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Cristobal J, Hegazy R, Richard JP. Glycerol 3-Phosphate Dehydrogenase: Role of the Protein Conformational Change in Activation of a Readily Reversible Enzyme-Catalyzed Hydride Transfer Reaction. Biochemistry 2024; 63:1016-1025. [PMID: 38546289 PMCID: PMC11025551 DOI: 10.1021/acs.biochem.3c00702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 02/26/2024] [Accepted: 03/13/2024] [Indexed: 04/17/2024]
Abstract
Kinetic parameters are reported for glycerol 3-phosphate dehydrogenase (GPDH)-catalyzed hydride transfer from the whole substrate glycerol 3-phosphate (G3P) or truncated substrate ethylene glycol (EtG) to NAD, and for activation of the hydride transfer reaction of EtG by phosphite dianion. These kinetic parameters were combined with parameters for enzyme-catalyzed hydride transfer in the microscopic reverse direction to give the reaction equilibrium constants Keq. Hydride transfer from G3P is favored in comparison to EtG because the carbonyl product of the former reaction is stabilized by hyperconjugative electron donation from the -CH2R keto substituent. The kinetic data show that the phosphite dianion provides the same 7.6 ± 0.1 kcal/mol stabilization of the transition states for enzyme-catalyzed reactions in the forward [reduction of NAD by EtG] and reverse [oxidation of NADH by glycolaldehyde] directions. The experimental evidence that supports a role for phosphite dianion in stabilizing the active closed form of the GPDH (EC) relative to the ca. 6 kcal/mol more unstable open form (EO) is summarized.
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Affiliation(s)
- Judith
R. Cristobal
- Department
of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
| | - Rania Hegazy
- Department
of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
| | - John P. Richard
- Department
of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
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2
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Hegazy R, Richard JP. Triosephosphate Isomerase: The Crippling Effect of the P168A/I172A Substitution at the Heart of an Enzyme Active Site. Biochemistry 2023; 62:2916-2927. [PMID: 37768194 PMCID: PMC10586322 DOI: 10.1021/acs.biochem.3c00414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 09/01/2023] [Indexed: 09/29/2023]
Abstract
The P168 and I172 side chains sit at the heart of the active site of triosephosphate isomerase (TIM) and play important roles in the catalysis of the isomerization reaction. The phosphodianion of substrate glyceraldehyde 3-phosphate (GAP) drives a conformational change at the TIM that creates a steric interaction with the P168 side chain that is relieved by the movement of P168 that carries the basic E167 side chain into a clamp that consists of the hydrophobic I172 and L232 side chains. The P168A/I172A substitution at TIM from Trypanosoma brucei brucei (TbbTIM) causes a large 120,000-fold decrease in kcat for isomerization of GAP that eliminates most of the difference in the reactivity of TIM compared to the small amine base quinuclidinone for deprotonation of catalyst-bound GAP. The I172A substitution causes a > 2-unit decrease in the pKa of the E167 carboxylic acid in a complex to the intermediate analog PGA, but the P168A substitution at the I172A variant has no further effect on this pKa. The P168A/I172A substitutions cause a 5-fold decrease in Km for the isomerization of GAP from a 0.9 kcal/mol stabilization of the substrate Michaelis complexes. The results show that the P168 and I172 side chains play a dual role in destabilizing the ground-state Michaelis complex to GAP and in promoting stabilization of the transition state for substrate isomerization. This is consistent with an important role for these side chains in an induced fit reaction mechanism [Richard, J. P. (2022) Enabling Role of Ligand-Driven Conformational Changes in Enzyme Evolution. Biochemistry 61, 1533-1542].
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Affiliation(s)
- Rania Hegazy
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United
States
| | - John P. Richard
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United
States
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3
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Cristobal J, Nagorski RW, Richard JP. Utilization of Cofactor Binding Energy for Enzyme Catalysis: Formate Dehydrogenase-Catalyzed Reactions of the Whole NAD Cofactor and Cofactor Pieces. Biochemistry 2023; 62:2314-2324. [PMID: 37463347 PMCID: PMC10399567 DOI: 10.1021/acs.biochem.3c00290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/29/2023] [Indexed: 07/20/2023]
Abstract
The pressure to optimize enzymatic rate accelerations has driven the evolution of the induced-fit mechanism for enzyme catalysts where the binding interactions of nonreacting phosphodianion or adenosyl substrate pieces drive enzyme conformational changes to form protein substrate cages that are activated for catalysis. We report the results of experiments to test the hypothesis that utilization of the binding energy of the adenosine 5'-diphosphate ribose (ADP-ribose) fragment of the NAD cofactor to drive a protein conformational change activates Candida boidinii formate dehydrogenase (CbFDH) for catalysis of hydride transfer from formate to NAD+. The ADP-ribose fragment provides a >14 kcal/mol stabilization of the transition state for CbFDH-catalyzed hydride transfer from formate to NAD+. This is larger than the ca. 6 kcal/mol stabilization of the ground-state Michaelis complex between CbFDH and NAD+ (KNAD = 0.032 mM). The ADP, AMP, and ribose 5'-phosphate fragments of NAD+ activate CbFDH for catalysis of hydride transfer from formate to nicotinamide riboside (NR). At a 1.0 M standard state, these activators stabilize the hydride transfer transition states by ≈5.5 (ADP), 5.5 (AMP), and 4.4 (ribose 5'-phosphate) kcal/mol. We propose that activation by these cofactor fragments is partly or entirely due to the ion-pair interaction between the guanidino side chain cation of R174 and the activator phosphate anion. This substitutes for the interaction between the α-adenosyl pyrophosphate anion of the whole NAD+ cofactor that holds CbFDH in the catalytically active closed conformation.
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Affiliation(s)
- Judith
R. Cristobal
- Department
of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United
States
| | - Richard W. Nagorski
- Department
of Chemistry, Illinois State University, Normal, Illinois 61790-4160, United
States
| | - John P. Richard
- Department
of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United
States
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4
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Hegazy R, Cordara G, Wierenga RK, Richard JP. The Role of Asn11 in Catalysis by Triosephosphate Isomerase. Biochemistry 2023. [PMID: 37162263 DOI: 10.1021/acs.biochem.3c00133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Four catalytic amino acids at triosephosphate isomerase (TIM) are highly conserved: N11, K13, H95, and E167. Asparagine 11 is the last of these to be characterized in mutagenesis studies. The ND2 side chain atom of N11 is hydrogen bonded to the O-1 hydroxyl of enzyme-bound dihydroxyacetone phosphate (DHAP), and it sits in an extended chain of hydrogen-bonded side chains that includes T75' from the second subunit. The N11A variants of wild-type TIM from Trypanosoma brucei brucei (TbbTIM) and Leishmania mexicana (LmTIM) undergo dissociation from the dimer to monomer under our assay conditions. Values of Kas = 8 × 103 and 1 × 106 M-1, respectively, were determined for the conversion of monomeric N11A TbbTIM and LmTIM into their homodimers. The N11A substitution at the variant of LmTIM previously stabilized by the E65Q substitution gives the N11A/E65Q variant that is stable to dissociation under our assay conditions. The X-ray crystal structure of N11A/E65Q LmTIM shows an active site that is essentially superimposable on that for wild-type TbbTIM, which also has a glutamine at position 65. A comparison of the kinetic parameters for E65Q LmTIM and N11A/E65Q LmTIM-catalyzed reactions of (R)-glyceraldehyde 3-phosphate (GAP) and (DHAP) shows that the N11A substitution results in a (13-14)-fold decrease in kcat/Km for substrate isomerization and a similar decrease in kcat for DHAP but only a 2-fold decrease in kcat for GAP.
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Affiliation(s)
- Rania Hegazy
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
| | - Gabriele Cordara
- Biocenter Oulu, University of Oulu, P.O. Box 5000, FIN-90014 Oulu, Finland
| | - Rik K Wierenga
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, P.O. Box 5400, FIN-90014 Oulu, Finland
| | - John P Richard
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
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Cristobal JR, Richard JP. Kinetics and mechanism for enzyme-catalyzed reactions of substrate pieces. Methods Enzymol 2023; 685:95-126. [PMID: 37245916 PMCID: PMC10251411 DOI: 10.1016/bs.mie.2023.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The most important difference between enzyme and small molecule catalysts is that only enzymes utilize the large intrinsic binding energies of nonreacting portions of the substrate in stabilization of the transition state for the catalyzed reaction. A general protocol is described to determine the intrinsic phosphodianion binding energy for enzymatic catalysis of reactions of phosphate monoester substrates, and the intrinsic phosphite dianion binding energy in activation of enzymes for catalysis of phosphodianion truncated substrates, from the kinetic parameters for enzyme-catalyzed reactions of whole and truncated substrates. The enzyme-catalyzed reactions so-far documented that utilize dianion binding interactions for enzyme activation; and, their phosphodianion truncated substrates are summarized. A model for the utilization of dianion binding interactions for enzyme activation is described. The methods for the determination of the kinetic parameters for enzyme-catalyzed reactions of whole and truncated substrates, from initial velocity data, are described and illustrated by graphical plots of kinetic data. The results of studies on the effect of site-directed amino acid substitutions at orotidine 5'-monophosphate decarboxylase, triosephosphate isomerase, and glycerol-3-phosphate dehydrogenase provide strong support for the proposal that these enzymes utilize binding interactions with the substrate phosphodianion to hold the protein catalysts in reactive closed conformations.
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Affiliation(s)
- Judith R Cristobal
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, NY, United States
| | - John P Richard
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, NY, United States.
