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. Author manuscript; available in PMC: 2015 Jul 1.
Published in final edited form as: Proteins. 2013 Nov 23;82(7):1128–1141. doi: 10.1002/prot.24478

Table I.

5CRO lattice: MM-PBSA energies of crystal packing interfacesa

Interfaceb ΔEvdwc ΔEele ΔEele + ΔGPB ΔGtot
1 −73.46 ± 0.74d 191.26 ± 11.45 36.62 ± 2.08 −49.19 ± 1.60
−76.19 ± 1.46 44.54 ± 11.73 36.11 ± 1.94 −52.57 ± 1.76
2 −73.47 ± 0.86 241.91 ± 8.42 41.18 ± 1.27 −44.37 ± 0.98
−73.94 ± 1.02 73.65 ± 9.42 35.11 ± 1.18 −50.57 ± 1.13
3 −10.49 ± 0.77 8.98 ± 3.72 −5.07 ± 1.52 −19.78 ± 1.62
−10.07 ± 0.91 −30.12 ± 5.43 −1.85 ± 1.97 −15.92 ± 1.75
4 −8.99 ± 0.66 7.07 ± 5.07 −4.67 ± 1.35 −17.94 ± 1.18
−8.89 ± 0.54 −15.55 ± 9.73 1.30 ± 2.24 −11.25 ± 2.14
5 −47.27 ± 0.66 62.35 ± 4.26 3.73 ± 1.22 −52.58 ± 1.35
−45.61 ± 0.87 31.83 ±11.04 9.67 ± 2.22 −44.29 ± 2.20
6 −48.18 ± 0.58 64.25 ± 4.99 4.46 ± 1.59 −52.73 ± 1.71
−46.38 ± 0.75 21.16 ± 6.03 9.35 ± 1.94 −45.56 ± 1.94
7 −23.18 ± 1.71 92.14 ±10.72 8.43 ± 1.38 −19.62 ± 1.64
−23.00 ± 1.13 18.69 ± 7.24 8.84 ± 0.99 −18.98 ± 1.07
8 −20.72 ± 1.91 80.54 ± 6.38 14.13 ± 1.20 −10.65 ± 1.08
−15.86 ± 1.47 29.45 ± 4.91 10.66 ± 1.04 −8.53 ± 0.89
9e −21.12 ± 0.80 272.41 ± 3.23 16.95 ± 0.92 −7.85 ± 0.53
−19.53 ± 1.19 143.22 ± 2.86 12.96 ± 0.58 −9.92 ± 1.08
10 −46.28 ± 0.39 340.35 ± 4.75 26.09 ± 0.79 −25.89 ± 0.70
−42.00 ± 0.82 217.03 ± 3.83 21.74 ± 0.73 −25.65 ± 0.90
11 −23.43 ± 0.73 232.25 ± 3.01 17.87 ± 0.31 −9.76 ± 0.68
−21.09 ± 0.84 137.38 ± 3.42 15.18 ± 0.62 −9.56 ± 0.45
12 −44.91 ± 0.55 266.81 ± 3.21 20.76 ± 0.55 −29.97 ± 0.58
−42.76 ± 0.40 199.12 ± 3.12 22.95 ± 0.41 −25.31 ± 0.67
13 −16.78 ± 0.96 273.33 ± 2.65 14.39 ± 0.60 −5.24 ± 0.67
−21.09 ± 0.89 159.84 ± 2.80 13.71 ± 0.72 −10.87 ± 0.62
14 −15.45 ± 0.85 346.50 ± 3.59 13.15 ± 0.46 −4.94 ± 0.61
−16.56 ± 0.66 174.10 ± 2.24 11.19 ± 0.39 −8.14 ± 0.55
a

For each packing interface, MM-PBSA energies (kcal/mol) are presented for the WT (rows with normal font) and mutant (rows with italicized font) crystal simulations.

b

The source and target chains for each interface are the following: 1: A(x,y,z), C(x,y,z); 2: B(x,y,z), O(x,y,z); 3: A(x,y,z), O(x,y,z); 4: B(x,y,z), C(x,y,z); 5: A(x,y,z), B(x,y,z); 6: C(x,y,z), O(x,y,z); 7: C(x,y,z), A(-y-1,x-y-1,z); 8: B(x,y,z), A(-y-1,x-y-1,z); 9: B(x,y,z), A(-x-2/3,-x+y-1/3,-z-1/3); 10: B(x,y,z), B(-x-2/3,-x+y-1/3,-z-1/3); 11: B(x,y,z), B(x-y-2/3,-y-4/3,-z-1/3); 12: C(x,y,z), C(y,x,-z); 13: O(x,y,z), C(y,x,-z); 14: O(x,y,z), O(-y-1,x-y,z). For the heterotypic interfaces (1, 2, 3, 4, 5, 6, 7, 8, 9, 13, and 14), each energy term is averaged over 18 unique copies in the unit cell. Energy terms for the homotypic interfaces (10, 11, and 12) are averaged over nine unique copies.

c

ΔEvdw: van der Waals energy; ΔEele: MM electrostatic energy; ΔEele + ΔGPB: net electrostatic contribution (where ΔGPB is the electrostatic solvation free energy, determined using the PB equation); ΔGtot: total binding energy. The individual solvation free energy terms (ΔGnp and ΔGPB) are not presented.

c

Standard errors are computed as σ/N1/2, where σ is the standard deviation of the averages over the total number of copies (N) of an interface in the unit cell.

d

Interfaces with mutation sites (9, 11, 13, and 14) are denoted by bold and underlined font.