Gopal Srinivasa M, Klumpers Fabian, Herrmann Christian, Schäfer Lars V
Center for Theoretical Chemistry, Faculty of Chemistry and Biochemistry, Ruhr-University Bochum, D-44780 Bochum, Germany.
Physical Chemistry I, Faculty of Chemistry and Biochemistry, Ruhr-University Bochum, D-44780 Bochum, Germany.
Phys Chem Chem Phys. 2017 May 3;19(17):10753-10766. doi: 10.1039/c6cp07899k.
Solvation plays an important role in virtually all biomolecular recognition and binding processes. However, the consequences of changes in solvation conditions often remain elusive. In this work, we combined isothermal titration calorimetry (ITC) and molecular dynamics (MD) simulations to investigate the effect of solvent composition on the thermodynamics of protein-ligand binding. We studied the binding of p-aminobenzamidine (PAB) to trypsin in various water/methanol mixtures as a model system for a biomolecular complex. Our ITC experiments show that the free energy of binding changes only very modestly with methanol concentration, and that this small change is due to strong enthalpy-entropy compensation. The MD and free energy simulations not only reproduce the experimental binding free energies, but also provide atomic-level insights into the mechanisms behind the thermodynamic observations. The more favorable binding enthalpy at increased methanol concentrations (when compared to pure water) is attributed to stronger protein-ligand and intramolecular protein-protein interactions. The stronger protein-ligand interaction is linked to a small-scale conformational rearrangement of the L2 binding pocket loop, which senses the solvent environment. Remarkably, the stronger interactions do not substantially reduce the configurational entropy of the protein. Instead, the more disfavorable entropy contribution to the binding free energy at increased methanol concentrations is due to the desolvation of the ligand from the bulk, which is more favorable in pure aqueous solution than in the presence of methanol. Our work thus underpins the importance of including conformational flexibility, even for an overall rather rigid complex, since even small-amplitude motions can significantly alter the binding energetics. Furthermore, the ability of our combined ITC/MD approach to assign different thermodynamic contributions to distinct conformational states might contribute to an enhanced understanding of biomolecular binding processes in general.
溶剂化在几乎所有生物分子识别和结合过程中都起着重要作用。然而，溶剂化条件变化的后果往往仍不明确。在这项工作中，我们结合等温滴定量热法（ITC）和分子动力学（MD）模拟，研究了溶剂组成对蛋白质-配体结合热力学的影响。我们研究了对氨基苯甲脒（PAB）在各种水/甲醇混合物中与胰蛋白酶的结合，将其作为生物分子复合物的模型系统。我们的ITC实验表明，结合自由能随甲醇浓度的变化非常小，而且这种小变化是由于强烈的焓-熵补偿。MD和自由能模拟不仅重现了实验结合自由能，还提供了原子水平上对热力学观测背后机制的见解。甲醇浓度增加时（与纯水相比）更有利的结合焓归因于更强的蛋白质-配体和分子内蛋白质-蛋白质相互作用。更强的蛋白质-配体相互作用与L2结合口袋环的小规模构象重排有关，该环能感知溶剂环境。值得注意的是，更强的相互作用并没有显著降低蛋白质的构象熵。相反，甲醇浓度增加时对结合自由能更不利的熵贡献是由于配体从本体中去溶剂化，这在纯水溶液中比在有甲醇存在时更有利。因此，我们的工作强调了即使对于整体相当刚性的复合物，纳入构象灵活性的重要性，因为即使是小幅度的运动也能显著改变结合能。此外，我们结合ITC/MD方法将不同热力学贡献分配给不同构象状态的能力，可能有助于总体上增强对生物分子结合过程的理解。
