QM-MM PREDICTIONS OF PHOTOINDUCED ELECTRON TRANSFER IN PROTEINS

这个子项目是利用资源的许多研究子项目之一。 由NIH/NCRR资助的中心拨款提供。对子项目的主要支持 子项目的首席调查员可能是由其他来源提供的， 包括美国国立卫生研究院的其他来源。为子项目列出的总成本可能 表示该子项目使用的中心基础设施的估计数量， 不是由NCRR赠款提供给次级项目或次级项目工作人员的直接资金。 我们需要资源来实现更现实的QM-MM计算，旨在通过详细的基本了解两种现象来探索蛋白质极其崎岖的静电图景，这两种现象被广泛用于研究蛋白质的结构和动力学：色氨酸(Trp)荧光猝灭(通过激发态的电子转移)和色氨酸荧光波长因大激发态偶极子的水化而移动。未来三年的重点将是(1)了解蛋白质的超快(0.5-100ps)荧光强度衰减(猝灭)和波长漂移实验，(2)蛋白质单分子荧光中所见的猝灭速率的惊人波动，以及(3)用于监测蛋白质折叠的猝灭变化的潜在机制。这些都是前沿实验工作的领域。该项目建立在前9年NSF主要为计算工作提供支持的基础上，这些工作导致了利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，以及在理解先前未解释但被广泛利用的伴随蛋白质结构变化的Trp荧光强度变化方面取得了前所未有的进展。这项工作最近得到了国家科学基金会(国家科学基金会提案ID：0847047)的资助，时间为2009年8月至2012年7月。我们最近在动力学模拟过程中对现实的电子转移耦合元素进行了从头计算，意外地理解了为什么波长和猝灭经常是强耦合和关联的。在拟议的多ns尺度模拟的帮助下，该项目现在立即能够对有争议的概念做出有洞察力的贡献，即时间分辨的波长移动仅代表溶剂化动力学，而不是蛋白质构象中溶剂化动力学和长期异质性的混合。这与上文第(1)和(2)项特别相关。我们工作的一个恒定主题表明了巨大的局部电场强度和方向在确定蛋白质中的荧光行为方面的至高无上的重要性。新出现的一种观点鼓励了这些领域的持续努力，即酶的催化能力在很大程度上是由于特定定向的、预先组织的静电环境，其能量可能来自折叠能量的减少。Callis团队一直以来的一个不变主题是，有序的静电环境加上巨大的波动，正是决定了荧光是强是弱，以及它的平均波长是短还是长。这与Marcus和其他人最近令人兴奋的观察结果完美地吻合，即静电场中波动的时间行为与蛋白质在生物重要性的时间尺度(毫秒到秒)上的其他属性的时间行为是相同的。两名学生和一名博士后将从事以下子项目：(A)QM-MM模拟研究超高速TDSS测量中溶剂松弛和异质性的关系，以及(B)预测Villin头盔折叠过程中的色氨酸荧光强度。PI要求50万个SU。

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.