PREDICTIONS OF MULTIMERIC GLOBULAR PROTEIN ASSEMBLY

多聚体球状蛋白组装的预测

• 批准号: 2292016
• 负责人: JEFFREY SKOLNICK
• 金额: $ 2.44万
• 依托单位: SCRIPPS RESEARCH INSTITUTE, THE
• 依托单位国家: 美国
• 财政年份: 1994
• 资助国家: 美国
• 起止时间: 1994-02-01 至 1997-01-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/2292016
• 关键词: chemical models; computer program /software; conformation; globular protein; glucagon; hydrogen bond; insulin; intermolecular interaction; proinsulin; protein folding; protein sequence; protein structure

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.

球状蛋白的三维结构的预测 从其氨基酸序列以及阐明机制 蛋白质折叠代表极其重要的未解决问题的问题 当代分子生物学。提议的总体目标 FIRCA项目是NIH计划项目的扩展，第二个PO1- GM38794-O6标题为“蛋白质折叠和大分子的结构基础 组装”是一种预测次要的方法的发展 第三和第四纪结构以及折叠途径 仅来自氨基酸序列的球状蛋白数量。该方法 基于蛋白质折叠的分层方法。首先，高 由α-碳加成的蛋白质的分辨率晶格模型 减少晶格侧链说明提供了整体折叠 途径和折叠构象。由此产生的晶格结构是 估计Alpha-Carbons具有2-4埃埃斯特rms的偏差 实验确定的天然的相应骨干原子 结构。这些晶格结构将提供一组预测 二级结构和侧链接触约束 一种旨在产生完整原子的分子动力学改进协议 结构。特别是，将在此解决以下内容 建议：（1）。该方法包括减少，离散模型 设计用于折叠单个结构域，单体球状蛋白将是 扩展以治疗多聚蛋白。现象学相互作用 参数将得出以反映界面的相对偏好 互动。 （2）。该方法将在四个螺旋中进行测试 由Degrado和同事设计的捆绑包，由四个短 肽，两个更长的肽和一个长多肽，其中氨基 螺旋区域的酸序列是高度简化的，在 所有情况。 （3）。 ROP二聚体的折叠，其天然构型是 由两个螺旋的关联形成的四个螺旋线圈线圈束 发夹将进行检查。折叠过程和产生的第四纪 将结构与重新设计的单体获得的结构进行比较 顺序。 （4）。鸟类的单体二聚体平衡的性质 将探索胰腺多肽和Crambin。这些分子 表示孤立的单体和多聚体形式的情况 球状蛋白是稳定的。 （5）。胰高血糖素的稳定性 将探索单体培训平衡的功能。这个分子 仅在与三聚体的关联或更高的关联时采用明确定义的构象 订购多聚机。 （6）。胰岛素和促胰岛素的折叠过程将 被解决。这代表了非常重要的情况 只能在 预处理形式；即，成熟的蛋白质处于亚稳态。