Molecular recognition in the streptavidin-biotin system

链霉亲和素-生物素系统中的分子识别

• 批准号: 7754050
• 负责人: TERRY P LYBRAND
• 金额: $ 30.97万
• 依托单位: VANDERBILT UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 1995
• 资助国家: 美国
• 起止时间: 1995-06-01 至 2012-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7754050
• 关键词: Active Sites; Affinity; Behavior; Binding; Binding Proteins; Binding Sites; Biological Models; Biology; Biotin; Calorimetry; Carbamoyl Transferases; Catalysis; Characteristics; Collection; Complex; Coupled; Covalent Interaction; Dihydrofolate Reductase; Dissociation; Distal; Drug Design; Enzymes; Equilibrium; Event; Free Energy; Funding; Hemoglobin; Homologous Gene; Lead; Ligand Binding; Ligands; Maps; Measurable; Measurement; Measures; Mutation; Play; Point Mutation; Positioning Attribute; Proteins; Protocols documentation; Reaction; Research Personnel; Resolution; Role; Site; Streptavidin; Structural Protein; Structure; System; Temperature; Testing; Thermodynamics; Water; base; biotin-streptavidin complex; design; molecular dynamics; molecular recognition; mutant; programs; protein structure; research study; simulation

DESCRIPTION (provided by applicant): The streptavidin/biotin complex involves one of the strongest non-covalent interactions observed in biology, and is an ideal model system for the study of high-affinity protein/ligand interactions. Analysis of high- resolution crystal structures for the streptavidin/biotin complex reveals numerous favorable protein-ligand contacts characteristic of a tightly bound complex. However, our extensive structural and thermodynamic characterization of numerous streptavidin mutants strongly suggests that direct protein-ligand contacts cannot fully explain the extremely tight biotin binding. Our previous studies also suggest that biotin follows a well defined reaction coordinate during ligand binding and dissociation reactions, and that certain mutations can alter the activation energy barrier for the binding/dissociation reactions, without any significant effect on the equilibrium structure. These results lead us to propose that streptavidin equilibrium dynamics, or structural fluctuations, help determine the equilibrium binding energy and activation energy barrier. We will test this hypothesis by performing molecular dynamics simulations and detailed crystallographic analyses of anisotropic temperature factors for wild-type and selected mutant streptavidin/biotin complexes, and then look for correlations between structural fluctuations and calorimetric measurements in wild-type versus mutant complexes. Our previous results also suggest that specific water molecules play a key energetic role in the biotin binding/dissociation reactions. We will use molecular dynamics simulations to test this proposal by further characterizing water interactions in the streptavidin binding site. We will use these simulation results to suggest mutations that can alter the equilibrium water behavior in the complex, and thus modulate the ligand binding free energy and/or activation energy. These studies will enhance our understanding of high-affinity protein/ligand binding interactions, and will help us elucidate important concepts that should be useful in structure-based ligand design projects. Such information will be helpful in rational drug design applications for therapeutically important protein targets.

描述（由申请人提供）：链霉亲和素/生物素复合物涉及生物学中观察到的最强的非共价相互作用之一，并且是研究高亲和力蛋白质/配体相互作用的理想模型系统。对链霉亲和素/生物素复合物的高分辨率晶体结构的分析揭示了紧密结合的复合物的许多有利的蛋白质-配体接触特征。然而，我们对众多链霉亲和素突变体的广泛结构和热力学表征强烈表明，直接的蛋白质-配体接触不能完全解释极其紧密的生物素结合。我们之前的研究还表明，生物素在配体结合和解离反应过程中遵循明确的反应坐标，并且某些突变可以改变结合/解离反应的活化能垒，而不会对平衡结构产生任何显着影响。这些结果使我们提出链霉亲和素平衡动力学或结构波动有助于确定平衡结合能和活化能垒。我们将通过对野生型和选定的突变型链霉亲和素/生物素复合物进行分子动力学模拟和各向异性温度因素的详细晶体学分析来测试这一假设，然后寻找野生型与突变型复合物的结构波动和量热测量之间的相关性。我们之前的结果还表明，特定的水分子在生物素结合/解离反应中发挥着关键的能量作用。我们将使用分子动力学模拟通过进一步表征链霉亲和素结合位点中的水相互作用来测试这一提议。我们将使用这些模拟结果来建议可以改变复合物中平衡水行为的突变，从而调节配体结合自由能和/或活化能。这些研究将增强我们对高亲和力蛋白质/配体结合相互作用的理解，并将帮助我们阐明在基于结构的配体设计项目中有用的重要概念。这些信息将有助于治疗重要蛋白质靶标的合理药物设计应用。

项目成果

Second-contact shell mutation diminishes streptavidin-biotin binding affinity through transmitted effects on equilibrium dynamics.

第二次接触壳突变通过对平衡动力学的传递效应降低了链霉亲和素-生物素结合亲和力。

• DOI: 10.1021/bi201221j
• 发表时间: 2012-01-17
• 期刊: Biochemistry
• 影响因子: 2.9
• 作者: Baugh, Loren;Isolde Le Trong;Cerutti, David S.;Mehta, Nital;Guelich, Susanne;Stayton, Patrick S.;Stenkamp, Ronald E.;Lybrand, Terry P.
• 通讯作者: Lybrand, Terry P.

Simulations of a protein crystal: explicit treatment of crystallization conditions links theory and experiment in the streptavidin-biotin complex.

蛋白质晶体的模拟：结晶条件的明确处理将链霉亲和素-生物素复合物中的理论和实验联系起来。

• DOI: 10.1021/bi800894u
• 发表时间: 2008-11-18
• 期刊: Biochemistry
• 影响因子: 2.9
• 作者: Cerutti, David S.;Le Trong, Isolde;Stenkamp, Ronald E.;Lybrand, Terry P.
• 通讯作者: Lybrand, Terry P.

A Streptavidin Binding Site Mutation Yields an Unexpected Result: An Ionized Asp128 Residue Is Not Essential for Strong Biotin Binding.

链霉亲和素结合位点突变产生了意想不到的结果：电离的 Asp128 残基对于强生物素结合并不是必需的。

• 发表时间: 2016-09-20
• 影响因子: 2.9
• 作者: Baugh, Loren;Le Trong, Isolde;Stayton, Patrick S;Stenkamp, Ronald E;Lybrand, Terry P
• 通讯作者: Lybrand, Terry P

Dynamics of the streptavidin-biotin complex in solution and in its crystal lattice: distinct behavior revealed by molecular simulations.

链霉亲和素-生物素复合物在溶液中及其晶格中的动力学：分子模拟揭示的独特行为。

• DOI: 10.1021/jp9010372
• 发表时间: 2009-05-14
• 期刊: The journal of physical chemistry. B
• 作者: Cerutti DS;Le Trong I;Stenkamp RE;Lybrand TP
• 通讯作者: Lybrand TP

A distal point mutation in the streptavidin-biotin complex preserves structure but diminishes binding affinity: experimental evidence of electronic polarization effects?

链霉亲和素-生物素复合物中的远端点突变保留了结构，但降低了结合亲和力：电子极化效应的实验证据？

• DOI: 10.1021/bi1005392
• 发表时间: 2010-06-08
• 期刊: Biochemistry
• 影响因子: 2.9
• 作者: Baugh, Loren;Le Trong, Isolde;Cerutti, David S.;Guelich, Susanne;Stayton, Patrick S.;Stenkamp, Ronald E.;Lybrand, Terry P.
• 通讯作者: Lybrand, Terry P.