Modeling protein stability: a theoretical analysis of the stability of T4 lysozyme mutants.
Modeling protein stability: a theoretical analysis of the stability of T4 lysozyme mutants.
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DOI：
10.1093/protein/10.7.789
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发表时间：
1997-07
期刊：
影响因子：
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通讯作者：
D. Veenstra;Peter A. Kollman
中科院分区：
文献类型：
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作者：
D. Veenstra;Peter A. Kollman
进行自由能计算以确定T4溶菌酶正缬氨酸(Nvl)和O-甲基-丝氨酸(Mse)的非天然氨基酸突变体以及残基133处的丙氨酸(其在天然序列中是亮氨酸)的相对稳定性。进行这些计算既是为了评估该方法的有效性，也是为了更好地了解有助于蛋白质稳定性的力量。使用不同长度的肽来模拟变性状态。采用约束来强制对扰动侧链的侧链chi1二面体进行采样，并通过使用不同的约束集来研究蛋白质重新包装对突变的影响。此外，还确定了折叠和展开状态下模拟的收敛行为和滞后。计算结果与实验相符，Mse-->Nvl 为+1.84 对比+1.56 kcal/mol，Nvl-->Ala 为-3.48 对比-2.2 至-3.6 kcal/mol。我们发现，在精心选择的系统上仔细进行自由能计算可以为蛋白质稳定性提供有用的见解。我们的结果表明，天然状态下堆积相互作用的丧失是突变体不稳定的主要来源，突变体减少了埋藏的非极性表面积的数量，并且主链的微妙反应影响了稳定性丧失的程度。我们发现 chi1 二面体的构象自由度对蛋白质稳定性有显着影响，并且氨基酸侧链的溶剂化受到与肽主链相互作用的强烈影响。
Free energy calculations were conducted to determine the relative stability of the unnatural amino acid mutants of T4 lysozyme norvaline (Nvl) and O-methyl-serine (Mse) and of alanine at residue 133, which is leucine in the native sequence. These calculations were performed both to assess the validity of the methodology and to gain a better understanding of the forces which contribute to protein stability. Peptides of different length were used to model the denatured state. Restraints were employed to force sampling of the side chain chi1 dihedral of the perturbed side chain, and the effect of protein repacking in response to mutation was studied through the use of different constraint sets. In addition, the convergence behavior and hysteresis of the simulations in the folded and unfolded states were determined. The calculated results agree well with experiment, + 1.84 versus + 1.56 kcal/mol for Mse-->Nvl and -3.48 versus -2.2 to -3.6 kcal/mol for Nvl-->Ala. We find that free energy calculations can provide useful insights to protein stability when conducted carefully on a well chosen system. Our results suggest that loss of packing interactions in the native state is a major source of destabilization for mutants which decrease the amount of buried nonpolar surface area and that subtle responses of the backbone affect the magnitude of the loss of stability. We show that the conformational freedom of the chi1 dihedral has a noticeable effect on protein stability and that the solvation of amino acid side chains is strongly influenced by interactions with the peptide backbone.