Background
Methods
Influenza sequences and sequence alignments
Pairwise comparison of aligned sequences
Parameterization and calculation of change in biophysical properties
aa | A | R | N | D | C | Q | E | G | H | I | L |
---|---|---|---|---|---|---|---|---|---|---|---|
∆ASA
tot
a
| 54.6 | 199.6 | 112.9 | 99.4 | 92 | 122.3 | 124.5 | 0 | 144.9 | 135.9 | 143.8 |
∆ASA
np
| 62.9 | 85.3 | 28.5 | 42.2 | 40.8 | 46.7 | 55.9 | 25.7 | 99.5 | 139.5 | 144.4 |
∆ASA
pol
| 28.7 | 151.3 | 113.3 | 87 | 96.1 | 110.1 | 103.6 | 28.7 | 74.1 | 28.7 | 28.7 |
Q
b
| 0 | 1.00 | 0 | −1.00 | −0.11 | 0 | −1.00 | 0 | 0.05 | 0 | 0 |
aa
|
K
|
M
|
F
|
P
| S |
T
|
W
|
Y
|
V
|
Deleted/missing
c
| |
∆ASA
tot
| 155.6 | 158 | 172 | 90.7 | 71.7 | 105.4 | 222.4 | 190.2 | 105.6 | 300 | |
∆ASA
np
| 122.4 | 122.1 | 172 | 100.8 | 44.2 | 74.8 | 200.5 | 154.3 | 113 | 258.3 | |
∆ASA
pol
| 70.3 | 73 | 28.7 | 15.6 | 64.4 | 63.4 | 52.4 | 71.6 | 26.2 | 64.4 | |
Q
| 1.00 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
Structural analysis, assignment of antigenic sites, and statistical analysis
Effect of alignment on biophysical parameters
Results and discussion
Sequence alignment and parameterization
Prediction of novel sites in potential antigenic sites in H1 and B HA
H1a | |||||
---|---|---|---|---|---|
Ca2
b
|
Sb
|
Sa
|
H1C
c
|
Ca1
|
Cb
|
132b
d,e
, 133, (140), (143), 144, (145), 149, (224), 225 | 156
f
, (159)g, 189–90, 192–3, (196), 197, (198) | (128), 129, 163, 165, (166–7), 247-8 | 86, 272–7, 279–82, 286 | (169), 173, (207), 212, 240, 241, 242, 243-5 | 51, (74–5), 77, (78–9), (117), 149, 255–6, 259-66 |
H3
h
| |||||
A
|
B
|
C
|
D
|
E
| |
121, 122, (123), 124, (125), 126, (127), (129), 131, (132), 133, (134), 135, (136), 137–8, 140, 142, (143), 144–5, (146), | 155, 156, (157), 158–60, 186, 188–9, (190), 192, 193, (194), (196), 197, 198–9, 246-7 | 49, 50, 53–4, 271, 273, 275, 276, 278 | 167, 201–2, (203–6), 207, 214, 216, (217– 8), 219–20, 222–3, 225–7, 242 | 62, (63), 75, 78, (79–82), 83, 91–2, 94 | |
B
i
| |||||
BA
|
BB1
j
|
BB2
9
|
BC
3
|
BD
|
BE
|
136-7, 141, 146, (147), 148–9, 150, 154 | 194, 195, 196, 197, 199, 200, 205-6 | 162,162a-c, 163, (164), 165 | 47-8, 80–1, 116, 276, 281 | 121-2, 125, 126–7, 129, 179–80, 181, 248–9, 252-5 | 56, 58, 68–9, 71, 73, 75, 76 |
Site-specific differences in biophysical properties in H1 HA
Antigenic Sitea | pb antigenic site vs. non-antigenic site residues | ||||
---|---|---|---|---|---|
Δabs | ΔΔASAtot | ΔΔASAnp | ΔΔASApol | ΔQ | |
H1 | |||||
Ca2
| p < 0.01 |
NS
|
NS
|
NS
| p < 0.05 |
Sb
| p < 0.001 |
NS
|
NS
|
NS
|
NS
|
Sa
|
NS
|
NS
|
NS
|
NS
|
NS
|
H1C
| p < 0.001 |
NS
|
NS
| p < 0.05 |
NS
|
Ca1
| p < 0.05 | p < 0.001 |
NS
|
NS
|
NS
|
Cb
| p < 0.001 | p < 0.05 |
NS
| p < 0.01 |