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Richard JP. The Role of the Substrate Phosphodianion in Catalysis by Orotidine 5'-Monophosphate Decarboxylase. Biochemistry 2023; 62:969-970. [PMID: 36791154 PMCID: PMC10052792 DOI: 10.1021/acs.biochem.3c00031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Affiliation(s)
- John P Richard
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
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7
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Richard JP, Moran GR. Preface. Methods Enzymol 2023; 685:xvii-xx. [PMID: 37245917 DOI: 10.1016/s0076-6879(23)00190-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
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Fernandez P, Richard JP. Adenylate Kinase-Catalyzed Reactions of AMP in Pieces: Specificity for Catalysis at the Nucleoside Activator and Dianion Catalytic Sites. Biochemistry 2022; 61:2766-2775. [PMID: 36413937 PMCID: PMC9731266 DOI: 10.1021/acs.biochem.2c00531] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 10/31/2022] [Indexed: 11/23/2022]
Abstract
The pressure to optimize the enzymatic rate acceleration for adenylate kinase (AK)-catalyzed phosphoryl transfer has led to the evolution of an induced-fit mechanism, where the binding energy from interactions between the protein and substrate adenosyl group is utilized to drive a protein conformational change that activates the enzyme for catalysis. The adenine group of adenosine contributes 11.8 kcal mol-1 to the total ≥14.7 kcal mol-1 adenosine stabilization of the transition state for AK-catalyzed phosphoryl transfer to AMP. The relative third-order rate constants for activation of adenylate kinase, by the C-5 truncated adenosine 1-(β-d-erythrofuranosyl)adenine (EA), for catalysis of phosphoryl transfer from ATP to phosphite dianion (HP, kcat/KHPKAct = 260 M-2 s-1), fluorophosphate (47 M-2 s-1), and phosphate (9.6 M-2 s-1), show that substitution of -F for -H and of -OH for -H at HP results, respectively, in decreases in the reactivity of AK for catalysis of phosphoryl transfer due to polar and steric effects of the -F and -OH substituents. The addition of a 5'-CH2OH to the EA activator results in a 3.0 kcal mol-1 destabilization of the transition state for AK-activated phosphoryl transfer to HP due to a steric effect. This is smaller than the 8.3 kcal mol-1 steric effect of the 5'-CH2OH substituent at OMP on HP-activated OMPDC-catalyzed decarboxylation of 1-(β-d-erythrofuranosyl)orotate. The 2'-OH ribosyl substituent shows significant interactions with the transition states for AK-catalyzed phosphoryl transfer from ATP to AMP and for adenosine-activated AK-catalyzed phosphoryl transfer from ATP to HP.
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Affiliation(s)
- Patrick
L. Fernandez
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, New York14260−3000, United States
| | - John P. Richard
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, New York14260−3000, United States
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9
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Abstract
Many enzymes that show a large specificity in binding the enzymatic transition state with a higher affinity than the substrate utilize substrate binding energy to drive protein conformational changes to form caged substrate complexes. These protein cages provide strong stabilization of enzymatic transition states. Using part of the substrate binding energy to drive the protein conformational change avoids a similar strong stabilization of the Michaelis complex and irreversible ligand binding. A seminal step in the development of modern enzyme catalysts was the evolution of enzymes that couple substrate binding to a conformational change. These include enzymes that function in glycolysis (triosephosphate isomerase), the biosynthesis of lipids (glycerol phosphate dehydrogenase), the hexose monophosphate shunt (6-phosphogluconate dehydrogenase), and the mevalonate pathway (isopentenyl diphosphate isomerase), catalyze the final step in the biosynthesis of pyrimidine nucleotides (orotidine monophosphate decarboxylase), and regulate the cellular levels of adenine nucleotides (adenylate kinase). The evolution of enzymes that undergo ligand-driven conformational changes to form active protein-substrate cages is proposed to proceed by selection of variants, in which the selected side chain substitutions destabilize a second protein conformer that shows compensating enhanced binding interactions with the substrate. The advantages inherent to enzymes that incorporate a conformational change into the catalytic cycle provide a strong driving force for the evolution of flexible protein folds such as the TIM barrel. The appearance of these folds represented a watershed event in enzyme evolution that enabled the rapid propagation of enzyme activities within enzyme superfamilies.
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Affiliation(s)
- John P Richard
- Department of Chemistry, University at Buffalo, the State University of New York, Buffalo, New York 14260-3000, United States
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10
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Cristobal JR, Richard JP. Glycerol-3-Phosphate Dehydrogenase: The K120 and K204 Side Chains Define an Oxyanion Hole at the Enzyme Active Site. Biochemistry 2022; 61:856-867. [PMID: 35502876 PMCID: PMC9119304 DOI: 10.1021/acs.biochem.2c00053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The cationic K120 and K204 side chains lie close to the C-2 carbonyl group of substrate dihydroxyacetone phosphate (DHAP) at the active site of glycerol-3-phosphate dehydrogenase (GPDH), and the K120 side chain is also positioned to form a hydrogen bond to the C-1 hydroxyl of DHAP. The kinetic parameters for unactivated and phosphite dianion-activated GPDH-catalyzed reduction of glycolaldehyde and acetaldehyde (AcA) show that the transition state for the former reaction is stabilized by ca 5 kcal/mole by interactions of the C-1 hydroxyl group with the protein catalyst. The K120A and K204A substitutions at wild-type GPDH result in similar decreases in kcat, but Km is only affected by the K120A substitution. These results are consistent with 3 kcal/mol stabilizing interactions between the K120 or K204 side chains and a negative charge at the C-2 oxygen at the transition state for hydride transfer from NADH to DHAP. This stabilization resembles that observed at oxyanion holes for other enzymes. There is no detectable rescue of the K204A variant by ethylammonium cation (EtNH3+), compared with the efficient rescue of the K120A variant. This is consistent with a difference in the accessibility of the variant enzyme active sites to exogenous EtNH3+. The K120A/K204A substitutions cause a (6 × 106)-fold increase in the promiscuity of wild-type hlGPDH for catalysis of the reduction of AcA compared to DHAP. This may reflect conservation of the active site for an ancestral alcohol dehydrogenase, whose relative activity for catalysis of reduction of AcA increases with substitutions that reduce the activity for reduction of the specific substrate DHAP.
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Affiliation(s)
- Judith R Cristobal
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
| | - John P Richard
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
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11
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Pereira MS, de Araújo SS, Nagem RAP, Richard JP, Brandão TAS. The role of remote flavin adenine dinucleotide pieces in the oxidative decarboxylation catalyzed by salicylate hydroxylase. Bioorg Chem 2022; 119:105561. [PMID: 34965488 PMCID: PMC8824312 DOI: 10.1016/j.bioorg.2021.105561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 11/19/2021] [Accepted: 12/11/2021] [Indexed: 02/03/2023]
Abstract
Salicylate hydroxylase (NahG) has a single redox site in which FAD is reduced by NADH, the O2 is activated by the reduced flavin, and salicylate undergoes an oxidative decarboxylation by a C(4a)-hydroperoxyflavin intermediate to give catechol. We report experimental results that show the contribution of individual pieces of the FAD cofactor to the observed enzymatic activity for turnover of the whole cofactor. A comparison of the kinetic parameters and products for the NahG-catalyzed reactions of FMN and riboflavin cofactor fragments reveal that the adenosine monophosphate (AMP) and ribitol phosphate pieces of FAD act to anchor the flavin to the enzyme and to direct the partitioning of the C(4a)-hydroperoxyflavin reaction intermediate towards hydroxylation of salicylate. The addition of AMP or ribitol phosphate pieces to solutions of the truncated flavins results in a partial restoration of the enzymatic activity lost upon truncation of FAD, and the pieces direct the reaction of the C(4a)-hydroperoxyflavin intermediate towards hydroxylation of salicylate.
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Affiliation(s)
- Mozart S. Pereira
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | - Simara S. de Araújo
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | - Ronaldo A. P. Nagem
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | - John P. Richard
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000,CORRESPONDING AUTHOR: ;
| | - Tiago A. S. Brandão
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil.,CORRESPONDING AUTHOR: ;
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Cristobal JR, Brandão TAS, Reyes AC, Richard JP. Protein-Ribofuranosyl Interactions Activate Orotidine 5'-Monophosphate Decarboxylase for Catalysis. Biochemistry 2021; 60:3362-3373. [PMID: 34726391 DOI: 10.1021/acs.biochem.1c00589] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The role of a global, substrate-driven, enzyme conformational change in enabling the extraordinarily large rate acceleration for orotidine 5'-monophosphate decarboxylase (OMPDC)-catalyzed decarboxylation of orotidine 5'-monophosphate (OMP) is examined in experiments that focus on the interactions between OMPDC and the ribosyl hydroxyl groups of OMP. The D37 and T100' side chains of OMPDC interact, respectively, with the C-3' and C-2' hydroxyl groups of enzyme-bound OMP. D37G and T100'A substitutions result in 1.4 kcal/mol increases in the activation barrier ΔG⧧ for catalysis of decarboxylation of the phosphodianion-truncated substrate 1-(β-d-erythrofuranosyl)orotic acid (EO) but result in larger 2.1-2.9 kcal/mol increases in ΔG⧧ for decarboxylation of OMP and for phosphite dianion-activated decarboxylation of EO. This shows that these substitutions reduce transition-state stabilization by the Q215, Y217, and R235 side chains at the dianion binding site. The D37G and T100'A substitutions result in <1.0 kcal/mol increases in ΔG⧧ for activation of OMPDC-catalyzed decarboxylation of the phosphoribofuranosyl-truncated substrate FO by phosphite dianions. Experiments to probe the effect of D37 and T100' substitutions on the kinetic parameters for d-glycerol 3-phosphate and d-erythritol 4-phosphate activators of OMPDC-catalyzed decarboxylation of FO show that ΔG⧧ for sugar phosphate-activated reactions is increased by ca. 2.5 kcal/mol for each -OH interaction eliminated by D37G or T100'A substitutions. We conclude that the interactions between the D37 and T100' side chains and ribosyl or ribosyl-like hydroxyl groups are utilized to activate OMPDC for catalysis of decarboxylation of OMP, EO, and FO.
