Comparative Binding Energy (COMBINE) Barnase Barstar

Comparative Binding Energy (COMBINE)

1. Comparative Binding Energy (COMBINE)
Analysis of Barnase-Barstar Interfacial Mutants
barstar
barnase
• High binding affinity (Kd=10
-14
M)
•Polar binding interface: positive(+2e) on
BN, negative (-6e) on BS
•Hot-spots Residues at the interface
Binding features:

2. 65 complexes with interfacial mutations
Arg59
Glu73
Arg83
His102
Arg87
Lys27
Glu80
Glu76
Trp38
Thr42
Tyr29
Asp39
Asp35
Trp44
Barnase
Barstar

3. 65 complexes with different interfacial mutations
No. Complex Exp. Binding delta_G Desol_BN Desol_BS Elec_inter Elect_binding_G
1 wtwt -19 83.29 75.7 -149.629 9.359
2 wtK27Awm -13.6 61.78 64.66 -121.787 4.658
3 wtR59A -13.8 67.68 69.38 -120.451 16.608
4 D39AR59A -7.7 60.52 23.06 -45.371 38.204
5 wtR87A -13.5 75.58 70.4 -111.981 33.999
6 wtH102Awm -12.9 75.93 73.32 -131.979 17.279
7 Y29FWTWMx -19.1 74.54 66.27 -129.535 11.274
8 Y29AWT -15.6 76.86 66.26 -131.241 11.88
9 D35Awtwm -14.5 82.35 51.48 -121.022 12.814
10 W38FWT -17.4 80.2 72.81 -147.522 5.49
11 D39Awt -11.3 78.3 44.99 -89.331 33.96
12 T42Awt -17.2 82.07 73.01 -142.04 13.042
13 W44FWT -19 82.54 74.96 -148.134 9.37
14 E76wt -17.7 76.34 70.45 -133.19 13.595
15 E80AWT -18.5 77.67 70.21 -140.513 7.366
16 Y29AK27AWM -10.4 56.34 56.68 -104.906 8.114
17 D35AK27Awm -9.5 58.45 41.3 -91.552 8.19
18 W38FK27AWM -12.6 59.29 62.5 -115.126 6.671
19 D39AK27Awm -10.8 52.85 41.48 -74.609 19.723
20 T42AK27Awm -13.3 59.23 63.75 -118.2 4.773
21 E76AK27AWM -12.3 54.36 59.53 -103.754 10.137
22 E80AK27Awm -13.5 58.31 61.2 -116.631 2.877
23 Y29AR59A -10.9 61.75 60.39 -102.207 19.926
24 D35AR59AWM -12.7 63.45 48.5 -100.483 11.458
25 W38FR59A -12.8 66.82 68.36 -119.921 15.255
26 T42AR59A -12.2 65.87 66.64 -112.196 20.308
27 E76AR59A -14.1 65.73 66.76 -118.262 14.23
28 E80AR59A -13.9 65.04 67.33 -118.106 14.257
29 Y29AR83Q -10.7 65.36 62.63 -85.188 42.797
30 D35AR83QWM -9.4 67.83 47.64 -72.423 43.046

