Merging Physical Bioinformatics and Molecular Simulations: Investigating the Function and Docking of HisH/HisF Complexes

蛋白质复合体的瞬时形成和氨导向活性部位是组氨酸生物合成调控的主要因素。该项目的目的是通过结合分子动力学模拟、生物信息学和实验生物化学的方法，研究对接过程的能量格局和氨通过假定的蛋白质通道的传导。这种通过球状蛋白的通道呈现了一种以前没有研究过的新场景。氨传输的自由能分布将由恒速操纵的分子动力学轨迹利用雅金斯基恒等式以及其他统计机械抽样程序重建。这项研究的总体目标是了解蛋白质-蛋白质相互作用形成大分子复合体的机制。生物信息学方法将被用来建议对接过程的路径，这可以使用引导和交互分子动力学协议来探索。将物理生物信息学和分子模拟技术结合起来，在更现实的环境中对这一过程进行建模，为了解这些蛋白质如何沟通以实现代谢调节提供了机会。最近发表的关于细胞色素c2到光合细菌反应中心的瞬时蛋白复合体的结构为将能量景观分析应用于小分子氧化还原蛋白与完整膜蛋白的对接提供了另一个宝贵的机会。组氨酸生物合成是研究复杂代谢网络的模型系统。组氨酸的调节生产依赖于位于几个多肽链上的九个活性部位之间的复杂相互作用。有人认为，通过蛋白质-蛋白质相互作用形成蛋白质复合体是调节这一代谢途径的主要因素。了解这些蛋白质是如何交流的，将对我们理解生物系统中瞬时复合体的形成机制产生影响。这项工作将涉及实验生物学家和计算生物物理学家之间的合作，结果将被纳入课程“计算化学生物学”，该课程面向对化学、生物学和计算机科学相结合的研究感兴趣的本科生和一年级研究生。在这个项目中开发的对接算法和方法将通过NSF赞助的计算生物物理学暑期学校和免费分发的可视化程序VMD的插件提供给更广泛的科学界。这项工作由分子和细胞生物科学部的分子生物物理学计划和化学部的理论和计算化学计划共同资助。

The transient formation of protein complexes and the channeling of ammonia to the active site are major factors in the regulation of histidine biosynthesis. The objective of this project is to investigate the energy landscape of the docking process and the conduction of ammonia through a putative protein channel by integrating methods from molecular dynamics simulations, bioinformatics, and experimental biochemistry. This channel through a globular protein presents a novel scenario not previously studied. The free energy profile of the ammonia transport will be reconstructed from constant velocity steered molecular dynamics trajectories using the Jarzynski identity as well as other statistical mechanical sampling procedures. The overall goal of this research is to understand the mechanism of protein-protein interactions in the formation of large complexes. A bioinformatics approach will be used to suggest pathways for the docking process which can be probed using both steered and interactive molecular dynamics protocols. Merging the techniques of physical bioinformatics and molecular simulations to model this process in a more realistic environment provides an opportunity to understand how these proteins communicate to achieve metabolic regulation. Recently published structures on the transient protein complex of cytochrome c2 to the reaction center of photosynthetic bacteria offer another valuable opportunity to apply the energy landscape analysis to the docking of small redox proteins to integral membrane proteins.Histidine biosynthesis is a model system for studying complex metabolic networks. Regulated production of histidine depends on the complex interplay between nine active sites located on several polypeptide chains. It has been suggested that the formation of protein complexes through protein-protein interactions is a major factor in the regulation of this metabolic pathway. An understanding of how these proteins communicate will have an impact on our understanding of the mechanism of the formation of transient complexes in biological systems. This work will involve a collaboration between experimental biologists and computational biophysicists and the results will be incorporated into the course "Computational Chemical Biology" which is aimed at undergraduates and first-year graduate students interested in research at the interface of chemistry, biology and computer science. The algorithms and approaches to docking developed in this project will be made available to the broader scientific community through a NSF sponsored Summer School on Computational Biophysics and through plugins for the visualization program VMD that is freely distributed. This work is funded jointly by the Molecular Biophysics Program in the Division of Molecular and Cellular Biosciences and the Theoretical and Computational Chemistry Program in the Chemistry Division.