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Affiliation(s)
- Judith R Cristobal
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
| | - Tiago A S Brandão
- Department of Chemistry, ICEx, Federal University of Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | - Archie C Reyes
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
| | - John P Richard
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
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Fernandez PL, Richard JP. Adenylate Kinase-Catalyzed Reaction of AMP in Pieces: Enzyme Activation for Phosphoryl Transfer to Phosphite Dianion. Biochemistry 2021; 60:2672-2676. [PMID: 34435776 DOI: 10.1021/acs.biochem.1c00535] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The binding of adenosine 5'-triphosphate (ATP) and adenosine 5'-monophosphate (AMP) to adenylate kinase (AdK) drives closure of lids over the substrate adenosyl groups. We test the hypothesis that this conformational change activates AdK for catalysis. The rate constants for Homo sapiens adenylate kinase 1 (HsAdK1)-catalyzed phosphoryl group transfer to AMP, kcat/Km = 7.0 × 106 M-1 s-1, and phosphite dianion, (kHPi)obs ≤1 × 10-4 M-1 s-1, show that the binding energy of the adenosyl group effects a ≥7.0 × 1010-fold rate acceleration of phosphoryl transfer from ATP. The third-order rate constant of kcat/KHPiKEA = 260 M-2 s-1 for 1-(β-d-erythrofuranosyl)adenine (EA)-activated phosphoryl transfer to phosphite dianion was determined, and the isohypophosphate reaction product characterized by 31P NMR. The results demonstrate the following: (i) a ≥14.7 kcal/mol stabilization of the transition state for phosphoryl transfer by the adenosyl group of AMP and a ≥2.6 × 106-fold rate acceleration from the EA-driven conformational change and (ii) the recovery of ≥8.7 kcal/mol of this transition state stabilization for EA-activated phosphoryl transfer from ATP to phosphite.
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Affiliation(s)
- Patrick L Fernandez
- Department of Chemistry, University at Buffalo, Buffalo, New York 14260-3000, United States
| | - John P Richard
- Department of Chemistry, University at Buffalo, Buffalo, New York 14260-3000, United States
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14
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Abstract
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Linear free energy relationships (LFERs) for substituent effects on reactions that
proceed through similar transition states provide insight into transition state
structures. A classical approach to the analysis of LFERs showed that differences in the
slopes of Brønsted correlations for addition of substituted alkyl alcohols to
ring-substituted 1-phenylethyl carbocations and to the β-galactopyranosyl
carbocation intermediate of reactions catalyzed by β-galactosidase provide
evidence that the enzyme catalyst modifies the curvature of the energy surface at the
saddle point for the transition state for nucleophile addition. We have worked to
generalize the use of LFERs in the determination of enzyme mechanisms. The defining
property of enzyme catalysts is their specificity for binding the transition state with
a much higher affinity than the substrate. Triosephosphate isomerase (TIM), orotidine
5′-monophosphate decarboxylase (OMPDC), and glycerol 3-phosphate dehydrogenase
(GPDH) show effective catalysis of reactions of phosphorylated substrates and strong
phosphite dianion activation of reactions of phosphodianion truncated substrates, with
rate constants kcat/Km
(M–1 s–1) and
kcat/KdKHPi
(M–2 s–1), respectively. Good linear logarithmic
correlations, with a slope of 1.1, between these kinetic parameters determined for
reactions catalyzed by five or more variant forms of each catalyst are observed, where
the protein substitutions are mainly at side chains which function to stabilize the cage
complex between the enzyme and substrate. This shows that the enzyme-catalyzed reactions
of a whole substrate and substrate pieces proceed through transition states of similar
structures. It provides support for the proposal that the dianion binding energy of
whole phosphodianion substrates and of phosphite dianion is used to drive the conversion
of these protein catalysts from flexible and entropically rich ground states to stiff
and catalytically active Michaelis complexes that show the same activity toward
catalysis of the reactions of whole and phosphodianion truncated substrates. There is a
good linear correlation, with a slope of 0.73, between values of the dissociation
constants log Ki for release of the transition state analog
phosphoglycolate (PGA) trianion and log
kcat/Km for isomerization of
GAP for wild-type and variants of TIM. This correlation shows that the substituted amino
acid side chains act to stabilize the complex between TIM and the PGA trianion and that
ca. 70% of this stabilization is observed at the transition state for
substrate deprotonation. The correlation provides evidence that these side chains
function to enhance the basicity of the E165 side chain of TIM, which deprotonates the
bound carbon acid substrate. There is a good linear correlation, with a slope of 0.74,
between the values of ΔG‡ and
ΔG° determined by electron valence bond (EVB) calculations
to model deprotonation of dihydroxyacetone phosphate (DHAP) in water and when bound to
wild-type and variant forms of TIM to form the enediolate reaction intermediate. This
correlation provides evidence that the stabilizing interactions of the transition state
for TIM-catalyzed deprotonation of DHAP are optimized by placement of amino acid side
chains in positions that provide for the maximum stabilization of the charged reaction
intermediate, relative to the neutral substrate.
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Affiliation(s)
- John P. Richard
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
| | - Judith R. Cristobal
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
| | - Tina L. Amyes
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
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15
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Zhou S, Nguyen BT, Richard JP, Kluger R, Gao J. Correction to "Origin of Free Energy Barriers of Decarboxylation and the Reverse Process of CO 2 Capture in Dimethylformamide and in Water". J Am Chem Soc 2021; 143:6018. [PMID: 33822616 DOI: 10.1021/jacs.1c03001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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16
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Fernandez PL, Nagorski RW, Cristobal JR, Amyes TL, Richard JP. Phosphodianion Activation of Enzymes for Catalysis of Central Metabolic Reactions. J Am Chem Soc 2021; 143:2694-2698. [PMID: 33560827 PMCID: PMC7919737 DOI: 10.1021/jacs.0c13423] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
![]()
The activation barriers ΔG⧧ for
kcat/Km for the reactions of
whole substrates catalyzed by 6-phosphogluconate dehydrogenase, glucose 6-phosphate
dehydrogenase, and glucose 6-phosphate isomerase are reduced by 11–13 kcal/mol by
interactions between the protein and the substrate phosphodianion. Between 4 and 6
kcal/mol of this dianion binding energy is expressed at the transition state for
phosphite dianion activation of the respective enzyme-catalyzed reactions of truncated
substrates d-xylonate or d-xylose. These and earlier results from
studies on β-phosphoglucomutase, triosephosphate isomerase, and glycerol
3-phosphate dehydrogenase define a cluster of six enzymes that catalyze reactions in
glycolysis or of glycolytic intermediates, and which utilize substrate dianion binding
energy for enzyme activation. Dianion-driven conformational changes, which convert
flexible open proteins to tight protein cages for the phosphorylated substrate, have
been thoroughly documented for five of these six enzymes. The clustering of metabolic
enzymes which couple phosphodianion-driven conformational changes to enzyme activation
suggests that this catalytic motif has been widely propagated in the proteome.
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Affiliation(s)
- Patrick L Fernandez
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
| | - Richard W Nagorski
- Department of Chemistry, Illinois State University, Normal, Illinois 61790-4160, United States
| | - Judith R Cristobal
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
| | - Tina L Amyes
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
| | - John P Richard
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
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17
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Zhou S, Nguyen BT, Richard JP, Kluger R, Gao J. Origin of Free Energy Barriers of Decarboxylation and the Reverse Process of CO 2 Capture in Dimethylformamide and in Water. J Am Chem Soc 2021; 143:137-141. [PMID: 33375792 DOI: 10.1021/jacs.0c12414] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In aqueous solution, biological decarboxylation reactions proceed irreversibly to completion, whereas the reverse carboxylation processes are typically powered by the hydrolysis of ATP. The exchange of the carboxylate of ring-substituted arylacetates with isotope-labeled CO2 in polar aprotic solvents reported recently suggests a dramatic change in the partition of reaction pathways. Yet, there is little experimental data pertinent to the kinetic barriers for protonation and thermodynamic data on CO2 capture by the carbanions of decarboxylation reactions. Employing a combined quantum mechanical and molecular mechanical simulation approach, we investigated the decarboxylation reactions of a series of organic carboxylate compounds in aqueous and in dimethylformamide solutions, revealing that the reverse carboxylation barriers in solution are fully induced by solvent effects. A linear Bell-Evans-Polanyi relationship was found between the rates of decarboxylation and the Gibbs energies of reaction, indicating diminishing recombination barriers in DMF. In contrast, protonation of the carbanions by the DMF solvent has large free energy barriers, rendering the competing exchange of isotope-labeled CO2 reversible in DMF. The finding of an intricate interplay of carbanion stability and solute-solvent interaction in decarboxylation and carboxylation could be useful to designing novel materials for CO2 capture.
