Synthesis and Study of Minimal Protein Folding Models: Molecular Torsion Balance

最小蛋白质折叠模型的合成与研究：分子扭转平衡

• 批准号: 7413629
• 负责人: CRAIG S WILCOX
• 金额: $ 27.02万
• 依托单位: UNIVERSITY OF PITTSBURGH AT PITTSBURGH
• 依托单位国家: 美国
• 财政年份: 2007
• 资助国家: 美国
• 起止时间: 2007-05-01 至 2011-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7413629
• 关键词: Address; Affect; Affinity; Amino Acids; Attention; Behavior; Benchmarking; Binding; Binding Sites; Biochemistry; Biological; Biological Models; Biological Phenomena; Catalysis; Chemicals; Communities; Competitive Binding; Complex; Computing Methodologies; Controlled Study; Data; Dependence; Drug Design; Drug Receptors; Enzymes; Equilibrium; Event; Free Energy; Halogens; Heart; Hydrogen Bonding; Hydrophobic Interactions; Hydrophobic Surfaces; Hydrophobicity; Indium; Individual; Ionic Strengths; Knowledge; Measures; Mediating; Methods; Molecular; Molecular Conformation; Molecular Models; Object Attachment; Pharmaceutical Preparations; Principal Investigator; Proteins; Relative (related person); Reporting; Risk; Science; Scientist; Side; Sodium Chloride; Solvents; Structure; Surface; System; Temperature; Testing; Theoretical model; Thermodynamics; Torsion; Water; Week; aqueous; behavior influence; concept; design; functional group; insight; interest; macromolecule; mimetics; model design; novel; programs; protein folding; receptor binding; research study; size; small molecule; theories; tool

DESCRIPTION (provided by applicant): Testing and improvement in our understanding of the molecular forces that influence biological phenomena (events including protein folding, protein-protein recognition, drug-receptor binding, and enzyme catalysis) require precise observations in well-controlled experiments. We developed a tool - the 'molecular torsion balance' - for measuring the relative energies of two well separated thermodynamic states which differ only in their conformation. These precision molecular tools can reliably measure differential energy effects on conformation as small as 0.05 kcal/mol. We propose to use these molecules in aqueous systems and to acquire quantitative data relevant to five important binding motifs that are central elements in theories of protein stability. The subprojects are designed to provide data directly relevant to understanding biological recognition (folding and binding) and useful for testing current biocomputational methods and theories. We will investigate: 1) The effects of salt bridges on conformational stability. Our experiments will provide quantitative comparisons of the strength of solvent-exposed salt bridges most common in biological molecules, and on the effects of ionic strength and temperature on these effects. 2) Hydrophobic binding and the effect of non-polar surfaces on water-mediated conformational stability. The Lum-Chandler-Weeks (LCW) theory of hydrophobicity makes intriguing predictions on how hydrophobicity changes with the sizes of alkyl surfaces. We seek to verify this prediction and quantify the differences. 3) The effects of halogens and the 'halogen bond' on conformation stability in water. The introduction of halogens into drug molecules is reported to change binding site affinities. 4) Neighboring group effects on hydrophobic interactions. How do nearby functional groups influence the 'stickiness' of hydrophobic surfaces? Is there an effect on the structure of water that can change the excess free energy at hydrophobic-water interfaces? 5) A beta-turn mimetic molecular torsion balance. A moderate risk -high impact subproject will allow direct comparisons of the energy of pair-wise amino acid interactions in anti-parallel orientation and the effects of amino acid changes on short beta-strand stability. Knowledge gained in these experimental studies will be available for testing current computational methods and theories of biological recognition and in identifying guiding principles for design of biologically active agents.

描述（由申请人提供）：我们对影响生物学现象的分子力的测试和改进（包括蛋白质折叠，蛋白质 - 蛋白质识别，药物 - 受体结合和酶催化的事件）需要在良好控制的实验中进行精确观察。我们开发了一种工具 - “分子扭转平衡” - 用于测量两个良好分离的热力学状态的相对能量，这仅在它们的构象上有所不同。这些精确的分子工具可以可靠地测量小至0.05 kcal/mol的构象的差异效应。我们建议在水系统中使用这些分子，并获取与五个重要的结合基序相关的定量数据，这些基序是蛋白质稳定性理论中的核心元素。该子项目旨在提供与理解生物学识别（折叠和结合）直接相关的数据，并且可用于测试当前的生物计算方法和理论。我们将研究：1）盐桥对构象稳定性的影响。我们的实验将提供定量的比较，以比较在生物分子中最常见的溶剂暴露盐桥的强度，以及离子强度和温度对这些作用的影响。 2）疏水结合和非极性表面对水介导的构象稳定性的影响。 Lum-Chandler-Weeks（LCW）的疏水理论对疏水性如何随烷基表面的尺寸变化提供了有趣的预测。我们试图验证这一预测并量化差异。 3）卤素和“卤素键”对水构象稳定性的影响。据报道，将卤素引入药物分子中会改变结合位点的亲和力。 4）相邻组对疏水相互作用的影响。附近的功能组如何影响疏水表面的“粘性”？是否会对水结构产生影响，可以改变疏水性水界面的多余自由能？ 5）β转向模拟分子扭转平衡。中等风险的高影响子标记将可以直接比较抗平行方向中成对氨基酸相互作用的能量以及氨基酸变化对短β-链链稳定性的影响。这些实验研究中获得的知识将用于测试当前的计算方法和生物识别理论，并确定设计生物活性剂的指导原理。