4. 32 D39AR83Q -12.6 55.34 42.26 -75.182 22.416
33 T42AR83Q1wm -12.9 66.04 68.45 -90.987 43.506
34 E76AR83Q -12.3 63.86 67.18 -83.349 47.686
35 E80AR83Q -13.3 68.43 69.37 -96.995 40.802
36 Y29AR87A -11 70.18 61.85 -102.068 29.963
37 T42AR87A -12 72.96 68.27 -103.662 37.568
38 E76AR87A -12.2 69.28 66.45 -96.035 39.696
39 E80AR87A -12.9 72.71 68.65 -107.539 33.82
40 Y29AH102AWM -12.7 69.04 62.5 -112.803 18.736
41 Y29FH102AWMx -13.5 69.12 63.08 -112.538 19.669
42 W38FH102AWM -11.4 75.04 71.71 -130.846 15.908
43 D39AH102Awm -10.1 70.31 43.2 -80.129 33.379
44 T42AH102Awm -10.9 74.47 70.98 -123.278 22.171
45 E76AH102AWM -11.5 71.25 68.4 -117.52 22.128
46 E80AH102AWM -12.3 74.11 70.37 -128.723 15.757
47 D35AE73Wwm -13.3 97.49 51.49 -141.319 7.661
48 D39AE73A -11.9 86.44 44.05 -95.671 34.825
49 D39AE73Q -11.8 98.07 44.89 -99.043 43.918
50 E76AE73Q -15.5 100.37 71.19 -159.859 11.704
51 wtE73A -16.7 91.86 70.78 -166.59 -3.953
52 wtE73C -16.5 97.02 73.44 -171.877 -1.42
53 wtE73F -16.8 104.48 76.16 -181.322 -0.674
54 wtE73Q -17.6 104.47 75.68 -174.595 5.553
55 wtE73S -16 93.75 71.2 -168.858 -3.913
56 wtE73Y -16.6 96.73 73.9 -176.256 -5.623
57 D35AE73Awm -12.6 95.94 48.24 -133.672 10.504
58 D35AE73Fwm -12.6 103.76 52.4 -142.665 13.491
59 D39AE73F -11.6 95.04 44.16 -96.927 42.276
60 D39AR87A -11.9 68.25 44.93 -84.455 28.724
61 E76AE73W -15.5 94.18 71.18 -163.989 1.37
62 W38FR87A -12 75.12 69.55 -110.615 34.049
63 WTE73W -17.4 97.84 75.42 -179.2 -5.934
64 WTR83Q -13.6 67.07 70.61 -95.287 42.397
65 D39AE73W -12.4 91.53 44.32 -97.266 38.585
65 complexes with different interfacial mutations

5. Electrostatic Desolvation Free Energy Calculation
•UHBD6.1: Solving the Poisson-Boltzmann equation using a finite
difference method
Pdesol
ele
G


LP
ele
Ldesol
ele
Pdesol
ele
bind
ele
EGGG


Ldesol
ele
G


LP
ele
E

LP
ele
E


6. Electrostatic Eesolvation Energy of Barnase
Electrostatic Eesolvation Energy of Barstar
R
2
<0.1
R
2
=0.41

7. R
2
=0.63
R
2
=0.35
Electrostatic Interaction Energy between Barnase and Barstar
Electrostatic Binding Free Energy

8. Energy Decomposition to each BN-BS
residue pair
•Each complex was energy-minimized in AMBER7.0 with AMBER94 ff
•Lennard-Jones interactions were calculated for each BN-BS residue pair
(110 x 89 = 9790)
•Coulomic interactions were calculated for each BN-BS residue pair
(110 x 89 = 9790)
•Desolvation energies of BN and BS were calculated in UHBD6.1
Each complex: 19582 (=9790+9790+2) energy terms

9. Chemometric Analysis
•Principal Component Analysis (PCA)
•Partial Least Squares Analysis (PLS)
CuwuwGwGwG
i
ele
i
ele
i
i
vdw
i
vdw
i
L
desol
L
desol
R
desol
R
desol
 
Contribution of each energy term:
Importance of each residue pair
Contribution of translational and
rotational entropy change

10. Data
set
#Complexes#LV R
2
Q
2
SDEP
(kcal/mol)
Constant C
(kcal/mol)
G 65
4 0.65 0.57 1.67 -2.928
5 0.85 0.74 1.29 +1.63
6 0.91 0.86 0.97 +5.364
7 0.93 0.88 0.87 +6.351
Table 1. Predictive Performance of the COMBINE Model

11. D
3
9
D
3
5
G
3
1
T
4
2
A
3
6
W
3
8
E
7
6
E
8
0
E
7
6
v
d
w
Y
2
9
v
d
w
D
3
9
v
d
w
T
4
2
v
d
w
R
8
3
R
8
7
R
5
9
H
1
0
2
D
7
5
K
2
7
E
7
3
R
5
9
v
d
w
H
1
0
2
v
d
w
R
8
3
v
d
w
K
2
7
v
d
w
-0.5
0
0.5
1
1.5
2
Normalized Coefficients at 6 LV
Barstar Barnase