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Daniel Ladant and Thérèse E. Malliavin
Chenal, Ana-Cristina Sotomayor-Perez,
Edithe Selwa, Marilyne Davi, Alexandre
Studies
Molecular Dynamics and Mutagenesis
Adenylyl Cyclase by Calmodulin:
Bordetella pertussisAllosteric Activation of
Molecular Biophysics:
published online June 6, 2014J. Biol. Chem.
10.1074/jbc.M113.530410Access the most updated version of this article at doi:
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Mutants of AC and AC/CaM interaction 1
June 5, 2014
Allosteric activation of Bordetella pertussis adenylyl
cyclase by calmodulin: molecular dynamics and
mutagenesis studies
Edithe Selwa1,3, Marilyne Davi2, Alexandre Chenal2, Ana-Cristina Sotomayor-P´erez2,
Daniel Ladant*2 and Th´er`ese E Malliavin*1
1 Institut Pasteur and CNRS UMR 3528, rue du Dr Roux, Unit´e de Bioinformatique Struc-
turale, 75015 Paris, France
2
Institut Pasteur and CNRS UMR 3528, rue du Dr Roux, Unit´e de Biochimie des Interactions
Macromol´eculaires, 75015 Paris, France
3
Universit´e Pierre et Marie Curie, Cellule Pasteur UPMC, rue du Dr Roux, 75015 Paris, France
Corresponding authors:
Th´er`ese E Malliavin, Unit´e de Bioinformatique Structurale, UMR CNRS 3528, rue du Dr
Roux, 75015 Paris, France; mail: therese.malliavin@pasteur.fr, tel.: 00 33 1 45 68 88 54
Daniel Ladant, Unit´e de Biochimie des Interactions Macromol´eculaires, UMR CNRS 3528,
rue du Dr Roux, 75015 Paris, France; mail: daniel.ladant@pasteur.fr, tel.: 00 33 1 45 68
84 00
Keywords: adenylyl cyclase,Bordetella pertussis, calcium, calmodulin affin-
ity, allostery, molecular dynamics
June 5, 2014
Running Title: AC mutants and AC/CaM interaction
Background: Adenylyl cyclase (AC)
from Bordetella pertussis is activated when
it interacts with calmodulin (CaM).
Results: A triple mutant of AC, which
was predicted by molecular modeling, exhib-
ited a highly reduced affinity for CaM.
Conclusion: This study suggests that
a long-range connection between CaM and
the AC catalytic loop is crucial for AC acti-
vation.
Significance: Molecular modeling
identified critical molecular determinants for
the allosteric activation of AC.
ABSTRACT
Adenylyl cyclase (AC) toxin is an es-
sential toxin that allows Bordetella per-
tussis to invade eukaryotic cells, where
it is activated after binding to calmod-
ulin (CaM). Based on the crystal
structure of the AC catalytic domain
in complex with the C-terminal half
of CaM (C-CaM), our previous molec-
ular dynamics simulations (Selwa et
al., Proteins 80, 1028–1040, 2012) sug-
gested that three residues, i.e., Arg338,
http://www.jbc.org/cgi/doi/10.1074/jbc.M113.530410The latest version is at
JBC Papers in Press. Published on June 6, 2014 as Manuscript M113.530410
Copyright 2014 by The American Society for Biochemistry and Molecular Biology, Inc.
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Mutants of AC and AC/CaM interaction 2
Asn347, and Asp360, might be impor-
tant for stabilizing the AC/CaM in-
teraction. These residues belong to a
loop-helix-loop motif (LHL) at the C-
terminal end of AC, which is located
at the interface between CaM and the
AC catalytic loop. In the present
study, we conducted the in silico and
in vitro characterization of three AC
variants, where one (Asn347; ACm1A),
two (Arg338 and Asp360; ACm2A), or
three residues (Arg338, Asn347, and
Asp360; ACm3A) were substituted
with Ala. Biochemical studies showed
that the affinities of ACm1A and
ACm2A for CaM were not affected
significantly, whereas that of ACm3A
was reduced dramatically. To under-
stand the effects of these modifica-
tions, molecular dynamics (MD) sim-
ulations were performed based on the
modified proteins. The MD trajecto-
ries recorded for the ACm3A/C-CaM
complex showed that the calcium-
binding loops of C-CaM exhibited
large fluctuations, which could be
related to the weakened interaction
between ACm3A and its activator.
Overall, our results suggest that the
LHL motif at the C-terminal end of
AC is crucial during CaM-binding for
stabilizing the AC catalytic loop in an
active configuration.
INTRODUCTION
The adenylyl cyclase toxin (CyaA) from
Bordetella pertussis, the causative agent of
whooping cough, plays an essential role
in host invasion [1–3]. CyaA is able to
invade eukaryotic target cells where it is
activated by interacting with calmodulin
(CaM), thereby overproducing cAMP, which
disorganizes cellular signaling processes and
triggers host cell death [4–12]. Several crys-
tallographic structures have been reported
of the CyaA catalytic domain (AC) in com-
plex with the C terminal moiety of CaM
(C-CaM) [13] (Figure 1). These structures
are physiologically relevant because C-CaM
has been shown [14] to be as potent in acti-
vating the enzymatic activity of AC as the
full-length CaM. In the AC/C-CaM com-
plex (Figure 1a), the AC domain includes
three main regions, CA (residues 7–61, 187–
197, 261–299, and 313–345; colored in green)
in the middle of the structure, and CB
(residues 62–186, colored in orange) and
SA (residues 192–254, colored in purple) at
the two extremities. The C-terminal tail
(residues 346–364, colored in cyan) and the
C-loop of the catalytic site (residues 300–
312, colored in yellow) are found in the CA
region. At the C-terminal end of AC, a
loop-helix-loop motif (LHL) that includes
residues from Arg338 to Asp360 (Figure 1c)
is present at the interface between C-CaM
and a major AC catalytic loop that spans
residues 300–312. In C-CaM, the calcium
ions are bound to EF-hands 3 and 4, where
EF-hand 3 is close to the interaction inter-
face with AC.
In a previous study [15], we analyzed
the interaction between the catalytic do-
main of AC from B. pertussis and C-CaM
based on the molecular dynamics (MD) tra-
jectories using maps of the energetic influ-
ences [16, 17]. Three residues in the LHL
motif, i.e., Arg338, Asn347, and Asp360 (Fig-
ure 1b), were predicted to be important for
the stability of the AC/CaM interaction,
where Arg338 and Asp360 make contact with
C-CaM, whereas Asn347 is in direct contact
with the AC catalytic loop. In the present
study, to further characterize the potential
roles of these residues in AC/CaM interac-
tions, we performed in silico MD simulations
and in vitro biochemical and biophysical
studies of the three modified AC proteins,
where one (Asn347; ACm1A), two (Arg338
and Asp360; ACm2A), or three residues
(Arg338, Asn347, and Asp360; ACm3A) were
substituted with Ala. We found that the
ACm3A variant exhibited a strongly re-
duced affinity for CaM, whereas the affini-
ties of the ACm1A and ACm2A variants
were similar to that of the wild-type enzyme.
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Mutants of AC and AC/CaM interaction 3
This demonstrated the strong synergistic ef-
fects of the three mutations. The MD sim-
ulations showed that the differences in the
behavior of the modified and wild-type com-
plexes were related to differences in the in-
ternal mobility of the C-CaM calcium loops.
These differences in mobility may induce di-
rect or indirect weakening of the C-CaM/AC
interaction observed in the ACm3A modi-
fied protein. These results, as well as an
analysis of the geometrical strain, suggest
that the LHL motif at the C-terminal end
of AC is important for establishing a long-
range connection between CaM binding and
the stabilization of the AC catalytic loop in
an active configuration, thus it is a criti-
cal module during the allosteric activation
of AC by CaM.
1 EXPERIMENTAL PRO-
CEDURES
MD simulations
The wild-type AC/C-CaM complexes in
the presence (ACwt 2Ca) and absence
(ACwt 0Ca) of calcium were prepared as de-
scribed previously [15] and the three mod-
ified systems, i.e., ACm1A, ACm2A, and
ACm3A, were generated in the following
manner. The last snapshot of the simula-
tion WT2Ca T1 (see Table I for the defi-
nition of this trajectory) was extracted and
the sidechains of the modified residues were
replaced by Ala sidechains using the LEaP
module from AMBER 10 [18] and the force
field FF99SB [19]. Na+ counterions were
added to neutralize the system.
The five systems, i.e., ACwt 2Ca,
ACwt 0Ca, ACm1A, ACm2A, and ACm3A
(Table I) were then hydrated in a box of
TIP3P [20] water molecules using cutoff val-
ues of 10 or 12.5 ˚A and periodic boundary
conditions. The calcium Lennard-Jones pa-
rameters of the Ca2+ ions comprised a van
der Waals radius R of 1.7131 ˚A, and a well
depth of 0.459789 kcal/mol [21].
The MD trajectories were initiated and
ran as described previously 15. For each sys-
tem, two simulations were recorded, which
were labeled using the system name and the
strings “T1” and “T2” (Table I).
The formation of hydrogen bonds be-
tween protein acceptor and donor groups
was monitored by selecting donor and ac-
ceptor pairs with a proximity of less than 3
˚Aevery ten recorded frames. This selection
was implemented using the Biskit python li-
brary [22]. In the following, the AC and
C-CaM residues are labeled based on their
numbers in the crystallographic structure
1YRT [13] and the C-CaM residue numbers
are followed by the letter a.
Along the MD trajectories, the geomet-
ric strain [23] of a residue i was calculated
using the following equation:
p(i) =
j
(dij − dij )2
[1−tanh( dij −7)]/2
(1)
where (dij − dij )2 is the intantaneous de-
viation from the average of the distance dij
between the α carbons of residues i and
j. It was shown previously [23] that hinge
residues are characterized by large p(i) val-
ues.
Plasmids
Plasmid pTRAC384GK was used to express
the wild-type AC (corresponding to the first
384 codons of CyaA, followed by the two
residues Gly and Lys), as described pre-
viously 24. Plasmids pKTRACm2A and
pKTRACm3A, which were used to express
ACm2A and ACm3A, respectively, were
constructed from plasmid pKTRAC, an ex-
pression vector for the CyaC and CyaA pro-
teins of B. pertussis. This plasmid was ob-
tained from plasmid pTRACG [25] by re-
placing the ampicillin (Amp) resistance gene
with a kanamycin (Kan) resistant gene from
plasmid pKT25 [26]. In pKTRAC, both the
cyaC and cyaA genes are expressed under
the control of the λ phage Pr promoter. The
plasmid has a ColE1 replication origin and it
also expresses a thermosensitive λ repressor
cI857, which strongly represses gene tran-
scription at the λ Pr promoter at tempera-
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Mutants of AC and AC/CaM interaction 4
tures below 32 ◦C. Thus, expression of the
CyaC and CyaA proteins can be triggered
by shifting the cells to 37–42 ◦C.
Plasmid pKTRACm3A was constructed
by subcloning between the unique AgeI and
BamHI sites of pKTRAC, a synthetic gene
(synthesized by GeneArt, Life Technologies
SAS, France) that encodes CyaA residues
320–384, followed by the two residues Gly
and Lys, and where the three codons,
Arg338, Asn347, and Asp360, were changed
to Ala codons (the sequence of the ACm3A
gene is available upon request).
Plasmid pKTRACm2A was constructed
by subcloning between the unique SnaBI
and BsiWI sites of plasmid pKTRACm3A
using a double-stranded synthetic oligonu-
cleotide produced via the hybridization
of the following two oligonucleotides: 5’-
GTTTTCTACGAAAACCGCGC-3’ and 5’-
GTACGCGCGGTTTTCGTAGAAAAC-3’
(Eurofins MWG GmbH, Ebersberg, Ger-
many), thereby restoring the wild-type
Asn347 codon (the SnaBI site was abol-
ished after oligonucleotide insertion; see
Figure S1). The DNA sequences of the
modified cyaA’ genes in pKTRACm2A and
pKTRACm3A were confirmed by DNA se-
quencing (Eurofins MWG GmbH, Ebers-
berg, Germany).
Plasmid pKT7AC contained a synthetic
AC gene (synthesized by GeneArt, Life
Technologies SAS, France) that encoded the
first 384 codons of CyaA, which was op-
timized for high expression in Escherichia
coli, followed by the two residues Gly and
Lys (the full DNA sequence is available
upon request). This synthetic AC gene was
cloned under the control of a T7 promoter
and a synthetic RBS sequence in the vector
pMK-RQ (GeneArt, Life Technologies SAS,
France), a plasmid with a ColE1 replication
origin and a Kan resistance gene.
Plasmid pKT7ACm1A was used
to express ACm1A and it was con-
structed by subcloning between the
unique SnaBI and BsiWI sites of plas-
mid pKT7AC, a double-stranded syn-
thetic oligonucleotide, which was obtained
by hybridizing two oligonucleotides: 5’-
GTGTTCTACGAAGCTCGCGC-3’ and 5’-
GTACGCGCGAGCTTCGTAGAACAC-3’
(Eurofins MWG GmbH, Ebersberg, Ger-
many), thereby replacing the wild-type
Asn347 codon with an Ala codon (sequence
available upon request). The DNA sequence
of the modified cyaA’ gene in pKT7ACm1A
was confirmed by DNA sequencing (Eurofins
MWG GmbH, Ebersberg, Germany).
