1. Electrostatic Interactions Between
Complement Regulator
CD46(SCR1-2) and Adenovirus
Ad11/Ad21 Fiber Protein Knob
Carl Chen
UC Riverside
Bioengineering

2. Motivation
• Adenoviruses target several systems in the body,
including the respiratory and kidney areas.
• There are no direct antiviral treatments for adenoviruses
due to the wide range of symptoms.
Persson, et al. Adenovirus type 11 binding alters the conformation of its receptor CD46. 2007

3. Background
• Over 50 serotypes of adenovirus. Ad11 and Ad21 are
subtypes of type B.
• Viral globular knob binds to 2 SCR domains of CD46 to
infect a variety of cells.
SCR-1
SCR-2
SCR-3
SCR-4
CD46
Ad11k or Ad21k
P1
P2
Persson, et al. Structure of the extracellular portion of CD46 provides insights into its interactions. 2010

4. Trimer of Trimers
P1
P3 P2
SCR-1
SCR-1
SCR-1
SCR-2SCR-2
SCR-2
Persson, et al. Structure of the extracellular portion of CD46 provides insights into its interactions. 2010

5. CD46(SCR1-2)-Ad11k
CD46
Ad11k
SCR-1 SCR-2
P1 = chain A
P2 = chain E
Interface
Petteren, et al, “UCSF Chimera”, 2004

6. CD46(SCR1-2)-Ad21k
CD46
SCR-1 SCR-2
P1 = chain B
P2 = chain C
Interface
Ad21k
Petteren, et al, “UCSF Chimera”, 2004

7. What Contributes to Adenovirus Binding?
• Ad11 ka = 1.18 x 106 M-1s-1, kb = 0.015 s-1
• Ad21 ka = 1.35 x 106 M-1s-1, kb = 0.383 s-1
Cupelli, et al. Structure of adenovirus type 21 knob in complex with CD46 reveals key differences. 2009

8. ___
___
+++ _ _ _
_ _ _
+ + +
+
+
+
+
Ad11
Ad21 CD46
recognition
binding
Electrostatics Association Model
Gorham, et al. Electrostatic clustering and free energy calculations. 2011

9. Electrostatic Surface Map for CD46(SCR1-2)-Ad11k
Ad11k CD46(SCR1-2)
E196(A)
D284(A) R279(A)R280(A)
D300(E)
R266(E)
K119
E63
K29
R25
D27
Binding
E285(A)
Petteren, et al, “UCSF Chimera”, 2004

10. Electrostatic Surface Map for CD46(SCR1-2)-Ad21k
Ad21k
E148(B)
R195(B)
E208(B)
R279(B) R247(B)
E299(C)
D179(C)
K119
R69
E63
K32 K29
D27
Binding
E302(C)
E292(B)
Petteren, et al, “UCSF Chimera”, 2004
CD46(SCR1-2)

11. Application of AESOP
• Performed Alanine scan mutations in both complexes to
determine effects of thermodynamic stability on binding.
Ad11 or Ad21 CD46 Complex
DGA
solvation DGB
solvation DGAB
solvation
DGref
DGsolu
ep = es = 20
ep = 20
es = 78.54
k = 0
k = 150
reference state
solvated state
Gorham, et al. Electrostatic clustering and free energy calculations. 2011

12. CD46(SCR1-2) Free Energy Plot (Ad11k)
3.5—5.0 Å
5.0—8.0 Å
“R: A language and environment for statistical computing”, 2011

13. CD46(SCR1-2) Free Energy Plot (Ad21k)
3.5—5.0 Å
5.0—8.0 Å
“R: A language and environment for statistical computing”, 2011

14. DGbind values for CD46(SCR1-2) mutants
CD46 ΔGbind (for Ad11 Complex) CD46 ΔGbind (for Ad21 Complex)
mutant kJ/mol mutant kJ/mol mutant kJ/mol mutant kJ/mol
WT 0 D27A (B) -6.20 WT 0 D27A (N) -1.61
D47A (B) -0.03 D47A (N) 0.12
H43A (B) 2.30 D57A (B) -0.21 H43A (N) 0.05 D57A (N) -0.01
H50A (B) -0.01 D58A (B) -0.13 H50A (N) 0.02 D58A (N) 0.11
H90A (B) 0.01 D70A (B) -0.35 H90A (N) 0.00 D70A (N) -0.30
K15A (B) 0.92 E2A (B) 0.09 K15A (N) 1.25 E2A (N) -0.01
K17A (B) -0.17 E3A (B) -0.05 K17A (N) 0.90 E3A (N) -0.41
K29A (B) 1.93 E11A (B) -0.74 K29A (N) 0.34 E8A (N) -0.10
K31A (B) 0.40 E21A (B) 0.10 K31A (N) 0.94 E11A (N) -0.61
K32A (B) 0.69 E24A (B) 0.14 K32A (N) -1.59 E21A (N) -0.09
K110A (B) 2.43 E63A (B) 6.39 K110A (N) 1.31 E24A (N) -0.58
K119A (B) 4.58 E84A (B) 0.40 K119A (N) 5.04 E63A (N) 8.44
K125A (B) 0.12 E8A (B) 0.06 K125A (N) 0.31 E84A (N) 0.24
E95A (B) 0.06 E95A (N) -0.12
R25A (B) 4.06 E102A (B) -0.50 R25A (N) 1.16 E102A (N) -1.76
R48A (B) 0.13 E103A (B) -0.08 R48A (N) -0.28 E103A (N) -0.39
R62A (B) -0.29 E108A (B) -1.14 R62A (N) -0.02 E108A (N) -1.26
R69A (B) 1.55 E124A (B) -0.54 R69A (N) 1.06 E124A (N) -0.78

