Dynamics and Mechanism of Water-Protein Interactions

水-蛋白质相互作用的动力学和机制

• 批准号: 8316362
• 负责人: DONGPING ZHONG
• 金额: $ 28.98万
• 依托单位: OHIO STATE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-09-01 至 2015-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8316362
• 关键词: Active Sites; Address; Amino Acids; Architecture; Benchmarking; Binding; Binding Sites; Biological Process; Catalysis; Chemical Structure; Chemicals; Complex; Coupled; Coupling; DNA; DNA-Directed DNA Polymerase; Data; Docking; Drug Design; Enzymes; Evolution; Future; Goals; Heterogeneity; Hydration status; Investigation; Isotopes; Knowledge; Lasers; Lead; Life; Maps; Mediation; Membrane Proteins; Methodology; Methods; Modeling; Molecular; Motion; Mutation; Nature; Neurodegenerative Disorders; Optics; Prevention; Property; Protein Dynamics; Protein Engineering; Proteins; Relaxation; Research; Resolution; Role; Scanning; Science; Series; Site-Directed Mutagenesis; Spectrum Analysis; Structural Protein; Structure; Surface; System; Temperature; Time; Tryptophan; Water; biological systems; flexibility; globular protein; improved; insight; interfacial; molecular dynamics; molecular recognition; mutant; novel; practical application; protein aggregation; protein protein interaction; protein structure; simulation

DESCRIPTION (provided by applicant): Protein hydration is a long-standing and unresolved problem in protein science and water-protein interactions/dynamics are essential to a protein's structure, dynamics and function. The elucidation of such coupling motions at the molecular level not only has fundamental significance in understanding protein stability and flexibility, folding, misfolding and aggregation, recognition and binding, and enzyme catalysis, but also has a significant impact on practical applications such as drug design. Various methods and strategies have been used to characterize water motions around proteins, but such studies have been challenging and difficult because the dynamics are ultrafast and heterogeneous. A general molecular picture has not been obtained yet. We have recently developed a methodology by integrating state-of-the-art femtosecond laser spectroscopy and site-directed mutagenesis and have reached femtosecond temporal resolution and single-residue spatial resolution. Using intrinsic amino acid tryptophan as a local optical probe, we have recently mapped out the global water motions around an a-helical globular protein with unprecedented details. In this proposal, we will systematically characterize water motions around small structural motifs, on surfaces of ¿-sheet globular proteins, and at interfaces of protein-DNA complexes. Specifically, Aim 1 is to elucidate the hydration dynamics evolution by systematic characterization of water motions from an a-helix, to a ¿-hairpin, to a small cage, and to a mini-protein. With the fundamental understanding of water motions around these elemental structure units, in Aim 2 we extend to characterize the global surface hydration dynamics around two ¿-sheet globular proteins. Combined with recently characterized water dynamics around the a-helical globular protein, we hope that such systematic comparisons will reveal the different dynamic nature of water motions around different protein architectures with different size, rigidity, chemical identity. Finally, in Aim 3, we investigate the interfacial hydration dynamics by systematic characterization of water motions at the interfaces of two protein-DNA complexes to address the dynamic role of water motions in mediation of protein-DNA recognition. The new knowledge obtained from these systematic investigations is fundamental to a wide variety of biological processes and also significant to a series of practical applications.

描述（由申请人提供）：蛋白质水合是蛋白质科学中一个长期存在且未解决的问题，水-蛋白质相互作用/动力学对蛋白质的结构、动力学和功能至关重要。在分子水平上阐明这种耦合运动不仅对理解蛋白质的稳定性和柔性、折叠、错误折叠和聚集、识别和结合以及酶催化具有基础性意义，而且对药物设计等实际应用具有重要影响。已经使用了各种方法和策略来表征蛋白质周围的水运动，但这些研究具有挑战性和困难性，因为动力学是超快和异质的。一个普遍的分子图像还没有得到。我们最近开发了一种方法，通过整合国家的最先进的飞秒激光光谱和定点诱变，并已达到飞秒时间分辨率和单残基空间分辨率。利用内源性氨基酸色氨酸作为局部光学探针，我们最近绘制出了全球水运动周围的a-螺旋球状蛋白质前所未有的细节。在这个建议中，我们将系统地描述水运动周围的小结构图案，在表面上的<$-sheet球状蛋白质，并在蛋白质-DNA复合物的界面。具体而言，目的1是阐明水的运动从一个α-螺旋，一个<$-发夹，一个小笼子，和一个迷你蛋白质的系统表征的水化动力学演变。随着对这些基本结构单元周围水运动的基本理解，在目标2中，我们扩展到表征两个<$-折叠球状蛋白周围的全球表面水合动力学。结合最近表征的α-螺旋球状蛋白周围的水动力学，我们希望这种系统的比较将揭示不同的蛋白质结构周围的水运动的不同动力学性质，具有不同的大小，刚度，化学身份。最后，在目标3中，我们通过系统表征两种蛋白质-DNA复合物界面处的水运动来研究界面水合动力学，以解决水运动在蛋白质-DNA识别介导中的动态作用。从这些系统的研究中获得的新知识是各种生物过程的基础，对一系列实际应用也很重要。