Purification of AC proteins
The wild-type AC, ACm2A, and ACm3A
were expressed in the E. coli BLR
strain (Novagen, Darmstadt, Germany)
by transformation with the plasmids
pTRAC384GK, pKTRACm2A, and pK-
TRACm3A, respectively. The transfor-
mants were grown at 30 ◦C in LB medium
that contained either 100 µg/mL Amp
(for plasmid pTRAC384GK) or 50 µg/mL
Kan (for plasmids pKTRACm2A or pK-
TRACm3A). When the culture reached an
optical density of 0.6–0.8 at 600 nm, expres-
sion of the proteins was triggered by shifting
the growth temperature to 42 ◦C. After 150
min of additional growth at 42 ◦C, the cells
were collected by centrifugation (20 min,
10,000 × g, 4 ◦C) and the cell pellets were
frozen at -20 ◦C.
ACm1A was expressed in the E. coli
KRX strain (Promega, Madison, USA),
which was transformed with the plas-
mid pKT7ACm1A. The transformants were
grown at 37 ◦C in LB medium containing
50 µg/mL Kan to an optical density of 0.6–
0.8. Next, expression of the proteins was
triggered by the addition of 0.1% rhamnose
(to induce the expression of the chromoso-
mally encoded T7 RNA polymerase). After
180 min of additional growth at 37 ◦C, the
cells were collected by centrifugation, as de-
scribed above.
The cell pellets were resuspended in 20
mM HEPES-Na, pH 7.5, and disrupted by
sonication at 4 ◦C. The sonicated suspen-
sion was centrifuged for 20 min at 13,000 ×
g and 4 ◦C. The supernatant was discarded
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Mutants of AC and AC/CaM interaction 5
and the pellet was resuspended in 8 M urea
with 20 mM HEPES-Na (pH 7.5), and ag-
itated overnight at 4 ◦C. After 20 min of
centrifugation at 13,000 × g at 4 ◦C, the su-
pernatant (“urea extract”) that contained
the solubilized AC proteins was collected.
The AC proteins were purified accord-
ing to a previously described protocol us-
ing two sequential chromatographic treat-
ments with DEAE-Sepharose [24]. Briefly,
the urea extract was first loaded onto a
DEAE-Sepharose column (20 mL packed
resin) equilibrated in 8 M urea with 20
mM HEPES-Na (pH 7.5). In these con-
ditions, the AC protein did not bind to
the resin and it was recovered in the flow-
through (FT) fractions. The collected FT
fractions were then diluted five times with
20 mM HEPES-Na (pH 7.5) and applied to
a second DEAE-Sepharose column (20 mL
packed resin), which had been equilibrated
in 20 mM HEPES-Na (pH 7.5). In these
conditions, the AC proteins were retained
on the resin and, after extensive washing
with 20 mM HEPES-Na (pH 7.5), the pro-
teins were eluted in a soluble form using 20
mM HEPES-Na (pH 7.5) containing 100–
200 mM NaCl. All of the AC protein prepa-
rations exceeded a purity of 95% according
to SDS-PAGE analysis (Figure 6A). The AC
protein content was determined based on the
absorption spectra using an extinction coef-
ficient at 278 nm of 28,000 M−1/cm−−1.
AC enzymatic activity assays
The activity of AC was measured using a
sensitive colorimetric assay, which was re-
ported recently [27]. AC converts ATP into
cAMP and pyrophosphate (PPi), and the
latter can be hydrolyzed further by an ex-
ogenously added pyrophosphatase into two
phosphate molecules (Pi), which can be
quantified using a standard colorimetric as-
say based on the change in the absorbance of
malachite green dye in the presence of phos-
phomolybdate complexes. The amount of
Pi produced was determined using the Pi
color Lock TM ALS colorimetric assay from
Innova Biosciences (Cambridge, UK).
The AC enzymatic assays were per-
formed using a 96-well microtiter plate at
30◦C in a final volume of 50 µL, which con-
tained 50 mM Tris-HCl (pH 8.0), 10 mM
MgCl2, 0.1 mM CaCl2, 0.5 mg/mL bovine
serum albumin, 2 Unit/mL of E. coli inor-
ganic pyrophosphatase (Sigma-Aldrich; the
amount of pyrophosphatase added to the re-
action medium was found to be sufficient
to ensure the immediate and complete con-
version of the released PPi into Pi), 0–1
µM of CaM, and 0.1–1 nM (depending on
the specific activity) of AC proteins (di-
luted from stock solutions in 10 mM Tris-
HCl with 0.2% Tween 20, pH 8.0). The mix-
tures were pre-incubated for 10 min at 30◦C.
Then, the enzymatic reactions were initiated
by adding 2 mM ATP (final concentration)
and the microplate was incubated at 30◦C
with agitation. At various incubation times
(typically 2–10 min), 10 µL samples were
taken from each well and transferred into a
second 96-well microtiter plate, where each
well contained 100 µL of a Pi-ALS mixture
made of 2 volumes of H2O plus 8 volumes
of Pi ColorLock ALS reagent (provided in
the Pi-ALS kit from Innova Biosciences).
The enzymatic reaction was stopped imme-
diately by the acidic conditions of the Pi-
ALS mixture. After 10–13 min incubation
at room temperature, 10 µL of stabilizer so-
lution (from the Pi-ALS kit) was added to
prevent further nonenzymatic breakdown of
the phosphorylated substrate in acidic con-
ditions (according to the kit instructions).
After further incubation for 30–60 min at
room temperature, the optical density at
595 nm (OD595) was recorded using a mi-
croplate reader (Tecan, Lyon, France). A
standard curve was obtained in parallel by
adding known concentrations of Pi to the
Pi-ALS mixture, which was used to convert
the OD595values into moles of PPi produced.
The enzymatic activity was calculated based
on the initial velocity of PPi synthesis (in
the conditions described above, the accumu-
lation of PPi was linear with time).
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Mutants of AC and AC/CaM interaction 6
Biophysical characterization of AC
proteins
Size exclusion chromatography (SEC) was
performed using a Superdex 200 column
(GE Healthcare), which was controlled by
a GPCmax module that was connected on-
line to a triple detector array (TDA) model
302 (Viscotek Ltd, Houston, Basingstoke,
U.K.), as described previously [28]. The
running buffer was buffer A (20 mM Hepes,
100 mM NaCl, pH 7.4) and the protein
concentrations were 10–20 µM. Synchrotron
radiation circular dichroism (SR-CD) ex-
periments were conducted at the SOLEIL
synchrotron facility (DISCO beamline, Gif-
sur-Yvette, France), as described previ-
ously [29]. Briefly, the SR-CD spectra were
recorded at 25◦C using an integration time
of 1.2 s and a bandwidth of 1 nm, with a
1-nm resolution step. Each far-UV spec-
trum represented the average of at least
three individual scans. Optical cells with
a 26 µm path-length and CaF2 windows
(Hellma) were used for recording CD sig-
nals in the far-UV region (180–260 nm).
The protein concentrations were 25–50 µM
for AC proteins and 250 µM for CaM in
buffer A. Equimolar mixtures of enzyme and
activator were used to obtain the AC-CaM
and ACm3A-CaM spectra. The thermo-
dynamic stability of the AC proteins was
investigated by following their urea-induced
denaturation (at 25◦C, in buffer A), which
was monitored by tryptophan fluorescence
spectroscopy as described previously [30]
using an FP-6200 spectrofluorimeter (Jasco,
Japan) in a Peltier-thermostated cell holder,
with a 1-cm path length quartz cell (101.QS,
Hellma). The thermodynamic parameters
(urea concentration required to unfold half
the population of native proteins, [urea]1/2,
the cooperativity, m, and free energy, ∆G)
were deduced from the fluorescence data, as
described previously 30.
RESULTS
C-CaM/AC interface in the crystal-
lographic structures
To explore the potential role of AC residues
Arg338, Asn347, and Asp360 in CaM-induced
activation, as suggested previously [15], we
first checked the conservation of the atomic
contacts established by these residues in
the crystallographic structures of the AC/C-
CaM complex [13]. The analysis of the
hydrogen bonds and water-mediated con-
tacts established between C-CaM and AC
residues showed that the residues Arg338
and Asp360 were often involved in hydrogen
bonds or in water-mediated contacts with
C-CaM (data not shown, but available on
request). Furthermore, most of the contacts
and hydrogen bonds between the LHL mo-
tif (residues 338–360) (Figure 1c) and other
AC residues were present in more than three
crystallographic structures (data not shown,
but available on request), thereby suggest-
ing that the LHL motif plays an important
role in the stabilization of the AC structure.
C-CaM/AC interaction along MD
trajectories
Six independent MD simulations were
recorded using the AC/C-CaM complex,
where AC was modified in three dif-
ferent ways. Two simulations, i.e.,
”T1” and ”T2,” were performed for each
AC variant, ACm1A (N347A), ACm2A
(R338A, D360A), and ACm3A(R338A,
N347A, D360A) (Figure 1b). The aim of
these simulations was to analyze the rela-
tive stability of the different ACm/C-CaM
complexes and to relate these to the obser-
vations described previously based on the X-
ray crystallographic structures.
The conformational drift of the AC/C-
CaM complex was monitored during
trajectories ACm1A T1, ACm2A T1,
ACm3A T1, ACm1A T2, ACm2A T2, and
ACm3A T2 (Figure 2). The global RMSD
calculated for the different AC/C-CaM com-
plexes (Figures 2a and 2e) were similar
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Mutants of AC and AC/CaM interaction 7
for all variants and they rapidly reached
a plateau around 3 ˚A. The RMSD plateau
was similar to that obtained based on the
MD trajectories of the wild-type AC/C-
CaM complex (Figure 2a in Ref [15]). Thus,
these modifications did not destabilize the
overall AC structure at least during the
timescales considered by the MD trajecto-
ries.
The conformational drifts (RMSD) of
the different protein regions in the two sets
of simulations (Figures 2b-d and 2f-h) were
very similar for CB (orange curves), the C
loop (yellow curves), the F, G, H, and H’
α helices, and the loop at the extremity of
SA, which all had RMSD plateaus that were
similar to or less than 2 ˚A. The CA region
(green curves), SA region (violet curves),
and C-terminal tail (cyan curves) had more
significant drifts, where the RMSD values
were larger than 4 ˚A. The CA and C ter-
minal drifts are not surprising because the
modified residues were located in these re-
gions. Interestingly, the increased internal
mobility of the C terminal tail is analogous
to that observed in a wild-type AC/C-CaM
complex (Figure 3a, b of Ref [15]) when the
Ca2+ ions were removed (Figure 3a, b of
Ref [15]). The latter had a lower affinity
in vitro, thus the modifications of residues
Arg338, Asn347, and Asp360 may have de-
creased the affinity of C-CaM for AC.
The water-mediated connections be-
tween AC and C-CaM were also ana-
lyzed along the MD trajectories (data not
shown). The connections that involved the
C-terminal tail of AC were present mainly
in one or two trajectories, which shows that
the interaction at this interface underwent
reorganizations.
C-CaM and AC fluctuations in the
MD trajectories
The behavior of C-CaM was monitored
along the two series of mutant trajectories
and compared with previous observations
[15] obtained using the wild type AC/C-
CaM complex.
In the simulation of the wild-type AC/C-
CaM complex in the absence of calcium ions
(WT0Ca T1) (Figure 3a, solid red curve),
the calcium loop of EF-hand 3 (i.e., between
α helices V and VI) and the C-terminal part
of α helix V exhibited highly increased fluc-
tuations (RMSF). A similar increase was ob-
served in ACm3A T1 (Figure 3b, solid red
curve) but in ACm2A T2 and ACm3A T2
(Figure 3b, dashed green and red curves),
increased fluctuations were found in the cal-
cium loop of EF-hand 4 (i.e., between α
helices VII and VIII). Interestingly, the in-
creased fluctuations in the C-terminal part
of α helix V in ACm3A T1 was associated
with the small number of hydrogen bonds
that connect C-CaM and C tail, i.e., only a
single hydrogen bond is present for over 80%
of the trajectory length between Arg90a and
Glu346.
Analysis of the internal fluctuations of
AC along the various trajectories (data not
shown) detected no major variations be-
tween the different modified proteins, which
agreed with the similar global RMSD that
was observed for all trajectories (Figure 2).
The fluctuations measured in the wild-type
systems were similar to those observed in
the modified proteins, where the largest dif-
ferences were observed for the 226–232 loop
and the C-terminal tail of the protein. It
should be noted that the loop 226–232 is not
visible in the X-ray crystallographic struc-
tures, thereby indicating that it is probably
a highly flexible region.
The coordination of calcium ions by the
C-CaM residues was stable in the EF-hand
3 along the trajectories of the modified pro-
teins (data available on request), but there
were some variations in the EF-hand 4. In-
deed, the calcium coordination by Asp133
in the EF-hand 4 was perturbed in the
two series of simulations. This perturba-
tion agrees with the increased fluctuation
observed in the calcium loop of EF-hand
4 for ACm2A T2 and ACm3A T2 (Figure
3b), and with the increase in the EF-hand 4
angle up to about 100◦.
The C-CaM conformations were ex-
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Mutants of AC and AC/CaM interaction 8
tracted from ACm2A T2 and ACm3A T2
(Figure 4) at times when different distances
were observed between Asp133-Oδ1/Oδ2 and
the calcium ion. In both simulations, the
sidechain of Asp133 moved apart and at
the end of the trajectory, the calcium ion
was coordinated by the backbone carbonyl,
instead of the sidechain. This conforma-
tional tendency of Asp133 was increased in
ACm3A T2 compared with ACm2A T2. In-
terestingly, in a steered MD study of the cal-
cium dissociation in CaM [31], it was found
that Asp133 was among the latest residues to
lose calcium coordination. The destabiliza-
tion of the calcium/Asp133 interaction ob-
served in the present study corresponds to
the destabilization of one of the strongest
interactions that defines the calcium coor-
dination in EF-hand 4. Thus, this desta-
bilization indicates that the AC mutations
decreased the calcium binding to CaM.
