Juffer A H, Eisenhaber F, Hubbard S J, Walther D, Argos P
European Molecular Biology Laboratory, Heidelberg, Germany.
Protein Sci. 1995 Dec;4(12):2499-509. doi: 10.1002/pro.5560041206.
Atomic solvation parameters (ASP) are widely used to estimate the solvation contribution to the thermodynamic stability of proteins as well as the free energy of association for protein-ligand complexes. They are also included in several molecular mechanics computer programs. In this work, a total of eight atomic solvation parametric sets has been employed to calculate the solvation contribution to the free energy of folding delta Gs for 17 proteins. A linear correlation between delta Gs and the number of residues in each protein was found for each ASP set. The calculations also revealed a great variety in the absolute value and in the sign of delta Gs values such that certain ASP sets predicted the unfolded state to be more stable than the folded, whereas others yield precisely the opposite. Further, the solvation contribution to the free energy of association of helix pairs and to the disassociation of loops (connection between secondary structural elements in proteins) from the protein tertiary structures were computed for each of the eight ASP sets and discrepancies were evident among them.
原子溶剂化参数（ASP）被广泛用于估算溶剂化对蛋白质热力学稳定性的贡献以及蛋白质-配体复合物的结合自由能。它们也被纳入了多个分子力学计算机程序中。在这项工作中，总共使用了八个原子溶剂化参数集来计算17种蛋白质折叠自由能ΔGs的溶剂化贡献。对于每个ASP集，都发现ΔGs与每种蛋白质中的残基数之间存在线性相关性。计算还揭示了ΔGs值的绝对值和符号存在很大差异，以至于某些ASP集预测未折叠状态比折叠状态更稳定，而其他ASP集则得出恰恰相反的结果。此外，针对八个ASP集中的每一个，都计算了溶剂化对螺旋对结合自由能以及环（蛋白质二级结构元件之间的连接）从蛋白质三级结构解离的自由能的贡献，并且它们之间存在明显差异。
