US-Turkey Cooperative Research Project: Studies on the Folding Dynamics of Proteins

0352868 PalazogluDescription：该项目支持加州大学戴维斯分校化学工程和材料科学系Ahmet Palazoglu博士与土耳其伊斯坦布尔Koc大学计算机工程系Attila Gursoy博士以及Koc大学化学和生物工程系Burak Erman博士和Yaman Arkun博士之间的合作伙伴关系。研究的重点是蛋白质折叠动力学的研究，重点是开发能够可靠预测折叠机制的快速仿真平台，并分析模拟的轨迹，以了解蛋白质折叠到其自然状态的基本特征。为了模拟折叠动态，他们计划使用粗粒度的快速折叠算法。具体地说，将使用粗粒度的GO类型模型。他们将在最优控制理论的基础上探索新的方向，将蛋白质引导到已知的自然状态。此外，他们计划使用主成分分析(PCA)来表征快速折叠GO-型模型获得的大量轨迹，并进行小波分解，以提供对其空间和时间特征的多分辨率分析。粗粒GO模型还将得到更广泛的水中蛋白质严格分子动力学(MD)的模拟，并将探讨不同的精度水平。范围：拟议的蛋白质折叠动力学研究是结构生物学中的一个密集研究领域。PI‘s预计这项研究的结果将对理解蛋白质从变性状态进化到自然状态过程中涉及的基本机制产生重大影响。两个小组在拟议工作的相关内容方面拥有互补的专业知识，两个小组之间的协作工作已经有了简短的历史。该项目将有来自土耳其的一名初级研究员担任首席国际和平研究所和来自两个机构的研究生。研究团队在美国和土耳其之间的旅行将以这样的方式组织，以便在年内为互动和实质性研究提供充足的时间。拟议的研究将有助于培养研究生，并提供一个协同环境，让他们能够体会到多学科研究的好处。这些结果将通过科学文献传播，也将在主要的私人投资机构的网页上提供。拟议的活动将加深我们对蛋白质如何发挥作用的了解，并将对整个社会的福祉产生直接影响。

0352868 PalazogluDescription: This project supports a partnership between the Dr. Ahmet Palazoglu, Department of Chemical Engineering and Material Science, The University of California, Davis, California and a team of Turkish scientists including Dr. Attila Gursoy, Department of Computer Engineering, Koc University, Istanbul, Turkey and Dr. Burak Erman and Dr. Yaman Arkun, both of the Department of Chemical and Biological Engineering at Koc University. The focus of the research is the study of protein folding dynamics, with the emphasis on developing fast simulation platforms that can reliably predict the mechanisms of folding and analyzing the simulated trajectories to understand the fundamental features of how the protein folds to its native state. For simulating the folding dynamics, they plan to use coarse-grained fast-folding algorithms. Specifically, a coarse-grained Go-type model will be utilized. They will explore new directions, based on optimal control theory, in steering the protein to its known native state. Furthermore, they plan to use the principal components analysis (PCA) to characterize the large number of trajectories obtained by the fast-folding Go-type model, and perform wavelet decomposition to provide a multi-resolution analysis of their spatial and temporal features. The coarse-grained Go model will also be complemented by more extensive simulations of rigorous molecular dynamics (MD) for proteins in water and different accuracy levels will be probed.Scope: The proposed research on protein folding dynamics is a field of intense study in structural biology. The PI's expect the results of this research to have significant repercussions in understanding the fundamental mechanisms involved during the evolution of the protein from its denatured state to its native state. The two teams have complementary expertise in the related elements of the proposed work, and there is already a brief history of collaborative work between the two groups. The project will involve a junior researcher from Turkey as the lead PI and graduate students from both institutions. The travel between the U.S. and Turkey by the research teams will be organized in such a way as to provide ample time for interaction and substantial research during the year. The proposed research will help train graduate students and provide a synergistic environment in which they can appreciate the benefits of multi-disciplinary research. The results will be disseminated through scientific literature and will also be available on the Web pages of the leading PIs. The proposed activity will enhance our understanding of how proteins function and will have a direct impact on the well being of the society at large.