Overall, the perturbations of the EF-
hand angles and calcium coordination are
precursory indicators of the decrease in the
C-CaM affinity for calcium ions [32,33]. On
longer time scales, this decrease could lead
to the dissociation of calcium ions from C-
CaM and to a decrease in the affinity of AC
for C-CaM, as shown previously [14].
Network of interactions involving
LHL along the MD trajectories
The LHL motif, which contains the three
modified residues, lies at the interface be-
tween C-CaM and the AC catalytic loop.
The hydrogen bonds established by the
residues in the LHL motif were analyzed
in the different AC/C-CaM complexes (data
available on request). Only long-range hy-
drogen bonds (that connected residues sep-
arated by more than ten residues in the
protein sequence) were considered in order
to exclude interactions related to local sec-
ondary structures. Most of these hydrogen
bonds were conserved along the MD tra-
jectories, except for one hydrogen bond be-
tween Asn35 and Tyr342, which was present
only in the modified complexes, and two hy-
drogen bonds between Glu346 and Leu357,
and between Tyr350 and Glu308, which were
observed in less than two simulations. A
lower number of stable hydrogen bonds that
involved modified residues were observed
in the ACm3A T1 and ACm3A T2 simula-
tions. Indeed, Asn347 established hydrogen
bonds with the residues Glu301, Gln302, and
Asn304, which are located in the catalytic
loop. These hydrogen bonds were disrupted
by the change from Asn347 to Ala, except for
the hydrogen bonds that involved the Asn347
backbone hydrogen. Similarly, the hydro-
gen bonds between Asp360 and Arg338 dis-
appeared when Asp360 or Arg338 were mod-
ified to Ala. These observations show that
the overall structure of the LHL motif is con-
served in all systems, and that the LHL con-
nection to C-CaM on one side, as well as to
the C-loop on the other side, were signifi-
cantly weakened in the presence of the triple
modification.
The hydrogen bonds that involved LHL
residues, as well as the protein fluctua-
tions and the correlations in the fluctua-
tion, indicated that there was limited vari-
ation among the protein variants (data not
shown). Thus, the possibility of long-range
communication through LHL was investi-
gated using a parameter that was poten-
tially more sensitive to small variations in
geometry. The geometric strain, as defined
by Chiappori et al. [23] (see Materials and
Methods), exhibits sufficient sensitivity be-
cause it depends on the geometry of the en-
vironment of the analyzed residue within a
sphere of 7 ˚A while it also follows the dis-
tance variations with respect to the average
distance values.
The variations in the geometric strain
along the MD trajectories exhibited corre-
lated transitions between the given residues,
which were due to simultaneous displace-
ments of the environments of these residues.
To summarize these variations, the time
correlation matrices of the geometric strain
were analyzed. The strain correlation peaks
(in pink/yellow) correspond to residue pairs
that are undergoing correlated displace-
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Mutants of AC and AC/CaM interaction 9
ments in their environment, thus they are
mechanically correlated. In order to esti-
mate the reliability of the correlation pre-
dictions, the calculation was repeated five
times by selecting at each time, one data-
point over five along the analyzed time
interval. The average values were calcu-
lated among LHL residues (Figure 5) and
among the LHL, C-loop and calcium loop
residues (data not shown but available on
request). The standard deviations obtained
from the repeated calculation of the corre-
lations allowed us to estimate the error on
the correlation, which was 4–6.5% for cor-
relations greater than 0.15. In all trajecto-
ries, the peaks were observed repeatedly be-
tween residues in the α-helix at 346–355. A
general attenuation of the correlations, with
pixel colors changing from pink to yellow,
was observed for the trajectories recorded
in the protein variants compared with those
recorded in the wild type. This suggests
that there was a decrease in the long-range
correlation along the LHL for the modified
proteins.
In vitro characterization of AC vari-
ants that harbored mutations at po-
sitions 338, 347 or 360
To further delineate the effect of the muta-
tions on the activity of AC and its affinity for
CaM, the three variants ACm1A, ACm2A,
and ACm3A were characterized in vitro (see
Materials and Methods). The three modi-
fied proteins and the wild-type catalytic do-
main (AC) were overexpressed in E. coli and
purified to homogeneity, as described pre-
viously ( [24], see Materials and Methods).
The results of the SDS-PAGE analysis of the
purified preparations are shown in Figure
6A.
The enzymatic activities of each AC
variant were determined at different CaM
concentrations, which ranged from 0.03
nM to 1 µM. Figure 6B shows the CaM-
dependency of the enzymatic activity for
each variant as a percentage of the maximal
activity (100 %) determined at the saturat-
ing CaM concentration of 1 µM. The affini-
ties of the AC enzymes for CaM, which were
defined as the CaM concentration at half-
maximal activation K1/2, were determined
(Figure 6C) by curve-fitting with a single
binding isotherm, according to A = AMax
(C/C+ K1/2) where C is the concentration
of CaM, A is the activity at the concentra-
tion C of CaM, and AMax is the maximal
activity measured in the presence of 1 µM
CaM.
As shown in Figures 6B and C, wild-type
AC (labeled ACWT in Figure 6C) exhibited
a kcat of 4600 s−1 (at saturating CaM and 2
mM ATP) and a half-maximal CaM activa-
tion K1/2 of 0.11 nM, which agreed well with
previous studies [13, 24, 34]. The ACm1A
variant, where the Asn347 residue that in-
teracted with the catalytic loop was mod-
ified to Ala, exhibited an enzymatic activ-
ity that was reduced by about half (kcat ∼
2250 s−1) compared with the wild type and
a ∼ five-fold lower affinity for CaM (KCaM
1/2
of 0.61 nM). The dual mutations R338A and
D360A in the ACm2A variant did not af-
fect the catalytic efficiency (kcat ∼ 6000 s−1
was even slightly higher than that of the
wild type) but the affinity for CaM was re-
duced by about six-fold (KCaM
1/2 of 0.66 nM),
as might be expected with modifications at
the CaM interface. Finally, the triple mu-
tant ACm3A was the enzyme that was af-
fected most significantly, where its catalytic
turnover (kcat ∼ 650 s−1) was decreased sig-
nificantly compared with the wild-type AC
(ca 15% of the wild type turnover) and its
affinity for CaM (KCaM
1/2 of 26 nM) was re-
duced by more than 200 times.
These data indicate that the separate
single (N347A) and dual (R338A, and
D360A) modifications had limited effects on
the catalytic and CaM-binding properties of
AC, whereas their combination in a single
enzyme (ACm3A) had strong synergistic ef-
fects on both the enzymatic activity and the
affinity for CaM. This fully supports our pre-
diction that the LHL region is critical for
the allosteric coupling of CaM binding to the
stabilization of the catalytic loop in an enzy-
byguestonJune8,2014http://www.jbc.org/Downloadedfrom
Mutants of AC and AC/CaM interaction 10
matically active configuration. The two- to
five-fold higher KATP
M levels of all the mod-
ified AC enzymes compared with the wild-
type AC also demonstrate that the LHL mo-
tif is important for maintaining the optimal
conformation of the active site.
To verify that the triple modification of
R338A, N347A, and D360A in ACm3A did
not affect the structural integrity of the pro-
tein, we performed the following biophysi-
cal analyses. First, the proteins were ana-
lyzed by SEC followed by triple detector ar-
ray (SEC-TDA) to determine whether the
mutations affected their oligomeric status.
SEC-TDA provides the molecular masses
of the eluted species by combining static
right angle light scattering with UV ab-
sorbance. The results showed that both
the wild-type and ACm3A proteins were
monomeric species in solution (Figure 7A).
The secondary structure contents of the
CaM and AC proteins, either isolated or in
complexes, were analyzed by SRCD in the
far-UV range. The shapes of the far-UV
CD spectra of wild-type AC and ACm3A
were similar (Figure 7B). The addition of
CaM induced similar changes in the over-
all secondary structure content of both AC
proteins. These results clearly indicate that
the secondary structure content of ACm3A
was not affected by the mutations. Fi-
nally, the thermodynamic stability of both
AC proteins was characterized. The urea-
induced denaturation of the AC proteins
was monitored by tryptophan fluorescence.
The denaturation profiles (Figure 7C). and
the thermodynamic parameters (Figure 7D)
obtained for both proteins were very similar.
Overall, these experiments indicate that the
three modifications in ACm3A did not af-
fect the structural properties or the overall
stability of the protein.
DISCUSSION
Maps of the energetic influences [16, 17]
that were calculated [15] previously using
the AC/C-CaM complex allowed us to iden-
tify three residues, i.e., Arg338, Asn347, and
Asp360, that might affect the interaction be-
tween AC and C-CaM. In the present study,
we characterized three modified proteins,
i.e., ACm1A (N347A), ACm2A (R338A,
D360A), and ACm3A (R338A, N347A and
D360A), using in silico MD simulations and
based on in vitro biochemical and biophysi-
cal studies.
Our in vitro studies showed that the
affinity of the triple mutant ACm3A for
CaM was greatly reduced whereas that
of the single (ACm1A) or dual mutant
(ACm2A) was not affected significantly
compared with that of the wild-type en-
zyme. These results indicate that these
three mutations had a strong synergistic ef-
fect on the CaM-binding affinity. A similar
synergistic effect was noted for the catalytic
efficiency of the enzyme because the enzy-
matic activity of ACm3A was also reduced
significantly (about 15% of the wild-type en-
zyme activity), whereas that of ACm1A was
about 50% of the wild-type activity. The
lower activity of the ACm1A and ACm3A
variants might be expected because the
Asn347 residue interacts directly with the
catalytic loop. Thus, any perturbation of
the interaction between Asn347 and the cat-
alytic loop might directly affect the catalytic
efficiency of AC.
The dynamical behaviors of the three
modified proteins in complex with C-CaM
were also analyzed in silico based on two
series of MD simulations. High variabil-
ity in the establishment of hydrogen bonds
in the complex was observed in the dif-
ferent modified proteins, as well as among
repeated trajectories. However, this vari-
ability could not be assigned to simula-
tion artifacts because similar variability was
observed among the four crystallographic
structures of the complex AC/C-CaM [13].
The analysis of the trajectories recorded
using modified and wild-type AC/C-CaM
complexes, which were conducted in paral-
lel with the experimental characterization
of the AC/CaM interaction, identified two
different routes that allowed the affinity of
AC for C-CaM to decrease. In the first
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Mutants of AC and AC/CaM interaction 11
simulation of the triple modified protein
(ACm3A T1), a destabilization of the cal-
cium loop of EF-hand 3 was observed, as
well as a large decrease in the interactions
between C-CaM and the CA region. In the
second trajectory recorded using ACm3A
(ACm3A T2), a destabilization of the cal-
cium coordination in the EF-hand 4 of C-
CaM led to the disruption of the hydrogen
bond between the Asp133 sidechain and cal-
cium. This could be the first step in the pos-
sible dissociation of calcium from C-CaM. It
is known that calcium-free CaM has a lower
affinity for AC [14], thus the destabilization
of calcium coordination would result in a re-
duction of the CaM affinity for AC.
Guo et al. [13] described the crys-
tallographic structure of the complex
AC/C-CaM and characterized one AC
modification: the double modification
E346A/R348A in the C terminal tail. The
modified protein exhibited a reduced enzy-
matic activity as well as a reduced affinity
for CaM. The two amino acids changed
in the E346A/R348A mutant flanked the
Asn347 residue that was modified in the
present study. The hydrogen bonds that in-
volve Glu346 and Arg348 residues varied in
the wild-type AC when calcium ions or C-
CaM were removed from the system, as well
as in the trajectories of the modified AC pro-
tein, but no systematic variations were de-
tected. However, the observations of Guo
et al. [13] based on the E346A/R348A AC
variant agree well with our present study,
as well as supporting the hypothesis that
the LHL motif is critical for linking CaM
binding with the stabilization of the AC cat-
alytic loop in a configuration that is favor-
able for catalysis. Indeed, the LHL mo-
tif is in direct contact with C-CaM on one
side via the Arg338 and Asp360 residues,
as well as the catalytic loop on the other
side via the Asn347 residue. Thus, it is
ideally positioned to relay information re-
lated to CaM-binding on the distant cat-
alytic site of the AC enzyme via a dense
network of atomic contacts, which primar-
ily involve the Arg338, Asn347, and Asp360
residues, as demonstrated in our MD simu-
lations. Long-range communications within
the LHL motif were further suggested by our
analysis of the geometric strain along the
MD trajectories of the different ACs. There-
fore, the LHL motif appears to be a crit-
ical module for the allosteric activation of
AC by CaM. The analysis performed in the
present study was more qualitative than the
method proposed recently by Weinkam et
al. [35,36], but we should note that the avail-
ability of only one structure of AC in com-
plex with Ca2+-loaded C-CaM, as well as
the conformational equilibrium that is prob-
ably adopted by AC in the unbound state,
prevent a more straightforward application
of this method.
From a more general perspective, the de-
tection of the residue networks that are re-
sponsible for long-range communication in-
side a given protein has been attracting
much interest during the last decade [37–41].
These networks are thought to be involved
in biomolecular interactions [42] with fun-
damental roles in many biological processes
[43]. Homologous protein sequence align-
ments [44–46] or analysis of the covariance of
the NMR chemical shifts [47] have predicted
long-range protein communication networks
that agree with experimental observations.
Some of these analyses have facilitated pro-
tein engineering [48]. In the present study,
we combined MD and mutagenesis to iden-
tify a long-range communication network re-
lated to the activation of a key virulence
factor derived from a bacterial pathogen.
This investigation may facilitate new meth-
ods for interfering with the AC-CaM inter-
action, thereby allowing a novel drug discov-
ery approach [49].
ACKNOWLEDGMENTS
We acknowledge SOLEIL for providing the
synchrotron radiation facilities (Proposal
IDs 20110586 and 20120444) and we thank
Frank Wien for assistance with using the
DISCO beamline. Edithe Selwa was sup-
ported by an allocation doctorale from
byguestonJune8,2014http://www.jbc.org/Downloadedfrom
Mutants of AC and AC/CaM interaction 12
MENRT, which was distributed by Uni-
versit´e Pierre et Marie Curie (Paris VI).
