1. PROTEIN CHAINMAIL
ABSTRACT EXAMPLES OF CHAINMAIL IN VIRUSES
GENERAL STRUCTURE
CONCLUSIONS
REFERENCES
ACKNOWLEDGEMENTS
T=16 Gamma-Herpesvirus RRV Forms ChainmailSince the discovery of a covalent chainmail interaction in bacteriophage HK97
more than a decade ago by X-ray crystallography, new findings have exposed
variations upon this common theme for constructing dsDNA viruses. Recent tech-
nical advances in single particle analysis by cryo electron microscopy (cryoEM)
have allowed the trace of the chainmail feature in dsDNA viruses from simple
bacteriophages to complex mammalian herpesviruses. Pseudo-atomic structures
of P22-like phages exhibit mechanisms for capsid stability by the addition of a
conserved external I-domain to the HK97 fold without the usage of crosslinks
or decoration proteins. The atomic structures of bacteriophages BPP-1 and ɛ15
showcase a novel topology of the classic HK97 capsid protein fold, as well as
the jellyroll motif in an auxiliary protein that serves to cement the major capsid
protein subunits. A different type of auxiliary protein with similar stabilizing func-
tions is found in phage lambda. A pseudo-atomic model of SIO-2, a phage with a
triangulation number of T=12, reveals yet another variation of utilizing decoration
proteins that bind to the center of hexon capsomers to stabilize base HK97-like
fold subunits. Lastly, the tumor herpesvirus RRV displays a complex, four-lev-
el hierarchical non-covalent organization including an HK97-like fold found in
the floor region. These high resolution structures reveal a strategy of employ-
ing variations of the canonical HK97-like chainmail to construct viral highly sta-
ble dsDNA viral capsids, and should help unlock the enigma of viral evolution.
Chainmail is a system formed by concatenated rings. In double-stranded DNA phages with icosahedral capsids, protein chainmail is a structural organization composed
of interlocking protein rings. It is named after the metal chainlink armor worn by medieval knights. Like the armor, chainmail in viruses serves as a protection mechanism.
Alternative Topologies to Build the HK97-like (Johnson) Fold for Protein Chainmail
Joshua Chiou1
, Z. Hong Zhou1,2
1 Department of Microbiology, Immunology, and Molecular Genetics , University of California, Los Angeles, CA 90095
2 California NanoSystems Institute, University of California, Los Angeles, CA 90095
1. [HK97] WIkoff et al. 2000. Science 289, 2129-2133.
2. [BPP-1] Zhang et al. 2013. eLife 2013;2:e01299.
3. [RRV] Zhou et al. 2014. Structure 22: 1385-1398.
This work was supported in part by grants from the NIH (GM071940 and
AI094386 to Z.H.Z). We acknowledge the use of instruments at the Electron Im-
aging Center for Nanomachines supported by UCLA and by instrumentation
grants from NIH (1S10RR23057, 1S10OD018111) and NSF (DBI-1338135).
Figure 1.
A) Concept of chainmail versus Borromean rings. Breaking one ring of a chain-
mail would not affect the integrity of the whole, unlike the case of Borromean rings.
B) Covalent protein chainmail of HK97 by isopeptide bonds. Chainmail is a struc-
tural organization of concatenated rings found in the capsids of icosahedral dsD-
NA viruses, and allows capsids to withstand internal forces exerted by the dsDNA.
C) Basic building blocks of the HK97-like (Johnson) fold include the N (cyan), α
(green), and β (magenta) primary elements. Variations of the Johnson fold can
occur based on differences in connectivity between the basic building blocks.
Capsid Protein of HK97 Displays the Johnson Fold
Figure 3.
A) The capsid protein of HK97 (Wikoff
et. al., 2000), gp5 contains the John-
sonfold.Variantsofthisfoldhavebeen
identified in viruses, archaea, and
bacteria. Major structural elements
include the N-arm, E-loop, 3-strand-
ed β sheet including the P-loop, spine
helix, G-loop, and 5-stranded β sheet,
contained in two major domains.
B) HK97 Johnson fold topology shows
thatbuildingblocksarearrangedinthe
order N-α-β, a circular arrangement.
Alternative Toplogy of the Johnson Fold in BPP-1
Figure 4.
A) The capsid protein of BPP-1
(Zhang et al., 2013), a phage infect-
ing the bacteria Bordetella pertus-
sis, which causes whooping cough.
This figure shows that the Johnson
folds of HK97 and BPP-1 contain sim-
ilar secondary structure elements.
B) Building blocks of Johnson fold in
BPP-1 are arranged in the order N-β-α
whichswitchesthetopologyoftheJohn-
son fold to be permuted non-circularly.
Figure 6.
Even large, complex structures such as the 1300 Å, T=16 gamma-herpesvirus
RRV (Zhou et al., 2014) displays the Johnson fold. In RRV, the Johnson-fold do-
main is located in the floor region of the major capsid protein. Fitting the Johnson
fold of HK97 into the Johnson-fold domain highlights similarities between the folds.
Viruses likely originated from ancient cells through encapsulating cellular plasmids
or genome fragments by cellular proteins. Indeed, cellular complexes resembling
the structure and topology of HK97 gp5 have been found in both bacteria and ar-
chaea. Similarly, it is natural to expect that cellular proteins with the BPP-1 topology
of the Johnson fold also exist elsewhere. The gene encoding one of these topolo-
gies may have evolved from the other through non-circular permutation in ancient
cells through horizontal gene transfer – a rule for evolution at the age of prokary-
otic world. Adaptation to challenging environments of higher level organisms such
as animal cells could have given rise to acquisition of additional structures via
insertions at locations of the loops of the Johnson fold, as revealed in eukaryotic
viruses such as gamma-herpesvirus RRV. In all of these cases, the chainmail or-
ganization is conserved despite variations and additions to the subunits that com-
pose the capsid, differences in capsid size, and differences in capsid complexity,
suggesting that understanding chainmail may provide insight into viral evolution.
Auxiliary Protein Stabilizes BPP-1 at the 2-fold Axis
Figure 5.
A) The local two-fold axis of BPP-1. Hexamer 1 and hexamer 2 are composed of
capsid proteins and are stabilized by auxiliary proteins dimers at the two-fold axis.
B) Zoomed-in view of the auxiliary protein dimer, showing the augmented
10-stranded β sheet formed by strands of this dimer and the N-terminal β strands
of capsid protein. The C-termini of the dimer are exposed at the capsid surface.
C) Salt bridges form between the capsid protein and auxiliary protein of BPP-1. In
this sense, the auxiliary protein acts like a glue to stabilize or cement the capsid.
Figure 2.
A) Like HK97, BPP-1 also attains the chainmail system, albiet through alter-
native means. Because BPP-1 lacks the strong isopeptide bonds that form co-
valent crosslinks in HK97, it uses non-covalent interactions for stabilization.
B) The density of the Johnson fold in BPP-1, showing the basic building blocks.
C)Additional support for the trace of the density, which supports evidence of a new
topology of the Johnson fold. The density is well resolved, as seen by the fitting.
T=7 Bacteriophage BPP-1 Forms Chainmail