Dynamic and Catalysis by Alcohol Dehydrogenases

醇脱氢酶的动力学和催化

• 批准号: 7287745
• 负责人: BRYCE V PLAPP
• 金额: $ 26.85万
• 依托单位: UNIVERSITY OF IOWA
• 依托单位国家: 美国
• 财政年份: 2006
• 资助国家: 美国
• 起止时间: 2006-09-15 至 2010-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7287745
• 关键词: Active Sites; Affect; Affinity; Alcohol dehydrogenase; Alcoholism; Alcohols; Amino Acid Substitution; Amino Acids; Benzaldehyde; Benzyl Alcohol; Benzyl Alcohols; Binding; Binding Sites; Carbon; Catalysis; Catalytic Domain; Chemicals; Coenzymes; Complex; Conserved Sequence; Coupled; Data; Development; Dissociation; Distant; Drug Design; Elements; Enzymes; Equilibrium; Equus caballus; Ethanol Metabolism; Evolution; Global Change; Hydrogen; Kinetics; Ligand Binding; Ligands; Liquid substance; Liver; Medical; Molecular Conformation; Motion; Multienzyme Complexes; Muscle Rigidity; Mutate; Mutation; NADH; Parents; Pathology; Pathway interactions; Phase; Pliability; Principal Investigator; Probability; Proteins; Protons; Range; Rate; Reaction; Relative (related person); Research; Research Personnel; Resolution; Role; Rotation; Scaffolding Protein; Series; Side; Site; Site-Directed Mutagenesis; Specificity; Structure; System; Techniques; Temperature; Tertiary Protein Structure; Testing; Therapeutic Agents; Translations; Variant; X-Ray Crystallography; Zinc; analog; base; carbonyl compound; catalyst; chemical binding; computer studies; design; dimer; enzyme structure; fluidity; improved; inhibitor/antagonist; interest; oxidation; programs; protein structure; reaction rate; scaffold; size; three dimensional structure; vibration

DESCRIPTION (provided by applicant): The long-term objectives of this research are to determine the roles of protein structure, flexibility, adaptability and dynamics in enzyme catalysis. The overall hypothesis is that residues at or distant from the active site contribute to catalysis by affecting protein motions and fluidity, conformational changes, and subunit interactions. Horse liver alcohol dehydrogenase is a good system for studying structural and dynamics effects on catalysis. Three-dimensional structures of various complexes have been determined by X-ray crystallography for two conformational states, and rate and dissociation constants for each step in the mechanism, including the chemical step (hydride transfer), can be estimated from steady-state and transient kinetics. Site-directed mutagenesis will be used to substitute amino acid residues in different regions of the enzyme, and the effects on the catalytic mechanism, structure and dynamics will be quantitatively evaluated. (1) Residues in the hinge region between the catalytic and coenzyme binding domains and the domain contact regions will be altered in order to change the rate and extent of the conformational change, and allosteric interactions through the subunits will be studied with heterodimeric enzymes. (2) Amino acid residues that may contribute to protein promoting vibrations and residues buried in core regions will be mutated in order to change the protein fluidity and dynamics. "Extraneous" structural elements or Q-loops will be deleted to test the role of the protein scaffold. (3) Three-dimensional structures of wild-type and mutated enzymes complexed with substrate analogs will be determined by X-ray crystallography at high resolution, and dynamic information will be extracted by analysis of translation, libration, screw-rotation displacements (TLS parameters) for domains and subdomains that cooperate in catalysis. The dynamics hypothesis will be supported if the directions and amplitudes of motion are correlated with rates of hydride transfer. The kinetic, structural and dynamic results should improve our understanding of catalysis and facilitate rational drug design. Redesign of enzymes for medical and industrial applications should become more "rational" when the connections between protein structure and catalysis are better understood. Development of new catalysts based on protein scaffolds will benefit from a better understanding of protein motions and dynamics. Furthermore, the design of therapeutic agents must incorporate information about protein motions, as specificities are affected by amino acid residues that are distant from the active site. Studies on substrate and inhibitor specificities of alcohol dehydrogenases suggest that active sites are adaptable and that binding affinities are not easily explained with a static structure. Design of better inhibitors for treating the pathology of alcoholism depends on understanding the dynamics of catalysis by the rate-limiting enzyme in the pathway of alcohol metabolism.

描述(申请人提供)：这项研究的长期目标是确定蛋白质结构、灵活性、适应性和动力学在酶催化中的作用。总的假设是，在活性中心或远离活性中心的残基通过影响蛋白质的运动和流动性、构象变化和亚单位相互作用来促进催化。马肝醇脱氢酶是研究结构和动力学对催化作用影响的良好体系。用X-射线单晶衍射法测定了各种络合物的两种构象的三维结构，并根据稳态和暂态动力学估算了该反应各步骤的速率和离解常数，包括化学步骤(氢化物转移)。利用定点突变技术替代酶不同区域的氨基酸残基，定量评价其对酶催化机理、结构和动力学的影响。(1)为了改变构象变化的速度和程度，催化和辅酶结合区之间的铰链区和结构域接触区的残基将被改变，并将用异二聚体酶研究通过亚基的变构相互作用。(2)可能有助于促进蛋白质振动的氨基酸残基和埋藏在核心区的残基将发生突变，以改变蛋白质的流动性和动力学。“无关的”结构元件或Q-环将被删除，以测试蛋白质支架的作用。(3)利用高分辨率的X射线结晶学方法，测定与底物类似物结合的野生型和突变酶的三维结构，并通过分析协同催化的结构域和亚结构域的平移、振动、螺杆旋转位移(TLS参数)来提取动力学信息。如果运动的方向和幅度与氢化物转移速率相关联，则动力学假说将得到支持。动力学、结构和动力学的结果将加深我们对催化的理解，并有助于合理的药物设计。当更好地理解蛋白质结构和催化之间的联系时，用于医疗和工业应用的酶的重新设计应该变得更加“合理”。基于蛋白质支架的新型催化剂的开发将受益于对蛋白质运动和动力学的更好理解。此外，治疗剂的设计必须包含有关蛋白质运动的信息，因为特异性受到远离活性部位的氨基酸残基的影响。对乙醇脱氢酶底物和抑制剂特异性的研究表明，活性部位是适应的，结合亲和力不容易用静态结构解释。设计更好的治疗酒精中毒病理的抑制剂依赖于了解酒精代谢途径中限速酶的催化动力学。