Studies of Molecular Recognition in Biological Systems

生物系统中分子识别的研究

• 批准号: 7677441
• 负责人: STEPHEN MARTIN
• 金额: $ 29.41万
• 依托单位: UNIVERSITY OF TEXAS AT AUSTIN
• 依托单位国家: 美国
• 财政年份: 2008
• 资助国家: 美国
• 起止时间: 2008-08-20 至 2011-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7677441
• 关键词: Acute; Adopted; Affect; Affinity; Binding; Biology; Calorimetry; Cations; Chemicals; Classification; Complex; Computing Methodologies; Crystallography; Data; Disease; Entropy; Free Energy; Generations; Hydrogen Bonding; Hydrophobicity; Knowledge; Ligand Binding; Ligands; Methods; Modeling; Modification; Molecular Conformation; Muscle Rigidity; NMR Spectroscopy; Organic Chemistry; Phosphotyrosine; Protein Binding; Protein Dynamics; Proteins; Relative (related person); Signal Transduction; Solvents; Structure; Texas; Therapeutic; Therapeutic Agents; Thermodynamics; Titrations; Universities; Variant; Vertebral column; X-Ray Crystallography; base; biological systems; computational chemistry; design; enthalpy; flexibility; insight; interdisciplinary approach; microcalorimetry; molecular dynamics; molecular recognition; novel; professor; protein structure; public health relevance; research study; small molecule; src Homology Region 2 Domain; tool

DESCRIPTION (provided by applicant): Correlating structural modifications of small molecules with changes in their protein binding affinities is a fundamental problem in chemical biology. The difficulty associated with predicting energetics in protein-ligand interactions is exacerbated by an acute lack of detailed experimental data pertaining to how specific variations in ligand structure affect compensating changes in binding enthalpies and entropies in protein-ligand interactions. Contributing to the complexity of the problem is a paucity of information regarding how variations in ligand structure affect protein dynamics in protein-ligand complexes and whether differential changes in such dynamics have a significant effect upon binding energetics. Toward developing a better understanding of molecular recognition in biological systems, we have adopted a unique, multidisciplinary approach in which synthetic organic chemistry, microcalorimetry, protein crystallography, NMR spectroscopy, and computational chemistry are integrated in systematic studies to investigate explicitly how specific variations in ligand structure affect energetics, structure and dynamics in protein-ligand interactions in a well-defined biological system. Briefly, we will design and synthesize pseudopeptides that are derived from pTyr-Val-Asn and vary in their rigidity and/or preorganization, hydrophobicity, cation-@ stabilizing ability, and hydrogen bond accepting ability. The thermodynamic parameters for binding of these pseudopeptides to the Grb2 SH2 domain will be determined using isothermal titration calorimetry, and free energies of solvent transfer of representative compounds will be determined by solvent partition experiments. The consequences of varying ligand structure upon structure and dynamics of the protein in the complex will be studied by X-ray crystallography and NMR. Molecular dynamics simulations will be conducted using experimental data to refine the models and methods, so we can calculate relative binding energetics and probe changes in protein dynamics that occur upon binding ligands having different structures and affinities. The results will be analyzed, and correlations between specific changes in ligand structure with variations in thermodynamic binding parameters and protein flexibility will be identified so it can be ascertained whether changes in ligand structure can be correlated with changes in binding enthalpies and entropies and whether changes in flexibility of the Grb2 SH2 domain contribute significantly to the energetics of ligand binding. Insights obtained from these studies will be used to design second generation pseudopeptides having higher binding affinities for the Grb2 SH2 domain as these will be useful as tools for signal biology and as potential therapeutic leads. PUBLIC HEALTH RELEVANCE: The highly integrated experiments proposed herein are uniquely designed to determine how specific changes in ligand structure affect enthalpies, entropies and dynamics in protein-ligand complexes. The results of these studies will enhance our knowledge of molecular recognition in biological systems and contribute to developing experimental and computational methods that will facilitate the structure-based design of small molecules having high affinities for protein targets. Such tools are indispensable to medicinal chemists as they optimize ligand binding affinities and transform novel leads into selective and potent therapeutic agents to treat diseases.

描述（由申请人提供）：将小分子的结构修饰与蛋白质结合亲和力的变化相关联是化学生物学的基本问题。由于急性缺乏与配体结构中的特定变化如何影响蛋白质 - 培养基相互作用的结合焓和熵的变化有关，与预测蛋白质配体相互作用中的能量相关的难度加剧了。有助于问题的复杂性的原因是关于配体结构的变化如何影响蛋白质配体复合物中的蛋白质动力学以及这种动力学中的差异变化是否对结合能量学有显着影响。我们采用了一种独特的多学科方法，以更好地了解生物系统中的分子识别方法，在这种方法中，合成有机化学，微量钙化，蛋白质晶体学，NMR光谱和计算化学是在系统的研究中整合的，从而在系统研究中整合了良好的体系良好的蛋白质和动力学，从而在系统的研究中进行了良好的研究。简而言之，我们将设计和合成源自ptyr-val-asn的伪肽，并在其刚性和/或预组织，疏水性，阳离子@稳定能力以及氢键接受能力方面变化。这些假肽与GRB2 SH2结构域结合的热力学参数将使用等温滴定量热法确定，并通过溶剂分区实验确定代表性化合物的溶剂转移的自由能。 X射线晶体学和NMR会研究不同配体结构对蛋白质结构和动力学的后果。将使用实验数据进行分子动力学模拟，以完善模型和方法，因此我们可以计算相对结合能的能量和探针变化，而蛋白质动力学的结合配体具有不同的结构和亲和力。 The results will be analyzed, and correlations between specific changes in ligand structure with variations in thermodynamic binding parameters and protein flexibility will be identified so it can be ascertained whether changes in ligand structure can be correlated with changes in binding enthalpies and entropies and whether changes in flexibility of the Grb2 SH2 domain contribute significantly to the energetics of ligand binding.从这些研究中获得的见解将用于设计对GRB2 SH2结构域具有较高结合亲和力的第二代伪肽，因为这些将作为信号生物学和潜在的治疗铅的工具有用。公共卫生相关性：本文提出的高度综合实验的设计是唯一设计的，旨在确定配体结构的特定变化如何影响蛋白质配体配合物的焓，熵和动态。这些研究的结果将增强我们对生物系统分子识别的了解，并有助于开发实验和计算方法，这些方法将促进基于结构的小分子的基于结构的设计，对蛋白质靶标具有高亲和力。这种工具对于药物学家优化配体结合亲和力并将新颖的铅转化为选择性且有效的治疗剂以治疗疾病的方法是必不可少的。