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.
