Electrostatic effects of the native state ensemble

本机态系综的静电效应

• 批准号: 8097249
• 负责人: Bertrand Garcia-Moreno
• 金额: $ 34.19万
• 依托单位: JOHNS HOPKINS UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-07-01 至 2013-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8097249
• 关键词: Accounting; Acids; Benchmarking; Binding; Biochemical Process; Biological; Biological Process; Characteristics; Charge; Computer Simulation; Computing Methodologies; Coupled; Coupling; DHFR gene; DNA Sequence Rearrangement; Data; Dependence; Development; Drug Design; Electrostatics; Equilibrium; Goals; Hydrogen; Ligand Binding; Measurement; Measures; Medical; Methods; Micrococcal Nuclease; Molecular; Molecular Conformation; NMR Spectroscopy; Physics; Process; Proteins; Relaxation; Resistance; Role; Sampling; Structure; Surface; Testing; Thermodynamics; Time; Toxin; Vertebral column; Virus Activation; aspartylglutamate; base; conformational conversion; design; flexibility; improved; insight; interest; ionization; molecular dynamics; novel; protein folding; protein structure function; public health relevance; research study; response

DESCRIPTION (provided by applicant): Electrostatic energy is useful to correlate the structure and the function of proteins. For this reason, improved understanding of the molecular determinants of pKa values and electrostatic energies, and the development of computational methods for structure- based electrostatics calculations, continues to be of great interest. Most computational methods are not yet sufficiently accurate to be useful to describe biochemical processes, especially those where the change in the charge of a protein is coupled to a change in conformation. Furthermore, the physical basis of electrostatic effects in proteins is not well understood. The studies that are proposed examine the hypothesis that local conformational fluctuations that involve rearrangement of the backbone contribute significantly to the magnitude of pKa values and electrostatic energies of proteins. Preliminary data suggest that the hypothesis is likely to be correct. Neither local conformational fluctuations of proteins nor the structural responses of proteins to changes in their charged state can be reproduced reliably with existing computational approaches. One of the problems is that the range and character of fluctuations of proteins in the slow time scales characteristic of equilibrium and biological processes have not been characterized. The goal of the equilibrium thermodynamic studies that are proposed is (1) to improve understanding the relationship between local conformational stability and pKa values of surface ionizable residues; (2) to describe the coupling between local structural fluctuations, ligand binding, and global conformational transitions; (3) to examine the contributions from local unfolding to the ionization energetics of internal residues. These experimental studies will contribute the physical insight and the data needed to guide improvements to existing methods for structure-based calculation of electrostatic effects in proteins. They will also be used to test and develop a new method for structure-based calculations of electrostatic effects that combines standard electrostatics continuum methods for pKa calculations with a statistical thermodynamic method to describe the distribution of microstates in the native state ensemble. PUBLIC HEALTH RELEVANCE: The principles and the computational methods emerging from these studies will impact our understanding of pH-driven conformational transitions of medical and biological relevance, such as activation of viruses and toxins. The computational method that will be developed could be useful in problems in drug design, and for the design of proteins and macromolecular switches.

描述（由申请人提供）：静电能可用于关联蛋白质的结构和功能。出于这个原因，pKa值和静电能的分子决定因素的更好的理解，以及基于结构的静电计算的计算方法的发展，仍然是非常感兴趣的。大多数计算方法还不够精确，不能用来描述生物化学过程，特别是那些蛋白质电荷变化与构象变化相结合的过程。此外，蛋白质中静电效应的物理基础还没有得到很好的理解。所提出的研究检查的假设，即本地构象波动，涉及重排的骨干贡献显着的pKa值和蛋白质的静电能的大小。初步数据表明，这一假设很可能是正确的。无论是局部构象波动的蛋白质，也不是蛋白质的结构响应，其带电状态的变化可以可靠地再现与现有的计算方法。其中一个问题是，在平衡和生物过程的特点缓慢的时间尺度的蛋白质的波动的范围和特点还没有得到表征。提出的平衡热力学研究的目标是：（1）提高对局部构象稳定性和表面可电离残基的pKa值之间的关系的理解;（2）描述局部结构波动，配体结合和全局构象转变之间的耦合;（3）检查局部解折叠对内部残基电离能学的贡献。这些实验研究将有助于物理洞察力和所需的数据，以指导改进现有的方法，基于结构的计算蛋白质中的静电效应。它们还将用于测试和开发一种基于结构的静电效应计算的新方法，该方法将标准的静电连续方法与统计热力学方法相结合，用于pKa计算，以描述原生状态系综中微观态的分布。 公共卫生相关性：这些研究中出现的原理和计算方法将影响我们对pH驱动的医学和生物学相关构象转变的理解，例如病毒和毒素的活化。将开发的计算方法可能是有用的药物设计中的问题，并为蛋白质和大分子开关的设计。