Computational Methods for Proteins

结构柔性在蛋白质功能中扮演着重要的角色，对于蛋白质-蛋白质和蛋白质-配体识别机制是必不可少的，被称为诱导-和选择-适合。通常参与这种过程的表面环可以在从随机线圈到定义良好的结构的柔性状态中占优势，其中环驻留在由局部结构波动定义的单一宽微态(WM)中。一个回路也可以表现出中等的灵活性，其中几个WM在热力学平衡中被大量填充。到目前为止，大环的结构确定在同调研究中仍然是一个悬而未决的问题。现有的方法都没有系统地解决循环灵活性的问题。我们最近发展了一种处理柔韧性的统计力学方法，并成功地应用于预测环肽在DMSO中的溶液结构和数量。在这个项目中，它将扩展到水中的蛋白质环。这种方法包括：(1)原子溶剂化参数(ASP)的新优化；(2)用局域扭转变形(LTD)方法进行构象搜索以确定最稳定的WMS；(3)用蒙特卡罗方法模拟这些WMS，并用我们的局域态(LS)方法计算它们的自由能(因此布居)。环能量由一个力场和一个溶剂化项定义，而溶剂化项依赖于asp。优化后的ASP是将环路的全局能量最小结构变成环路的X射线结构的那些。这一过程不同于常见的基于小分子从气相转移到水的自由能的ASPs的推导。我们已经根据OPLS和琥珀力场优化了核糖核酸酶A环的天冬氨酸。琥珀获得了特别好的结果。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。CASP5解决的问题也将受到攻击。我们将集中于参与酶结合、催化和识别过程的环的中间灵活性，这些过程在合理的药物设计中是重要的。为了能够处理长循环，LTD和LS方法的效率将得到提高。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、对接和穿线。

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.