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Affiliation(s)
- Shaoyuan Zhou
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 581055, China.,Institute of Theoretical Chemistry, Jilin University, Changchun 100231, China
| | - Bach T Nguyen
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - John P Richard
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 47907, United States
| | - Ronald Kluger
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Jiali Gao
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 581055, China.,Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States
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18
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He R, Cristobal JR, Gong NJ, Richard JP. Hydride Transfer Catalyzed by Glycerol Phosphate Dehydrogenase: Recruitment of an Acidic Amino Acid Side Chain to Rescue a Damaged Enzyme. Biochemistry 2020; 59:4856-4863. [PMID: 33305938 PMCID: PMC7784668 DOI: 10.1021/acs.biochem.0c00801] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
![]()
K120 of glycerol 3-phosphate dehydrogenase (GPDH) lies close to the carbonyl group of
the bound dihydroxyacetone phosphate (DHAP) dianion. pH rate (pH 4.6–9.0)
profiles are reported for kcat and
(kcat/Km)dianion
for wild type and K120A GPDH-catalyzed reduction of DHAP by NADH, and for
(kcat/KdKam)
for activation of the variant-catalyzed reduction by
CH3CH2NH3+, where
Kam and Kd are apparent
dissociation constants for CH3CH2NH3+ and
DHAP, respectively. These profiles provide evidence that the K120 side chain cation,
which is stabilized by an ion-pairing interaction with the D260 side chain, remains
protonated between pH 4.6 and 9.0. The profiles for wild type and K120A variant GPDH
show downward breaks at a similar pH value (7.6) that are attributed to protonation of
the K204 side chain, which also lies close to the substrate carbonyl oxygen. The pH
profiles for
(kcat/Km)dianion
and
(kcat/KdKam)
for the K120A variant show that the monoprotonated form of the variant is activated for
catalysis by CH3CH2NH3+ but has no
detectable activity, compared to the diprotonated variant, for unactivated reduction of
DHAP. The pH profile for kcat shows that the monoprotonated
K120A variant is active toward reduction of enzyme-bound DHAP, because of activation by
a ligand-driven conformational change. Upward breaks in the pH profiles for
kcat and
(kcat/Km)dianion
for K120A GPDH are attributed to protonation of D260. These breaks are consistent with
the functional replacement of K120 by D260, and a plasticity in the catalytic roles of
the active site side chains.
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Affiliation(s)
- Rui He
- Department of Chemistry, University at Buffalo, The State University of New York at Buffalo, Buffalo, New York 14260-3000, United States
| | - Judith R Cristobal
- Department of Chemistry, University at Buffalo, The State University of New York at Buffalo, Buffalo, New York 14260-3000, United States
| | - Naiji Jabin Gong
- Department of Chemistry, University at Buffalo, The State University of New York at Buffalo, Buffalo, New York 14260-3000, United States
| | - John P Richard
- Department of Chemistry, University at Buffalo, The State University of New York at Buffalo, Buffalo, New York 14260-3000, United States
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19
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Mhashal AR, Romero-Rivera A, Mydy LS, Cristobal JR, Gulick AM, Richard JP, Kamerlin SCL. Modeling the Role of a Flexible Loop and Active Site Side Chains in Hydride Transfer Catalyzed by Glycerol-3-phosphate Dehydrogenase. ACS Catal 2020; 10:11253-11267. [PMID: 33042609 PMCID: PMC7536716 DOI: 10.1021/acscatal.0c02757] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 08/31/2020] [Indexed: 11/30/2022]
Abstract
![]()
Glycerol-3-phosphate
dehydrogenase is a biomedically important
enzyme that plays a crucial role in lipid biosynthesis. It is activated
by a ligand-gated conformational change that is necessary for the
enzyme to reach a catalytically competent conformation capable of
efficient transition-state stabilization. While the human form (hlGPDH) has been the subject of extensive structural and
biochemical studies, corresponding computational studies to support
and extend experimental observations have been lacking. We perform
here detailed empirical valence bond and Hamiltonian replica exchange
molecular dynamics simulations of wild-type hlGPDH
and its variants, as well as providing a crystal structure of the
binary hlGPDH·NAD R269A variant where the enzyme
is present in the open conformation. We estimated the activation free
energies for the hydride transfer reaction in wild-type and substituted hlGPDH and investigated the effect of mutations on catalysis
from a detailed structural study. In particular, the K120A and R269A
variants increase both the volume and solvent exposure of the active
site, with concomitant loss of catalytic activity. In addition, the
R269 side chain interacts with both the Q295 side chain on the catalytic
loop, and the substrate phosphodianion. Our structural data and simulations
illustrate the critical role of this side chain in facilitating the
closure of hlGPDH into a catalytically competent
conformation, through modulating the flexibility of a key catalytic
loop (292-LNGQKL-297). This, in turn, rationalizes a tremendous 41,000
fold decrease experimentally in the turnover number, kcat, upon truncating this residue, as loop closure is
essential for both correct positioning of key catalytic residues in
the active site, as well as sequestering the active site from the
solvent. Taken together, our data highlight the importance of this
ligand-gated conformational change in catalysis, a feature that can
be exploited both for protein engineering and for the design of allosteric
inhibitors targeting this biomedically important enzyme.
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Affiliation(s)
- Anil R. Mhashal
- Department of Chemistry—BMC, Uppsala University, Box 576, Uppsala SE-751 23, Sweden
| | - Adrian Romero-Rivera
- Department of Chemistry—BMC, Uppsala University, Box 576, Uppsala SE-751 23, Sweden
| | - Lisa S. Mydy
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York 14203-1121, United States
| | - Judith R. Cristobal
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
| | - Andrew M. Gulick
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York 14203-1121, United States
| | - John P. Richard
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
| | - Shina C. L. Kamerlin
- Department of Chemistry—BMC, Uppsala University, Box 576, Uppsala SE-751 23, Sweden
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20
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Abstract
![]()
The D37 and T100′
side chains of orotidine 5′-monophosphate
decarboxylase (OMPDC) interact with the C-3′ and C-2′
ribosyl hydroxyl groups, respectively, of the bound substrate. We
compare the intra-subunit interactions of D37 with the inter-subunit
interactions of T100′ by determining the effects of the D37G,
D37A, T100′G, and T100′A substitutions on the following:
(a) kcat and kcat/Km values for the OMPDC-catalyzed decarboxylations
of OMP and 5-fluoroorotidine 5′-monophosphate (FOMP) and (b)
the stability of dimeric OMPDC relative to the monomer. The D37G and
T100′A substitutions resulted in 2 kcal mol–1 increases in ΔG† for kcat/Km for the decarboxylation
of OMP, while the D37A and T100′G substitutions resulted in
larger 4 and 5 kcal mol–1 increases, respectively,
in ΔG†. The D37G and T100′A
substitutions both resulted in smaller 2 kcal mol–1 decreases in ΔG† for the
decarboxylation of FOMP compared to that of OMP. These results show
that the D37G and T100′A substitutions affect the barrier to
the chemical decarboxylation step while the D37A and T100′G
substitutions also affect the barrier to a slow, ligand-driven enzyme
conformational change. Substrate binding induces the movement of an
α-helix (G′98–S′106) toward the substrate
C-2′ ribosyl hydroxy bound at the main subunit. The T100′G
substitution destabilizes the enzyme dimer by 3.5 kcal mol–1 compared to the monomer, which is consistent with the known destabilization
of α-helices by the internal Gly side chains [Serrano, L., et
al. (1992) Nature, 356, 453–455].
We propose that the T100′G substitution weakens the α-helical
contacts at the dimer interface, which results in a decrease in the
dimer stability and an increase in the barrier to the ligand-driven
conformational change.
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Affiliation(s)
- Tiago A S Brandão
- Department of Chemistry, ICEx, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil
| | - John P Richard
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260-3000, United States
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21
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Cristobal JR, Reyes AC, Richard JP. The Organization of Active Site Side Chains of Glycerol-3-phosphate Dehydrogenase Promotes Efficient Enzyme Catalysis and Rescue of Variant Enzymes. Biochemistry 2020; 59:1582-1591. [PMID: 32250105 PMCID: PMC7207223 DOI: 10.1021/acs.biochem.0c00175] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
A comparison of the
values of kcat/Km for reduction of dihydroxyacetone phosphate
(DHAP) by NADH catalyzed by wild type and K120A/R269A variant glycerol-3-phosphate
dehydrogenase from human liver (hlGPDH) shows that
the transition state for enzyme-catalyzed hydride transfer is stabilized
by 12.0 kcal/mol by interactions with the cationic K120 and R269 side
chains. The transition state for the K120A/R269A variant-catalyzed
reduction of DHAP is stabilized by 1.0 and 3.8 kcal/mol for reactions
in the presence of 1.0 M EtNH3+ and guanidinium
cation (Gua+), respectively, and by 7.5 kcal/mol for reactions
in the presence of a mixture of each cation at 1.0 M, so that the
transition state stabilization by the ternary E·EtNH3+·Gua+ complex is 2.8 kcal/mol greater
than the sum of stabilization by the respective binary complexes.
This shows that there is cooperativity between the paired activators
in transition state stabilization. The effective molarities (EMs)
of ∼50 M determined for the K120A and R269A side chains are
≪106 M, the EM for entropically controlled reactions.
The unusually efficient rescue of the activity of hlGPDH-catalyzed reactions by the HPi/Gua+ pair
and by the Gua+/EtNH3+ activator
pair is due to stabilizing interactions between the protein and the
activator pieces that organize the K120 and R269 side chains at the
active site. This “preorganization” of side chains promotes
effective catalysis by hlGPDH and many other enzymes.
The role of the highly conserved network of side chains, which include
Q295, R269, N270, N205, T264, K204, D260, and K120, in catalysis is
discussed.
