Electrostatic Interactions Between Complement Regulator

CD46(SCR1-2) and Adenovirus Ad11/Ad21 Fiber Protein Knob

Carl ChenUC Riverside

Bioengineering

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

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 Ad21kP1

P2

Persson, et al. Structure of the extracellular portion of CD46 provides insights into its interactions. 2010

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

CD46(SCR1-2)-Ad11k

CD46

Ad11k

SCR-1 SCR-2

P1 = chain AP2 = chain E

Interface

Petteren, et al, “UCSF Chimera”, 2004

CD46(SCR1-2)-Ad21k

CD46

SCR-1 SCR-2

P1 = chain B

P2 = chain C

Interface

Ad21k

Petteren, et al, “UCSF Chimera”, 2004

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

_ _ __ _ _+ + + _ _ _

_ _ _+ + +

+

++

+

Ad11Ad21 CD46

recognition

binding

Electrostatics Association Model

Gorham, et al. Electrostatic clustering and free energy calculations. 2011

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

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)

Application of AESOP

• Performed Alanine scan mutations in both complexes to determine effects of thermodynamic stability on binding.

Ad11 or Ad21 CD46 Complex

DGAsolvation DGB

solvation DGABsolvation

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

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

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

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) -1.61D47A (B) -0.03 D47A (N) 0.12

H43A (B) 2.30 D57A (B) -0.21 H43A (N) 0.05 D57A (N) -0.01H50A (B) -0.01 D58A (B) -0.13 H50A (N) 0.02 D58A (N) 0.11H90A (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) -0.01K17A (B) -0.17 E3A (B) -0.05 K17A (N) 0.90 E3A (N) -0.41K29A (B) 1.93 E11A (B) -0.74 K29A (N) 0.34 E8A (N) -0.10K31A (B) 0.40 E21A (B) 0.10 K31A (N) 0.94 E11A (N) -0.61K32A (B) 0.69 E24A (B) 0.14 K32A (N) -1.59 E21A (N) -0.09K110A (B) 2.43 E63A (B) 6.39 K110A (N) 1.31 E24A (N) -0.58K119A (B) 4.58 E84A (B) 0.40 K119A (N) 5.04 E63A (N) 8.44K125A (B) 0.12 E8A (B) 0.06 K125A (N) 0.31 E84A (N) 0.24

E95A (B) 0.06 E95A (N) -0.12R25A (B) 4.06 E102A (B) -0.50 R25A (N) 1.16 E102A (N) -1.76R48A (B) 0.13 E103A (B) -0.08 R48A (N) -0.28 E103A (N) -0.39R62A (B) -0.29 E108A (B) -1.14 R62A (N) -0.02 E108A (N) -1.26R69A (B) 1.55 E124A (B) -0.54 R69A (N) 1.06 E124A (N) -0.78

Ad11k Free Energy Plot

3.5—5.0 Å

5.0—8.0 Å

“R: A language and environment for statistical computing”, 2011

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) 0.03R189A (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) 0.88H188A (E) -0.01 R208A (E) 0.10 D155A (E) 0.06 E152A (E) 0.12H218A (A) 0.00 R249A (A) 0.28 D200A (A) -0.27 E196A (A) 3.84H218A (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) -0.50K157A (A) -0.02 R266A (E) 4.28 D246A (E) -0.06 E250A (E) -0.04K157A (E) 0.06 R279A (A) 3.15 D265A (A) -0.08 E252A (A) -0.23K164A (A) -0.01 R279A (E) 0.07 D265A (E) 1.39 E252A (E) -0.01K164A (E) 0.06 R280A (A) 3.70 D272A (A) 0.51 E285A (A) -4.29K213A (A) -0.83 R280A (E) 0.09 D272A (E) 0.18 E285A (E) -0.19K213A (E) 0.00 R291A (A) -1.12 D284A (A) 3.74 E303A (A) -0.05K219A (A) -0.03 R291A (E) 0.06 D284A (E) -0.25 E303A (E) 0.96K219A (E) 0.01 R322A (A) 0.01 D300A (A) -0.13 E323A (A) -0.16K233A (A) 0.06 R322A (E) 0.03 D300A (E) 1.46 E323A (E) -0.09K233A (E) 0.14 D324A (A) 0.00K251A (A) 0.37 D324A (E) -0.06K251A (E) 0.00 D325A (A) 0.04

D325A (E) -0.05

Ad21k Free Energy Plot

3.5—5.0 Å

5.0—8.0 Å

“R: A language and environment for statistical computing”, 2011

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

Intermolecular Coulombic InteractionsInteractions 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 4.3GLU 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 4.5Interactions 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 4.6LYS 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 weakAd11k unfavorable: 1 salt bridge, 1 weakAd11k contributing: 1 salt bridge, 4 weak

Ad21k favorable: 3 salt bridge, 4 weakAd21k unfavorable: 1 salt bridge, 4 weakAd21k contributing: 2 salt bridge

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 ChargedBlue = Positively Charged

Ad11k H-bonds: 12SASA: 641 Å

Red = Negatively ChargedBlue = Positively Charged

Ad21k H-bonds: 8SASA: 768 Å

Questions?