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Biomolecular Interactions and Enzymatic Processes

生物分子相互作用和酶促过程

基本信息

批准号：
10462598
负责人：
JIALI GAO
金额：
$ 32.4万
依托单位：
UNIVERSITY OF MINNESOTA
依托单位国家：
美国
项目类别：
财政年份：
1992
资助国家：
美国
起止时间：
1992-09-30 至 2024-07-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10462598
关键词：
Address Amino Acids Animal Migration Binding Biochemical Process Biochemical Reaction Biological Biological Process Biophysics Biosensor Cell physiology Cells Charge Complex Computing Methodologies Contracts Coupled DNA Data Development Dissociation Drosophila genus Electron Transport Electrons Energy Transfer Engineering Environment Enzymes Flavins Free Energy Funding Gene Activation Generations Goals Grant Harvest Homologous Protein Imaging Device Investigation Jet Lag Syndrome Life Light Maps Mechanics Methodology Methods Modeling Molecular Nature Nuclear Pathway interactions Photochemistry Photoreceptors Photosynthesis Phototropism Plants Play Principal Investigator Procedures Process Protein Conformation Proteins Protons Reaction Research Research Project Grants Respiration Role Signal Transduction Structure Techniques Time Travel Tryptophan Water Work absorption chemical bond chromophore cofactor computer studies conformational conversion cost cryptochrome density design dimer experimental study improved insight interest interfacial intermolecular interaction molecular dynamics novel optogenetics photoactivation prevent programs protein protein interaction quantum receptor response simulation theories tool ultraviolet

项目摘要

Program Director/Principal Investigator (Last, First, Middle): Gao, Jiali Project Summary A multi-faceted research project is directed aimed at computational studies of photochemically induced processes and interactions in photoreceptor proteins. The theoretical approach centers on molecular dynamics and nonadiabatic quantum dynamics simulations of the ultrafast excited energy transfer and charge transfer as well as the subsequent protein conformation change that triggers signal transduction. We employ multiscale simulation techniques, including combined quantum mechanical and molecular mechanical (QM/MM) methods to describe intermolecular interactions. A major goal is to increase the capability of QM/MM methods to model photochemical processes and to achieve greater accuracy than conventional approaches. We propose to develop multistate density functional theory (MSDFT) to define excitation, charge, and spin localized states. We also plan on further explore the computationally efficient multistate tight-binding density functional theory (MS-DFTB) to perform long-time dynamics simulations. The MSDFT method follows a dynamic-then-static ansatz, in which dynamic correlation is incorporated into the basis states in the first place. As such, the basis configurations in the active space are highly contracted, which significantly reduce the number of configurations needed and the computational costs. Yet, MSDFT is also accurate. Applying the MSDFT/CHARMM combination, we aim to understand the nature of the photochemical and photophysical processes following light absorption in cryptochromes. In addition, we aim to understand the light harvesting mechanism of the ultraviolet-B receptor UVR8, and its light-induced dimer photodissociation process. A long- term goal is to understand the nature of protein-protein interactions between UVR8 and homologous proteins. PHS 398/2590 (Rev. 06/09) Page Continuation Format Page

项目负责人/主要研究者（末、首、中）：高佳丽项目摘要一个多方面的研究项目是针对计算研究的光化学诱导光感受器蛋白的过程和相互作用。理论方法以分子动力学为中心和非绝热量子动力学模拟的超快激发能量转移和电荷转移，以及随后引发信号转导的蛋白质构象变化。我们采用多尺度模拟技术，包括结合量子力学和分子力学（QM/MM）方法来描述分子间的相互作用。一个主要目标是提高QM/MM方法的建模能力光化学过程，并实现更高的精度比传统的方法。我们建议发展多态密度泛函理论（MSDFT）来定义激发、电荷和自旋局域态。我们还计划进一步探索计算效率高的多态紧束缚密度泛函理论（MS-DFTB）执行长期动态模拟。MSDFT方法遵循动态-静态在这种方法中，首先将动态相关性并入基态。因此，根据活动空间中的配置高度收缩，这显著减少了所需的配置和计算成本。然而，MSDFT也是准确的。应用 MSDFT/CHARMM组合，我们的目标是了解光化学和光物理的性质，隐花色素中光吸收后的过程。此外，我们的目标是了解光收集紫外线B受体UVR 8的作用机制及其光诱导的二聚体光解过程。很长的- 术语目标是了解UVR 8和同源蛋白之间蛋白质-蛋白质相互作用的性质。 PHS 398/2590（Rev.06/09）