comparative binding energy (combine) analysis of barnase-barstar interfacial mutants
DESCRIPTION
Comparative Binding Energy (COMBINE) Analysis of Barnase-Barstar Interfacial Mutants. Binding features:. High binding affinity (Kd=10 -14 M) Polar binding interface: positive(+2e) on BN, negative (-6e) on BS Hot-spots Residues at the interface. barstar. barnase. - PowerPoint PPT PresentationTRANSCRIPT
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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:
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65 complexes with interfacial mutations
Arg59
Glu73
Arg83
His102
Arg87Lys27
Glu80
Glu76Trp38
Thr42
Tyr29Asp39
Asp35
Trp44
Barnase
Barstar
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65 complexes with different interfacial mutationsNo. Complex Exp. Binding delta_G Desol_BN Desol_BS Elec_inter Elect_binding_G1 wtwt -19 83.29 75.7 -149.629 9.3592 wtK27Awm -13.6 61.78 64.66 -121.787 4.6583 wtR59A -13.8 67.68 69.38 -120.451 16.6084 D39AR59A -7.7 60.52 23.06 -45.371 38.2045 wtR87A -13.5 75.58 70.4 -111.981 33.9996 wtH102Awm -12.9 75.93 73.32 -131.979 17.2797 Y29FWTWMx -19.1 74.54 66.27 -129.535 11.2748 Y29AWT -15.6 76.86 66.26 -131.241 11.889 D35Awtwm -14.5 82.35 51.48 -121.022 12.81410 W38FWT -17.4 80.2 72.81 -147.522 5.4911 D39Awt -11.3 78.3 44.99 -89.331 33.9612 T42Awt -17.2 82.07 73.01 -142.04 13.04213 W44FWT -19 82.54 74.96 -148.134 9.3714 E76wt -17.7 76.34 70.45 -133.19 13.59515 E80AWT -18.5 77.67 70.21 -140.513 7.36616 Y29AK27AWM -10.4 56.34 56.68 -104.906 8.11417 D35AK27Awm -9.5 58.45 41.3 -91.552 8.1918 W38FK27AWM -12.6 59.29 62.5 -115.126 6.67119 D39AK27Awm -10.8 52.85 41.48 -74.609 19.72320 T42AK27Awm -13.3 59.23 63.75 -118.2 4.77321 E76AK27AWM -12.3 54.36 59.53 -103.754 10.13722 E80AK27Awm -13.5 58.31 61.2 -116.631 2.87723 Y29AR59A -10.9 61.75 60.39 -102.207 19.92624 D35AR59AWM -12.7 63.45 48.5 -100.483 11.45825 W38FR59A -12.8 66.82 68.36 -119.921 15.25526 T42AR59A -12.2 65.87 66.64 -112.196 20.30827 E76AR59A -14.1 65.73 66.76 -118.262 14.2328 E80AR59A -13.9 65.04 67.33 -118.106 14.25729 Y29AR83Q -10.7 65.36 62.63 -85.188 42.79730 D35AR83QWM -9.4 67.83 47.64 -72.423 43.046
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32 D39AR83Q -12.6 55.34 42.26 -75.182 22.41633 T42AR83Q1wm -12.9 66.04 68.45 -90.987 43.50634 E76AR83Q -12.3 63.86 67.18 -83.349 47.68635 E80AR83Q -13.3 68.43 69.37 -96.995 40.80236 Y29AR87A -11 70.18 61.85 -102.068 29.96337 T42AR87A -12 72.96 68.27 -103.662 37.56838 E76AR87A -12.2 69.28 66.45 -96.035 39.69639 E80AR87A -12.9 72.71 68.65 -107.539 33.8240 Y29AH102AWM -12.7 69.04 62.5 -112.803 18.73641 Y29FH102AWMx -13.5 69.12 63.08 -112.538 19.66942 W38FH102AWM -11.4 75.04 71.71 -130.846 15.90843 D39AH102Awm -10.1 70.31 43.2 -80.129 33.37944 T42AH102Awm -10.9 74.47 70.98 -123.278 22.17145 E76AH102AWM -11.5 71.25 68.4 -117.52 22.12846 E80AH102AWM -12.3 74.11 70.37 -128.723 15.75747 D35AE73Wwm -13.3 97.49 51.49 -141.319 7.66148 D39AE73A -11.9 86.44 44.05 -95.671 34.82549 D39AE73Q -11.8 98.07 44.89 -99.043 43.91850 E76AE73Q -15.5 100.37 71.19 -159.859 11.70451 wtE73A -16.7 91.86 70.78 -166.59 -3.95352 wtE73C -16.5 97.02 73.44 -171.877 -1.4253 wtE73F -16.8 104.48 76.16 -181.322 -0.67454 wtE73Q -17.6 104.47 75.68 -174.595 5.55355 wtE73S -16 93.75 71.2 -168.858 -3.91356 wtE73Y -16.6 96.73 73.9 -176.256 -5.62357 D35AE73Awm -12.6 95.94 48.24 -133.672 10.50458 D35AE73Fwm -12.6 103.76 52.4 -142.665 13.49159 D39AE73F -11.6 95.04 44.16 -96.927 42.27660 D39AR87A -11.9 68.25 44.93 -84.455 28.72461 E76AE73W -15.5 94.18 71.18 -163.989 1.3762 W38FR87A -12 75.12 69.55 -110.615 34.04963 WTE73W -17.4 97.84 75.42 -179.2 -5.93464 WTR83Q -13.6 67.07 70.61 -95.287 42.39765 D39AE73W -12.4 91.53 44.32 -97.266 38.585
65 complexes with different interfacial mutations
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Electrostatic Desolvation Free Energy Calculation
• UHBD6.1: Solving the Poisson-Boltzmann equation using a finite difference method
PdesoleleG
LPele
Ldesolele
Pdesolele
bindele EGGG
LdesoleleG
LPeleE
LPeleE
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Electrostatic Eesolvation Energy of Barnase
Electrostatic Eesolvation Energy of Barstar
R2<0.1
R2=0.41
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R2=0.63
R2=0.35
Electrostatic Interaction Energy between Barnase and Barstar
Electrostatic Binding Free Energy
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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
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Chemometric Analysis
• Principal Component Analysis (PCA)
• Partial Least Squares Analysis (PLS)
CuwuwGwGwGi
elei
elei
i
vdwi
vdwi
Ldesol
Ldesol
Rdesol
Rdesol
Contribution of each energy term: Importance of each residue pair
Contribution of translational and rotational entropy change
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Data set
#Complexes #LV R2 Q2 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
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D39
D35
G31
T42
A36
W38
E76
E80
E76vdw
Y29vdw
D39vdw
T42vdwR83 R87 R59 H102 D75 K27 E73
R59vdw
H102vdw
R83vdw
K27vdw
-0.5
0
0.5
1
1.5
2
Normalized Coefficients at 6 LV
Barstar Barnase