15. Ad11k Free Energy Plot
3.5—5.0 Å
5.0—8.0 Å
“R: A language and environment for statistical computing”, 2011

16. DGbind values for Ad11k mutants
Ad11 ΔGbind values
mutant kJ/mol mutant kJ/mol mutant kJ/mol mutant kJ/mol
WT 0 R189A (A) 0.39 D129A (A) 0.08 E142A (A) 0.03
R189A (E) -0.19 D129A (E) 0.03 E142A (E) 0.11
H188A (A) 0.04 R208A (A) 1.02 D155A (A) 1.00 E152A (A) 0.88
H188A (E) -0.01 R208A (E) 0.10 D155A (E) 0.06 E152A (E) 0.12
H218A (A) 0.00 R249A (A) 0.28 D200A (A) -0.27 E196A (A) 3.84
H218A (E) 0.00 R249A (E) 0.03 D200A (E) -0.14 E196A (E) -0.04
R266A (A) 0.10 D246A (A) -0.41 E250A (A) -0.50
K157A (A) -0.02 R266A (E) 4.28 D246A (E) -0.06 E250A (E) -0.04
K157A (E) 0.06 R279A (A) 3.15 D265A (A) -0.08 E252A (A) -0.23
K164A (A) -0.01 R279A (E) 0.07 D265A (E) 1.39 E252A (E) -0.01
K164A (E) 0.06 R280A (A) 3.70 D272A (A) 0.51 E285A (A) -4.29
K213A (A) -0.83 R280A (E) 0.09 D272A (E) 0.18 E285A (E) -0.19
K213A (E) 0.00 R291A (A) -1.12 D284A (A) 3.74 E303A (A) -0.05
K219A (A) -0.03 R291A (E) 0.06 D284A (E) -0.25 E303A (E) 0.96
K219A (E) 0.01 R322A (A) 0.01 D300A (A) -0.13 E323A (A) -0.16
K233A (A) 0.06 R322A (E) 0.03 D300A (E) 1.46 E323A (E) -0.09
K233A (E) 0.14 D324A (A) 0.00
K251A (A) 0.37 D324A (E) -0.06
K251A (E) 0.00 D325A (A) 0.04
D325A (E) -0.05

17. Ad21k Free Energy Plot
3.5—5.0 Å
5.0—8.0 Å
“R: A language and environment for statistical computing”, 2011

18. DGbind values for Ad21k mutants
Ad21 ΔGbind values
mutant kJ/mol mutant kJ/mol mutant kJ/mol mutant kJ/mol
K139A (B) -0.08 WT 0 D151A (B) 1.06 E148A (B) 1.62
K139A (C) 0.00 D151A (C) 0.51 E148A (C) 0.31
K156A (B) -0.04 H254A (B) -0.03 D154A (B) 1.23 E208A (B) -0.99
K156A (C) -0.38 H254A (C) 0.01 D154A (C) 0.50 E208A (C) 0.18
K163A (B) -0.05 D179A (B) -0.02 E225A (B) 0.04
K163A (C) -0.04 R195A (B) -5.30 D179A (C) 1.86 E225A (C) 0.03
K188A (B) 0.05 R195A (C) -0.22 D199A (B) -0.11 E250A (B) 0.37
K188A (C) -0.14 R247A (B) 0.91 D199A (C) 0.10 E250A (C) -0.05
K212A (B) -1.90 R247A (C) -0.07 D207A (B) -0.45 E292A (B) 2.02
K212A (C) -0.30 R265A (B) 0.2 D207A (C) 0.25 E292A (C) 0.16
K216A (B) -0.08 R265A (C) 1.66 D248A (B) -0.01 E299A (B) -0.11
K216A (C) -0.16 R279A (B) 3.29 D248A (C) -0.04 E299A (C) 1.22
K218A (B) -0.03 R279A (C) -0.04 D264A (B) -0.20 E302A (B) -0.10
K218A (C) -0.07 R319A (B) -0.07 D264A (C) -0.81 E302A (C) 2.47
K231A (B) 0.08 R319A (C) -0.03 D321A (B) 0.04 E320A (B) -0.06
K231A (C) 0.01 D321A (C) -0.01 E320A (C) -0.01
K298A (B) 0.06 D322A (B) 0.04
K298A (C) 0.03 D322A (C) 0.00