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Affiliation(s)
- Judith R Cristobal
- Department of Chemistry, University at Buffalo, State University of New York, Buffalo, New York 14260-3000, United States
| | - Archie C Reyes
- Department of Chemistry, University at Buffalo, State University of New York, Buffalo, New York 14260-3000, United States
| | - John P Richard
- Department of Chemistry, University at Buffalo, State University of New York, Buffalo, New York 14260-3000, United States
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22
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Kulkarni YS, Amyes TL, Richard JP, Kamerlin SCL. Uncovering the Role of Key Active-Site Side Chains in Catalysis: An Extended Brønsted Relationship for Substrate Deprotonation Catalyzed by Wild-Type and Variants of Triosephosphate Isomerase. J Am Chem Soc 2019; 141:16139-16150. [PMID: 31508957 PMCID: PMC7032883 DOI: 10.1021/jacs.9b08713] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
We report results of detailed empirical valence bond simulations that model the effect of several amino acid substitutions on the thermodynamic (ΔG°) and kinetic activation (ΔG⧧) barriers to deprotonation of dihydroxyacetone phosphate (DHAP) and d-glyceraldehyde 3-phosphate (GAP) bound to wild-type triosephosphate isomerase (TIM), as well as to the K12G, E97A, E97D, E97Q, K12G/E97A, I170A, L230A, I170A/L230A, and P166A variants of this enzyme. The EVB simulations model the observed effect of the P166A mutation on protein structure. The E97A, E97Q, and E97D mutations of the conserved E97 side chain result in ≤1.0 kcal mol-1 decreases in the activation barrier for substrate deprotonation. The agreement between experimental and computed activation barriers is within ±1 kcal mol-1, with a strong linear correlation between ΔG⧧ and ΔG° for all 11 variants, with slopes β = 0.73 (R2 = 0.994) and β = 0.74 (R2 = 0.995) for the deprotonation of DHAP and GAP, respectively. These Brønsted-type correlations show that the amino acid side chains examined in this study function to reduce the standard-state Gibbs free energy of reaction for deprotonation of the weak α-carbonyl carbon acid substrate to form the enediolate phosphate reaction intermediate. TIM utilizes the cationic side chain of K12 to provide direct electrostatic stabilization of the enolate oxyanion, and the nonpolar side chains of P166, I170, and L230 are utilized for the construction of an active-site cavity that provides optimal stabilization of the enediolate phosphate intermediate relative to the carbon acid substrate.
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Affiliation(s)
- Yashraj S Kulkarni
- Science for Life Laboratory, Department of Chemistry - BMC , Uppsala University, BMC , Box 576, S-751 23 Uppsala , Sweden
| | - Tina L Amyes
- Department of Chemistry , University at Buffalo, SUNY , Buffalo , New York 14260-3000 , United States
| | - John P Richard
- Department of Chemistry , University at Buffalo, SUNY , Buffalo , New York 14260-3000 , United States
| | - Shina C L Kamerlin
- Science for Life Laboratory, Department of Chemistry - BMC , Uppsala University, BMC , Box 576, S-751 23 Uppsala , Sweden
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23
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Goryanova B, Amyes TL, Richard JP. Role of the Carboxylate in Enzyme-Catalyzed Decarboxylation of Orotidine 5'-Monophosphate: Transition State Stabilization Dominates Over Ground State Destabilization. J Am Chem Soc 2019; 141:13468-13478. [PMID: 31365243 PMCID: PMC6735427 DOI: 10.1021/jacs.9b04823] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
![]()
Kinetic
parameters kex (s–1)
and kex/Kd (M–1 s–1) are reported
for exchange
for deuterium in D2O of the C-6 hydrogen of 5-fluororotidine
5′-monophosphate (FUMP) catalyzed by the Q215A,
Y217F, and Q215A/Y217F variants of yeast orotidine 5′-monophosphate
decarboxylase (ScOMPDC) at pD 8.1, and by the Q215A
variant at pD 7.1–9.3. The pD rate profiles for wildtype ScOMPDC and the Q215A variant are identical, except for
a 2.5 log unit downward displacement in the profile for the Q215A
variant. The Q215A, Y217F and Q215A/Y217F substitutions cause 1.3–2.0
kcal/mol larger increases in the activation barrier for wildtype ScOMPDC-catalyzed deuterium exchange compared with decarboxylation,
because of the stronger apparent side chain interaction with the transition
state for the deuterium exchange reaction. The stabilization of the
transition state for the OMPDC-catalyzed deuterium exchange reaction
of FUMP is ca. 19 kcal/mol smaller than the transition
state for decarboxylation of OMP, and ca. 8 kcal/mol
smaller than for OMPDC-catalyzed deprotonation of FUMP to form the vinyl carbanion intermediate common to OMPDC-catalyzed
reactions OMP/FOMP and UMP/FUMP. We propose
that ScOMPDC shows similar stabilizing interactions
with the common portions of decarboxylation and deprotonation transition
states that lead to formation of this vinyl carbanion intermediate,
and that there is a large ca. (19–8) = 11 kcal/mol stabilization
of the former transition state from interactions with the nascent
CO2 of product. The effects of Q215A and Y217F substitutions
on kcat/Km for decarboxylation of OMP are expressed mainly as
an increase in Km for the reactions catalyzed
by the variant enzymes, while the effects on kex/Kd for deuterium exchange are
expressed mainly as an increase in kex. This shows that the Q215 and Y217 side chains stabilize the Michaelis
complex to OMP for the decarboxylation reaction, compared
with the complex to FUMP for the deuterium exchange reaction.
These results provide strong support for the conclusion that interactions
which stabilize the transition state for ScOMPDC-catalyzed
decarboxylation at a nonpolar enzyme active site dominate over interactions
that destabilize the ground-state Michaelis complex.
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Affiliation(s)
- Bogdana Goryanova
- Department of Chemistry , University at Buffalo, SUNY , Buffalo , New York 14260-3000 , United States
| | - Tina L Amyes
- Department of Chemistry , University at Buffalo, SUNY , Buffalo , New York 14260-3000 , United States
| | - John P Richard
- Department of Chemistry , University at Buffalo, SUNY , Buffalo , New York 14260-3000 , United States
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24
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Abstract
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The enormous rate accelerations observed
for many enzyme catalysts
are due to strong stabilizing interactions between the protein and
reaction transition state. The defining property of these catalysts
is their specificity for binding the transition state with a much
higher affinity than substrate. Experimental results are presented
which show that the phosphodianion-binding energy of phosphate monoester
substrates is used to drive conversion of their protein catalysts
from flexible and entropically rich ground states to stiff and catalytically
active Michaelis complexes. These results are generalized to other
enzyme-catalyzed reactions. The existence of many enzymes in flexible,
entropically rich, and inactive ground states provides a mechanism
for utilization of ligand-binding energy to mold these catalysts into
stiff and active forms. This reduces the substrate-binding energy
expressed at the Michaelis complex, while enabling the full and specific
expression of large transition-state binding energies. Evidence is
presented that the complexity of enzyme conformational changes increases
with increases in the enzymatic rate acceleration. The requirement
that a large fraction of the total substrate-binding energy be utilized
to drive conformational changes of floppy enzymes is proposed to favor
the selection and evolution of protein folds with multiple flexible
unstructured loops, such as the TIM-barrel fold. The effect of protein
motions on the kinetic parameters for enzymes that undergo ligand-driven
conformational changes is considered. The results of computational
studies to model the complex ligand-driven conformational change in
catalysis by triosephosphate isomerase are presented.
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Affiliation(s)
- John P Richard
- Department of Chemistry , SUNY, University at Buffalo , Buffalo , New York 14260-3000 , United States
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25
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Mydy LS, Cristobal JR, Katigbak RD, Bauer P, Reyes AC, Kamerlin SCL, Richard JP, Gulick AM. Human Glycerol 3-Phosphate Dehydrogenase: X-ray Crystal Structures That Guide the Interpretation of Mutagenesis Studies. Biochemistry 2019; 58:1061-1073. [PMID: 30640445 DOI: 10.1021/acs.biochem.8b01103] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Human liver glycerol 3-phosphate dehydrogenase ( hlGPDH) catalyzes the reduction of dihydroxyacetone phosphate (DHAP) to form glycerol 3-phosphate, using the binding energy associated with the nonreacting phosphodianion of the substrate to properly orient the enzyme-substrate complex within the active site. Herein, we report the crystal structures for unliganded, binary E·NAD, and ternary E·NAD·DHAP complexes of wild type hlGPDH, illustrating a new position of DHAP, and probe the kinetics of multiple mutant enzymes with natural and truncated substrates. Mutation of Lys120, which is positioned to donate a proton to the carbonyl of DHAP, results in similar increases in the activation barrier to hlGPDH-catlyzed reduction of DHAP and to phosphite dianion-activated reduction of glycolaldehyde, illustrating that these transition states show similar interactions with the cationic K120 side chain. The K120A mutation results in a 5.3 kcal/mol transition state destabilization, and 3.0 kcal/mol of the lost transition state stabilization is rescued by 1.0 M ethylammonium cation. The 6.5 kcal/mol increase in the activation barrier observed for the D260G mutant hlGPDH-catalyzed reaction represents a 3.5 kcal/mol weakening of transition state stabilization by the K120A side chain and a 3.0 kcal/mol weakening of the interactions with other residues. The interactions, at the enzyme active site, between the K120 side chain and the Q295 and R269 side chains were likewise examined by double-mutant analyses. These results provide strong evidence that the enzyme rate acceleration is due mainly or exclusively to transition state stabilization by electrostatic interactions with polar amino acid side chains.
