The association of proteins with small molecules and macromolecular targets is at the center of biology. The rates and mechanisms of these association processes constitute fundamental knowledge and provide avenues for designing therapeutic agents. The long-term objective of this project is the determination, via theory, simulation, and experiment, of association rates and mechanisms. Efforts in the pervious funding periods have culminated in the transient-complex theory. This computational methodology has allowed the protein association problem to be solved when the molecules are relatively rigid so that overall translational/rotational diffusion is rate- determining. The preset project aims to tackle the much more challenging problem where conformational change is closely coupled with the association process, and essential for biological function.
The specific aims are the determination of rate constants and mechanisms for three classes of systems: (1) protein-protein association;(2) protein-ligand binding;and (3) Site-specific protein-DNA binding. The research will integrate computation and experiment, and bring methodological breakthroughs that enable realistic modeling of conformational changes in calculating protein association rate constants. The knowledge gained will shed light on important protein functions and offer broad mechanistic insights.

Public Health Relevance

The proposed research will advance fundamental understanding on the association of proteins with small molecules and macromolecular targets. This understanding may provide new avenues for designing more selective drugs.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM058187-15
Application #
8604395
Study Section
Macromolecular Structure and Function D Study Section (MSFD)
Program Officer
Wehrle, Janna P
Project Start
1998-08-01
Project End
2016-12-31
Budget Start
2014-01-01
Budget End
2014-12-31
Support Year
15
Fiscal Year
2014
Total Cost
$245,766
Indirect Cost
$75,949
Name
Florida State University
Department
Physics
Type
Schools of Arts and Sciences
DUNS #
790877419
City
Tallahassee
State
FL
Country
United States
Zip Code
32306
Zhou, Huan-Xiang; Pang, Xiaodong (2018) Electrostatic Interactions in Protein Structure, Folding, Binding, and Condensation. Chem Rev 118:1691-1741
Hicks, Alan; Zhou, Huan-Xiang (2018) Temperature-induced collapse of a disordered peptide observed by three sampling methods in molecular dynamics simulations. J Chem Phys 149:072313
Zhou, Huan-Xiang; Wollmuth, Lonnie P (2017) Advancing NMDA Receptor Physiology by Integrating Multiple Approaches. Trends Neurosci 40:129-137
Zhou, Huan-Xiang (2017) Gating Motions and Stationary Gating Properties of Ionotropic Glutamate Receptors: Computation Meets Electrophysiology. Acc Chem Res 50:814-822
Pang, Xiaodong; Zhou, Huan-Xiang (2017) Rate Constants and Mechanisms of Protein-Ligand Binding. Annu Rev Biophys 46:105-130
Ou, Li; Matthews, Megan; Pang, Xiaodong et al. (2017) The dock-and-coalesce mechanism for the association of a WASP disordered region with the Cdc42 GTPase. FEBS J 284:3381-3391
Guo, Cong; Zhou, Huan-Xiang (2016) Unidirectional allostery in the regulatory subunit RI? facilitates efficient deactivation of protein kinase A. Proc Natl Acad Sci U S A 113:E6776-E6785
Lensink, Marc F; Velankar, Sameer; Kryshtafovych, Andriy et al. (2016) Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment. Proteins 84 Suppl 1:323-48
Dai, Jian; Zhou, Huan-Xiang (2016) Semiclosed Conformations of the Ligand-Binding Domains of NMDA Receptors during Stationary Gating. Biophys J 111:1418-1428
Guo, Jingjing; Zhou, Huan-Xiang (2016) Protein Allostery and Conformational Dynamics. Chem Rev 116:6503-15

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