We propose to bring our Enzyme Dynamics Program into an uncharted area of inquiry with this renewal: bridging the gap from observation to design. Progress made thus far, developing powerful new approaches and a deep knowledge of the dynamical nature of enzymes, has set the stage for a fundamentally new approach to enzyme and inhibitor design based on dynamics. The overall objective of the research is the development of rational design principles based on dynamics for both 'allosteric'effectors and inhibitors for naturally occurring enzymes and rationally designed synthetic enzymes. The key to achieving this goal is to understand protein architectural design features that yield specific, functionally important dynamics. We bring together a skilled research group of diverse backgrounds all aimed at understanding enzyme function. This group has proven its ability to work closely in collaborative research over a decade. Importantly, we bring to bear unique, advanced, and effective experimental and theoretical approaches sensitive to the characteristics of protein structure and the dynamics this structure engenders on multiple time scales, from fs to ms or longer. This Program consists of four Projects with, collectively, two overall Aims: (1) To determine, via integrated application of experiment and theory, the elements of protein structure that create specific dynamics that are part of enzymatic catalysis on all relevant timescales. We will study how protein dynamics, particularly focused on the energy landscape of the Michaelis complex and motion of the promoting vibrations, is coupled to allostery and how this concept can be expanded to fully elucidate allosteric regulation of proteins. This presents a potential paradigm shift for protein and enzyme regulation via new drug action. In addition, a deeper understanding of transition state passage leaves us with the view that transition state inhibitors often do not function by """"""""locking in"""""""" a specific structure, but rather by preserving dynamics at the transition state. We will investigate this new principle of strong inhibitor bindin via dynamic preservation as a paradigm for enzyme function and inhibition. (2) To use the understanding of how important functional dynamics are coded into the protein structure gained in (1) as a means to manipulate them in order to modify protein function. This objective comprises several parts. One is to design active site inhibitors against the dynamical nature of the enzyme. Another is to design small molecules to modify the dynamical nature through an 'allosteric'action which will either down or up-regulate activity and/or binding of substrate. The third is to develop methods to design rate controlling dynamics on a variety of timescales into engineered enzymes.

Public Health Relevance

Our studies are aimed at determining the elements of protein structure that create specific dynamics important for catalytic mechanism. We will understand design features that either up or down regulate enzymatic activity. This Program Project is perhaps the most advanced in the world to develop our understanding of dynamics in enzyme interactions. The goal of this research is to lay a foundation for the development and rational design of 'allosteric'effectors or active site inhibitors based on dynamics.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Program Projects (P01)
Project #
2P01GM068036-11
Application #
8668387
Study Section
Special Emphasis Panel (ZRG1-VH-F (40))
Program Officer
Wehrle, Janna P
Project Start
2004-05-01
Project End
2019-04-30
Budget Start
2014-08-15
Budget End
2015-04-30
Support Year
11
Fiscal Year
2014
Total Cost
$1,880,381
Indirect Cost
$410,137
Name
Albert Einstein College of Medicine
Department
Biochemistry
Type
Schools of Medicine
DUNS #
110521739
City
Bronx
State
NY
Country
United States
Zip Code
10461
Pan, Xiaoliang; Schwartz, Steven D (2016) Conformational Heterogeneity in the Michaelis Complex of Lactate Dehydrogenase: An Analysis of Vibrational Spectroscopy Using Markov and Hidden Markov Models. J Phys Chem B 120:6612-20
Dzierlenga, Michael W; Schwartz, Steven D (2016) Targeting a Rate-Promoting Vibration with an Allosteric Mediator in Lactate Dehydrogenase. J Phys Chem Lett 7:2591-6
Antoniou, Dimitri; Schwartz, Steven D (2016) Phase Space Bottlenecks in Enzymatic Reactions. J Phys Chem B 120:433-9
Wang, Zhen; Antoniou, Dimitri; Schwartz, Steven D et al. (2016) Hydride Transfer in DHFR by Transition Path Sampling, Kinetic Isotope Effects, and Heavy Enzyme Studies. Biochemistry 55:157-66
Dzierlenga, M W; Varga, M J; Schwartz, S D (2016) Path Sampling Methods for Enzymatic Quantum Particle Transfer Reactions. Methods Enzymol 578:21-43
Zoi, Ioanna; Suarez, Javier; Antoniou, Dimitri et al. (2016) Modulating Enzyme Catalysis through Mutations Designed to Alter Rapid Protein Dynamics. J Am Chem Soc 138:3403-9
Reddish, Michael J; Vaughn, Morgan B; Fu, Rong et al. (2016) Ligand-Dependent Conformational Dynamics of Dihydrofolate Reductase. Biochemistry 55:1485-93
Varga, Matthew J; Schwartz, Steven D (2016) Enzymatic Kinetic Isotope Effects from First-Principles Path Sampling Calculations. J Chem Theory Comput 12:2047-54
Pan, Xiaoliang; Schwartz, Steven D (2015) Free energy surface of the Michaelis complex of lactate dehydrogenase: a network analysis of microsecond simulations. J Phys Chem B 119:5430-6
Dzierlenga, Michael W; Antoniou, Dimitri; Schwartz, Steven D (2015) Another Look at the Mechanisms of Hydride Transfer Enzymes with Quantum and Classical Transition Path Sampling. J Phys Chem Lett 6:1177-81

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