Ana Cristina Sotomayor P´erez was sup-
ported by an Institut Pasteur PTR grant
(PTR#374). This project was supported by
the Institut Pasteur and the Centre National
de la Recherche Scientifique (CNRS UMR
3528, Biologie Structurale et Agents Infec-
tieux). Data not shown in the manuscript
may be obtained from the authors (Daniel
Ladant: daniel.ladant@pasteur.fr; Th´er`ese
Malliavin: therese.malliavin@pasteur.fr) on
request.
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[48] Lee, J., Natarajan, M., Nashine, V., Socolich, M., Vo, T., Russ, W., Benkovic, S.,
and Ranganathan, R. (2008) Surface sites for engineering allosteric control in proteins.
Science 322, 438–442
[49] Seifert, R. and Dove, S. (2012) Towards selective inhibitors of adenylyl cyclase toxin
from Bordetella pertussis. Trends Microbiol 20, 343–351
[50] Eswar, N., Eramian, D., Webb, B., Shen, M., and Sali, A. (2008) Protein structure
modeling with MODELLER. Methods Mol Biol 426, 145–159
byguestonJune8,2014http://www.jbc.org/Downloadedfrom
Mutants of AC and AC/CaM interaction 16
FIGURE LEGENDS
Figure 1
a) X-ray crystallographic structure of the catalytic domain (AC) of adenyl cyclase
(CyaA, PDB entry 1YRT) drawn in cartoons. Helices F, G, and H colored in purple form
the SA region (residues 192–254). The loop 226–232 (Hom loop) colored in salmon at
the left extremity of SA colored in purple was missing from the X-ray crystallographic
structure and was modeled using Modeller9v4 [50]. The other protein regions are colored
in green (CA: residues 7–61, 187–197, 261–299, and 313–345), orange (CB: residues 62–
186), cyan (C-terminal tail/C tail: residues 346–364), and yellow (catalytic loop/C loop:
residues 300–312). The C-CaM lobe, which is colored in red, interacts with SA and the
C-terminal tail. Calcium ions are represented by silver beads. b) The modified residues,
i.e., Arg338, Asn347, and Asp360, located in CA and the C terminal tail, are indicated by
sticks. c) The LHL motif localized between the C-CaM/AC interface and the catalytic
loop is colored in brown.
Figure 2
Conformational drifts estimated based on the α carbon coordinates RMSD from the
starting conformations in the T1 (a-d) and T2 (e-h) series of simulations. (a, e) Drift cal-
culated based on the Cα carbons in the AC domain for ACm1A (black), ACm2A (green),
and ACm3A (red). (b–d,f–h) Drift calculated based on different regions of the AC domain,
which were analyzed for ACm1A (b, f), ACm2A (c, g), and ACm3A (d, h). The color
codes of the different protein regions are shown in panel (d). The AC regions are defined
as follows. 1) CA: residues 7–61, 187–197, 261–299, and 313–345. 2) Catalytic loop (C
Loop): residues 300–312. 3) C-terminal tail (C tail): residues 346–364. 4) CB: residues
62–186. 5) SA: residues 198–260. Helices H, F, G, and H’ correspond to residues 234–253,
198-210, 214-223, 256-260.
Figure 3
Fluctuations of the residues (RMSF: ˚A) observed in C-CaM based on the trajectories
recorded for: (a) wild-type and (b) modified C-CaM/AC complexes. The trajectory names
are shown in the legends. The WT2Ca trajectories were run on two Ca2+-loaded AC/C-
CaM complexes, whereas the WT0Ca trajectories were run on the AC/C-CaM complex
in the absence of calcium ions. The fluctuations were calculated based on the trajectories
after removing their first 10 ns.
Figure 4
C-CaM conformation extracted from ACm2A T2 and ACm3A T2, which are colored
according to the simulation times indicated. The N- and C-terminal ends are indicated,
as well as Asp-133, which is shown in black. The calcium ions are shown as gray spheres,
and the carboxyl oxygens of the Asp-133 sidechain are colored in red.
Figure 5
Correlation between geometric strains among the LHL residues, displayed for each
recorded trajectory. The time-correlation matrices were calculated between the variations
of the geometric strains of LHL residues and the first ten nanoseconds were discarded from
the analysis. In order to estimate the reliability of the prediction of correlation, the cal-
culation was repeated five times by selecting at each time, one data-point over five along
the analyzed time interval. The average values calculated for the LHL residues are shown
byguestonJune8,2014http://www.jbc.org/Downloadedfrom
Mutants of AC and AC/CaM interaction 17
in the figure. The intensity scale varies from 1.0 (pink) to –0.2 (dark green).
Figure 6
A. SDS-PAGE analysis of the purified AC variants, wild type AC, and CaM. The pro-
teins were separated by electrophoresis on a 4–12% SDS-polyacrylamide gel (Life Tech-
nologies). After migration, the gel was stained with PageBlue protein staining solution
(Thermo Fisher Scientific). B. Activation of modified ACs by CaM. The activity of the
purified wild-type AC and/or the variants were measured (as described in the Materials
and Methods) in the presence of the indicated CaM concentrations, and the results are
expressed as the percentage of the maximal activity (measured in the presence of 1µM
CaM). C. Catalytic properties of AC variants. The parameters were determined within
an error of ± 10%. ∆G is the calculated energy of association between CaM and AC.
Figure 7
A. SEC-TDA analysis of the oligomerization state of ACwt and ACm3A. Red curve:
right angle light scattering; blue curve: UV absorbance; green curve: molecular masses of
the eluted species. See the Materials and Methods for details. B. Synchrotron radiation
circular dichroism spectra of CaM and AC proteins in isolation or in a 1:1 complex. MRE:
mean residual ellipticity. See the Materials and Methods for details. C. Thermodynamic
stability of AC proteins following urea-induced denaturation. The ratio of the fluorescence
intensity at 360 and 320 nm (excitation wavelength = 295 nm) for the proteins as a func-
tion of the urea concentration was measured as described in the Materials and Methods.
D. Thermodynamics parameters of the urea-induced denaturation of AC proteins.
byguestonJune8,2014http://www.jbc.org/Downloadedfrom
Mutants of AC and AC/CaM interaction 18
Table I Details of the molecular systems simulated in molecular dynamics
(MD) trajectories.
Systems ACwt 2Ca ACwt 0Ca
Trajectories WT2Ca T1 WT0Ca T1
WT2Ca T2 WT0Ca T2
Number of Na+
counter-ions 14 18
Water box 92.6 x 106.9 91.3 x 106.9
dimensions x 103.3 ˚A3 x 106.4 ˚A3
Number of
water molecules 26455 27056
Total number
of atoms 85825 87630
Length (ns) 30 30
Table I
Systems ACm1A ACm2A ACm3A
Trajectories ACm1A T1 ACm2A T1 ACm3A T1
ACm1A T2 ACm2A T2 ACm3A T2
Number of Na+
counter-ions 14 18 14
Water box 109.6 x 82.8 108.1 x 82.8 109.6 x 82.8
dimensions x 111.7 ˚A3 x 111.7 ˚A3 x 111.7 ˚A3
Number of
water molecules 29003 29008 29008
Total number
of atoms 93465 93468 93464
Length (ns) 50 50 50
byguestonJune8,2014http://www.jbc.org/Downloadedfrom
Mutants of AC and AC/CaM interaction 19
Figure 1
a) C-CaM
C-tail
C-Loop
CA
CB
SAHom
loop
G
F
H
b) c)
L16
ASN-347
ARG-338
ASP-360
Figure 1
byguestonJune8,2014http://www.jbc.org/Downloadedfrom
Mutants of AC and AC/CaM interaction 20
Figure 2
Figure 2
byguestonJune8,2014http://www.jbc.org/Downloadedfrom
Mutants of AC and AC/CaM interaction 21
Figure 3
RMSF(A°)
79 84 89 94 99 105 111 117 123 129 135 141 147
0123
a)
Helix V Helix VI Helix VII Helix VIII
WT2Ca_T1
WT2Ca_T2
WT0Ca_T1
WT0Ca_T2
RMSF(A°)
79 84 89 94 99 104 110 116 122 128 134 140 146
0123
b)
Helix V Helix VI Helix VII Helix VIII
ACm1A_T1
ACm1A_T2
ACm2A_T1
ACm2A_T2
ACm3A_T1
ACm3A_T2
Residue number
RMSF(A°)RMSF(A°)
Figure 3 byguestonJune8,2014http://www.jbc.org/Downloadedfrom
Mutants of AC and AC/CaM interaction 22
Figure 4
ACm2A_T2
Asp 133
COO-
C N ACm3A_T2 C
N
Asp 133
COO-
10 ns
20 ns
25 ns
start
Figure 4
byguestonJune8,2014http://www.jbc.org/Downloadedfrom
Mutants of AC and AC/CaM interaction 23
Figure 5
Residuenumber
345350355360
ACm1A_T1 ACm1A_T2Residuenumber
345350355360
ACm2A_T1 ACm2A_T2
Residuenumber
345350355360
ACm3A_T1 ACm3A_T2
Residuenumber
345350355360
WT2Ca_T1 WT2Ca_T2
Residue number
Residuenumber
340 345 350 355 360
345350355360
WT0Ca_T1
Residue number
Residue number
340 345 350 355 360
WT0Ca_T2
Residue number
−0.2 0.0 0.2 0.4 0.6 0.8 1.0 1.2
ResiduenumberResiduenumberResiduenumberResiduenumberResiduenumber
Figure 5
byguestonJune8,2014http://www.jbc.org/Downloadedfrom
Mutants of AC and AC/CaM interaction 24
Figure 6
A
170 -
130-
95-
72-
55-
43-
34-
26-
17-
10-
AC
ACm
3AACm
2AACm
1A
CaM
B
C kcat KATP
M KCaM
1/2 ∆G kcat/ KM
(s−1) (mM) (nM) (kcal.mol−1) 106 M−1s−1
ACwt 4600 0.60 0.11 13.8 7.6
ACm1A 2250 2.2 0.61 12.8 1.0
ACm2A 6000 1.5 0.66 12.7 4.0
ACm3A 650 3.0 26.7 10.5 0.2
Figure 6
byguestonJune8,2014http://www.jbc.org/Downloadedfrom
Mutants of AC and AC/CaM interaction 25
Figure 7
050100150 AC
A
uu
mm[2472:3101]
01020304050
050100150
uv
ACm3A
uu
mm[2472:3101]
10 11 12 13 14 15 16 17 18
01020304050
UV wavelength
Signalintensity(AU)Signalintensity(AU)
Molecularmass(kDa)Molecularmass(kDa)
−20−100102030
180 200 220 240
B
wavelength (nm)
MRE,Kdeg*cm2/dmol
ACm3A
ACm3A:CaM
ACWT
ACWT:CaM
CaM
q q
q
q
q
q
q q q q q q q
0.60.81.01.21.41.61.82.0
q q
q
q q q q q q
q
q
q
q
q q
q
q
q
q
q q q q q q q
q q q q
q
q
q
q q
q
q
q q
0 0.5 1 1.5 2 2.5 3 3.5 4 5 6 7 8
C
urea (M)
ratiooffluorescenceintensity360/320
ACm3A
ACm3A:CaM
ACWT
ACWT:CaM
D
proteins AC WT ACm3A
[urea]1/2
(M) 1.8 1.7
∆G,
kcal.mol−1 2.4 2.6
m
parameter 1335 1490
Figure 7
byguestonJune8,2014http://www.jbc.org/Downloadedfrom

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J. biol. chem. 2014-selwa-jbc.m113.530410

  • 1. Daniel Ladant and Thérèse E. Malliavin Chenal, Ana-Cristina Sotomayor-Perez, Edithe Selwa, Marilyne Davi, Alexandre Studies Molecular Dynamics and Mutagenesis Adenylyl Cyclase by Calmodulin: Bordetella pertussisAllosteric Activation of Molecular Biophysics: published online June 6, 2014J. Biol. Chem. 10.1074/jbc.M113.530410Access the most updated version of this article at doi: .JBC Affinity SitesFind articles, minireviews, Reflections and Classics on similar topics on the Alerts: When a correction for this article is posted• When this article is cited• to choose from all of JBC's e-mail alertsClick here http://www.jbc.org/content/early/2014/06/06/jbc.M113.530410.full.html#ref-list-1 This article cites 0 references, 0 of which can be accessed free at byguestonJune8,2014http://www.jbc.org/DownloadedfrombyguestonJune8,2014http://www.jbc.org/Downloadedfrom
  • 2. Mutants of AC and AC/CaM interaction 1 June 5, 2014 Allosteric activation of Bordetella pertussis adenylyl cyclase by calmodulin: molecular dynamics and mutagenesis studies Edithe Selwa1,3, Marilyne Davi2, Alexandre Chenal2, Ana-Cristina Sotomayor-P´erez2, Daniel Ladant*2 and Th´er`ese E Malliavin*1 1 Institut Pasteur and CNRS UMR 3528, rue du Dr Roux, Unit´e de Bioinformatique Struc- turale, 75015 Paris, France 2 Institut Pasteur and CNRS UMR 3528, rue du Dr Roux, Unit´e de Biochimie des Interactions Macromol´eculaires, 75015 Paris, France 3 Universit´e Pierre et Marie Curie, Cellule Pasteur UPMC, rue du Dr Roux, 75015 Paris, France Corresponding authors: Th´er`ese E Malliavin, Unit´e de Bioinformatique Structurale, UMR CNRS 3528, rue du Dr Roux, 75015 Paris, France; mail: therese.malliavin@pasteur.fr, tel.: 00 33 1 45 68 88 54 Daniel Ladant, Unit´e de Biochimie des Interactions Macromol´eculaires, UMR CNRS 3528, rue du Dr Roux, 75015 Paris, France; mail: daniel.ladant@pasteur.fr, tel.: 00 33 1 45 68 84 00 Keywords: adenylyl cyclase,Bordetella pertussis, calcium, calmodulin affin- ity, allostery, molecular dynamics June 5, 2014 Running Title: AC mutants and AC/CaM interaction Background: Adenylyl cyclase (AC) from Bordetella pertussis is activated when it interacts with calmodulin (CaM). Results: A triple mutant of AC, which was predicted by molecular modeling, exhib- ited a highly reduced affinity for CaM. Conclusion: This study suggests that a long-range connection between CaM and the AC catalytic loop is crucial for AC acti- vation. Significance: Molecular modeling identified critical molecular determinants for the allosteric activation of AC. ABSTRACT Adenylyl cyclase (AC) toxin is an es- sential toxin that allows Bordetella per- tussis to invade eukaryotic cells, where it is activated after binding to calmod- ulin (CaM). Based on the crystal structure of the AC catalytic domain in complex with the C-terminal half of CaM (C-CaM), our previous molec- ular dynamics simulations (Selwa et al., Proteins 80, 1028–1040, 2012) sug- gested that three residues, i.e., Arg338, http://www.jbc.org/cgi/doi/10.1074/jbc.M113.530410The latest version is at JBC Papers in Press. Published on June 6, 2014 as Manuscript M113.530410 Copyright 2014 by The American Society for Biochemistry and Molecular Biology, Inc. byguestonJune8,2014http://www.jbc.org/Downloadedfrom
