Computational Methods for Proteins

结构灵活性在蛋白质功能中起着重要作用，并且对于蛋白质-蛋白质和蛋白质-配体识别机制（称为诱导和选择匹配）至关重要。 通常参与这种过程的表面环可以在从无规卷曲到明确定义的结构的柔性状态中占主导地位，其中环驻留在由局部结构波动定义的单个宽微观状态（WM）中。 回路也可以表现出中等灵活性，其中几个WM在热力学平衡中显著地填充。 大环结构的确定至今仍是同源性研究中一个未解决的问题。现有的方法都没有以系统的方式解决环路灵活性的问题。 我们最近发展了一种处理柔性的统计力学方法，并成功地应用于预测环肽在DMSO中的溶液结构和群体。 在这个项目中，它将扩展到水中的蛋白质环。 该方法包括（1）一种新的原子溶剂化参数（ASP）优化，（2）广泛的构象搜索使用我们的本地扭转变形（LTD）方法识别最稳定的WM，和（3）模拟这些WM的Monte Carlo和计算它们的自由能（因此人口）与我们的本地状态（LS）方法。 回路能量由力场和溶剂化项定义，溶剂化项取决于ASP。 优化的ASP是循环的全局能量最小结构变为循环的X射线结构的ASP。 这个过程不同于ASP的常见推导，其基于小分子从气相转移到水的自由能。 我们已经优化了基于OPLS和AMBER力场的核糖核酸酶A环的ASP。 使用AMBER获得了非常好的结果。 将通过研究抗体的高变环和其他已知的环结构来测试ASPS的可转移性。CASP 5解决的问题也将受到攻击。 我们将集中在参与酶结合，催化和识别过程，在合理的药物设计是重要的环的中间灵活性。 为了能够处理长循环，将提高LTD和LS方法的效率。 我们独特的工具适用于结构生物学中的各种问题，如蛋白质工程，对接和线程。

Structural flexibility plays an important role in protein function and is essential for the protein-protein and protein-ligand recognition mechanisms known as induced- and selected-fit. Surface loops, which typically participate in such processes, can prevail in flexibility states ranging from a random coil to a well defined structure, where a loop resides in a single wide microstate (WM), defined by local structural fluctuations. A loop can also exhibit intermediate flexibility, where several WMs are populated significantly in thermodynamic equilibrium. To date structure determination of large loops is still an unsolved problem in homology studies. None of the existing approaches has addressed the problem of loop flexibility in a systematic way. A statistical mechanics methodology for treating flexibility was developed recently by us and applied successfully to predict the solution structures and populations of cyclic peptides in DMSO. In this project it will be extended to protein loops in water. This methodology consists of (1) a novel optimization of atomic solvation parameters (ASPs), (2) an extensive conformational search using our local torsional deformations (LTD) method for identifying the most stable WMs, and (3) simulating these WMs by Monte Carlo and calculating their free energies (hence populations) with our local states (LS) method. The loop energy is defined by a force field and a solvation term which depends on the ASPs. The optimized ASPs are those for which the global energy minimum structure of the loop becomes the loop's X-ray structure. This procedure differs from the common derivation of ASPs, which is based on the free energy of transfer of small molecules from the gas phase to water. We have already optimized ASPs for a loop of ribonuclease A based on the OPLS and AMBER force fields. Exceptionally good results obtained with AMBER. The transferability of the ASPS will be tested by studying hypervariable loops of antibodies and other known loop structures. Problems addressed by CASP5 will be attacked as well. We shall concentrate on the intermediate flexibility of loops participating in enzyme binding, catalysis, and recognition processes that are important in rational drug design. To be able to treat long loops, the efficiency of the LTD and LS methods will be enhanced. Our unique tools are applicable to a wide range of problems in structural biology, such as protein engineering, docking, and threading.