Cytochrome COxidase (CeO) is an important enzyme involved in the electron transfer pathway in cellular respiration. CeO activates molecular oxygen to prevent the release of potentially toxic oxygen intermediates and at the same time, uses the free energy from oxygen reduction to pump protons across the membrane in a stoichiometric fashion, creating the proton concentration gradient required for ATP synthesis. Compromise of CeO activity is implicated in serious human health threats such as various neurodegenerative diseases, muscular dystrophies and colon cancer. Therefore, investigation of the functional mechanism of CeO at a molecular level not only has fundamental value but also contributes to understanding the molecular origin of these diseases and aiding the design of effective therapeutic strategies. In this project, we propose to use quantum mechanical/molecular mechanical (QM/MM) techniques to study several actively debated mechanistic issues in CeO. Specifically, we have the following aims: (i). Use pKa calculations with QM/MM methods to help identify the most likely candidate(s) for the loading site of pumped protons among His334 and the propionates of the heme co-factor. (ii). Via analysis of the energetics (including barrier) of Glu286 isomerization and key proton transfer steps in wild type CeO, establish the identity of the """"""""gating element(s)"""""""" that prevent the backflow of protons. Define conformational and electrostatic contributions to gating. Together with experimental analyses, these investigations at the atomic level will firmly establish the molecular properties of CeO that are essential to its function. Continued development of an approximate density functional approach will find application in the study of a broad range of biomolecules, especially those involve vectorial chemistry.

Public Health Relevance

We propose to integrate combined quantum mechanical/molecular mechanical (QM/MM) and continuum electrostatic techniques to investigate several key mechanistic questions regarding proton pumping in Cytochrome c oxidase (CcO). Together with experimental studies in our collaborators' groups, these investigations at the atomic level will firmly establish the molecular properties of CcO that are essential to its function, which ultimately can contribute to understanding the molecular origin of human diseases that implicate CcO malfunction.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM084028-02
Application #
7944150
Study Section
Macromolecular Structure and Function D Study Section (MSFD)
Program Officer
Anderson, Vernon
Project Start
2009-09-30
Project End
2012-08-31
Budget Start
2010-09-01
Budget End
2012-08-31
Support Year
2
Fiscal Year
2010
Total Cost
$274,778
Indirect Cost
Name
University of Wisconsin Madison
Department
Chemistry
Type
Schools of Arts and Sciences
DUNS #
161202122
City
Madison
State
WI
Country
United States
Zip Code
53715
Goyal, Puja; Yang, Shuo; Cui, Qiang (2015) Microscopic basis for kinetic gating in Cytochrome c oxidase: insights from QM/MM analysis. Chem Sci 6:826-841
Goyal, Puja; Qian, Hu-Jun; Irle, Stephan et al. (2014) Molecular simulation of water and hydration effects in different environments: challenges and developments for DFTB based models. J Phys Chem B 118:11007-27
Gaus, Michael; Lu, Xiya; Elstner, Marcus et al. (2014) Parameterization of DFTB3/3OB for Sulfur and Phosphorus for Chemical and Biological Applications. J Chem Theory Comput 10:1518-1537
Yoo, Jejoong; Jackson, Meyer B; Cui, Qiang (2013) A comparison of coarse-grained and continuum models for membrane bending in lipid bilayer fusion pores. Biophys J 104:841-52
Goyal, Puja; Lu, Jianxun; Yang, Shuo et al. (2013) Changing hydration level in an internal cavity modulates the proton affinity of a key glutamate in cytochrome c oxidase. Proc Natl Acad Sci U S A 110:18886-91
Yoo, Jejoong; Cui, Qiang (2013) Three-dimensional stress field around a membrane protein: atomistic and coarse-grained simulation analysis of gramicidin A. Biophys J 104:117-27
Yoo, Jejoong; Cui, Qiang (2013) Membrane-mediated protein-protein interactions and connection to elastic models: a coarse-grained simulation analysis of gramicidin A association. Biophys J 104:128-38
Fu, Ye; Jia, Guifang; Pang, Xueqin et al. (2013) FTO-mediated formation of N6-hydroxymethyladenosine and N6-formyladenosine in mammalian RNA. Nat Commun 4:1798
Daily, Michael D; Yu, Haibo; Phillips Jr, George N et al. (2013) Allosteric activation transitions in enzymes and biomolecular motors: insights from atomistic and coarse-grained simulations. Top Curr Chem 337:139-64
Hou, Guanhua; Cui, Qiang (2013) Stabilization of different types of transition states in a single enzyme active site: QM/MM analysis of enzymes in the alkaline phosphatase superfamily. J Am Chem Soc 135:10457-69

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