QM-MM PREDICTIONS OF PHOTOINDUCED ELECTRON TRANSFER IN PROTEINS

蛋白质中光诱导电子转移的 QM-MM 预测

• 批准号: 8364314
• 负责人: PATRIK R CALLIS
• 金额: $ 0.11万
• 依托单位: CARNEGIE-MELLON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-09-15 至 2013-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8364314
• 关键词: Area; Behavior; Biological; Biomedical Research; Coupled; Coupling; Electron Transport; Electrostatics; Elements; Environment; Enzymes; Fluorescence; Funding; Grant; Heterogeneity; High Performance Computing; Hydration status; Measurement; Monitor; National Center for Research Resources; Positioning Attribute; Principal Investigator; Property; Protein Conformation; Protein Dynamics; Proteins; Relaxation; Research; Research Infrastructure; Resources; Solvents; Source; Students; Time; Tryptophan; United States National Institutes of Health; Variant; Work; cost; electric field; millisecond; protein folding; protein structure; research study; simulation; single molecule; villin

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. We request resources to enable significantly more realistic QM-MM computations that aim to explore the extremely rugged electrostatic landscape of proteins through a detailed fundamental understanding of two phenomena that are widely exploited to study protein structure and dynamics: tryptophan (Trp) fluorescence quenching (by electron transfer from the excited state) and tryptophan fluorescence wavelength shifts due to hydration of the large excited state dipole. Particular focus during the next three years will be on (1) understanding ultrafast (0.5 -100 ps) fluorescence intensity decay (quenching) and wavelength shift experiments on proteins, (2) the spectacular fluctuation of quenching rates seen in single-molecule fluorescence of proteins, and (3) the underlying mechanisms of quenching variation used to monitor protein folding. These are areas of cutting edge experimental work. The project builds on 9 previous years of NSF support for mostly computational work that led to unprecedented progress in understanding Trp fluorescence wavelength variability in proteins using electrostatics, and to unprecedented progress in understanding of the previously unexplained--but widely exploited--Trp fluorescence intensity changes accompanying changes in protein structure. This work has recently been funded by NSF (NSF Proposal ID: 0847047) for the period Aug 2009-July 2012. Our recent ab initio computations of realistic electron transfer coupling elements during dynamics simulations led unexpectedly to an understanding of why wavelength and quenching are often strongly coupled and correlated. With the aid of the proposed multiple ns-scale simulations, the project is now immediately in a position to make insightful contributions to the contested notion that time resolved wavelength shifts speak solely to solvation dynamics, rather than a mixture of solvation dynamics and long term heterogeneity in protein conformation. This is particularly relevant to items (1) and (2) above. A constant theme of our work has shown the supreme importance of the enormous local electric field strength and direction in determining fluorescence behavior in proteins. Continued effort in these areas is encouraged by the emerging view that the catalytic power of enzymes is largely due to a specifically oriented, preorganized electrostatic environment, whose energy may come from reduction in folding energy. A constant theme from the Callis group has been that an ordered electrostatic environment coupled with large fluctuations is precisely what determines whether fluorescence will be strong or weak, and whether its average wavelength will be short or long. This meshes perfectly with the exciting recent observation by Marcus and others that the temporal behavior of fluctuations in electrostatic field is in common with that of other properties of proteins over the time scale of biological importance (milliseconds to seconds). Two students and a postdoctoral associate will work on subprojects entitled: (A) QM-MM simulations examining the relationship of solvent relaxation and heterogeneity in ultrafast TDSS measurements, and (B) Prediction of tryptophan fluorescence intensities during folding of the villin headpiece. The PI requests 500, 000 SU.

这个子项目是许多利用资源的研究子项目之一 由NIH/NCRR资助的中心拨款提供。子项目的主要支持 子项目的主要研究者可能是由其他来源提供的， 包括其他NIH来源。 列出的子项目总成本可能 代表子项目使用的中心基础设施的估计数量， 而不是由NCRR赠款提供给子项目或子项目工作人员的直接资金。 我们请求资源，使显着更现实的QM-MM计算，旨在探索极其崎岖的静电景观的蛋白质通过详细的基本了解被广泛利用研究蛋白质的结构和动力学的两种现象：色氨酸（Trp）荧光淬灭（通过电子转移从激发态）和色氨酸荧光波长偏移由于水合的大激发态偶极子。未来三年的重点将是（1）理解蛋白质的超快（0.5 - 100 ps）荧光强度衰减（猝灭）和波长漂移实验，（2）在蛋白质单分子荧光中看到的猝灭速率的壮观波动，以及（3）用于监测蛋白质折叠的猝灭变化的潜在机制。这些都是尖端实验工作的领域。该项目建立在NSF前9年对主要计算工作的支持基础上，这些工作导致了使用静电学理解蛋白质中Trp荧光波长变异性的前所未有的进展，以及对以前无法解释但被广泛利用的Trp荧光强度变化的理解的前所未有的进展伴随蛋白质结构的变化。这项工作最近由NSF资助（NSF提案ID：0847047），资助期限为2009年8月至2012年7月。我们最近的从头计算的现实电子转移耦合元件的动力学模拟过程中意外地导致理解为什么波长和淬火往往强烈耦合和相关。借助于所提出的多个ns尺度模拟，该项目现在能够立即对有争议的概念做出有见地的贡献，即时间分辨波长偏移仅与溶剂化动力学有关，而不是溶剂化动力学和蛋白质构象长期异质性的混合物。这与上述第（1）和（2）项特别有关。我们工作的一个不变的主题已经显示了巨大的局部电场强度和方向在决定蛋白质的荧光行为中的极端重要性。在这些领域的持续努力是鼓励新兴的观点，酶的催化能力在很大程度上是由于一个特定的定向，预组织的静电环境，其能量可能来自折叠能量的减少。Callis小组的一个不变的主题是，有序的静电环境加上大的波动正是决定荧光是强还是弱，以及其平均波长是短还是长的因素。这与马库斯等人最近令人兴奋的观察结果完美吻合，即静电场波动的时间行为与蛋白质在生物学重要性时间尺度（毫秒到秒）上的其他性质是共同的。两名学生和一名博士后助理将从事题为：（A）QM-MM模拟检查溶剂弛豫和超快TDSS测量异质性的关系，和（B）预测色氨酸荧光强度在绒毛头部折叠。PI要求50万SU。