Alvarez-Garcia Daniel, Barril Xavier
Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona , Av. Joan XXIII s/n, 08028 Barcelona, Spain.
Institut de Biomedicina de la Universitat de Barcelona (IBUB) , Barcelona, Spain.
J Chem Theory Comput. 2014 Jun 10;10(6):2608-14. doi: 10.1021/ct500182z. Epub 2014 May 30.
Conceptually, the simplistic lock and key model has been superseded by more realistic views of molecular recognition that take into account the intrinsic dynamics of biological macromolecules. However, it is still common for structure-based drug discovery methods to represent the receptor as static structures. The practical advantages of this approximation, the notable success attained over the past few decades with such simple models and the absence of clear guidelines for weighing the pros and cons of accounting for flexibility may prompt some investigators to stretch the rigid model beyond its scope. Here, we investigate the relationship between protein flexibility and binding free energy and present some useful hints for understanding when, and to what extent, flexibility should be considered. Using molecular dynamics simulations of hen egg-white lysozyme (HEWL) with explicit aqueous/organic solvent mixtures and a range of restraint conditions, we find out how artificially restricted mobility affects binding hot spots. Barring sampling errors or an inappropriate choice of reference structure, we find that decreased mobility (measured as B-factors) leads to artifactually more negative binding free energies, but a logarithmic relationship between both terms attenuates the errors. Consequently, ignoring flexibility may be an acceptable approximation for intrinsically rigid regions (such as the active site of enzymes) but may lead to larger errors elsewhere. For the same reason, local conformational sampling yields very accurate predictions and, owing to its practical advantages, may be preferable to full conformational sampling for many applications.
从概念上讲，简单的锁钥模型已被更现实的分子识别观点所取代，这些观点考虑了生物大分子的内在动力学。然而，基于结构的药物发现方法仍普遍将受体表示为静态结构。这种近似方法的实际优势、过去几十年来使用此类简单模型所取得的显著成功，以及在权衡考虑灵活性的利弊方面缺乏明确指导方针，可能会促使一些研究人员将刚性模型扩展到其适用范围之外。在此，我们研究蛋白质灵活性与结合自由能之间的关系，并给出一些有用的提示，以帮助理解何时以及在何种程度上应考虑灵活性。通过对鸡蛋清溶菌酶（HEWL）在含有明确水/有机溶剂混合物及一系列限制条件下进行分子动力学模拟，我们探究了人为限制的流动性如何影响结合热点。排除采样误差或参考结构选择不当的情况，我们发现流动性降低（以B因子衡量）会导致人为地产生更负的结合自由能，但两者之间的对数关系会减弱误差。因此，对于本质上刚性的区域（如酶的活性位点），忽略灵活性可能是一种可接受的近似，但在其他地方可能会导致更大的误差。出于同样的原因，局部构象采样能产生非常准确的预测，并且由于其实际优势，在许多应用中可能比完全构象采样更可取。