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Affiliation(s)
- Lisa S Mydy
- Department of Structural Biology , University at Buffalo, SUNY , Buffalo , New York 14203 , United States
| | - Judith R Cristobal
- Department of Chemistry , University at Buffalo, SUNY , Buffalo , New York 14260-3000 , United States
| | - Roberto D Katigbak
- Department of Chemistry , University at Buffalo, SUNY , Buffalo , New York 14260-3000 , United States
| | - Paul Bauer
- Science for Life Laboratory, Department of Cell and Molecular Biology , Uppsala University , BMC Box 596, S-751 24 Uppsala , Sweden
| | - Archie C Reyes
- Department of Chemistry , University at Buffalo, SUNY , Buffalo , New York 14260-3000 , United States
| | - Shina Caroline Lynn Kamerlin
- Science for Life Laboratory, Department of Cell and Molecular Biology , Uppsala University , BMC Box 596, S-751 24 Uppsala , Sweden
| | - John P Richard
- Department of Chemistry , University at Buffalo, SUNY , Buffalo , New York 14260-3000 , United States
| | - Andrew M Gulick
- Department of Structural Biology , University at Buffalo, SUNY , Buffalo , New York 14203 , United States
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26
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Reyes AC, Plache DC, Koudelka AP, Amyes TL, Gerlt JA, Richard JP. Enzyme Architecture: Breaking Down the Catalytic Cage that Activates Orotidine 5'-Monophosphate Decarboxylase for Catalysis. J Am Chem Soc 2018; 140:17580-17590. [PMID: 30475611 PMCID: PMC6317530 DOI: 10.1021/jacs.8b09609] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report the results of a study of the catalytic role of a network of four interacting amino acid side chains at yeast orotidine 5'-monophosphate decarboxylase ( ScOMPDC), by the stepwise replacement of all four side chains. The H-bond, which links the -CH2OH side chain of S154 from the pyrimidine umbrella loop of ScOMPDC to the amide side chain of Q215 in the phosphodianion gripper loop, creates a protein cage for the substrate OMP. The role of this interaction in optimizing transition state stabilization from the dianion gripper side chains Q215, Y217, and R235 was probed by determining the kinetic parameter kcat/ Km for 16 enzyme variants, which include all combinations of single, double, triple, and quadruple S154A, Q215A, Y217F, and R235A mutations. The effects of consecutive Q215A, Y217F, and R235A mutations on Δ G⧧ for wild-type enzyme-catalyzed decarboxylation sum to 11.6 kcal/mol, but to only 7.6 kcal/mol when starting from S154A mutant. This shows that the S154A mutation results in a (11.6-7.6) = 4.0 kcal/mol decrease in transition state stabilization from interactions with Q215, Y217, and R235. Mutant cycles show that ca. 2 kcal/mol of this 4 kcal/mol effect is from the direct interaction between the S154 and Q215 side chains and that ca. 2 kcal/mol is from a tightening in the stabilizing interactions of the Y217 and R235 side chains. The sum of the effects of individual A154S, A215Q, F217Y and A235R substitutions at the quadruple mutant of ScOMPDC to give the corresponding triple mutants, 5.6 kcal/mol, is much smaller than 16.0 kcal/mol, the sum of the effects of the related four substitutions in wild-type ScOMPDC to give the respective single mutants. The small effect of substitutions at the quadruple mutant is consistent with a large entropic cost to holding the flexible loops of ScOMPDC in the active closed conformation.
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Affiliation(s)
- Archie C Reyes
- Department of Chemistry , University at Buffalo, SUNY , Buffalo , New York 14260-3000 , United States
| | - David C Plache
- Department of Chemistry , University at Buffalo, SUNY , Buffalo , New York 14260-3000 , United States
| | - Astrid P Koudelka
- Department of Chemistry , University at Buffalo, SUNY , Buffalo , New York 14260-3000 , United States
| | - Tina L Amyes
- Department of Chemistry , University at Buffalo, SUNY , Buffalo , New York 14260-3000 , United States
| | - John A Gerlt
- Department of Chemistry and Biochemistry , University of Illinois , Urbana , Illinois 61801 , United States
| | - John P Richard
- Department of Chemistry , University at Buffalo, SUNY , Buffalo , New York 14260-3000 , United States
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Reyes AC, Amyes TL, Richard JP. Primary Deuterium Kinetic Isotope Effects: A Probe for the Origin of the Rate Acceleration for Hydride Transfer Catalyzed by Glycerol-3-Phosphate Dehydrogenase. Biochemistry 2018; 57:4338-4348. [PMID: 29927590 PMCID: PMC6091503 DOI: 10.1021/acs.biochem.8b00536] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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Large
primary deuterium kinetic isotope effects (1° DKIEs)
on enzyme-catalyzed hydride transfer may be observed when the transferred
hydride tunnels through the energy barrier. The following 1°
DKIEs on kcat/Km and relative reaction driving force are reported for wild-type and
mutant glycerol-3-phosphate dehydrogenase (GPDH)-catalyzed reactions
of NADL (L = H, D): wild-type GPDH, ΔΔG⧧ = 0 kcal/mol, 1° DKIE = 1.5;
N270A, 5.6 kcal/mol, 3.1; R269A, 9.1 kcal/mol, 2.8; R269A + 1.0 M
guanidine, 2.4 kcal/mol, 2.7; R269A/N270A, 11.5 kcal/mol, 2.4. Similar
1° DKIEs were observed on kcat. The
narrow range of 1° DKIEs (2.4–3.1) observed for a 9.1
kcal/mol change in reaction driving force provides strong evidence
that these are intrinsic 1° DKIEs on rate-determining hydride
transfer. Evidence is presented that the intrinsic DKIE on wild-type
GPDH-catalyzed reduction of DHAP lies in this range. A similar range
of 1° DKIEs (2.4–2.9) on (kcat/KGA, M–1 s–1) was reported for dianion-activated hydride transfer from NADL to
glycolaldehyde (GA) [Reyes, A. C.; Amyes, T. L.; Richard, J.
P. J. Am. Chem. Soc.2016, 138, 14526–14529].
These 1° DKIEs are much smaller than those observed for enzyme-catalyzed
hydrogen transfer that occurs mainly by quantum mechanical tunneling.
These results support the conclusion that the rate acceleration for
GPDH-catalyzed reactions is due to the stabilization of the transition
state for hydride transfer by interactions with the protein catalyst.
The small 1° DKIEs reported for mutant GPDH-catalyzed and for
wild-type dianion-activated reactions are inconsistent with a model
where the dianion binding energy is utilized in the stabilization
of a tunneling ready state.
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Affiliation(s)
- Archie C Reyes
- Department of Chemistry , University at Buffalo, SUNY , Buffalo , New York 14260-3000 , United States
| | - Tina L Amyes
- Department of Chemistry , University at Buffalo, SUNY , Buffalo , New York 14260-3000 , United States
| | - John P Richard
- Department of Chemistry , University at Buffalo, SUNY , Buffalo , New York 14260-3000 , United States
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Zhai X, Reinhardt CJ, Malabanan MM, Amyes TL, Richard JP. Enzyme Architecture: Amino Acid Side-Chains That Function To Optimize the Basicity of the Active Site Glutamate of Triosephosphate Isomerase. J Am Chem Soc 2018; 140:8277-8286. [PMID: 29862813 PMCID: PMC6037162 DOI: 10.1021/jacs.8b04367] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
![]()
We report pH rate profiles for kcat and Km for the
isomerization reaction
of glyceraldehyde 3-phosphate catalyzed by wildtype triosephosphate
isomerase (TIM) from three organisms and by ten mutants of TIM; and,
for Ki for inhibition of this reaction
by phosphoglycolate trianion (I3–). The pH profiles for Ki show
that the binding of I3– to TIM (E) to form EH·I3– is accompanied by
uptake of a proton by the carboxylate side-chain of E165, whose function
is to abstract a proton from substrate. The complexes for several
mutants exist mainly as E–·I3– at high pH, in which cases the pH profiles define the pKa for deprotonation of EH·I3–. The linear
free energy correlation, with slope of 0.73 (r2 = 0.96), between kcat/Km for TIM-catalyzed isomerization and the disassociation
constant of PGA trianion for TIM shows that EH·I3– and the
transition state are stabilized by similar interactions with the protein
catalyst. Values of pKa = 10–10.5
were estimated for deprotonation of EH·I3– for wildtype TIM.
This pKa decreases to as low as 6.3 for
the severely crippled Y208F mutant. There is a correlation between
the effect of several mutations on kcat/Km and on pKa for EH·I3–. The results support a model where the strong basicity of
E165 at the complex to the enediolate reaction intermediate is promoted
by side-chains from Y208 and S211, which serve to clamp loop 6 over
the substrate; I170, which assists in the creation of a hydrophobic
environment for E165; and P166, which functions in driving the carboxylate
side-chain of E165 toward enzyme-bound substrate.
