Fluctuations and entropy in the energetics and function of protein complexes

蛋白质复合物的能量学和功能中的波动和熵

• 批准号: 8515476
• 负责人: A. JOSHUA WAND
• 金额: $ 35.04万
• 依托单位: UNIVERSITY OF PENNSYLVANIA
• 依托单位国家: 美国
• 财政年份: 2012
• 资助国家: 美国
• 起止时间: 2012-08-01 至 2016-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8515476
• 关键词: Abbreviations; Affinity; Bacteria; Binding; Biochemical; CaM kinase I activator; Calcium; Calcium Binding; Calibration; Calmodulin; Complement; Complex; Coupling; Cyclic AMP Receptor Protein; DNA; DNA Binding; DNA-Protein Interaction; Data; Dihydrofolate Reductase; Egg White; Entropy; Evolution; Free Energy; Genetic; Goals; Homo sapiens; Homologous Gene; Human Biology; Iris; Knowledge; Lac Repressors; Lactose; Libraries; Ligand Binding; Ligands; Literature; Measurement; Measures; Mediating; Methods; Molecular Conformation; Motion; Muramidase; Myosin Light Chain Kinase; Nature; Nitric Oxide Synthase Type I; Pharmacologic Substance; Phosphotransferases; Play; Prokaryotic Cells; Property; Protein Conformation; Protein Dynamics; Proteins; Proxy; Regulation; Relaxation; Repressor Proteins; Role; Series; Set protein; Signal Pathway; Signal Transduction; Solutions; Structure; System; Testing; Thermodynamics; Time; Transcriptional Regulation; Ubiquitin; Variant; Work; base; cdc42 GTP-Binding Protein; cost effective; defined contribution; design; human disease; improved; insulin receptor substrate 1 protein; meter; molecular recognition; p21 activated kinase; phosphoric diester hydrolase; pressure; protein complex; protein function; ras Proteins; response; rho; src Homology Domains

DESCRIPTION (provided by applicant): The fundamental premise of this proposal is that proteins are dynamic entities, that their internal motion is an expression of an inherent and significant amount of conformational entropy and that changes in conformation entropy can greatly influence the energetics of protein function. Below we will summarize recent results that support these assertions. Perhaps the simplest functional context is the binding of a ligand by a protein. Thus our general hypothesis is that the thermodynamics of protein-ligand interactions can be influenced via changes in the protein internal entropy. Though this idea has been in the literature for some time it is only recently that the experimental methods that are capable of illuminating it have become available. We will test the generality of a role for protein dynamics (and the entropy it represents) in molecular recognition by proteins and in the more sophisticated allosteric response. The former will build upon an existing array of examples that indicate a general roughly linear relationship between the contributions of a change in conformational entropy upon ligand binding and the overall binding entropy. Though such a relationship is not required its existence suggests that evolution has exploited conformational entropy in the optimization of protein-ligand thermodynamics. This idea will be quantitatively explored using the recently calibrated "entropy meter" that relies on a dynamical proxy for conformational entropy. Comprehensive measurements of internal protein motion will be undertaken using the now well-established solution NMR relaxation methods. In an effort to more fully understand the propagation of dynamics within the protein matrix, a high-pressure perturbation study of protein motion will be carried out to illuminate coupling of motion. Recent work by others on the catabolite activator protein suggests that conformational entropy may play a central role in protein-DNA recognition. We therefore propose to examine the structural and dynamic properties underlying protein-DNA recognition in the lac repressor. The lac repressor is a paradigm for genetic regulation in prokaryotes. Overall these studies will greatly expand our appreciation of the nature of protein motion and the role of the conformational entropy that it represents in the energetics of protein function.

描述（由申请人提供）：该提案的基本前提是蛋白质是动态实体，其内部运动是固有且大量构象熵的表达，并且构象熵的变化可以极大地影响蛋白质功能的能量学。下面我们将总结支持这些主张的最新结果。也许最简单的功能背景是配体与蛋白质的结合。因此，我们的一般假设是蛋白质-配体相互作用的热力学可以通过蛋白质内熵的变化来影响。尽管这个想法已经在文献中出现了一段时间，但直到最近才有能够阐明它的实验方法。我们将测试蛋白质动力学（及其代表的熵）在蛋白质分子识别和更复杂的变构反应中的作用的普遍性。前者将建立在现有的一系列示例的基础上，这些示例表明配体结合时构象熵变化的贡献与总体结合熵之间存在一般的大致线性关系。尽管这种关系不是必需的，但它的存在表明进化在蛋白质-配体热力学的优化中利用了构象熵。这个想法将使用最近校准的“熵计”进行定量探索，该“熵计”依赖于构象熵的动态代理。将使用现已成熟的溶液核磁共振弛豫方法对内部蛋白质运动进行全面测量。为了更全面地了解蛋白质基质内动力学的传播，将对蛋白质运动进行高压扰动研究，以阐明运动的耦合。其他人最近对分解代谢物激活蛋白的研究表明，构象熵可能在蛋白质-DNA 识别中发挥核心作用。因此，我们建议检查 lac 阻遏蛋白中蛋白质-DNA 识别的结构和动态特性。 lac 阻遏蛋白是原核生物遗传调控的范例。总的来说，这些研究将极大地扩展我们对蛋白质运动本质及其在蛋白质功能能量学中所代表的构象熵的作用的认识。