  • 3. Mutants of AC and AC/CaM interaction 2 Asn347, and Asp360, might be impor- tant for stabilizing the AC/CaM in- teraction. These residues belong to a loop-helix-loop motif (LHL) at the C- terminal end of AC, which is located at the interface between CaM and the AC catalytic loop. In the present study, we conducted the in silico and in vitro characterization of three AC variants, where one (Asn347; ACm1A), two (Arg338 and Asp360; ACm2A), or three residues (Arg338, Asn347, and Asp360; ACm3A) were substituted with Ala. Biochemical studies showed that the affinities of ACm1A and ACm2A for CaM were not affected significantly, whereas that of ACm3A was reduced dramatically. To under- stand the effects of these modifica- tions, molecular dynamics (MD) sim- ulations were performed based on the modified proteins. The MD trajecto- ries recorded for the ACm3A/C-CaM complex showed that the calcium- binding loops of C-CaM exhibited large fluctuations, which could be related to the weakened interaction between ACm3A and its activator. Overall, our results suggest that the LHL motif at the C-terminal end of AC is crucial during CaM-binding for stabilizing the AC catalytic loop in an active configuration. INTRODUCTION The adenylyl cyclase toxin (CyaA) from Bordetella pertussis, the causative agent of whooping cough, plays an essential role in host invasion [1–3]. CyaA is able to invade eukaryotic target cells where it is activated by interacting with calmodulin (CaM), thereby overproducing cAMP, which disorganizes cellular signaling processes and triggers host cell death [4–12]. Several crys- tallographic structures have been reported of the CyaA catalytic domain (AC) in com- plex with the C terminal moiety of CaM (C-CaM) [13] (Figure 1). These structures are physiologically relevant because C-CaM has been shown [14] to be as potent in acti- vating the enzymatic activity of AC as the full-length CaM. In the AC/C-CaM com- plex (Figure 1a), the AC domain includes three main regions, CA (residues 7–61, 187– 197, 261–299, and 313–345; colored in green) in the middle of the structure, and CB (residues 62–186, colored in orange) and SA (residues 192–254, colored in purple) at the two extremities. The C-terminal tail (residues 346–364, colored in cyan) and the C-loop of the catalytic site (residues 300– 312, colored in yellow) are found in the CA region. At the C-terminal end of AC, a loop-helix-loop motif (LHL) that includes residues from Arg338 to Asp360 (Figure 1c) is present at the interface between C-CaM and a major AC catalytic loop that spans residues 300–312. In C-CaM, the calcium ions are bound to EF-hands 3 and 4, where EF-hand 3 is close to the interaction inter- face with AC. In a previous study [15], we analyzed the interaction between the catalytic do- main of AC from B. pertussis and C-CaM based on the molecular dynamics (MD) tra- jectories using maps of the energetic influ- ences [16, 17]. Three residues in the LHL motif, i.e., Arg338, Asn347, and Asp360 (Fig- ure 1b), were predicted to be important for the stability of the AC/CaM interaction, where Arg338 and Asp360 make contact with C-CaM, whereas Asn347 is in direct contact with the AC catalytic loop. In the present study, to further characterize the potential roles of these residues in AC/CaM interac- tions, we performed in silico MD simulations and in vitro biochemical and biophysical studies of the three modified AC proteins, where one (Asn347; ACm1A), two (Arg338 and Asp360; ACm2A), or three residues (Arg338, Asn347, and Asp360; ACm3A) were substituted with Ala. We found that the ACm3A variant exhibited a strongly re- duced affinity for CaM, whereas the affini- ties of the ACm1A and ACm2A variants were similar to that of the wild-type enzyme. byguestonJune8,2014http://www.jbc.org/Downloadedfrom
  • 4. Mutants of AC and AC/CaM interaction 3 This demonstrated the strong synergistic ef- fects of the three mutations. The MD sim- ulations showed that the differences in the behavior of the modified and wild-type com- plexes were related to differences in the in- ternal mobility of the C-CaM calcium loops. These differences in mobility may induce di- rect or indirect weakening of the C-CaM/AC interaction observed in the ACm3A modi- fied protein. These results, as well as an analysis of the geometrical strain, suggest that the LHL motif at the C-terminal end of AC is important for establishing a long- range connection between CaM binding and the stabilization of the AC catalytic loop in an active configuration, thus it is a criti- cal module during the allosteric activation of AC by CaM. 1 EXPERIMENTAL PRO- CEDURES MD simulations The wild-type AC/C-CaM complexes in the presence (ACwt 2Ca) and absence (ACwt 0Ca) of calcium were prepared as de- scribed previously [15] and the three mod- ified systems, i.e., ACm1A, ACm2A, and ACm3A, were generated in the following manner. The last snapshot of the simula- tion WT2Ca T1 (see Table I for the defi- nition of this trajectory) was extracted and the sidechains of the modified residues were replaced by Ala sidechains using the LEaP module from AMBER 10 [18] and the force field FF99SB [19]. Na+ counterions were added to neutralize the system. The five systems, i.e., ACwt 2Ca, ACwt 0Ca, ACm1A, ACm2A, and ACm3A (Table I) were then hydrated in a box of TIP3P [20] water molecules using cutoff val- ues of 10 or 12.5 ˚A and periodic boundary conditions. The calcium Lennard-Jones pa- rameters of the Ca2+ ions comprised a van der Waals radius R of 1.7131 ˚A, and a well depth of 0.459789 kcal/mol [21]. The MD trajectories were initiated and ran as described previously 15. For each sys- tem, two simulations were recorded, which were labeled using the system name and the strings “T1” and “T2” (Table I). The formation of hydrogen bonds be- tween protein acceptor and donor groups was monitored by selecting donor and ac- ceptor pairs with a proximity of less than 3 ˚Aevery ten recorded frames. This selection was implemented using the Biskit python li- brary [22]. In the following, the AC and C-CaM residues are labeled based on their numbers in the crystallographic structure 1YRT [13] and the C-CaM residue numbers are followed by the letter a. Along the MD trajectories, the geomet- ric strain [23] of a residue i was calculated using the following equation: p(i) = j (dij − dij )2 [1−tanh( dij −7)]/2 (1) where (dij − dij )2 is the intantaneous de- viation from the average of the distance dij between the α carbons of residues i and j. It was shown previously [23] that hinge residues are characterized by large p(i) val- ues. Plasmids Plasmid pTRAC384GK was used to express the wild-type AC (corresponding to the first 384 codons of CyaA, followed by the two residues Gly and Lys), as described pre- viously 24. Plasmids pKTRACm2A and pKTRACm3A, which were used to express ACm2A and ACm3A, respectively, were constructed from plasmid pKTRAC, an ex- pression vector for the CyaC and CyaA pro- teins of B. pertussis. This plasmid was ob- tained from plasmid pTRACG [25] by re- placing the ampicillin (Amp) resistance gene with a kanamycin (Kan) resistant gene from plasmid pKT25 [26]. In pKTRAC, both the cyaC and cyaA genes are expressed under the control of the λ phage Pr promoter. The plasmid has a ColE1 replication origin and it also expresses a thermosensitive λ repressor cI857, which strongly represses gene tran- scription at the λ Pr promoter at tempera- byguestonJune8,2014http://www.jbc.org/Downloadedfrom
  • 5. Mutants of AC and AC/CaM interaction 4 tures below 32 ◦C. Thus, expression of the CyaC and CyaA proteins can be triggered by shifting the cells to 37–42 ◦C. Plasmid pKTRACm3A was constructed by subcloning between the unique AgeI and BamHI sites of pKTRAC, a synthetic gene (synthesized by GeneArt, Life Technologies SAS, France) that encodes CyaA residues 320–384, followed by the two residues Gly and Lys, and where the three codons, Arg338, Asn347, and Asp360, were changed to Ala codons (the sequence of the ACm3A gene is available upon request). Plasmid pKTRACm2A was constructed by subcloning between the unique SnaBI and BsiWI sites of plasmid pKTRACm3A using a double-stranded synthetic oligonu- cleotide produced via the hybridization of the following two oligonucleotides: 5’- GTTTTCTACGAAAACCGCGC-3’ and 5’- GTACGCGCGGTTTTCGTAGAAAAC-3’ (Eurofins MWG GmbH, Ebersberg, Ger- many), thereby restoring the wild-type Asn347 codon (the SnaBI site was abol- ished after oligonucleotide insertion; see Figure S1). The DNA sequences of the modified cyaA’ genes in pKTRACm2A and pKTRACm3A were confirmed by DNA se- quencing (Eurofins MWG GmbH, Ebers- berg, Germany). Plasmid pKT7AC contained a synthetic AC gene (synthesized by GeneArt, Life Technologies SAS, France) that encoded the first 384 codons of CyaA, which was op- timized for high expression in Escherichia coli, followed by the two residues Gly and Lys (the full DNA sequence is available upon request). This synthetic AC gene was cloned under the control of a T7 promoter and a synthetic RBS sequence in the vector pMK-RQ (GeneArt, Life Technologies SAS, France), a plasmid with a ColE1 replication origin and a Kan resistance gene. Plasmid pKT7ACm1A was used to express ACm1A and it was con- structed by subcloning between the unique SnaBI and BsiWI sites of plas- mid pKT7AC, a double-stranded syn- thetic oligonucleotide, which was obtained by hybridizing two oligonucleotides: 5’- GTGTTCTACGAAGCTCGCGC-3’ and 5’- GTACGCGCGAGCTTCGTAGAACAC-3’ (Eurofins MWG GmbH, Ebersberg, Ger- many), thereby replacing the wild-type Asn347 codon with an Ala codon (sequence available upon request). The DNA sequence of the modified cyaA’ gene in pKT7ACm1A was confirmed by DNA sequencing (Eurofins MWG GmbH, Ebersberg, Germany). Purification of AC proteins The wild-type AC, ACm2A, and ACm3A were expressed in the E. coli BLR strain (Novagen, Darmstadt, Germany) by transformation with the plasmids pTRAC384GK, pKTRACm2A, and pK- TRACm3A, respectively. The transfor- mants were grown at 30 ◦C in LB medium that contained either 100 µg/mL Amp (for plasmid pTRAC384GK) or 50 µg/mL Kan (for plasmids pKTRACm2A or pK- TRACm3A). When the culture reached an optical density of 0.6–0.8 at 600 nm, expres- sion of the proteins was triggered by shifting the growth temperature to 42 ◦C. After 150 min of additional growth at 42 ◦C, the cells were collected by centrifugation (20 min, 10,000 × g, 4 ◦C) and the cell pellets were frozen at -20 ◦C. ACm1A was expressed in the E. coli KRX strain (Promega, Madison, USA), which was transformed with the plas- mid pKT7ACm1A. The transformants were grown at 37 ◦C in LB medium containing 50 µg/mL Kan to an optical density of 0.6– 0.8. Next, expression of the proteins was triggered by the addition of 0.1% rhamnose (to induce the expression of the chromoso- mally encoded T7 RNA polymerase). After 180 min of additional growth at 37 ◦C, the cells were collected by centrifugation, as de- scribed above. The cell pellets were resuspended in 20 mM HEPES-Na, pH 7.5, and disrupted by sonication at 4 ◦C. The sonicated suspen- sion was centrifuged for 20 min at 13,000 × g and 4 ◦C. The supernatant was discarded byguestonJune8,2014http://www.jbc.org/Downloadedfrom
  • 6. Mutants of AC and AC/CaM interaction 5 and the pellet was resuspended in 8 M urea with 20 mM HEPES-Na (pH 7.5), and ag- itated overnight at 4 ◦C. After 20 min of centrifugation at 13,000 × g at 4 ◦C, the su- pernatant (“urea extract”) that contained the solubilized AC proteins was collected. The AC proteins were purified accord- ing to a previously described protocol us- ing two sequential chromatographic treat- ments with DEAE-Sepharose [24]. Briefly, the urea extract was first loaded onto a DEAE-Sepharose column (20 mL packed resin) equilibrated in 8 M urea with 20 mM HEPES-Na (pH 7.5). In these con- ditions, the AC protein did not bind to the resin and it was recovered in the flow- through (FT) fractions. The collected FT fractions were then diluted five times with 20 mM HEPES-Na (pH 7.5) and applied to a second DEAE-Sepharose column (20 mL packed resin), which had been equilibrated in 20 mM HEPES-Na (pH 7.5). In these conditions, the AC proteins were retained on the resin and, after extensive washing with 20 mM HEPES-Na (pH 7.5), the pro- teins were eluted in a soluble form using 20 mM HEPES-Na (pH 7.5) containing 100– 200 mM NaCl. All of the AC protein prepa- rations exceeded a purity of 95% according to SDS-PAGE analysis (Figure 6A). The AC protein content was determined based on the absorption spectra using an extinction coef- ficient at 278 nm of 28,000 M−1/cm−−1. AC enzymatic activity assays The activity of AC was measured using a sensitive colorimetric assay, which was re- ported recently [27]. AC converts ATP into cAMP and pyrophosphate (PPi), and the latter can be hydrolyzed further by an ex- ogenously added pyrophosphatase into two phosphate molecules (Pi), which can be quantified using a standard colorimetric as- say based on the change in the absorbance of malachite green dye in the presence of phos- phomolybdate complexes. The amount of Pi produced was determined using the Pi color Lock TM ALS colorimetric assay from Innova Biosciences (Cambridge, UK). The AC enzymatic assays were per- formed using a 96-well microtiter plate at 30◦C in a final volume of 50 µL, which con- tained 50 mM Tris-HCl (pH 8.0), 10 mM MgCl2, 0.1 mM CaCl2, 0.5 mg/mL bovine serum albumin, 2 Unit/mL of E. coli inor- ganic pyrophosphatase (Sigma-Aldrich; the amount of pyrophosphatase added to the re- action medium was found to be sufficient to ensure the immediate and complete con- version of the released PPi into Pi), 0–1 µM of CaM, and 0.1–1 nM (depending on the specific activity) of AC proteins (di- luted from stock solutions in 10 mM Tris- HCl with 0.2% Tween 20, pH 8.0). The mix- tures were pre-incubated for 10 min at 30◦C. Then, the enzymatic reactions were initiated by adding 2 mM ATP (final concentration) and the microplate was incubated at 30◦C with agitation. At various incubation times (typically 2–10 min), 10 µL samples were taken from each well and transferred into a second 96-well microtiter plate, where each well contained 100 µL of a Pi-ALS mixture made of 2 volumes of H2O plus 8 volumes of Pi ColorLock ALS reagent (provided in the Pi-ALS kit from Innova Biosciences). The enzymatic reaction was stopped imme- diately by the acidic conditions of the Pi- ALS mixture. After 10–13 min incubation at room temperature, 10 µL of stabilizer so- lution (from the Pi-ALS kit) was added to prevent further nonenzymatic breakdown of the phosphorylated substrate in acidic con- ditions (according to the kit instructions). After further incubation for 30–60 min at room temperature, the optical density at 595 nm (OD595) was recorded using a mi- croplate reader (Tecan, Lyon, France). A standard curve was obtained in parallel by adding known concentrations of Pi to the Pi-ALS mixture, which was used to convert the OD595values into moles of PPi produced. The enzymatic activity was calculated based on the initial velocity of PPi synthesis (in the conditions described above, the accumu- lation of PPi was linear with time). byguestonJune8,2014http://www.jbc.org/Downloadedfrom
