Previous work in this program project has identified motions that are involved in the catalytic function of enzymes. The hypothesis for our work in this renewal application is that by using theoretical and computational methods we can identify the structural elements that create dynamics related to catalysis on all timescales, and through these means we may create protein dynamics design paradigms for both rate enhancement, and enzyme inhibition. In order to complete this research program we will work on 5 distinct areas that are: 1) we will identify conformational movements necessary on all timescales for reaction. Just as we have followed trajectories and identified protein dynamics that form promoting vibrations and are part of the reaction coordinate, we will extend these calculations to the timescale of enzyme turnover. 2) We will identify structural elements in specific enzyme systems (lactate dehydrogenase and purine nucleoside phosphorylase) that create the specific dynamics. 3) We will identify allosteric binding sites and determine the effect of binding on protein dynamics. 4) We will identify how dynamics is involved in transition state inhibitor binding. 5) we will propose a redesign of "heavy" PNP that corrects dynamic defects we have previously identified and restores normal catalytic function. The overall thrust to all of the work in this program project has been the identification of dynamics as a central feature in enzyme function from the selection of a catalytically competent conformational substate to rapid promoting vibrations. We now proceed to the next step in this program - identification of dynamics as a design element in enzyme function. We propose to begin the process of developing this concept as a protein engineering tool.

Public Health Relevance

Enzymes perform the chemistry of life. They do so with far greater efficiency and specificity than any non-biological catalyst. One of the great challenges of our day is finding the design principles of enzymes so that we may create synthetic biological catalysts. The work described in this project will advance this goal.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Program Projects (P01)
Project #
2P01GM068036-11
Application #
8722196
Study Section
Special Emphasis Panel (ZRG1-VH-F (40))
Project Start
Project End
Budget Start
2014-08-15
Budget End
2015-04-30
Support Year
11
Fiscal Year
2014
Total Cost
$399,513
Indirect Cost
$16,750
Name
Albert Einstein College of Medicine
Department
Type
DUNS #
110521739
City
Bronx
State
NY
Country
United States
Zip Code
10461
Einarsdóttir, Olöf; McDonald, William; Funatogawa, Chie et al. (2015) The pathway of O?to the active site in heme-copper oxidases. Biochim Biophys Acta 1847:109-18
Reddish, Michael J; Peng, Huo-Lei; Deng, Hua et al. (2014) Direct evidence of catalytic heterogeneity in lactate dehydrogenase by temperature jump infrared spectroscopy. J Phys Chem B 118:10854-62
Kise, Drew P; Magana, Donny; Reddish, Michael J et al. (2014) Submillisecond mixing in a continuous-flow, microfluidic mixer utilizing mid-infrared hyperspectral imaging detection. Lab Chip 14:584-91
Wang, Zhen; Singh, Priyanka; Czekster, Clarissa M et al. (2014) Protein mass-modulated effects in the catalytic mechanism of dihydrofolate reductase: beyond promoting vibrations. J Am Chem Soc 136:8333-41
Peng, Huo-Lei; Deng, Hua; Dyer, R Brian et al. (2014) Energy landscape of the Michaelis complex of lactate dehydrogenase: relationship to catalytic mechanism. Biochemistry 53:1849-57
Masterson, Jean E; Schwartz, Steven D (2014) The enzymatic reaction catalyzed by lactate dehydrogenase exhibits one dominant reaction path. Chem Phys 442:132-136
Li, Guifeng; Magana, Donny; Dyer, R Brian (2014) Anisotropic energy flow and allosteric ligand binding in albumin. Nat Commun 5:3100
Schramm, Vern L (2013) Transition States, analogues, and drug development. ACS Chem Biol 8:71-81
Masterson, Jean E; Schwartz, Steven D (2013) Changes in protein architecture and subpicosecond protein dynamics impact the reaction catalyzed by lactate dehydrogenase. J Phys Chem A 117:7107-13
Motley, Matthew W; Schramm, Vern L; Schwartz, Steven D (2013) Conformational freedom in tight binding enzymatic transition-state analogues. J Phys Chem B 117:9591-7

Showing the most recent 10 out of 62 publications