Native State Conformational Ensemble of SEM5 SH3 Domain

SEM5 SH3 结构域的天然态构象集合

• 批准号: 6904633
• 负责人: VINCENT J. HILSER
• 金额: $ 23.84万
• 依托单位: UNIVERSITY OF TEXAS MED BR GALVESTON
• 依托单位国家: 美国
• 财政年份: 2001
• 资助国家: 美国
• 起止时间: 2001-08-01 至 2006-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6904633
• 关键词: calorimetry; chemical stability; chemical synthesis; computer simulation; fluorescence spectrometry; high performance liquid chromatography; intermolecular interaction; model design /development; molecular dynamics; molecular shape; molecular site; nuclear magnetic resonance spectroscopy; physical model; polymerase chain reaction; protein purification; protein structure function; proteins; protonation; site directed mutagenesis; structural biology; surface property; thermodynamics

Molecular recognition is one of the most important problems in structural biology. This issue is not just academic, as a clear understanding of the mechanism of recognition will facilitate development of rational design strategies to produce agonistic or antagonistic variants or ligand for clinically important proteins. Although it is clear that the conformational fluctuations (or dynamics) of proteins both affect and are affected by binding, no quantitative, predictive model for the role of dynamics in recognition is available. As a model system, this project investigates the nature and energetics of the native stage conformational ensemble of the SEM5 Sh3 domain from C. elegans. Our Specific Aims are: 1) experimental characterization of its region stability and dynamics, using NMR-detected hydrogen exchange and 15N relaxation; 2) determining the cooperativity of the conformational fluctuations, by measuring the effects of ALA to GLY mutations at positions showing differential stability in Aim 1; 3) correlating the mutations' effects on stability with those on ligand binding, to provide a quantitative description for the role of fluctuations in the recognition process; and 4) structural thermodynamic analysis of selected mutants to determine the energy of the different states, by solving the mutants' solution structures and modeling their flexible regions to the observed changes in their NOE constraints. These experiments are an essential step toward our long-term goal, a structure-based model for quantitatively describing the role of conformational heterogeneity in molecular recognition.

分子识别是结构生物学中最重要的问题之一。 这个问题不仅是学术，因为对识别机制的明确理解将有助于制定理性设计策略，以生成临床上重要蛋白质的激动或拮抗变体或配体。 尽管很明显，蛋白质的构象波动（或动力学）既影响又受结合影响，但没有用于识别动力学作用的定量，预测模型。 作为模型系统，该项目研究了秀丽隐杆线虫的SEM5 SH3域的天然阶段构象集合的性质和能量。 我们的具体目的是：1）使用NMR检测的氢交换和15N松弛的实验表征其区域稳定性和动力学； 2）通过测量ALA在AIM 1中显示出差异稳定性的位置的ALA对GLY突变的影响来确定构象波动的协同性； 3）将突变对稳定性的影响与配体结合的稳定性的影响相关联，以定量描述波动在识别过程中的作用； 4）通过求解突变体的溶液结构并将其柔性区域建模到其NOE约束中观察到的变化，对所选突变体的结构热力学分析来确定不同状态的能量。 这些实验是朝着我们的长期目标迈出的重要一步，这是一个基于结构的模型，用于定量描述构象异质性在分子识别中的作用。