Electrostatic effects of the native state ensemble

本机态系综的静电效应

• 批准号: 7848982
• 负责人: Bertrand Garcia-Moreno
• 金额: $ 34.59万
• 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/7848982
• 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)：静电能量有助于蛋白质的结构和功能的相互关系。因此，更好地理解pKa值和静电能的分子决定因素，以及发展基于结构的静电计算的计算方法，仍然是人们非常感兴趣的。大多数计算方法还不够准确，不足以描述生化过程，特别是那些蛋白质电荷的变化与构象变化相耦合的过程。此外，蛋白质中静电效应的物理基础还没有被很好地理解。所提出的研究检验了这样一种假设，即涉及骨架重排的局部构象波动对蛋白质的pKa值和静电能量的大小有显著贡献。初步数据显示，这一假设很可能是正确的。现有的计算方法既不能可靠地再现蛋白质的局部构象波动，也不能可靠地再现蛋白质对带电状态变化的结构响应。其中一个问题是，蛋白质在以平衡和生物过程为特征的慢时间尺度上的波动范围和特征尚未得到表征。平衡热力学研究的目的是(1)提高对局部构象稳定性与表面可电离残基pKa值之间的关系的理解；(2)描述局部结构涨落、配体结合和整体构象转变之间的耦合；(3)考察局部展开对内部残基电离能学的贡献。这些实验研究将有助于提供物理洞察力和所需的数据，以指导改进现有的基于结构的蛋白质静电效应计算方法。它们还将被用来测试和开发一种基于结构的静电效应计算的新方法，该方法将标准静电学连续统方法用于PKA计算与统计热力学方法相结合来描述本征态系综中微态的分布。 公共卫生相关性：这些研究产生的原理和计算方法将影响我们对pH驱动的医学和生物相关性构象转变的理解，例如病毒和毒素的激活。将开发的计算方法可能对药物设计中的问题以及蛋白质和大分子开关的设计有用。