Computer Simulation of Protein Structure and Dynamics

研究将集中在计算生物学的两个领域：(1)探索生物分子构象空间的方法的应用；(2)开发有助于测定可溶性蛋白和膜蛋白的蛋白质结构的方法。了解蛋白质折叠在许多情况下都是很重要的，比如蛋白质设计和寻找折叠过程与蛋白质初级序列相关的一般规则。计算机模拟蛋白质折叠的一个主要问题是，动态过程发生在几十年的时间里，从亚皮秒到毫秒甚至秒。我们采用的方法是限制蛋白质的运动，使其在固定的时间步长内从初始状态（如未展开状态）移动到最终折叠状态。这种“轨迹退火”方法有能力探索许多可能的途径，通过这些途径，蛋白质可以在保持系统处于生理温度的情况下折叠。我们将继续目前的轨迹退火研究，并将其应用于两种小蛋白质，它们的折叠特性已经在实验中得到了广泛的采样。轨迹退火模拟提供了根据各种折叠路径的概率变化来解释这些实验的可能性，这些变化很难在实验中观察到。随着大规模DNA测序项目的巨大进展，生物序列信息积累的快速增长给结构生物学界带来了巨大的压力，需要高通量地为新基因提供结构信息。在实验上，大规模的x射线晶体学和核磁共振测量现在的目标是在几十年甚至几年内确定所有（1000到10000）可用的蛋白质折叠。然而，仍然有许多可溶性蛋白质难以结晶，核磁共振方法可能无效。结构同源性是一个非常强大的工具，通过它我们可以尝试在计算机上为新基因分配功能，这些新基因在序列同源性方面与已知基因只有遥远的联系。我们将在我们现有的从头算结构预测计算方法的基础上，通过添加包含在小角x射线散射（SAXS）数据中的额外物理信息。这将提高我们的能力，找到一个给定的蛋白质与蛋白质的已知结构，但很少或没有序列同源性。我们也将扩展我们的方法重建低分辨率电子密度图从小角度散射数据到x射线散射膜蛋白结合在小泡。数据库中约25%的基因序列编码膜蛋白的表达。虽然已经确定了数千种可溶性蛋白的结构，但由于膜蛋白被周围脂质的疏水环境自然稳定，因此难以结晶，因此只知道少数膜蛋白的结构。通过将膜蛋白嵌入小脂质囊泡中，我们相信我们可以生成SAXS数据，该数据除了包含囊泡上的数据外，还包含蛋白质的形状和大小信息，以及囊泡散射与蛋白质散射之间的x射线干涉模式。通过制备一种可以改变囊泡大小的制备方法，我们相信我们可以扩展现有的重建方法，从囊泡贡献中整理出对散射的蛋白质贡献，从而获得膜蛋白的低分辨率结构信息。

Research will focus on two areas of computational biology - (1)application of methods which explore conformation space for biomolecules, and (2) development of methods to help in protein structure determination both for soluble proteins and for membrane proteins.Understanding protein folding is important in a number of contexts such as protein design and the more general issue of finding general rules relating the folding process to the primary sequence of the protein. A major problem for computer simulation of protein folding is the fact that the dynamics takes place over many decades of time, from sub-picoseconds to milliseconds or even seconds. The approach we adopt is to constrain the motions of a protein so that it moves from an initial state, such as an unfolded state, to a final folded state in a fixed number of time steps. This "trajectory annealing" approach has the capability to explore a number of possible pathways by which a protein may fold while keeping the system at a physiological temperature. We will continue our present studies of trajectory annealing and apply them to two small proteins whose folding properties have been extensively sampled experimentally. The trajectory annealing simulations offer the possibility of interpreting those experiments in terms of changes in probability of various pathways for folding which are very difficult to observe experimentally.As a result of the tremendous progress in large-scale DNA sequencing projects, rapid growth in accumulation of biological sequence information has put strong pressure on the structural biology community to produce structural information for new genes with high throughput. Experimentally, large scale X-ray crystallography and NMR measurements now aim to determine all (1000 to 10000) available protein folds within a few decades or even years. However there remain many soluble proteins which have difficulties in crystallizing and for which NMR methods may be ineffective. Structural homology is a very powerful tool by which we can try to assign functions in silico to new genes which bear only remote if any association with known genes in terms of sequence homology. We will build on our current computational methods of ab initio structure prediction by adding additional physical information contained in small angle x-ray scattering (SAXS) data. This will improve our ability to find structural homologs of a given protein with proteins of known structure but for which there is little or no sequence homology. We will also extend our methods of reconstructing low resolution electron density maps from small-angle scattering data to x-ray scattering from membrane proteins bound in small vesicles. Some 25% of gene sequences in the database code for expression of membrane proteins. Although structures for several thousand soluble proteins have been determined, only a handful of structures for membrane proteins are known owing to the difficulties of crystallizing proteins which are naturally stabilized by the hydrophobic environment of the s urrounding lipids. By embedding a membrane protein in small lipid vesicles, we believe we can generate SAXS data which contains information about the shape and size of the protein in addition to data on the vesicle, and also about the x-ray interference pattern between the scattering from the vesicle and the scattering from the protein. By making a preparation in which vesicle sizes can be varied, we believe we can extend our present reconstruction methods to sort out the protein contributions to the scattering from the vesicle contributions and hence obtain low resolution structural information on the membrane protein.