Muegge I, Tao H, Warshel A
Department of Chemistry, University of Southern California, Los Angeles 90089-1062, USA.
Protein Eng. 1997 Dec;10(12):1363-72. doi: 10.1093/protein/10.12.1363.
Dissecting ligand-protein binding free energies in individual contributions of protein residues (which are referred to here as 'group contributions') is of significant importance. For example, such contributions could help in estimating the corresponding mutational effects and in studies of drug resistance problems. However, the meaning of group contributions is not always uniquely defined and the approximations for rapid estimates of such contributions are not well developed. In this paper, the nature of group contributions to binding free energy is examined, focusing particularly on electrostatic contributions which are expected to be well behaved. This analysis examines different definitions of group contributions; the 'relaxed' group contributions that represent the change in binding energy upon mutation of the given residue to glycine, and the 'non-relaxed' group contributions that represent the scaled Coulomb interaction between the given residue and the ligand. Both contributions are defined and evaluated by the linear response approximation (LRA) of the PDLD/ S method. The present analysis considers the binding of pepstatin to endothiapepsin and 23 of its mutants as a test case for a neutral ligand. The 'non-relaxed' group contributions of 15 endothiapepsin residues show significant peaks in the 'electrostatic fingerprint'. The residues that contribute to the electrostatic fingerprint are located in the binding site of endothiapepsin. They include the aspartic dyad (Asp32, Asp215) with adjacent residues and the flap region. Twelve of these 15 residues have a heavy atom distance of <3.75 A to pepstatin. The contributions of 8 (10) of these 12 residues can be reconciled with the calculated 'relaxed' group contributions where one allows the protein and solvent (solvent only) to relax upon mutation of the given residue to glycine. On the other hand, it was found that residues at the second 'solvation shell' can have relaxed contributions that are not captured by the non-relaxed approach. Hence, whereas residues with significant non-relaxed electrostatic contributions are likely to contribute to binding, residues with small non-relaxed contributions may still affect the binding energy. At any rate, it is established here that even in the case of uncharged inhibitors it is possible to use the non-relaxed electrostatic fingerprint to detect 'hot' residues that are responsible for binding. This is significant since some versions of the non-relaxed approximation are faster by several orders of magnitude than more rigorous approaches. The general applicability of this approach is outlined, emphasizing its potential in studies of drug resistance where it is crucial to have a rapid way of anticipating the effect of mutation on both drug binding and catalysis.
剖析配体 - 蛋白质结合自由能中蛋白质残基的个体贡献（本文中称为“基团贡献”）具有重要意义。例如，此类贡献有助于估计相应的突变效应以及研究耐药性问题。然而，基团贡献的含义并非总是唯一确定的，且用于快速估计此类贡献的近似方法尚未充分发展。本文研究了基团对结合自由能贡献的本质，特别关注预期表现良好的静电贡献。该分析考察了基团贡献的不同定义；“松弛”的基团贡献表示给定残基突变为甘氨酸时结合能的变化，“非松弛”的基团贡献表示给定残基与配体之间的缩放库仑相互作用。这两种贡献均通过PDLD/S方法的线性响应近似（LRA）来定义和评估。本分析将胃蛋白酶抑制剂与内硫霉素及其23个突变体的结合作为中性配体的测试案例。15个内硫霉素残基的“非松弛”基团贡献在“静电指纹”中显示出显著峰值。对静电指纹有贡献的残基位于内硫霉素的结合位点。它们包括天冬氨酸二元组（Asp32、Asp215）及其相邻残基和侧翼区域。这15个残基中有12个与胃蛋白酶抑制剂的重原子距离小于3.75埃。这12个残基中的8个（10个）的贡献可以与计算得到的“松弛”基团贡献相协调，其中在给定残基突变为甘氨酸时允许蛋白质和溶剂（仅溶剂）松弛。另一方面，发现处于第二个“溶剂化壳层”的残基可能具有非松弛方法未捕捉到的松弛贡献。因此，虽然具有显著非松弛静电贡献的残基可能对结合有贡献，但具有小非松弛贡献的残基仍可能影响结合能。无论如何，本文确定即使在不带电荷抑制剂的情况下，也可以使用非松弛静电指纹来检测负责结合的“热点”残基。这很重要，因为某些版本的非松弛近似比更严格的方法快几个数量级。概述了该方法的一般适用性，强调了其在耐药性研究中的潜力，在耐药性研究中，快速预测突变对药物结合和催化的影响至关重要。
