Multiscale Modeling of Protein Kinase Structure, Catalysis and Allostery

蛋白激酶结构、催化和变构的多尺度建模

• 批准号: 10240612
• 负责人: Kwangho Nam
• 金额: $ 35.29万
• 依托单位: UNIVERSITY OF TEXAS ARLINGTON
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-09-15 至 2023-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10240612
• 关键词: Acceleration; Active Sites; Address; Affect; Algorithms; Behavior; Binding; Biochemical; Biology; Catalysis; Cells; Collaborations; Communities; Complex; Computer Models; Coupling; Data; Development; Disease; Enzyme Kinetics; Enzymes; Free Energy; Goals; Grant; Guanosine Triphosphate Phosphohydrolases; Health; Homeostasis; Human; Insulin Receptor; Investigation; Kinetics; Length; Ligand Binding; Link; Malignant Neoplasms; Mechanics; Methodology; Methods; Modeling; Molecular; Molecular Conformation; Motion; Motor; Pathologic; Pharmaceutical Preparations; Phosphorylation; Phosphotransferases; Play; Population; Process; Protein Dynamics; Protein Kinase; Proteins; Reaction; Regulation; Research; Role; Series; Structural Protein; Structure; System; Testing; Theoretical Studies; Time; Wolves; adenylate kinase; base; biophysical techniques; cofactor; density; design; experimental group; experimental study; human disease; improved; innovation; insight; interest; multi-scale modeling; novel; novel therapeutic intervention; parallelization; quantum; simulation; theories; tool

Multiscale Modeling of Protein Kinase Structure, Catalysis and Allostery PROJECT SUMMARY/ABSTRACT The long-term goal of this research is to advance our understanding of the catalytic and regulatory mechanisms of complex enzymatic systems and the roles of protein dynamics in enzyme function. Protein kinase (PK), the focus of this study, is an attractive system for this purpose, because it involves both large-scale conformational change and enzymatic catalysis. Moreover, because of its pathological significance, understanding PK’s molecular mechanism is of fundamental importance in kinase research and also may provide new insights into the development of improved therapies against kinases. Our central hypothesis, based on our recent studies and enzyme kinetic data, is that the catalytic activity of PK is closely associated with its regulatory function. Therefore, any change in regulatory activity affects the catalytic activity of the kinase, which occurs through allosteric modulation of underlying protein dynamics, and together control overall activity of PK. This contrasts with the conventional view that the inactive-to-active conformational change is the main mechanism for regulating kinase activity. Our objective in this grant is to examine these two contrasting views on the regulation of kinase activity by the parallel study of two important kinases, insulin receptor kinase (IRK) and adenylate kinase (AdK), which play critical roles in cell homeostasis, and elucidate their complete molecular mechanisms. These objectives will be accomplished through quantitative modeling of their conformational change, ligand binding and catalysis in key functional states, including the fully active and inactive states. The proposed research involves development of new multiscale simulation methods combining quantum, molecular and statistical mechanical methods and their extension to permit rapid and accurate determination of kinase mechanisms. Our specific AIMs are: (1) the development of effective multiscale simulation methods integrating the ab initio/density functional theory (AI/DFT) and semiempirical (SE) QM/MM methods with the string simulation methods in CHARMM, their acceleration through advanced parallelization and accelerator algorithms and reaction-specific parameterizations, and development of efficient alchemical free energy simulation methods overcoming the limitations of existing methods; 2) elucidation of the mechanisms of IRK catalysis and conformational change and the connection between its intrinsic protein motions and catalysis of IRK; and 3) determination of the catalytic mechanism of AdK and the role of active site residues in controlling the active site and global protein dynamics and the overall activity of AdK. The completion of the proposed study will deepen the mechanistic understanding of these kinases and the role of protein dynamics in their catalysis. Experimental verification of computational results will also be made by characterization of their kinetic and structural parameters via collaboration with an experimental group. Finally, the theoretical methods developed are general and can be applied readily to numerous enzymatic systems involving conformational changes and catalysis, such as ATP/GTPases and various motor proteins.

蛋白激酶结构、催化和变构的多尺度建模 项目概要/摘要 这项研究的长期目标是增进我们对催化和调节机制的理解 复杂的酶系统和蛋白质动力学在酶功能中的作用，即蛋白激酶（PK）。 这项研究的重点是为此目的的一个有吸引力的系统，因为它涉及大规模构象 此外，由于其病理意义，了解PK的作用。 分子机制在激酶研究中至关重要，也可能为激酶研究提供新的见解。 基于我们最近的研究，我们的中心假设是针对激酶的改进疗法的开发。 和酶动力学数据表明，PK的催化活性与其调节功能密切相关。 因此，调节活性的任何变化都会影响激酶的催化活性，这是通过以下方式发生的： 基础蛋白质动力学的变构调节，并共同控制 PK 的整体活性。 传统观点认为非活性到活性构象变化是调节的主要机制 我们这笔资助的目的是研究关于激酶调节的这两种截然不同的观点。 通过对两种重要激酶胰岛素受体激酶 (IRK) 和腺苷酸激酶 (AdK) 的平行研究来确定活性， 在细胞稳态中发挥关键作用，并阐明其完整的分子机制。 目标将通过其构象变化、配体结合和的定量建模来实现 拟议的研究涉及关键功能状态的催化，包括完全活性和非活性状态。 结合量子、分子和统计力学的新型多尺度模拟方法的开发 方法及其扩展，可以快速准确地确定我们的特定激酶机制。 目标是：（1）开发集成从头算/密度的有效多尺度模拟方法 泛函理论 (AI/DFT) 和半经验 (SE) QM/MM 方法以及弦模拟方法 CHARMM，通过先进的并行化和加速器算法以及特定反应进行加速 参数化，并开发有效的炼金术自由能模拟方法来克服 2）阐明IRK催化和构象变化的机制 及其内在蛋白质运动与IRK催化作用之间的联系；3)催化作用的测定； AdK 的机制以及活性位点残基在控制活性位点和整体蛋白质动力学中的作用 以及 AdK 的整体活动 所提出的研究的完成将加深对机制的理解。 这些激酶以及蛋白质动力学在其催化中的作用的实验验证。 结果还将通过与一个合作伙伴的合作来表征其动力学和结构参数 最后，所开发的理论方法是通用的，可以很容易地应用于 许多涉及构象变化和催化的酶系统，例如 ATP/GTP 酶和 各种运动蛋白。