  • 7. Mutants of AC and AC/CaM interaction 6 Biophysical characterization of AC proteins Size exclusion chromatography (SEC) was performed using a Superdex 200 column (GE Healthcare), which was controlled by a GPCmax module that was connected on- line to a triple detector array (TDA) model 302 (Viscotek Ltd, Houston, Basingstoke, U.K.), as described previously [28]. The running buffer was buffer A (20 mM Hepes, 100 mM NaCl, pH 7.4) and the protein concentrations were 10–20 µM. Synchrotron radiation circular dichroism (SR-CD) ex- periments were conducted at the SOLEIL synchrotron facility (DISCO beamline, Gif- sur-Yvette, France), as described previ- ously [29]. Briefly, the SR-CD spectra were recorded at 25◦C using an integration time of 1.2 s and a bandwidth of 1 nm, with a 1-nm resolution step. Each far-UV spec- trum represented the average of at least three individual scans. Optical cells with a 26 µm path-length and CaF2 windows (Hellma) were used for recording CD sig- nals in the far-UV region (180–260 nm). The protein concentrations were 25–50 µM for AC proteins and 250 µM for CaM in buffer A. Equimolar mixtures of enzyme and activator were used to obtain the AC-CaM and ACm3A-CaM spectra. The thermo- dynamic stability of the AC proteins was investigated by following their urea-induced denaturation (at 25◦C, in buffer A), which was monitored by tryptophan fluorescence spectroscopy as described previously [30] using an FP-6200 spectrofluorimeter (Jasco, Japan) in a Peltier-thermostated cell holder, with a 1-cm path length quartz cell (101.QS, Hellma). The thermodynamic parameters (urea concentration required to unfold half the population of native proteins, [urea]1/2, the cooperativity, m, and free energy, ∆G) were deduced from the fluorescence data, as described previously 30. RESULTS C-CaM/AC interface in the crystal- lographic structures To explore the potential role of AC residues Arg338, Asn347, and Asp360 in CaM-induced activation, as suggested previously [15], we first checked the conservation of the atomic contacts established by these residues in the crystallographic structures of the AC/C- CaM complex [13]. The analysis of the hydrogen bonds and water-mediated con- tacts established between C-CaM and AC residues showed that the residues Arg338 and Asp360 were often involved in hydrogen bonds or in water-mediated contacts with C-CaM (data not shown, but available on request). Furthermore, most of the contacts and hydrogen bonds between the LHL mo- tif (residues 338–360) (Figure 1c) and other AC residues were present in more than three crystallographic structures (data not shown, but available on request), thereby suggest- ing that the LHL motif plays an important role in the stabilization of the AC structure. C-CaM/AC interaction along MD trajectories Six independent MD simulations were recorded using the AC/C-CaM complex, where AC was modified in three dif- ferent ways. Two simulations, i.e., ”T1” and ”T2,” were performed for each AC variant, ACm1A (N347A), ACm2A (R338A, D360A), and ACm3A(R338A, N347A, D360A) (Figure 1b). The aim of these simulations was to analyze the rela- tive stability of the different ACm/C-CaM complexes and to relate these to the obser- vations described previously based on the X- ray crystallographic structures. The conformational drift of the AC/C- CaM complex was monitored during trajectories ACm1A T1, ACm2A T1, ACm3A T1, ACm1A T2, ACm2A T2, and ACm3A T2 (Figure 2). The global RMSD calculated for the different AC/C-CaM com- plexes (Figures 2a and 2e) were similar byguestonJune8,2014http://www.jbc.org/Downloadedfrom
  • 8. Mutants of AC and AC/CaM interaction 7 for all variants and they rapidly reached a plateau around 3 ˚A. The RMSD plateau was similar to that obtained based on the MD trajectories of the wild-type AC/C- CaM complex (Figure 2a in Ref [15]). Thus, these modifications did not destabilize the overall AC structure at least during the timescales considered by the MD trajecto- ries. The conformational drifts (RMSD) of the different protein regions in the two sets of simulations (Figures 2b-d and 2f-h) were very similar for CB (orange curves), the C loop (yellow curves), the F, G, H, and H’ α helices, and the loop at the extremity of SA, which all had RMSD plateaus that were similar to or less than 2 ˚A. The CA region (green curves), SA region (violet curves), and C-terminal tail (cyan curves) had more significant drifts, where the RMSD values were larger than 4 ˚A. The CA and C ter- minal drifts are not surprising because the modified residues were located in these re- gions. Interestingly, the increased internal mobility of the C terminal tail is analogous to that observed in a wild-type AC/C-CaM complex (Figure 3a, b of Ref [15]) when the Ca2+ ions were removed (Figure 3a, b of Ref [15]). The latter had a lower affinity in vitro, thus the modifications of residues Arg338, Asn347, and Asp360 may have de- creased the affinity of C-CaM for AC. The water-mediated connections be- tween AC and C-CaM were also ana- lyzed along the MD trajectories (data not shown). The connections that involved the C-terminal tail of AC were present mainly in one or two trajectories, which shows that the interaction at this interface underwent reorganizations. C-CaM and AC fluctuations in the MD trajectories The behavior of C-CaM was monitored along the two series of mutant trajectories and compared with previous observations [15] obtained using the wild type AC/C- CaM complex. In the simulation of the wild-type AC/C- CaM complex in the absence of calcium ions (WT0Ca T1) (Figure 3a, solid red curve), the calcium loop of EF-hand 3 (i.e., between α helices V and VI) and the C-terminal part of α helix V exhibited highly increased fluc- tuations (RMSF). A similar increase was ob- served in ACm3A T1 (Figure 3b, solid red curve) but in ACm2A T2 and ACm3A T2 (Figure 3b, dashed green and red curves), increased fluctuations were found in the cal- cium loop of EF-hand 4 (i.e., between α helices VII and VIII). Interestingly, the in- creased fluctuations in the C-terminal part of α helix V in ACm3A T1 was associated with the small number of hydrogen bonds that connect C-CaM and C tail, i.e., only a single hydrogen bond is present for over 80% of the trajectory length between Arg90a and Glu346. Analysis of the internal fluctuations of AC along the various trajectories (data not shown) detected no major variations be- tween the different modified proteins, which agreed with the similar global RMSD that was observed for all trajectories (Figure 2). The fluctuations measured in the wild-type systems were similar to those observed in the modified proteins, where the largest dif- ferences were observed for the 226–232 loop and the C-terminal tail of the protein. It should be noted that the loop 226–232 is not visible in the X-ray crystallographic struc- tures, thereby indicating that it is probably a highly flexible region. The coordination of calcium ions by the C-CaM residues was stable in the EF-hand 3 along the trajectories of the modified pro- teins (data available on request), but there were some variations in the EF-hand 4. In- deed, the calcium coordination by Asp133 in the EF-hand 4 was perturbed in the two series of simulations. This perturba- tion agrees with the increased fluctuation observed in the calcium loop of EF-hand 4 for ACm2A T2 and ACm3A T2 (Figure 3b), and with the increase in the EF-hand 4 angle up to about 100◦. The C-CaM conformations were ex- byguestonJune8,2014http://www.jbc.org/Downloadedfrom
  • 9. Mutants of AC and AC/CaM interaction 8 tracted from ACm2A T2 and ACm3A T2 (Figure 4) at times when different distances were observed between Asp133-Oδ1/Oδ2 and the calcium ion. In both simulations, the sidechain of Asp133 moved apart and at the end of the trajectory, the calcium ion was coordinated by the backbone carbonyl, instead of the sidechain. This conforma- tional tendency of Asp133 was increased in ACm3A T2 compared with ACm2A T2. In- terestingly, in a steered MD study of the cal- cium dissociation in CaM [31], it was found that Asp133 was among the latest residues to lose calcium coordination. The destabiliza- tion of the calcium/Asp133 interaction ob- served in the present study corresponds to the destabilization of one of the strongest interactions that defines the calcium coor- dination in EF-hand 4. Thus, this desta- bilization indicates that the AC mutations decreased the calcium binding to CaM. Overall, the perturbations of the EF- hand angles and calcium coordination are precursory indicators of the decrease in the C-CaM affinity for calcium ions [32,33]. On longer time scales, this decrease could lead to the dissociation of calcium ions from C- CaM and to a decrease in the affinity of AC for C-CaM, as shown previously [14]. Network of interactions involving LHL along the MD trajectories The LHL motif, which contains the three modified residues, lies at the interface be- tween C-CaM and the AC catalytic loop. The hydrogen bonds established by the residues in the LHL motif were analyzed in the different AC/C-CaM complexes (data available on request). Only long-range hy- drogen bonds (that connected residues sep- arated by more than ten residues in the protein sequence) were considered in order to exclude interactions related to local sec- ondary structures. Most of these hydrogen bonds were conserved along the MD tra- jectories, except for one hydrogen bond be- tween Asn35 and Tyr342, which was present only in the modified complexes, and two hy- drogen bonds between Glu346 and Leu357, and between Tyr350 and Glu308, which were observed in less than two simulations. A lower number of stable hydrogen bonds that involved modified residues were observed in the ACm3A T1 and ACm3A T2 simula- tions. Indeed, Asn347 established hydrogen bonds with the residues Glu301, Gln302, and Asn304, which are located in the catalytic loop. These hydrogen bonds were disrupted by the change from Asn347 to Ala, except for the hydrogen bonds that involved the Asn347 backbone hydrogen. Similarly, the hydro- gen bonds between Asp360 and Arg338 dis- appeared when Asp360 or Arg338 were mod- ified to Ala. These observations show that the overall structure of the LHL motif is con- served in all systems, and that the LHL con- nection to C-CaM on one side, as well as to the C-loop on the other side, were signifi- cantly weakened in the presence of the triple modification. The hydrogen bonds that involved LHL residues, as well as the protein fluctua- tions and the correlations in the fluctua- tion, indicated that there was limited vari- ation among the protein variants (data not shown). Thus, the possibility of long-range communication through LHL was investi- gated using a parameter that was poten- tially more sensitive to small variations in geometry. The geometric strain, as defined by Chiappori et al. [23] (see Materials and Methods), exhibits sufficient sensitivity be- cause it depends on the geometry of the en- vironment of the analyzed residue within a sphere of 7 ˚A while it also follows the dis- tance variations with respect to the average distance values. The variations in the geometric strain along the MD trajectories exhibited corre- lated transitions between the given residues, which were due to simultaneous displace- ments of the environments of these residues. To summarize these variations, the time correlation matrices of the geometric strain were analyzed. The strain correlation peaks (in pink/yellow) correspond to residue pairs that are undergoing correlated displace- byguestonJune8,2014http://www.jbc.org/Downloadedfrom
