Dynamic Elements: Effects of Co-Solvents on Peptide Folding Pathways

堪萨斯大学的Krzysztof Kuczera和Corey K.Johnson得到了化学部生命过程化学计划的一项奖项的支持，该奖项旨在使用实验和计算方法分析生物分子如何根据外部刺激修改其结构。对环境影响的反应变化是活细胞生物分子功能的一个重要方面，可能涉及对温度、pH和溶剂的反应。这个项目的重点是多肽，相对较小的分子-10-60个氨基酸长度-作为蛋白质的简单模型。库泽拉教授和约翰逊教授正在设计定制的多肽，以展示螺旋、片状和转体等形状。这些形状包含用于跟踪结构变化的“报告器”组件。时间分辨光谱分析是用来分析在正常条件下和在不同应力下的多肽结构和运动。计算方法的组合被用来模拟三维多肽结构。这种计算机建模策略的一个关键组成部分是识别多肽的“动态元素”-用于表征实验确定的多肽变化的代表性形状，包括折叠和展开。这项研究促进了对酶活性和细胞信号等基本生物学过程的理解，并将其应用于药物输送。教育活动包括将计算建模技术融入普通化学课堂，每年有1200多名学生。该团队扩展了广泛使用的计算机模拟界面，用于分子建模教育。虽然研究项目进行了培训，但参与该大学的多样性学者项目支持了少数族裔学生在化学方面的成功和留住。该项目背后的假设是，添加共溶剂导致的多肽折叠路径的变化是特定微观相互作用的结果。这项研究正在利用实验和计算相结合的方法来研究所设计的展示一系列螺旋、片状和转角的多肽的折叠路径变化。该项目使用了一系列先进的光谱方法，包括圆二色谱、核磁共振和FRET，通过分析荧光各向异性衰减(FAD)来探测旋转运动，并使用温度跳跃研究来分析动力学过程。这些研究是在缓冲液中进行的，并在变性剂、保护性渗透剂和粘性物质存在的情况下进行，以表征作为环境函数的动态效应。通过分子动力学(MD)的轨迹分析和复制交换MD模拟，利用聚集和动力学粗粒化来识别主要的、具有代表性的多肽构象，即它的“动态元素”。二面体约束的分子动力学和连续介质流体动力学被用来分析动力学元素的扩散和微观溶剂化模式，允许将观察到的光谱信号去卷积为来自特定结构和相互作用的贡献。对于每种多肽类型和环境，共溶剂对结构、局部和全局动力学以及对折叠、展开和中间态之间的平衡的影响被分析。通过将观察到的信号映射到特定的结构、相互作用和运动，动态元素方法提供的微观洞察力以全面的实验数据为基础，在新的细节水平上提供对肽和蛋白质的基本结构构件的结构、动力学和折叠路径的洞察。该项目将广泛的计算建模和主动学习活动(可视化、动力学数据分析、动力系统、基于主体的建模)整合到普通化学课程中，研究人员通过参与堪萨斯大学多元化学者计划和本科生研究经验计划，为招募和保留化学领域代表不足的群体做出贡献。该奖项反映了NSF的法定使命，并通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。

Krzysztof Kuczera and Corey K. Johnson of the University of Kansas are supported by an award from the Chemistry of Life Processes Program in the Division of Chemistry to analyze how biological molecules modify their structures in response to external stimuli, using experimental and computational approaches. Changes in response to environmental influences are a crucial aspect of biomolecular function in living cells, and can involve responses to temperature, pH, and solvents. This project focuses on peptides, relatively small molecules---10-60 amino acids in length---that serve as simple models of proteins. Professors Kuczera and Johnson are designing custom peptides tailored to exhibit shapes such as helices, sheets, and turns. These shapes incorporate "reporter" components for tracking structural changes. Time-resolved spectroscopy is used to analyze peptide structure and motion under normal conditions and under various stresses. A combination of computational approaches is used to model the three-dimensional peptide structures. A key component of this computer modeling strategy is the identification the peptide's "dynamic elements"--- representative shapes used to characterize the experimentally-determined peptide changes, including folding and unfolding. This research advances understanding of fundamental biological processes such as enzyme activity and cell signaling, and applications to drug delivery. Educational activities include the integration of computational modeling techniques into general chemistry classes, with over 1200 students annually. The team expands the widely-used computer simulation interface for use in molecular modeling education. While the research program trains, participation in the university's Diversity Scholars Program supports the success and retention of minority students in chemistry.The hypothesis underlying this project is that changes in peptide folding pathways induced by the addition of co-solvents are the result of specific microscopic interactions. The research is utilizing combined experimental and computational approaches to investigate folding path changes of designed peptides exhibiting an array of helices, sheets and turns. The project is using a range of advanced spectroscopic methods, including circular dichroism, NMR, and FRET, with analysis of fluorescence anisotropy decay (FAD) to probe rotational motion, and temperature-jump studies for analyzing kinetic processes. The studies are being performed in buffer, and in the presence of denaturants, protective osmolytes and viscogens, in order to characterize dynamical effects as a function of environment. Clustering and kinetic coarse-graining are employed to identify major, representative peptide conformers, its "dynamic elements", from trajectory analysis of molecular dynamics (MD) and replica-exchange MD simulations. Dihedral-restrained MD and continuum hydrodynamics are used to analyze diffusion and microscopic solvation patterns of the dynamic elements, allowing de-convolution of the observed spectroscopic signals into contributions from specific structures and interactions. For each peptide type and environment, co-solvent effects on structure, local and global dynamics and on equilibria between folded, unfolded, and intermediate states are analyzed. By mapping observed signals onto specific structures, interactions and motions, the microscopic insight provided by the dynamic elements approach, grounded in comprehensive experimental data, is providing insight into the structure, dynamics and folding pathways of the basic structural building blocks of peptides and proteins at new level of detail. The project is integrating extensive computational modeling and active learning activities (visualization, kinetic data analysis, dynamical systems, agent-based modeling) within the general chemistry curriculum, and the investigators are contributing to the recruitment and retention of underrepresented groups in chemistry, through participation in the University of Kansas Diversity Scholars Program and Research Experience for Undergraduates Program.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.