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.
Intended
Audience:
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