Computational Methods for Proteins

结构灵活性在蛋白质功能中起着重要作用，是蛋白质-蛋白质和蛋白质-配体识别机制（诱导和选择配合）的必要条件。表面回路通常参与这些过程，可以在从随机线圈到定义良好的结构的柔性状态中占上风，其中回路驻留在单个宽微状态（WM）中，由局部结构波动定义。一个回路也可以表现出中间的灵活性，其中几个wm在热力学平衡中被显著填充。迄今为止，大环的结构确定仍是同源性研究中未解决的问题。现有的方法都没有以系统的方式解决循环灵活性的问题。我们最近开发了一种处理柔性的统计力学方法，并成功地应用于预测DMSO中环肽的溶液结构和种群。在这个项目中，它将扩展到水中的蛋白质环。该方法包括：(1)原子溶剂化参数（asp）的新颖优化，(2)使用我们的局部扭转变形（LTD）方法进行广泛的构象搜索，以识别最稳定的WMs，以及(3)通过蒙特卡罗模拟这些WMs，并使用我们的局部状态（LS）方法计算它们的自由能（因此是种群）。环能量由力场和依赖于asp的溶剂化项来定义。优化的asp是指环的整体能量最小结构成为环的x射线结构。这一过程不同于asp的一般推导，后者是基于小分子从气相到水的自由转移能。我们已经基于ops和AMBER力场优化了核糖核酸酶a环的asp。琥珀获得了非常好的结果。ASPS的可转移性将通过研究抗体的高变环和其他已知环结构来测试。CASP5解决的问题也将受到攻击。我们将集中讨论参与酶结合、催化和识别过程的环的中间柔韧性，这在合理的药物设计中是重要的。为了能够处理长环路，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的广泛问题，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.