19. Intermolecular Coulombic Interactions
Interactions for CD46(SCR1-2)-Ad11k (Chain A) Interactions for CD46(SCR1-2)-Ad21k (Chain B)
CD46 res # atom Ad11 res # atom dist (Å) CD46 res # atom Ad21 res # atom dist (Å)
ARG 25 CZ GLU 285 CD 5 *GLU 11 CD GLU 148 CD 7.7
ARG 25 CZ ASP 284 CG 6.3 *ASP 27 CG GLU 208 CD 7.8
*ASP 27 CG GLU 285 CD 4.9 *LYS 29 NZ ARG 195 CZ 7.7
*ASP 27 CG ASP 284 CG 6.6 *LYS 29 NZ LYS 212 NZ 7.8
LYS 29 NZ GLU 196 CD 7.4 *LYS 32 NZ ARG 195 CZ 4.3
GLU 63 CD ARG 280 CZ 4 LYS 32 NZ GLU 148 CD 7.1
GLU 63 CD ARG 279 CZ 7.7 LYS 32 NZ GLU 292 CD 7.9
GLU 63 CD ARG 247 CZ 4.5
Interactions for CD46(SCR1-2)-Ad11k (Chain E) GLU 63 CD ARG 279 CZ 4
CD46 res # atom Ad11 res # atom dist (Å)
GLU 63 CD ARG 266 CZ 7.3 Interactions for CD46(SCR1-2)-Ad21k (Chain C)
LYS 119 NZ ASP 300 CG 6.1 CD46 res # atom Ad21 res # atom dist (Å)
ARG 69 CZ ASP 179 CG 6.1
LYS 119 NZ GLU 299 CD 4.6
LYS 119 NZ GLU 302 CD 7.3
Bold-face = Interactions < 5 Å
*Denotes unfavorable interactions
Bold-face = Interactions < 5 Å
*Denotes unfavorable interactions
Ad11k favorable: 2 salt bridge, 5 weak
Ad11k unfavorable: 1 salt bridge, 1 weak
Ad11k contributing: 1 salt bridge, 4 weak
Ad21k favorable: 3 salt bridge, 4 weak
Ad21k unfavorable: 1 salt bridge, 4 weak
Ad21k contributing: 2 salt bridge

20. Intermolecular Hydrogen Bonds
Interactions for CD46(SCR1-2)-Ad11k (Chain A) Interactions for CD46(SCR1-2)-Ad21k (Chain B)
CD46 res # atom Ad11 res # atom dist (Å) CD46 res # atom AD21 res # atom dist (Å)
TYR 28 O ASN 283 ND2 3.7 CYS 30 N ILE 281 O 3.2
CYS 30 N ILE 282 O 3 TYR 36 N THR 280 O 2.7
CYS 30 SG ILE 282 O 3.4 THR 64 OG1 THR 245 O 2.6
TYR 36 N ALA 281 O 2.9 SER 112 O ARG 247 NH1 3.3
TYR 36 O ASN 245 ND2 3.3
THR 42 N ASP 284 OD2 2.8 Interactions for CD46(SCR1-2)-Ad21k (Chain C)
THR 42 OG1 ASP 284 N 3.1 CD46 res # atom AD21 res # atom dist (Å)
HIS 43 ND1 ASP 284 OD2 2.8 ARG 69 O ASN 304 ND2 3.5
SER 112 OG GLU 196 OE2 3.1 TRP 116 N TYR 263 O 3.2
LYS 119 NZ SER 300 O 3
Interactions for CD46(SCR1-2)-Ad11k (Chain E) PRO 120 O SER 303 OG 3.3
CD46 res # atom Ad11 res # atom dist (Å)
THR 64 O ARG 266 NH1 2.9
THR 64 O ARG 266 NH2 3.5
ALA 114 O ARG 266 NH1 2.8
Red = Negatively Charged
Blue = Positively Charged
Ad11k H-bonds: 12
SASA: 641 Å
Red = Negatively Charged
Blue = Positively Charged
Ad21k H-bonds: 8
SASA: 768 Å

21. Questions?