# Studies on Enzyme Activation and Novel Modes of Inhibition. Administrative Supplement for Equipment

> **NIH NIH R35** · STATE UNIVERSITY OF NEW YORK AT BUFFALO · 2020 · $67,036

## Abstract

Progress in studies of enzyme mechanisms has slowed in recent years, in part because investigators have failed
to clearly define all of the important questions that must be addressed in order to move towards final conclusions
about these reaction mechanisms. Many of the studies described in this grant are designed to leverage the
potential for creative work directed towards answering the following question: "How do enzymes achieve their
specificity in transition state (TS) binding?" This potential has been harnessed in studies in Buffalo on the
mechanism of action of triosephosphate isomerase (TIM), orotidine 5'-monophosphate decarboxylase (OMPDC)
and glycerol 3-phosphate dehydrogenase (GPDH). These enzymes undergo dianion-driven conformational
changes from loose, unliganded, open enzymes to stiff, structured, catalytically active closed forms, which act
as “switches” that turn on the expression of tight transition state binding interactions. Four key question are
addressed in this grant, with the goals of generalizing earlier conclusions from TIM, OMPDC, and GPDH to other
enzymes, and of initiating new studies to develop novel inhibitors of TIM and OMPDC from pathogenic
organisms. Key Question 1: What other protein catalysts utilize binding interactions of their nonreacting substrate
fragments to drive enzyme-activating conformational changes? These experiments will probe whether the
binding energy from the adenosine ring of the substrate for adenylate kinase, or from the NAD cofactor of the
substrate for alcohol dehydrogenase, which drive conformational changes during catalysis by these enzymes,
act as a switch to turn on tight transition state binding interactions. Key Question 2: What interactions between
the catalytic and activation sites of TIM, OMPDC and GPDH enable utilization of the intrinsic substrate binding
energy for catalysis? Experiments are described to characterize a network of amino acid side chains involved in
catalysis by GPDH, and to characterize the mechanism for activation of OMPDC by the utilization of binding
interactions between the enzyme and the ribosyl hydroxyl groups of the substrates orotidine 5'-monophosphate
(OMP) and 5-F-OMP. Key Question 3: Are computational methods sufficiently advanced to model the effect of
site-directed mutations on the activation barrier for reactions catalyzed by TIM and GPDH? Calculations will be
carried out in collaboration with Professor Lynn Kamerlin in Uppsala, Sweden, to determine whether existing
EVB methods are able to model the results of extensive mutagenesis studies on these enzymes, with the goal
of expanding the limits of these computational methods. Key Question 4: What is the potential for selection of
peptides that show species specificity for inhibition of TIM and OMPDC from pathogenic organisms?
Experiments are proposed, in collaboration with Professor Hiroaki Suga at the University of Tokyo, Japan, to
identify species-specific inhibitors for TIM from Trypanosoma brucei a...

## Key facts

- **NIH application ID:** 10132086
- **Project number:** 3R35GM134881-01S1
- **Recipient organization:** STATE UNIVERSITY OF NEW YORK AT BUFFALO
- **Principal Investigator:** John P Richard
- **Activity code:** R35 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $67,036
- **Award type:** 3
- **Project period:** 2020-01-01 → 2024-12-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10132086

## Citation

> US National Institutes of Health, RePORTER application 10132086, Studies on Enzyme Activation and Novel Modes of Inhibition. Administrative Supplement for Equipment (3R35GM134881-01S1). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10132086. Licensed CC0.

---

*[NIH grants dataset](/datasets/nih-grants) · CC0 1.0*