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Affiliation(s)
- Xiang Zhai
- Department of Chemistry , University at Buffalo, SUNY , Buffalo , New York 14260-3000 United States
| | - Christopher J Reinhardt
- Department of Chemistry , University of Illinois at Urbana-Champaign , 600 S Mathews Avenue , Urbana , Illinois 61801 , United States
| | - M Merced Malabanan
- Department of Biochemistry , Vanderbilt University , 842 Robinson Research Building , Nashville , Tennessee 37205 , United States
| | - Tina L Amyes
- Department of Chemistry , University at Buffalo, SUNY , Buffalo , New York 14260-3000 United States
| | - John P Richard
- Department of Chemistry , University at Buffalo, SUNY , Buffalo , New York 14260-3000 United States
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Abstract
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The mystery associated with catalysis by what were once regarded
as protein black boxes, diminished with the X-ray crystallographic
determination of the three-dimensional structures of enzyme–substrate
complexes. The report that several high-resolution X-ray crystal structures
of orotidine 5′-monophosphate decarboxylase (OMPDC) failed
to provide a consensus mechanism for enzyme-catalyzed decarboxylation
of OMP to form uridine 5′-monophosphate, therefore, provoked
a flurry of controversy. This controversy was fueled by the enormous
1023-fold rate acceleration for this enzyme, which had
“jolted many biochemists’ assumptions about
the catalytic potential of enzymes.” Our studies on
the mechanism of action of OMPDC provide strong evidence that catalysis
by this enzyme is not fundamentally different from less proficient
catalysts, while highlighting important architectural elements that
enable a peak level of performance. Many enzymes undergo substrate-induced
protein conformational changes that trap their substrates in solvent
occluded protein cages, but the conformational change induced by ligand
binding to OMPDC is incredibly complex, as required to enable the
development of 22 kcal/mol of stabilizing binding interactions with
the phosphodianion and ribosyl substrate fragments of OMP. The binding
energy from these fragments is utilized to activate OMPDC for catalysis
of decarboxylation at the orotate fragment of OMP, through the creation
of a tight, catalytically active, protein cage from the floppy, open,
unliganded form of OMPDC. Such utilization of binding energy for ligand-driven
conformational changes provides a general mechanism to obtain specificity
in transition state binding. The rate enhancement that results from
the binding of carbon acid substrates to enzymes is partly due to
a reduction in the carbon acid pKa that
is associated with ligand binding. The binding of UMP to OMPDC results
in an unusually large >12 unit decrease in the pKa = 29 for abstraction of the C-6 substrate hydrogen,
due to stabilization of an enzyme-bound vinyl carbanion, which is
also an intermediate of OMPDC-catalyzed decarboxylation. The protein–ligand
interactions operate to stabilize the vinyl carbanion at the enzyme
active site compared to aqueous solution, rather than to stabilize
the transition state for the concerted electrophilic displacement
of CO2 by H+ that avoids formation of this reaction
intermediate. There is evidence that OMPDC induces strain into the
bound substrate. The interaction between the amide side chain of Gln-215
from the phosphodianion gripper loop and the hydroxymethylene side
chain of Ser-154 from the pyrimidine umbrella of ScOMPDC position the amide side chain to interact with the phosphodianion
of OMP. There are no direct stabilizing interactions between dianion
gripper protein side chains Gln-215, Tyr-217, and Arg-235 and the
pyrimidine ring at the decarboxylation transition state. Rather these
side chains function solely to hold OMPDC in the catalytically active
closed conformation. The hydrophobic side chains that line the active
site of OMPDC in the region of the departing CO2 product
may function to stabilize the decarboxylation transition state by
providing hydrophobic solvation of this product.
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Affiliation(s)
- John P. Richard
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
| | - Tina L. Amyes
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
| | - Archie C. Reyes
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
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30
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Kulkarni YS, Liao Q, Byléhn F, Amyes TL, Richard JP, Kamerlin SCL. Role of Ligand-Driven Conformational Changes in Enzyme Catalysis: Modeling the Reactivity of the Catalytic Cage of Triosephosphate Isomerase. J Am Chem Soc 2018. [PMID: 29516737 PMCID: PMC5867644 DOI: 10.1021/jacs.8b00251] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
![]()
We have previously performed empirical
valence bond calculations
of the kinetic activation barriers, ΔG‡calc, for the deprotonation of complexes
between TIM and the whole substrate glyceraldehyde-3-phosphate (GAP, Kulkarni et al.2017, 139, 10514–1052528683550). We now extend
this work to also study the deprotonation of the substrate pieces
glycolaldehyde (GA) and GA·HPi [HPi = phosphite
dianion]. Our combined calculations provide activation barriers, ΔG‡calc, for the TIM-catalyzed
deprotonation of GAP (12.9 ± 0.8 kcal·mol–1), of the substrate piece GA (15.0 ± 2.4 kcal·mol–1), and of the pieces GA·HPi (15.5 ± 3.5 kcal·mol–1). The effect of bound dianion on ΔG‡calc is small (≤2.6 kcal·mol–1), in comparison to the much larger 12.0 and 5.8 kcal·mol–1 intrinsic phosphodianion and phosphite dianion binding
energy utilized to stabilize the transition states for TIM-catalyzed
deprotonation of GAP and GA·HPi, respectively. This
shows that the dianion binding energy is essentially fully expressed
at our protein model for the Michaelis complex, where it is utilized
to drive an activating change in enzyme conformation. The results
represent an example of the synergistic use of results from experiments
and calculations to advance our understanding of enzymatic reaction
mechanisms.
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Affiliation(s)
- Yashraj S Kulkarni
- Science for Life Laboratory, Department of Cell and Molecular Biology , Uppsala University , BMC Box 596, S-751 24 Uppsala , Sweden
| | - Qinghua Liao
- Science for Life Laboratory, Department of Cell and Molecular Biology , Uppsala University , BMC Box 596, S-751 24 Uppsala , Sweden
| | - Fabian Byléhn
- Science for Life Laboratory, Department of Cell and Molecular Biology , Uppsala University , BMC Box 596, S-751 24 Uppsala , Sweden.,Department of Chemical Engineering , University College London , Torrington Place , London WC1E 7JE , United Kingdom
| | - Tina L Amyes
- Department of Chemistry , University at Buffalo, SUNY , Buffalo , New York 14260-3000 , United States
| | - John P Richard
- Department of Chemistry , University at Buffalo, SUNY , Buffalo , New York 14260-3000 , United States
| | - Shina C L Kamerlin
- Science for Life Laboratory, Department of Cell and Molecular Biology , Uppsala University , BMC Box 596, S-751 24 Uppsala , Sweden
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31
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Abstract
There is no consensus of opinion on the origin of the large rate accelerations observed for enzyme-catalyzed hydride transfer. The interpretation of recent results from studies on hydride transfer reactions catalyzed by alcohol dehydrogenase (ADH) focus on the proposal that the effective barrier height is reduced by quantum-mechanical tunneling through the energy barrier. This interpretation contrasts sharply with the notion that enzymatic rate accelerations are obtained through direct stabilization of the transition state for the nonenzymatic reaction in water. The binding energy of the dianion of substrate DHAP provides 11 kcal mol-1 stabilization of the transition state for the hydride transfer reaction catalyzed by glycerol-3-phosphate dehydrogenase (GPDH). We summarize evidence that the binding interactions between (GPDH) and dianion activators are utilized directly for stabilization of the transition state for enzyme-catalyzed hydride transfer. The possibility is considered, and then discounted, that these dianion binding interactions are utilized for the stabilization of a tunnel ready state (TRS) that enables efficient tunneling of the transferred hydride through the energy barrier, and underneath the energy maximum for the transition state. It is noted that the evidence to support the existence of a tunnel-ready state for the hydride transfer reactions catalyzed by ADH is ambiguous. We propose that the rate acceleration for ADH is due to the utilization of the binding energy of the cofactor NAD+/NADH in the stabilization of the transition state for enzyme-catalyzed hydride transfer.
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Affiliation(s)
- Archie C Reyes
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, USA.
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32
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He R, Reyes AC, Amyes TL, Richard JP. Enzyme Architecture: The Role of a Flexible Loop in Activation of Glycerol-3-phosphate Dehydrogenase for Catalysis of Hydride Transfer. Biochemistry 2018; 57:3227-3236. [PMID: 29337541 PMCID: PMC6001809 DOI: 10.1021/acs.biochem.7b01282] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
![]()
The side chain of Q295 of glycerol-3-phosphate
dehydrogenase from
human liver (hlGPDH) lies in a flexible loop, that
folds over the phosphodianion of substrate dihydroxyacetone phosphate
(DHAP). Q295 interacts with the side-chain cation from R269, which
is ion-paired to the substrate phosphodianion. Kinetic parameters kcat/Km (M–1 s–1) and kcat/KGAKHPi (M–2 s–1) were determined, respectively, for catalysis
of the reduction of DHAP and for dianion activation of catalysis of
reduction of glycolaldehyde (GA) catalyzed by wild-type, Q295G, Q295S,
Q295A, and Q295N mutants of hlGPDH. These mutations
result in up to a 150-fold decrease in (kcat/Km)DHAP and up to a 2.7 kcal/mol
decrease in the intrinsic phosphodianion binding energy. The data
define a linear correlation with slope 1.1, between the intrinsic
phosphodianion binding energy and the intrinsic phosphite dianion
binding energy for activation of hlGPDH-catalyzed
reduction of GA, that demonstrates a role for Q295 in optimizing this
dianion binding energy. The R269A mutation of wild-type GPDH results
in a 9.1 kcal/mol destabilization of the transition state for reduction
of DHAP, but the same R269A mutation of N270A and Q295A mutants result
in smaller 5.9 and 4.9 kcal/mol transition-state destabilization.
Similarly, the N270A or Q295A mutations of R269A GPDH each result
in large falloffs in the efficiency of rescue of the R269A mutant
by guanidine cation. We conclude that N270, which interacts for the
substrate phosphodianion and Q295, which interacts with the guanidine
side chain of R269, function to optimize the apparent
transition-state stabilization provided by the cationic side chain
of R269.
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Affiliation(s)
- Rui He
- Department of Chemistry , University at Buffalo, SUNY , Buffalo , New York 14260-3000 , United States
| | - Archie C Reyes
- Department of Chemistry , University at Buffalo, SUNY , Buffalo , New York 14260-3000 , United States
| | - Tina L Amyes
- Department of Chemistry , University at Buffalo, SUNY , Buffalo , New York 14260-3000 , United States
| | - John P Richard
- Department of Chemistry , University at Buffalo, SUNY , Buffalo , New York 14260-3000 , United States
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33
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Reyes AC, Amyes TL, Richard JP. Enzyme Architecture: Erection of Active Orotidine 5'-Monophosphate Decarboxylase by Substrate-Induced Conformational Changes. J Am Chem Soc 2017; 139:16048-16051. [PMID: 29058891 PMCID: PMC5720041 DOI: 10.1021/jacs.7b08897] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Orotidine
5′-monophosphate decarboxylase (OMPDC) catalyzes
the decarboxylation of 5-fluoroorotate (FO) with kcat/Km = 1.4 ×
10–7 M–1 s–1. Combining this and related kinetic parameters shows that the 31
kcal/mol stabilization of the transition state for decarboxylation
of OMP provided by OMPDC represents the sum of 11.8 and 10.6 kcal/mol
stabilization by the substrate phosphodianion and the ribosyl ring,
respectively, and an 8.6 kcal/mol stabilization from the orotate ring.
