Model studies in water to characterize the kinetic reactivity, equilibrium stability and mechanisms for the formation and reaction of putative carbanion, carbocation and quinone methide intermediates of enzyme-catalyzed reactions are proposed. The following problems will be studied: (1) Oxygen and thiol ester enolates have been proposed as intermediates for a wide range of enzymatic reactions. However, there is scant direct evidence for their formation in water or at enzyme active sites. We will generate the putative enolate intermediates of seven enzymatic reactions by general base-catalyzed deprotonation of the respective carbonyl precursors, and determine the relative thermodynamic stabilities of these enolates. (2) The relative advantage for metal ion catalysis of deprotonation at carbon is not known. This will be determined by a comparison of metal-ion activation of proton transfer with the activation provided by a CH3 + group. (3) A series of alpha-substituted enol phosphotriesters will be synthesized and their potential use as precursors to alpha-substituted enols and ketenes, or as suicide enzyme inhibitors will be explored. (4) The enzymatic source of methylglyoxal in mammalian tissues will be purified and characterized in order to determine whether it is identical with triosephosphate isomerase. This work may resolve the enigma of the metabolic role of glyoxalase I and II. (5) It is not known if the reaction catalyzed by isopentenyl pyrophosphate isomerase proceeds through a tertiary carbocation reaction intermediate or if it proceeds through a highly polar, carbocation-like, transition state of a concerted reaction mechanism. We will determine whether a model nonenzymatic 1,3-allylic isomerization reaction follows a stepwise or a concerted mechanism. (6) The rate law for the reactions of a simple quinone methide with nucleophilic reagents will be characterized in order to determine if these reactions are subject to general acid and/or general base catalysis. The results of this work will be compared with results of studies on nucleophilic addition reactions at the carbonyl group. (7) Experiments will be performed to determine whether there is a simple relationship between carbocation lifetime and the occurrence of general acid-base catalysis of oxocarbenium ion formation and breakdown. Advances in the understanding of enzyme mechanisms that result from model studies of nonenzymatic reactions may prove critical for drug design (enzyme inhibitors), to the understanding of metabolic pathways and diseases, and to the resolution of other health-related problems.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
7R01GM039754-07
Application #
3296925
Study Section
Physical Biochemistry Study Section (PB)
Project Start
1988-05-01
Project End
1997-04-30
Budget Start
1993-08-01
Budget End
1994-04-30
Support Year
7
Fiscal Year
1993
Total Cost
Indirect Cost
Name
State University of New York at Buffalo
Department
Type
Schools of Arts and Sciences
DUNS #
038633251
City
Buffalo
State
NY
Country
United States
Zip Code
14260
Zhai, Xiang; Reinhardt, Christopher J; Malabanan, M Merced et al. (2018) Enzyme Architecture: Amino Acid Side-Chains That Function To Optimize the Basicity of the Active Site Glutamate of Triosephosphate Isomerase. J Am Chem Soc 140:8277-8286
Reyes, Archie C; Amyes, Tina L; Richard, John P (2018) Primary Deuterium Kinetic Isotope Effects: A Probe for the Origin of the Rate Acceleration for Hydride Transfer Catalyzed by Glycerol-3-Phosphate Dehydrogenase. Biochemistry 57:4338-4348
Richard, John P; Amyes, Tina L; Reyes, Archie C (2018) Orotidine 5'-Monophosphate Decarboxylase: Probing the Limits of the Possible for Enzyme Catalysis. Acc Chem Res 51:960-969
Kulkarni, Yashraj S; Liao, Qinghua; Byléhn, Fabian et al. (2018) Role of Ligand-Driven Conformational Changes in Enzyme Catalysis: Modeling the Reactivity of the Catalytic Cage of Triosephosphate Isomerase. J Am Chem Soc 140:3854-3857
Amyes, T L; Malabanan, M M; Zhai, X et al. (2017) Enzyme activation through the utilization of intrinsic dianion binding energy. Protein Eng Des Sel 30:157-165
Amyes, Tina L; Richard, John P (2017) Substituent Effects on Carbon Acidity in Aqueous Solution and at Enzyme Active Sites. Synlett 28:2407-2421
Amyes, Tina L; Richard, John P (2017) Primary Deuterium Kinetic Isotope Effects From Product Yields: Rationale, Implementation, and Interpretation. Methods Enzymol 596:163-177
Reyes, Archie C; Amyes, Tina L; Richard, John P (2017) Enzyme Architecture: Erection of Active Orotidine 5'-Monophosphate Decarboxylase by Substrate-Induced Conformational Changes. J Am Chem Soc 139:16048-16051
Reyes, Archie C; Amyes, Tina L; Richard, John P (2017) A reevaluation of the origin of the rate acceleration for enzyme-catalyzed hydride transfer. Org Biomol Chem 15:8856-8866
Reyes, Archie C; Amyes, Tina L; Richard, John P (2016) Structure-Reactivity Effects on Intrinsic Primary Kinetic Isotope Effects for Hydride Transfer Catalyzed by Glycerol-3-phosphate Dehydrogenase. J Am Chem Soc 138:14526-14529

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