  • 10. Mutants of AC and AC/CaM interaction 9 ments in their environment, thus they are mechanically correlated. In order to esti- mate the reliability of the correlation pre- dictions, the calculation was repeated five times by selecting at each time, one data- point over five along the analyzed time interval. The average values were calcu- lated among LHL residues (Figure 5) and among the LHL, C-loop and calcium loop residues (data not shown but available on request). The standard deviations obtained from the repeated calculation of the corre- lations allowed us to estimate the error on the correlation, which was 4–6.5% for cor- relations greater than 0.15. In all trajecto- ries, the peaks were observed repeatedly be- tween residues in the α-helix at 346–355. A general attenuation of the correlations, with pixel colors changing from pink to yellow, was observed for the trajectories recorded in the protein variants compared with those recorded in the wild type. This suggests that there was a decrease in the long-range correlation along the LHL for the modified proteins. In vitro characterization of AC vari- ants that harbored mutations at po- sitions 338, 347 or 360 To further delineate the effect of the muta- tions on the activity of AC and its affinity for CaM, the three variants ACm1A, ACm2A, and ACm3A were characterized in vitro (see Materials and Methods). The three modi- fied proteins and the wild-type catalytic do- main (AC) were overexpressed in E. coli and purified to homogeneity, as described pre- viously ( [24], see Materials and Methods). The results of the SDS-PAGE analysis of the purified preparations are shown in Figure 6A. The enzymatic activities of each AC variant were determined at different CaM concentrations, which ranged from 0.03 nM to 1 µM. Figure 6B shows the CaM- dependency of the enzymatic activity for each variant as a percentage of the maximal activity (100 %) determined at the saturat- ing CaM concentration of 1 µM. The affini- ties of the AC enzymes for CaM, which were defined as the CaM concentration at half- maximal activation K1/2, were determined (Figure 6C) by curve-fitting with a single binding isotherm, according to A = AMax (C/C+ K1/2) where C is the concentration of CaM, A is the activity at the concentra- tion C of CaM, and AMax is the maximal activity measured in the presence of 1 µM CaM. As shown in Figures 6B and C, wild-type AC (labeled ACWT in Figure 6C) exhibited a kcat of 4600 s−1 (at saturating CaM and 2 mM ATP) and a half-maximal CaM activa- tion K1/2 of 0.11 nM, which agreed well with previous studies [13, 24, 34]. The ACm1A variant, where the Asn347 residue that in- teracted with the catalytic loop was mod- ified to Ala, exhibited an enzymatic activ- ity that was reduced by about half (kcat ∼ 2250 s−1) compared with the wild type and a ∼ five-fold lower affinity for CaM (KCaM 1/2 of 0.61 nM). The dual mutations R338A and D360A in the ACm2A variant did not af- fect the catalytic efficiency (kcat ∼ 6000 s−1 was even slightly higher than that of the wild type) but the affinity for CaM was re- duced by about six-fold (KCaM 1/2 of 0.66 nM), as might be expected with modifications at the CaM interface. Finally, the triple mu- tant ACm3A was the enzyme that was af- fected most significantly, where its catalytic turnover (kcat ∼ 650 s−1) was decreased sig- nificantly compared with the wild-type AC (ca 15% of the wild type turnover) and its affinity for CaM (KCaM 1/2 of 26 nM) was re- duced by more than 200 times. These data indicate that the separate single (N347A) and dual (R338A, and D360A) modifications had limited effects on the catalytic and CaM-binding properties of AC, whereas their combination in a single enzyme (ACm3A) had strong synergistic ef- fects on both the enzymatic activity and the affinity for CaM. This fully supports our pre- diction that the LHL region is critical for the allosteric coupling of CaM binding to the stabilization of the catalytic loop in an enzy- byguestonJune8,2014http://www.jbc.org/Downloadedfrom
  • 11. Mutants of AC and AC/CaM interaction 10 matically active configuration. The two- to five-fold higher KATP M levels of all the mod- ified AC enzymes compared with the wild- type AC also demonstrate that the LHL mo- tif is important for maintaining the optimal conformation of the active site. To verify that the triple modification of R338A, N347A, and D360A in ACm3A did not affect the structural integrity of the pro- tein, we performed the following biophysi- cal analyses. First, the proteins were ana- lyzed by SEC followed by triple detector ar- ray (SEC-TDA) to determine whether the mutations affected their oligomeric status. SEC-TDA provides the molecular masses of the eluted species by combining static right angle light scattering with UV ab- sorbance. The results showed that both the wild-type and ACm3A proteins were monomeric species in solution (Figure 7A). The secondary structure contents of the CaM and AC proteins, either isolated or in complexes, were analyzed by SRCD in the far-UV range. The shapes of the far-UV CD spectra of wild-type AC and ACm3A were similar (Figure 7B). The addition of CaM induced similar changes in the over- all secondary structure content of both AC proteins. These results clearly indicate that the secondary structure content of ACm3A was not affected by the mutations. Fi- nally, the thermodynamic stability of both AC proteins was characterized. The urea- induced denaturation of the AC proteins was monitored by tryptophan fluorescence. The denaturation profiles (Figure 7C). and the thermodynamic parameters (Figure 7D) obtained for both proteins were very similar. Overall, these experiments indicate that the three modifications in ACm3A did not af- fect the structural properties or the overall stability of the protein. DISCUSSION Maps of the energetic influences [16, 17] that were calculated [15] previously using the AC/C-CaM complex allowed us to iden- tify three residues, i.e., Arg338, Asn347, and Asp360, that might affect the interaction be- tween AC and C-CaM. In the present study, we characterized three modified proteins, i.e., ACm1A (N347A), ACm2A (R338A, D360A), and ACm3A (R338A, N347A and D360A), using in silico MD simulations and based on in vitro biochemical and biophysi- cal studies. Our in vitro studies showed that the affinity of the triple mutant ACm3A for CaM was greatly reduced whereas that of the single (ACm1A) or dual mutant (ACm2A) was not affected significantly compared with that of the wild-type en- zyme. These results indicate that these three mutations had a strong synergistic ef- fect on the CaM-binding affinity. A similar synergistic effect was noted for the catalytic efficiency of the enzyme because the enzy- matic activity of ACm3A was also reduced significantly (about 15% of the wild-type en- zyme activity), whereas that of ACm1A was about 50% of the wild-type activity. The lower activity of the ACm1A and ACm3A variants might be expected because the Asn347 residue interacts directly with the catalytic loop. Thus, any perturbation of the interaction between Asn347 and the cat- alytic loop might directly affect the catalytic efficiency of AC. The dynamical behaviors of the three modified proteins in complex with C-CaM were also analyzed in silico based on two series of MD simulations. High variabil- ity in the establishment of hydrogen bonds in the complex was observed in the dif- ferent modified proteins, as well as among repeated trajectories. However, this vari- ability could not be assigned to simula- tion artifacts because similar variability was observed among the four crystallographic structures of the complex AC/C-CaM [13]. The analysis of the trajectories recorded using modified and wild-type AC/C-CaM complexes, which were conducted in paral- lel with the experimental characterization of the AC/CaM interaction, identified two different routes that allowed the affinity of AC for C-CaM to decrease. In the first byguestonJune8,2014http://www.jbc.org/Downloadedfrom
  • 12. Mutants of AC and AC/CaM interaction 11 simulation of the triple modified protein (ACm3A T1), a destabilization of the cal- cium loop of EF-hand 3 was observed, as well as a large decrease in the interactions between C-CaM and the CA region. In the second trajectory recorded using ACm3A (ACm3A T2), a destabilization of the cal- cium coordination in the EF-hand 4 of C- CaM led to the disruption of the hydrogen bond between the Asp133 sidechain and cal- cium. This could be the first step in the pos- sible dissociation of calcium from C-CaM. It is known that calcium-free CaM has a lower affinity for AC [14], thus the destabilization of calcium coordination would result in a re- duction of the CaM affinity for AC. Guo et al. [13] described the crys- tallographic structure of the complex AC/C-CaM and characterized one AC modification: the double modification E346A/R348A in the C terminal tail. The modified protein exhibited a reduced enzy- matic activity as well as a reduced affinity for CaM. The two amino acids changed in the E346A/R348A mutant flanked the Asn347 residue that was modified in the present study. The hydrogen bonds that in- volve Glu346 and Arg348 residues varied in the wild-type AC when calcium ions or C- CaM were removed from the system, as well as in the trajectories of the modified AC pro- tein, but no systematic variations were de- tected. However, the observations of Guo et al. [13] based on the E346A/R348A AC variant agree well with our present study, as well as supporting the hypothesis that the LHL motif is critical for linking CaM binding with the stabilization of the AC cat- alytic loop in a configuration that is favor- able for catalysis. Indeed, the LHL mo- tif is in direct contact with C-CaM on one side via the Arg338 and Asp360 residues, as well as the catalytic loop on the other side via the Asn347 residue. Thus, it is ideally positioned to relay information re- lated to CaM-binding on the distant cat- alytic site of the AC enzyme via a dense network of atomic contacts, which primar- ily involve the Arg338, Asn347, and Asp360 residues, as demonstrated in our MD simu- lations. Long-range communications within the LHL motif were further suggested by our analysis of the geometric strain along the MD trajectories of the different ACs. There- fore, the LHL motif appears to be a crit- ical module for the allosteric activation of AC by CaM. The analysis performed in the present study was more qualitative than the method proposed recently by Weinkam et al. [35,36], but we should note that the avail- ability of only one structure of AC in com- plex with Ca2+-loaded C-CaM, as well as the conformational equilibrium that is prob- ably adopted by AC in the unbound state, prevent a more straightforward application of this method. From a more general perspective, the de- tection of the residue networks that are re- sponsible for long-range communication in- side a given protein has been attracting much interest during the last decade [37–41]. These networks are thought to be involved in biomolecular interactions [42] with fun- damental roles in many biological processes [43]. Homologous protein sequence align- ments [44–46] or analysis of the covariance of the NMR chemical shifts [47] have predicted long-range protein communication networks that agree with experimental observations. Some of these analyses have facilitated pro- tein engineering [48]. In the present study, we combined MD and mutagenesis to iden- tify a long-range communication network re- lated to the activation of a key virulence factor derived from a bacterial pathogen. This investigation may facilitate new meth- ods for interfering with the AC-CaM inter- action, thereby allowing a novel drug discov- ery approach [49]. ACKNOWLEDGMENTS We acknowledge SOLEIL for providing the synchrotron radiation facilities (Proposal IDs 20110586 and 20120444) and we thank Frank Wien for assistance with using the DISCO beamline. Edithe Selwa was sup- ported by an allocation doctorale from byguestonJune8,2014http://www.jbc.org/Downloadedfrom
