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. Author manuscript; available in PMC: 2012 Jun 12.
Published in final edited form as: J Phys Chem A. 2011 Mar 23;115(16):4042–4053. doi: 10.1021/jp110373f

Table 1.

Simulation setup

Proteina PDB codeb Backgroundc Neutrald Chargedd
DOWSER Na+ Cl− tot wat Na+ Cl− tot wat
L25E 3EVQ Δ+PHS 1 7 13 5228 8 13 5240
L25K 3ERQ Δ+PHS 2 7 13 5230 7 14 5216
L36K 3EJI Δ+PHS 1 7 14 5213 6 14 5216
L38E 3D6C PHS 1 6 15 5182 6 14 5179
L38K 2RKS PHS 2 5 14 5179 5 15 5174
T62K 3DMU PHS 2 5 14 5175 5 15 5168
V66D 2OXP PHS 2 6 15 5168 6 14 5167
V66E 1U9R PHS 3 6 15 5151 6 14 5153
V66K 2SNM WT 2 5 14 5214 5 15 5209
I72E 3ERO Δ+PHS 0 7 13 5241 8 13 5237
I72K 2RBM Δ+PHS 0 7 14 5198 6 14 5199
Y91E 3D4D Δ+PHS 1 7 13 5232 8 13 5229
I92D 2OEO Δ+PHS 3 7 14 5215 7 13 5210
I92E 1TR5 Δ+PHS 4 7 14 5189 7 13 5188
I92K 1TT2 Δ+PHS 6 7 14 5181 6 14 5187
L103K 3E5S Δ+PHS 0 7 13 5225 7 14 5219
V104K 3C1F Δ+PHS 1 7 13 5235 7 14 5223
L125K 3C1E Δ+PHS 0 7 13 5205 7 14 5205
a

Substitution used to make the variant protein;

b

PDB accession code of simulated protein;

c

background form of SNase in which the substitution was engineered;

d

number of DOWSER water molecules, Na+ and Cl− ions, and total number of water molecules included in the simulations.