Chemistry and Materials Science Seminar: Investigating Protein Dynamics and Functions with Multiscale Simulation and Modeling
Chemistry and Materials Science Seminar
Investigating Protein Dynamics and Functions with Multiscale Simulation and Modeling
Dr. Wenjun Zheng
Professor, Department of Physics
SUNY Buffalo
Event Details:
Protein structural and functional dynamics, spanning a wide range of time scales from nanoseconds to seconds, holds keys to the mechanisms of protein functions and dysfunctions. Molecular Dynamics (MD) simulation is the method of choice for exploring protein dynamics under physiological conditions with atomic resolution. However, MD simulation is computationally expensive, especially for large protein complexes in explicit solvent. As a cost-effective alternative, coarse-grained models have been developed using simplified structural representations (e.g., one point per amino acid) and force fields. For example, in an elastic network model (ENM), the carbon alpha atoms of nearby amino acids are connected by harmonic springs. The normal mode analysis of ENM can be used to predict a handful of low-frequency normal modes, which offer remarkably good descriptions of many global and local conformational changes in proteins as observed experimentally. Unlike MD simulation, ENM is computationally cheap and can be applied to large protein complexes without any limit in accessible time scale. Over the years, I have combined all-atom MD simulation and ENM-based modeling to perform multiscale simulations of key aspects of protein dynamics and energetics. Here, I will illustrate this powerful integrated approach with a few examples from my research projects, and envision how this can be useful in the new age of AI-assisted protein modeling.
Speaker Bio:
Dr Zheng obtained his BS from Zhejiang University in 1995, and MS from Chinese Academy of Science in 1998. He then pursed his PHD study in computational biophysics at Stanford University with Prof. Sebastian Doniach (1998-2003). Dr Zheng received his postdoc training at NIH/NHLBI with Dr. Bernard Brooks (2003-2007). In 2007, he started assistant professor position at State University of New York at Buffalo, and was promoted to professor in 2018. His research in computational biophysics has been funded by grants from National Science Foundation and American Heart Association.
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