  • 13. Mutants of AC and AC/CaM interaction 12 MENRT, which was distributed by Uni- versit´e Pierre et Marie Curie (Paris VI). Ana Cristina Sotomayor P´erez was sup- ported by an Institut Pasteur PTR grant (PTR#374). This project was supported by the Institut Pasteur and the Centre National de la Recherche Scientifique (CNRS UMR 3528, Biologie Structurale et Agents Infec- tieux). Data not shown in the manuscript may be obtained from the authors (Daniel Ladant: daniel.ladant@pasteur.fr; Th´er`ese Malliavin: therese.malliavin@pasteur.fr) on request. References [1] Ladant, D. and Ullmann, A. (1999) Bordetella pertussis adenylate cyclase: a toxin with multiple talents. Trends Microbiol 7, 172–176 [2] Vojtova, J., Kamanova, J., and Sebo, P. (2006) Bordetella adenylate cyclase toxin: a swift saboteur of host defense. Curr Opin Microbiol 9, 69–75 [3] Carbonetti, N. (2010) Pertussis toxin and adenylate cyclase toxin: key virulence factors of Bordetella pertussis and cell biology tools. Future Microbiol 5, 455–469 [4] Wolff, J., Cook, G., Goldhammer, A., and Berkowitz, S. (1980) Calmodulin activates prokaryotic adenylate cyclase. Proc Natl Acad Sci USA 77, 3841–3844 [5] Confer, D. and Eaton, J. (1982) Phagocyte impotence caused by an invasive bacterial adenylate cyclase. Science 217, 948–950 [6] Rogel, A., Schultz, J., Brownlie, R., Coote, J., Parton, R., and Hanski, E. (1989) Bordetella pertussis adenylate cyclase: purification and characterization of the toxic form of the enzyme. EMBO J 8, 2755–2760 [7] Goodwin, M. and Weiss, A. (1990) Adenylate cyclase toxin is critical for colonization and pertussis toxin is critical for lethal infection by Bordetella pertussis in infant mice. Infect Immun 58, 3445–3447 [8] Khelef, N., Zychlinsky, A., and Guiso, N. (1993) Bordetella pertussis induces apoptosis in macrophages: role of adenylate cyclase-hemolysin. Infect Immun 61, 4064–4071 [9] Harvill, E., Cotter, P., Yuk, M., and Miller, J. (1999) Probing the function of Bor- detella bronchiseptica adenylate cyclase toxin by manipulating host immunity. Infect Immun 67, 1493–1500 [10] Hewlett, E., Donato, G., and Gray, M. (2006) Macrophage cytotoxicity produced by adenylate cyclase toxin from Bordetella pertussis: more than just making cyclic AMP! Mol Mic 59, 447–459 [11] Cheung, G., Dickinson, P., Sing, G., Craigon, M., Ghazal, P., Parton, R., and Coote, J. (2008) Transcriptional responses of murine macrophages to the adenylate cyclase toxin of Bordetella pertussis. Microb Pathog 44, 61–70 [12] Kamanova, J., Kofronova, O., Masin, J., Genth, H., Vojtova, J., Linhartova, I., Be- nada, O., Just, I., and Sebo, P. (2008) Adenylate cyclase toxin subverts phagocyte function by RhoA inhibition and unproductive ruffling. J Immunol 181, 5587–5597 byguestonJune8,2014http://www.jbc.org/Downloadedfrom
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  • 15. Mutants of AC and AC/CaM interaction 14 [27] Laine, E., Goncalves, C., Karst, J., Lesnard, A., Rault, S., Tang, W., Malliavin, T., Ladant, D., and Blondel, A. (2010) Use of allostery to identify inhibitors of calmodulin- induced activation of Bacillus anthracis Edema Factor. Proc. Natl. Acad. Sci. U.S.A. 107, 11277–11282 [28] Karst, J., Sotomayor-P´erez, A., Guijarro, J., Raynal, B., Chenal, A., and Ladant, D. (2010) Calmodulin-induced conformational and hydrodynamic changes in the cat- alytic domain of Bordetella pertussis adenylate cyclase toxin. Biochemistry 49, 318– 328 [29] Sotomayor-P´erez, A., Subrini, O., Hessel, A., Ladant, D., and Chenal, A. (2013) Molecular Crowding Stabilizes Both the Intrinsically Disordered Calcium-Free State and the Folded Calcium-Bound State of a Repeat in Toxin (RTX) Protein. J Am Chem Soc 135, 11929–11934 [30] Chenal, A., Karst, J., Sotomayor-P´erez, A., Wozniak, A., Baron, B., England, P., and Ladant, D. (2010) Calcium-induced folding and stabilization of the intrinsically disordered RTX domain of the CyaA toxin. Biophys J 99, 3744–3753 [31] Zhang, Y., Tan, H., Lu, Y., Jia, Z., and Cheng, G. (2008) Ca(2+) dissociation from the C-terminal EF-hand pair in calmodulin: a steered molecular dynamics study. FEBS Lett 582, 1355–1361 [32] Zhang, M., Tanaka, T., and Ikura, M. (1995) Calcium-induced conformational transi- tion revealed by the solution structure of apo calmodulin. Nat Struct Biol 2, 758–767 [33] Finn, B., Evenas, J., Drakenberg, T., Waltho, J., Thulin, E., and Forsen, S. (1995) Calcium-induced structural changes and domain autonomy in calmodulin. Nat Struct Biol 2, 777–783 [34] Glaser, P., Elmaoglou-Lazaridou, A., Krin, E., Ladant, D., B´arzu, O., and Danchin, A. (1989) Identification of residues essential for catalysis and binding of calmodulin in Bordetella pertussis adenylate cyclase by site-directed mutagenesis. EMBO J 8, 967–972 [35] Weinkam, P., Pons, J., and Sali, A. (2012) Structure-based model of allostery predicts coupling between distant sites. PNAS 109, 4875–4880 [36] Weinkam, P., Chen, Y., Pons, J., and Sali, A. (2013) Impact of mutations on the allosteric conformational equilibrium. J Mol Biol 425, 647–661 [37] Chennubhotla, C. and Bahar, I. (2007) Signal propagation in proteins and relation to equilibrium fluctuations. PLoS Comput Biol 3, 1716–1726 [38] del Sol, A., Tsai, C., Ma, B., and Nussinov, R. (2009) The origin of allosteric func- tional modulation: multiple pre-existing pathways. Structure 17, 1042–1050 [39] Dubay, K., Bothma, J., and Geissler, P. (2011) Long-range intra-protein communi- cation can be transmitted by correlated side-chain fluctuations alone. PLoS Comput Biol 7, e1002168 [40] Kuzu, G., Keskin, O., Gursoy, A., and Nussinov, R. (2012) Constructing structural networks of signaling pathways on the proteome scale. Curr Opin Struct Biol 22, 367–377 byguestonJune8,2014http://www.jbc.org/Downloadedfrom
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  • 17. Mutants of AC and AC/CaM interaction 16 FIGURE LEGENDS Figure 1 a) X-ray crystallographic structure of the catalytic domain (AC) of adenyl cyclase (CyaA, PDB entry 1YRT) drawn in cartoons. Helices F, G, and H colored in purple form the SA region (residues 192–254). The loop 226–232 (Hom loop) colored in salmon at the left extremity of SA colored in purple was missing from the X-ray crystallographic structure and was modeled using Modeller9v4 [50]. The other protein regions are colored in green (CA: residues 7–61, 187–197, 261–299, and 313–345), orange (CB: residues 62– 186), cyan (C-terminal tail/C tail: residues 346–364), and yellow (catalytic loop/C loop: residues 300–312). The C-CaM lobe, which is colored in red, interacts with SA and the C-terminal tail. Calcium ions are represented by silver beads. b) The modified residues, i.e., Arg338, Asn347, and Asp360, located in CA and the C terminal tail, are indicated by sticks. c) The LHL motif localized between the C-CaM/AC interface and the catalytic loop is colored in brown. Figure 2 Conformational drifts estimated based on the α carbon coordinates RMSD from the starting conformations in the T1 (a-d) and T2 (e-h) series of simulations. (a, e) Drift cal- culated based on the Cα carbons in the AC domain for ACm1A (black), ACm2A (green), and ACm3A (red). (b–d,f–h) Drift calculated based on different regions of the AC domain, which were analyzed for ACm1A (b, f), ACm2A (c, g), and ACm3A (d, h). The color codes of the different protein regions are shown in panel (d). The AC regions are defined as follows. 1) CA: residues 7–61, 187–197, 261–299, and 313–345. 2) Catalytic loop (C Loop): residues 300–312. 3) C-terminal tail (C tail): residues 346–364. 4) CB: residues 62–186. 5) SA: residues 198–260. Helices H, F, G, and H’ correspond to residues 234–253, 198-210, 214-223, 256-260. Figure 3 Fluctuations of the residues (RMSF: ˚A) observed in C-CaM based on the trajectories recorded for: (a) wild-type and (b) modified C-CaM/AC complexes. The trajectory names are shown in the legends. The WT2Ca trajectories were run on two Ca2+-loaded AC/C- CaM complexes, whereas the WT0Ca trajectories were run on the AC/C-CaM complex in the absence of calcium ions. The fluctuations were calculated based on the trajectories after removing their first 10 ns. Figure 4 C-CaM conformation extracted from ACm2A T2 and ACm3A T2, which are colored according to the simulation times indicated. The N- and C-terminal ends are indicated, as well as Asp-133, which is shown in black. The calcium ions are shown as gray spheres, and the carboxyl oxygens of the Asp-133 sidechain are colored in red. Figure 5 Correlation between geometric strains among the LHL residues, displayed for each recorded trajectory. The time-correlation matrices were calculated between the variations of the geometric strains of LHL residues and the first ten nanoseconds were discarded from the analysis. In order to estimate the reliability of the prediction of correlation, the cal- culation was repeated five times by selecting at each time, one data-point over five along the analyzed time interval. The average values calculated for the LHL residues are shown byguestonJune8,2014http://www.jbc.org/Downloadedfrom
  • 18. Mutants of AC and AC/CaM interaction 17 in the figure. The intensity scale varies from 1.0 (pink) to –0.2 (dark green). Figure 6 A. SDS-PAGE analysis of the purified AC variants, wild type AC, and CaM. The pro- teins were separated by electrophoresis on a 4–12% SDS-polyacrylamide gel (Life Tech- nologies). After migration, the gel was stained with PageBlue protein staining solution (Thermo Fisher Scientific). B. Activation of modified ACs by CaM. The activity of the purified wild-type AC and/or the variants were measured (as described in the Materials and Methods) in the presence of the indicated CaM concentrations, and the results are expressed as the percentage of the maximal activity (measured in the presence of 1µM CaM). C. Catalytic properties of AC variants. The parameters were determined within an error of ± 10%. ∆G is the calculated energy of association between CaM and AC. Figure 7 A. SEC-TDA analysis of the oligomerization state of ACwt and ACm3A. Red curve: right angle light scattering; blue curve: UV absorbance; green curve: molecular masses of the eluted species. See the Materials and Methods for details. B. Synchrotron radiation circular dichroism spectra of CaM and AC proteins in isolation or in a 1:1 complex. MRE: mean residual ellipticity. See the Materials and Methods for details. C. Thermodynamic stability of AC proteins following urea-induced denaturation. The ratio of the fluorescence intensity at 360 and 320 nm (excitation wavelength = 295 nm) for the proteins as a func- tion of the urea concentration was measured as described in the Materials and Methods. D. Thermodynamics parameters of the urea-induced denaturation of AC proteins. byguestonJune8,2014http://www.jbc.org/Downloadedfrom
  • 19. Mutants of AC and AC/CaM interaction 18 Table I Details of the molecular systems simulated in molecular dynamics (MD) trajectories. Systems ACwt 2Ca ACwt 0Ca Trajectories WT2Ca T1 WT0Ca T1 WT2Ca T2 WT0Ca T2 Number of Na+ counter-ions 14 18 Water box 92.6 x 106.9 91.3 x 106.9 dimensions x 103.3 ˚A3 x 106.4 ˚A3 Number of water molecules 26455 27056 Total number of atoms 85825 87630 Length (ns) 30 30 Table I Systems ACm1A ACm2A ACm3A Trajectories ACm1A T1 ACm2A T1 ACm3A T1 ACm1A T2 ACm2A T2 ACm3A T2 Number of Na+ counter-ions 14 18 14 Water box 109.6 x 82.8 108.1 x 82.8 109.6 x 82.8 dimensions x 111.7 ˚A3 x 111.7 ˚A3 x 111.7 ˚A3 Number of water molecules 29003 29008 29008 Total number of atoms 93465 93468 93464 Length (ns) 50 50 50 byguestonJune8,2014http://www.jbc.org/Downloadedfrom
  • 20. Mutants of AC and AC/CaM interaction 19 Figure 1 a) C-CaM C-tail C-Loop CA CB SAHom loop G F H b) c) L16 ASN-347 ARG-338 ASP-360 Figure 1 byguestonJune8,2014http://www.jbc.org/Downloadedfrom
  • 21. Mutants of AC and AC/CaM interaction 20 Figure 2 Figure 2 byguestonJune8,2014http://www.jbc.org/Downloadedfrom
  • 22. Mutants of AC and AC/CaM interaction 21 Figure 3 RMSF(A°) 79 84 89 94 99 105 111 117 123 129 135 141 147 0123 a) Helix V Helix VI Helix VII Helix VIII WT2Ca_T1 WT2Ca_T2 WT0Ca_T1 WT0Ca_T2 RMSF(A°) 79 84 89 94 99 104 110 116 122 128 134 140 146 0123 b) Helix V Helix VI Helix VII Helix VIII ACm1A_T1 ACm1A_T2 ACm2A_T1 ACm2A_T2 ACm3A_T1 ACm3A_T2 Residue number RMSF(A°)RMSF(A°) Figure 3 byguestonJune8,2014http://www.jbc.org/Downloadedfrom
  • 23. Mutants of AC and AC/CaM interaction 22 Figure 4 ACm2A_T2 Asp 133 COO- C N ACm3A_T2 C N Asp 133 COO- 10 ns 20 ns 25 ns start Figure 4 byguestonJune8,2014http://www.jbc.org/Downloadedfrom
  • 24. Mutants of AC and AC/CaM interaction 23 Figure 5 Residuenumber 345350355360 ACm1A_T1 ACm1A_T2Residuenumber 345350355360 ACm2A_T1 ACm2A_T2 Residuenumber 345350355360 ACm3A_T1 ACm3A_T2 Residuenumber 345350355360 WT2Ca_T1 WT2Ca_T2 Residue number Residuenumber 340 345 350 355 360 345350355360 WT0Ca_T1 Residue number Residue number 340 345 350 355 360 WT0Ca_T2 Residue number −0.2 0.0 0.2 0.4 0.6 0.8 1.0 1.2 ResiduenumberResiduenumberResiduenumberResiduenumberResiduenumber Figure 5 byguestonJune8,2014http://www.jbc.org/Downloadedfrom
  • 25. Mutants of AC and AC/CaM interaction 24 Figure 6 A 170 - 130- 95- 72- 55- 43- 34- 26- 17- 10- AC ACm 3AACm 2AACm 1A CaM B C kcat KATP M KCaM 1/2 ∆G kcat/ KM (s−1) (mM) (nM) (kcal.mol−1) 106 M−1s−1 ACwt 4600 0.60 0.11 13.8 7.6 ACm1A 2250 2.2 0.61 12.8 1.0 ACm2A 6000 1.5 0.66 12.7 4.0 ACm3A 650 3.0 26.7 10.5 0.2 Figure 6 byguestonJune8,2014http://www.jbc.org/Downloadedfrom
  • 26. Mutants of AC and AC/CaM interaction 25 Figure 7 050100150 AC A uu mm[2472:3101] 01020304050 050100150 uv ACm3A uu mm[2472:3101] 10 11 12 13 14 15 16 17 18 01020304050 UV wavelength Signalintensity(AU)Signalintensity(AU) Molecularmass(kDa)Molecularmass(kDa) −20−100102030 180 200 220 240 B wavelength (nm) MRE,Kdeg*cm2/dmol ACm3A ACm3A:CaM ACWT ACWT:CaM CaM q q q q q q q q q q q q q 0.60.81.01.21.41.61.82.0 q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q 0 0.5 1 1.5 2 2.5 3 3.5 4 5 6 7 8 C urea (M) ratiooffluorescenceintensity360/320 ACm3A ACm3A:CaM ACWT ACWT:CaM D proteins AC WT ACm3A [urea]1/2 (M) 1.8 1.7 ∆G, kcal.mol−1 2.4 2.6 m parameter 1335 1490 Figure 7 byguestonJune8,2014http://www.jbc.org/Downloadedfrom