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Functional protein dynamics on enzyme catalysis from QM/MM simulations

When: 15:00, June 14, 2017
Where: 410 Meeting Room, Chemical Building

Enzymes are remarkable catalysts that can accelerate the reaction rates as much as 20 orders of magnitude. For example, orotidine 5‘-monophosphate decarboxylase (OMPDC) catalyzes the exchange of CO2 for a proton at the C6 position to form uridine 5'-monophosphate (UMP) with a rate increase of 1017 relative to the uncatalyzed reaction. In this talk, I will present analysis of the effect of protein dynamic fluctuations from combined quantum mechanical and molecular mechanical simulations of two proteins. It was found that specific dynamic motions of the proteins are intimately coupled to the function and catalytic mechanism of the catalyzed reactions, by directly affect activation barrier and by controlling the access of water in the active site. In one case, even small changes in the position of the substrate OMP could increase the barrier height by 5 to 10 kcal/mol due to hydrogen bonding interactions. In the LOV domain, a photoreceptor protein, distance mutations significant alter a gating mechanism for water access in the active site and its dark-state recover rate. Analyses of molecular dynamics trajectories help reveal the interplay of protein conformational dynamics and access of water in the active center of the proteins.

Speaker biography:

Prof. Jiali Gao

Address: Department of Chemistry, University of Minnesota,207 Pleasant Street, SE,Minneapolis, MN 55455, and

Professional Background

  • 2012 1000-Global Talent Professor of Theoretical Chemistry, Theoretical Chemistry Institute, Jilin University, Changchun, China.
  • 2010 Lee I. Smith Professor of Chemistry, University of Minnesota
  • 2006 Changjiang Professorship Award, Education Ministry, PR China and Xiamen University
  • 2000 - present Professor of Chemistry, and Fellow of the Minnesota Supercomputing Institute, University of Minnesota.

Research Interests:

Development and application of theoretical and computational methods in chemistry; Computer simulations of liquids, solutions, and biopolymers using empirical and combined quantum mechanical and classical potentials; Ab initio molecular dynamics; Algorithms for simulation of condensed phase systems using massively parallel computers; Understanding of the medium effect on chemical reactions in ambient and supercritical solutions, in heterogeneous catalytic materials, and in enzymes, and of photochemical processes in solutions and in proteins.

Awards and Honors

  • - 1000-Global Talent Professorship, 2013, Ministry of Organization, P.R. China
  • - IBM Faculty Fellowship Award, 2010, IBM
  • - Albert Hofmann Centennial Prize, 2006, The Organic Chemistry Institute, the University of Zurich
  • - Changjiang Professorship Award, Education Ministry, PR China, 2006.
  • - The #1 Most-Accessed Article of 2005 in the Journal of Chemical Theory and Computation, American Chemical Society Publications (JCTC, 2005, 1, 2.)
  • - Dirac Medal, 2000, The World Association for Theoretically Oriented Chemists.
  • - Hot Paper, The Scientist, Vol. 8, No. 21, October 31, 1994.
  • - Graduate Student Advisory Board, Purdue University (1985-1986)
  • - P.R.C.-U.S.A.-Chemical Graduate Program (CGP) Fellowship (1982-1983). This program was sponsored by Professor William von E. Doering and the Education Ministry, PRC. 40 students from China were admitted to study in the US in 1982.
  • - Recipient of Beijing University Mathematics Award (1981). Professional Membership
  • - American Chemical Society (1983-2001; 2007, 2009-2012, 2014-).
  • - Member-at-large, Western New York Section of the American Chemical Society (1993-1995).
  • - American Association for the Advancement of Science (1993-2001).