Microfolding: Study of Protein Conformation Change by Molecular Dynamics Calculations

Hermans博士建议进行分子动力学研究，以研究多肽和蛋白质的构象变化的平衡和动力学。我们将对被几层溶剂分子显式溶剂化的体系进行计算。(1)分4步计算构象自由能面：通过真空动力学模拟探索构象空间；每个自由能最小值附近的概率分布将由自由动力学计算；不同构象之间的自由能差异将通过施加扭矩的受限自由能模拟和分子取代的自由能模拟来确定；最小值之间的障碍将单独探讨。这些结果将与不同的方法（自由动力学、随机模型、过渡态动力学）结合使用，以确定障碍越过的速率，即构象变化的动力学参数。(2)他计划开发一种方法来先验地确定氨基酸替代对折叠肽结构和蛋白质天然折叠构象稳定性的影响。这将有两个目标，一是开发出能够持续再现现有实验测量的自由能变化的技术，二是利用动力学模拟唯一适合提供的关于结构和热力学的细节，从而量化潜在物理效应方面的差异。(3)拟以两个例子研究酶活性位点的构象柔韧性：丝氨酸蛋白酶的侧链柔韧性及其对不同底物特异性的可能关系；二氢叶酸还原酶抑制剂的柔韧性及其与不同物种酶特异性的关系。(4)最后，他将尝试根据自由能区分蛋白质分子部分的交替构象，即小表面环和肽基团，以开发一种适用于实验数据提供不足细节的结构确定的工具。***//

Dr. Hermans proposes molecular dynamics studies to investigate equilibria and kinetics of conformation change of peptides and proteins. Calculations will be done for systems which are explicitly solvated with several layers of solvent molecules. (1) Conformational free energy surfaces will be calculated in a 4-step process: conformation space will be explored by dynamics simulations in vacuo; probability distributions near each free energy minimum will be computed by free dynamics; free energy differences between conformations will be determined by restrained free-energy simulations with applied torques, and by free-energy simulations with molecular substitution; barriers between minima will be explored separately. These results will be used in conjunction with different approaches (free dynamics; a stochastic model; transition state dynamics) in order to determine the rates of barrier crossings, i.e.kinetic parameters of conformation changes. (2) He plans to develop a method for determining a priori the effect of amino acid replacement on the stability of folded peptide structures and of native, folded conformations of proteins. This will have as aims both to develop techniques that consistently reproduce available experimentally measured free energy changes, and to use the details about structure and thermodynamics that the dynamics simulations are uniquely suited to provide, and thereby quantitate the differences in terms of underlying physical effects. (3) He plans to study conformational flexibility in enzyme active sites in two examples: side chain flexibility in serine protease, and its possible relation to specificity for different substrates; inhibitor flexibility in dihydrofolate reductase and its relation to specificity for enzymes from different species. (4) Finally, he will attempt to distinguish alternate conformations of parts of protein molecules, namely, small surface loops and peptide groups, according to free energy, in order to develop a tool applicable in structure determinations where experimental data provide insufficient detail.***//