IBS-CMSD Colloquium_Dr. Holly Freedman (IBS CMSD)(Aug. 22, 2018)
IBS Center for Molecular Spectroscopy and Dynamics
COLLOQUIUM |
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SPEAKER
Dr. Holly Freedman (IBS
Center for Molecular Spectroscopy and Dynamics)
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TITLE
Some
Computational Studies of Molecular Structure and Dynamics Applied to Biomedical
Problems
■ ABSTRACT
First,
I will give two examples where I have applied computation to study the
structure and/or dynamics of biological systems relevant to problems in
virology. I will describe the prediction of a full-length model of the E1/E2
heterodimer comprising the HCV viral envelope, based on the partial crystal
structures of the envelope glycoproteins E1 and E2. A better understanding of
the structure and dynamics of the HCV viral envelope, which is responsible for
attachment and fusion, could aid in the development of a vaccine. Next, I will
discuss determining relative binding free energies of nucleotide analogues to
human mitochondrial DNA-dependent RNA polymerase (POLRMT), an important source
of off-target toxicity, by running molecular dynamics simulations on our Blue
Gene supercomputer. I will present a comparison of relative binding affinities
computed with free energy perturbation (FEP) to the experimental values. A better understanding of the dynamical
process of vibrational energy transfer in proteins following ATP hydrolysis may
also make it possible to design means of regulating such processes. In the
second half of my talk, we will consider the coupling of amide I vibrational
excitations to alpha-helical phonon modes, which was proposed by A. S. Davydov
to facilitate energy storage and propagation in proteins following ATP
hydrolysis. Because of the computational expense associated with fully quantum
mechanical treatments of systems with many degrees of freedom, practical
simulations of the Davydov-Scott model may be realized via a mixed
quantum-classical approach. A surface-hopping solution of the mixed
quantum-classical Liouville (MQCL) equation is implemented to study vibrational
delocalization in a one-dimensional model of a protein alpha helix.
■ DATE AND VENUE
August 22, 2018 (Wednesday, 4:00 - 5:00 pm)
Seminar Room A 116, KU R&D Center
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LANGUAGE
English