Sun Y C, Veenstra D L, Kollman P A
Department of Pharmaceutical Chemistry, University of California, San Francisco 94143-0446, USA.
Protein Eng. 1996 Mar;9(3):273-81. doi: 10.1093/protein/9.3.273.
Free energy calculations were carried out to determine the relative unfolding free energy of the Ile96 wild type and Ala96 mutant barnases. The total calculated free energies suggest that substitution of Ile96 with Ala destabilizes barnase by 3.9 kcal/mol, which is in good agreement with the independently determined experimental values of 4.0 and 3.3 kcal/mol and a previous simulation. However, a decomposition of the free energy finds the dominant contributions to this free energy arising from the noncovalent interactions between the perturbed group and distant residues of barnase in the sequence and water molecules and only a very small contribution from covalent interactions. This is in contrast to the previous simulation, using the dual topology methodology, which produced a decomposition with an approximately 60% free energy contribution from changes in covalent interactions. The use of the single topology employed in the present calculations and the dual topology employed in the previous study are analyzed in order to understand the contrast between the present results and the results of the previous study.
进行了自由能计算，以确定Ile96野生型和Ala96突变型巴那斯酶的相对解折叠自由能。计算得到的总自由能表明，将Ile96替换为Ala会使巴那斯酶的稳定性降低3.9千卡/摩尔，这与独立测定的4.0和3.3千卡/摩尔的实验值以及先前的模拟结果非常吻合。然而，对自由能的分解发现，该自由能的主要贡献来自受扰基团与巴那斯酶序列中远距离残基之间的非共价相互作用以及水分子，而共价相互作用的贡献非常小。这与先前使用双拓扑方法的模拟结果形成对比，该模拟结果显示共价相互作用变化对自由能的贡献约为60%。分析了本计算中使用的单拓扑和先前研究中使用的双拓扑，以理解本研究结果与先前研究结果之间的差异。
