PREDICTIONS OF MULTIMERIC GLOBULAR PROTEIN ASSEMBLY

球状蛋白质三维结构的预测 从它的氨基酸序列沿着阐明的机制 其中蛋白质折叠代表了极其重要的未解决的问题， 当代分子生物学建议的总体目标 FIRCA项目，是NIH计划项目第2号PO 1- GM 38794 - 06，标题为“蛋白质折叠和大分子的结构基础 大会”是一种方法的发展，以预测次级， 三级和四级结构，沿着折叠途径， 单从氨基酸序列中就可以发现球状蛋白的数量。述的方法 是基于蛋白质折叠的分层方法。一是高 由α-碳+组成的蛋白质的分辨率晶格模型 减少的离格侧链描述提供了整体折叠 路径和折叠构象。由此产生的晶格结构是 估计α-碳与 实验确定的天然的相应的主链原子 结构这些晶格结构将提供一组预测的 二级结构和侧链接触约束， 一个分子动力学改进协议，旨在产生完整的原子 结构.特别是，本报告将讨论以下问题： 建议：（1）.该方法包括减少，离散模型 设计折叠单域，单体球状蛋白将被 扩展到治疗多聚体蛋白。唯象交互作用 参数将被导出，以反映界面的相对偏好 交互.（二）、该方法将在一系列四螺旋上进行测试 由DeGrado及其同事设计的捆绑包，由四个短的 肽，两个较长的肽和一个长的多肽，其中氨基 螺旋区的酸序列高度简化， 所有案件。（三）、ROP二聚体的折叠，其天然构象是 四螺旋盘绕线圈束由两个螺旋线圈的组合形成， 毛泽东将被考察。折叠过程和由此产生的四元 结构将与重新设计的单体 顺序（四）、禽流感病毒单体-二聚体平衡的本质 胰多肽和海甘蓝素。这些分子 代表其中分离的单体和多聚体形式的 球状蛋白是稳定的。（五）、胰高血糖素作为一种 将探索单体-三聚体平衡的功能。这种分子 仅在与三聚体或更高聚体结合时采用明确的构象 订购多聚体。（六）、胰岛素和胰岛素原的折叠过程 被解决。这代表了非常重要的情况， 成熟蛋白质的天然构象只能在 预处理形式;即，成熟蛋白质处于亚稳态。

The prediction of the three dimensional structure of a globular protein from its amino acid sequence along with the elucidation of the mechanisms by which proteins fold represent extremely important unsolved problems of contemporary molecular biology. The overall objective of the proposed FIRCA project which is an extension of a NIH Program Project, No. 2 PO1- GM38794-O6 entitled, "Structural Basis of Protein Folding & Macromolecular Assembly" is the development of a methodology to predict the secondary, tertiary and quaternary structure along with the folding pathway of a number of globular proteins from the amino acid sequence alone. The method is based on a hierarchical approach to protein folding. First, high resolution lattice models of proteins comprised of an alpha-carbon plus reduced off lattice side chain description provide the overall folding pathway and folded conformations. The resulting lattice structures are estimated for the alpha-carbons to have a 2-4 Angstroms rms deviation from the corresponding backbone atoms of the experimentally determined native structure. These lattice structures will provide the set of predicted secondary structure and side chain contact constraints which are used in a molecular dynamics refinement protocol aimed at producing full atom structures. In particular, the following will be addressed in this proposal: (1). The methodology comprised of reduced, discretized models designed to fold single domain, monomeric globular proteins will be extended to treat multimeric proteins. Phenomenological interaction parameters will be derived to reflect relative preferences for interfacial interactions. (2). The methodology will be tested on series of four helix bundles designed by DeGrado and coworkers and composed of four short peptides, two longer peptides, and one long polypeptide, where the amino acid sequence of the helical regions is highly simplified and the same in all cases. (3). The folding of ROP dimer, whose native conformation is a four helix coiled coil bundle formed from the association of two helical hairpins, will be examined. The folding process and resulting quaternary structure will be compared to that obtained for the redesigned monomeric sequence. (4). The nature of the monomer-dimer equilibrium of avian pancreatic polypeptide and crambin will be explored. These molecules represent cases where both the isolated monomer and the multimeric form of the globular protein are stable. (5). The stability of glucagon as a function of the monomer-trimer equilibrium will be explored. This molecule adopts well defined conformations only on association to trimers or higher order multimers. (6). The folding process of insulin and proinsulin will be addressed. This represents the very important situation where the native conformation of a mature protein can be obtained only in the preprocessed form; i.e., the mature protein is in a metastable state.