Methods for Calculating the Free Energy of Proteins

描述(申请人提供)：本提案的主要目的是进一步发展第一个提案1中建立的用于计算绝对熵S和亥姆霍兹自由能F(F=E-TS，其中E是势能，7是绝对温度)的新方法。这种方法-假设的扫描蒙特卡罗(分子动力学)HSMC(MD)是我们处理生物大分子柔性的方法的重要组成部分，该方法还包括构象搜索技术的发展和简化的溶剂化模型；因此，HSMC(MD)也将被应用于在该方法框架内处理的问题。HSMC(MD)的主要优点是：(I)两个微态m和n之间的自由能差(例如，肽的螺旋和发夹)或结合到酶活性部位的两个配体之间的自由能差只需进行两次不同的模拟即可得到Fm和Fn，从而无需诉诸热力学积分即可得到AFMn=Fm-Fn；(Ii)该方法是精确的，因为该方法考虑了所有相互作用，唯一的近似是由于采样不足，(Iii)提供了F的严格下界和上界。HSMC(MD)最初是为多肽、水和自我回避行走而开发的。在这个建议(2)中，我们试图将其扩展到蛋白质中的链段，如侧链、表面环或由显性水溶解的配体。因此，该方法将用于研究在酶功能中起重要作用的移动环的结构偏好(酶：A-淀粉酶、磷酸三糖异构酶(TIM)、链霉亲和素和乙酰胆碱酯酶)。我们还将计算生物素和亚胺生物素与链霉亲和素结合的相对自由能和它们的绝对结合自由能，以及氨基酸与天冬氨酸-tRNA合成酶的结合自由能，并将我们的结果与实验和以前的计算工作进行比较。我们还将与Troy Wymore博士合作，预测CASP比赛中的环路结构。晶格模型被广泛用于合成聚合物和研究蛋白质折叠。因此，我们将改进晶格链模型的HSMC，并将其应用于几个这样的模型，特别是研究蛋白质钙调素模型中构象转变过程中访问的微态数量。新节目将在万维网上公布。

DESCRIPTION (provided by applicant): The main objective of this proposal is to further develop a novel method established in the first proposal, proposal 1, for calculating the absolute entropy, S and the Helmholtz free energy, F (F=E-TS where E is the potential energy and 7 the absolute temperature). This method - the hypothetical scanning Monte Carlo (molecular dynamics) HSMC(MD) is an important ingredient in our approach for treating flexibility in biological macromolecules which also includes development of conformational search techniques and simplified solvation models; thus, HSMC(MD) will also be applied to problems treated within the framework of this approach. The main advantages of HSMC(MD) are: (i) Free energy differences between two microstates m and n (e.g., a helix and a hairpin of a peptide) or between two ligands bound to an active site of an enzyme can be obtained by carrying out only two different simulations from which Fm and Fn are obtained leading to AFmn = Fm -Fn without the need to resort to thermodynamic integration, (ii) The method is exact in the sense that all interactions are considered and the only approximation is due to insufficient sampling, (iii) Rigorous lower and upper bounds for F are provided. HSMC(MD) was developed initially for peptides, water, and self-avoiding walks. In this proposal (2) we seek to extend it to chain segments in proteins such as side chains, surface loops or ligands solvated by explicit water. Thus, the method will be used for studying structural preferences in mobile loops that play an important role in enzyme function (of the enzymes: a-amylase, triose phosphate isomerase (TIM), streptavidin, and acetylcholinesterase). We shall also calculate the relative free energy of binding of biotin and iminobiotin to streptovidin and their absolute free energies of binding, and binding free energy of amino acids to aspartyl-tRNA synthetase, comparing our results to the experiment and to previous computational work. We shall also predict loop structures in the CASP competition collaborating with Dr. Troy Wymore. Lattice model are used extensively for synthetic polymers and for studying protein folding. Thus, we shall improve HSMC for lattice chain models and apply it to several such models, in particular to study the population of microstates visited during conformational transitions in a model of the protein calmodulin. The new programs will be posted on the World Wide Web.