NS
|
H3 | |||||
A
| p < 0.001 |
NS
|
NS
|
NS
|
NS
|
B
| p < 0.001 |
NS
|
NS
|
NS
|
NS
|
C
| p < 0.001 |
NS
|
NS
|
NS
|
NS
|
D
| p < 0.001 |
NS
|
NS
|
NS
|
NS
|
E
| p < 0.01 |
NS
|
NS
|
NS
|
NS
|
B | |||||
BA
| p < 0.001 | p < 0.001 | p < 0.001 | p < 0.001 | p < 0.01 |
BB1
| p < 0.001 | p < 0.01 | p < 0.001 | p < 0.01 | p < 0.001 |
BB2
| p < 0.001 | p < 0.01 | p < 0.001 | p < 0.01 | p < 0.01 |
BC
| p < 0.001 | p < 0.01 | p < 0.01 | p < 0.01 | p < 0.05 |
BD
| p < 0.001 | p < 0.001 | p < 0.001 | p < 0.001 | p < 0.01 |
BE
| p < 0.001 | p < 0.05 | p < 0.01 |
NS
| p < 0.05 |
Biophysical properties of frequently changing H3 residues
Differences in biophysical properties define separate adjacent antigenic sites in B HA
Observed changes in biophysical properties are dependent on alignment
Antigenic Sitea | pb from aligned sequencesc (p
b
from resorted sequencesd) | ||||
---|---|---|---|---|---|
Δabs | ΔΔASAtot | ΔΔASAnp | ΔΔASApol | ΔQ | |
H1 epitope residues vs. randome | |||||
Ca2
| p < 0.05 (NS) | NS (NS) | NS (NS) | NS (NS) | p < 0.05 (p < 0.05) |
Sb
| p < 0.05 (p < 0.01) | NS (NS) | NS (NS) | NS (NS) | p < 0.05 (NS) |
Sa
| NS (p < 0.05) | NS (NS) | NS (NS) | NS (NS) | NS (NS) |
H1C
| p < 0.01 (p < 0.05) | NS (NS) | NS (NS) | NS (NS) | NS (NS) |
Ca1
| NS (NS) | NS (p < 0.01) | NS (NS) | NS (NS) | NS (NS) |
Cb
| NS (NS) | NS (NS) | NS (NS) | NS (NS) | NS (NS) |
H3 epitope residues vs. randomf | |||||
A
| NS (p < 0.05) | NS (NS) | NS (NS) | NS (NS) | NS (NS) |
B
| p < 0.05 (p < 0.01) | NS (NS) | NS (NS) | NS (NS) | NS (NS) |
C
| NS (NS) | NS (NS) | NS (NS) | NS (NS) | NS (NS) |
D
| p < 0.05 (NS) | NS (NS) | NS (NS) | NS (NS) | NS (NS) |
E
| NS (NS) | NS (NS) | NS (NS) | NS (NS) | p < 0.05 (NS) |
B HA epitope residues vs. randomg | |||||
BA
| NS (p < 0.01) | NS (NS) | NS (NS) | NS (NS) | p < 0.05 (NS) |
BB1
| NS (p < 0.01) | NS (NS) | NS (p < 0.05) | NS (NS) | p < 0.001 (p < 0.05) |
BB2
| NS (p < 0.05) | NS (NS) | NS (NS) | NS (NS) | p < 0.05 (NS) |
BC
| NS (NS) | NS (NS) | NS (NS) | NS (NS) | p < 0.05 (NS) |
BD
| NS (NS) | NS (NS) | NS (NS) | NS (NS) | p < 0.05 (NS) |
BE
| NS (NS) | NS (NS) | NS (NS) | NS (NS) | NS (NS) |
Comparison of changes in biophysical properties to other techniques to identify evolutionarily important residues
aa | Δabs | ΔΔASAtot | ΔΔASAnp | ΔΔASApol | ΔQ | |
---|---|---|---|---|---|---|
Positively Selected in H1.a,b | 86
c
, 98d, 144, 163, 165, 189, 190, 225 | p < 0.001e |
NS
| p < 0.05 |
NS
| p < 0.001 |
“Predictive” in H3f | 121, 124, 133, 135, 138, 142, 145, 156, 158, 186, 190g, 193, 194g, 197, 201, 226, 262h, 275 | p < 0.001 |
NS
|
NS
|
NS
|
NS
|
Directionally selected in H3.i,b | 45, 135, 145, 155, 158, 229, 248 | p < 0.001 |
NS
|
NS
|
NS
| p < 0.01 |