The transition state for OMPDC-catalyzed decarboxylation of FO is stabilized by 5.2, 7.2, and 9.0 kcal/mol, respectively,
by 1.0 M phosphite dianion, d-glycerol 3-phosphate and d-erythritol 4-phosphate. The stabilization is due to the utilization
of binding interactions of the substrate fragments to drive an enzyme
conformational change, which locks the orotate ring of the whole substrate,
or the substrate pieces in a caged complex. We propose that enzyme-activation
is a possible, and perhaps probable, consequence of any substrate-induced
enzyme conformational change.
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Affiliation(s)
- Archie C Reyes
- Department of Chemistry, University at Buffalo, SUNY , Buffalo, New York 14260-3000, United States
| | - Tina L Amyes
- Department of Chemistry, University at Buffalo, SUNY , Buffalo, New York 14260-3000, United States
| | - John P Richard
- Department of Chemistry, University at Buffalo, SUNY , Buffalo, New York 14260-3000, United States
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34
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Amyes TL, Richard JP. Primary Deuterium Kinetic Isotope Effects From Product Yields: Rationale, Implementation, and Interpretation. Methods Enzymol 2017; 596:163-177. [PMID: 28911770 DOI: 10.1016/bs.mie.2017.06.043] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A simple and convenient method is described to determine primary deuterium kinetic isotope effects (1°DKIEs) on reactions where the hydron incorporated into the reaction product is derived from solvent water. The 1°DKIE may be obtained by 1H NMR analyses as the ratio of the yields of H- and D-labeled products from a reaction in 50:50 (v/v) HOH/DOD. The procedures for these 1H NMR analyses are reviewed. This product deuterium isotope effect (PDIE) is defined as 1/ϕEL for fractionation of hydrons between solvent and the transition state for the reaction examined. When the solvent is not the direct hydron donor, it is necessary to correct the PDIE for the fractionation factor ϕEL for partitioning of the hydron between the solvent and the direct donor EL. This method was used to determine the 1°DKIE on decarboxylation reactions catalyzed by wild-type orotidine 5'-monophosphate decarboxylase (OMPDC) and by mutants of OMPDC, and then in the determination of the 1°DKIE on the decarboxylation reaction catalyzed by 5-carboxyvanillate decarboxylase. The experimental procedures used in studies on OMPDC and the rationale for these procedures are described.
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Affiliation(s)
- Tina L Amyes
- University at Buffalo, SUNY, Buffalo, NY, United States
| | - John P Richard
- University at Buffalo, SUNY, Buffalo, NY, United States.
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35
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Kulkarni YS, Liao Q, Petrović D, Krüger DM, Strodel B, Amyes TL, Richard JP, Kamerlin SCL. Enzyme Architecture: Modeling the Operation of a Hydrophobic Clamp in Catalysis by Triosephosphate Isomerase. J Am Chem Soc 2017; 139:10514-10525. [PMID: 28683550 PMCID: PMC5543394 DOI: 10.1021/jacs.7b05576] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Triosephosphate isomerase (TIM) is a proficient catalyst of the reversible isomerization of dihydroxyacetone phosphate (DHAP) to d-glyceraldehyde phosphate (GAP), via general base catalysis by E165. Historically, this enzyme has been an extremely important model system for understanding the fundamentals of biological catalysis. TIM is activated through an energetically demanding conformational change, which helps position the side chains of two key hydrophobic residues (I170 and L230), over the carboxylate side chain of E165. This is critical both for creating a hydrophobic pocket for the catalytic base and for maintaining correct active site architecture. Truncation of these residues to alanine causes significant falloffs in TIM's catalytic activity, but experiments have failed to provide a full description of the action of this clamp in promoting substrate deprotonation. We perform here detailed empirical valence bond calculations of the TIM-catalyzed deprotonation of DHAP and GAP by both wild-type TIM and its I170A, L230A, and I170A/L230A mutants, obtaining exceptional quantitative agreement with experiment. Our calculations provide a linear free energy relationship, with slope 0.8, between the activation barriers and Gibbs free energies for these TIM-catalyzed reactions. We conclude that these clamping side chains minimize the Gibbs free energy for substrate deprotonation, and that the effects on reaction driving force are largely expressed at the transition state for proton transfer. Our combined analysis of previous experimental and current computational results allows us to provide an overview of the breakdown of ground-state and transition state effects in enzyme catalysis in unprecedented detail, providing a molecular description of the operation of a hydrophobic clamp in triosephosphate isomerase.
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Affiliation(s)
- Yashraj S Kulkarni
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University , BMC Box 596, Uppsala S-751 24, Sweden
| | - Qinghua Liao
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University , BMC Box 596, Uppsala S-751 24, Sweden
| | - Dušan Petrović
- Institute of Complex Systems: Structural Biochemistry, Forschungszentrum Jülich , Jülich 52425, Germany
| | - Dennis M Krüger
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University , BMC Box 596, Uppsala S-751 24, Sweden
| | - Birgit Strodel
- Institute of Complex Systems: Structural Biochemistry, Forschungszentrum Jülich , Jülich 52425, Germany.,Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf , Universitätsstrasse 1, Düsseldorf 40225, Germany
| | - Tina L Amyes
- Department of Chemistry, University at Buffalo, SUNY , Buffalo, New York 14260-3000, United States
| | - John P Richard
- Department of Chemistry, University at Buffalo, SUNY , Buffalo, New York 14260-3000, United States
| | - Shina C L Kamerlin
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University , BMC Box 596, Uppsala S-751 24, Sweden
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36
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Amyes TL, Malabanan MM, Zhai X, Reyes AC, Richard JP. Enzyme activation through the utilization of intrinsic dianion binding energy. Protein Eng Des Sel 2017; 30:157-165. [PMID: 27903763 DOI: 10.1093/protein/gzw064] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 11/14/2016] [Indexed: 11/12/2022] Open
Abstract
43 We consider 'the proposition that the intrinsic binding energy that results from the noncovalent interaction of a specific substrate with the active site of the enzyme is considerably larger than is generally believed. An important part of this binding energy may be utilized to provide the driving force for catalysis, so that the observed binding energy represents only what is left over after this utilization' [Jencks,W.P. (1975) Adv. Enzymol. Relat. Areas. Mol. Biol. , , 219-410]. The large ~12 kcal/mol intrinsic substrate phosphodianion binding energy for reactions catalyzed by triosephosphate isomerase (TIM), orotidine 5'-monophosphate decarboxylase and glycerol-3-phosphate dehydrogenase is divided into 4-6 kcal/mol binding energy that is expressed on the formation of the Michaelis complex in anchoring substrates to the respective enzyme, and 6-8 kcal/mol binding energy that is specifically expressed at the transition state in activating the respective enzymes for catalysis. A structure-based mechanism is described where the dianion binding energy drives a conformational change that activates these enzymes for catalysis. Phosphite dianion plays the active role of holding TIM in a high-energy closed active form, but acts as passive spectator in showing no effect on transition-state structure. The result of studies on mutant enzymes is presented, which support the proposal that the dianion-driven enzyme conformational change plays a role in enhancing the basicity of side chain of E167, the catalytic base, by clamping the base between a pair of hydrophobic side chains. The insight these results provide into the architecture of enzyme active sites and the development of strategies for the de novo design of protein catalysts is discussed.
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Affiliation(s)
- T L Amyes
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, NY 14260-3000, USA
| | - M M Malabanan
- Department of Biochemistry, Vanderbilt University, Nashville, TN37205-0146, USA
| | - X Zhai
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX77843-2128, USA
| | - A C Reyes
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, NY 14260-3000, USA
| | - J P Richard
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, NY 14260-3000, USA
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37
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Abstract
Methods are described for the determination of pKas for weak carbon acids in water. The application of these methods to the determination of the pKas for a variety of carbon acids including nitriles, imidazolium cations, amino acids, peptides and their derivatives and, α-iminium cations is presented. The substituent effects on the acidity of these different classes of carbon acids are discussed; and, the relevance of these results to catalysis of the deprotonation of amino acids by enzymes and by pyridoxal 5'-phosphate is reviewed. The procedure for estimating the pKa of uridine 5'-phosphate for C-6 deprotonation at the active site of orotidine 5'-phosphate decarboxylase is described, and the effect of a 5-F substituent on carbon acidity of the enzyme-bound substrate is discussed.
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Affiliation(s)
- Tina L Amyes
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, NY 14260-3000
| | - John P Richard
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, NY 14260-3000
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Reyes AC, Amyes TL, Richard JP. Enzyme Architecture: Self-Assembly of Enzyme and Substrate Pieces of Glycerol-3-Phosphate Dehydrogenase into a Robust Catalyst of Hydride Transfer. J Am Chem Soc 2016; 138:15251-15259. [PMID: 27792325 PMCID: PMC5291162 DOI: 10.1021/jacs.6b09936] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The stabilization of the transition
state for hlGPDH-catalyzed reduction of DHAP due
to the action of the phosphodianion
of DHAP and the cationic side chain of R269 is between 12.4 and 17
kcal/mol. The R269A mutation of glycerol-3-phosphate dehydrogenase
(hlGPDH) results in a 9.1 kcal/mol destabilization
of the transition state for enzyme-catalyzed reduction of dihydroxyacetone
phosphate (DHAP) by NADH, and there is a 6.7 kcal/mol stabilization of this transition state by 1.0 M guanidine cation (Gua+) [J. Am. Chem. Soc.2015, 137, 5312–5315]. The R269A mutant shows no detectable
activity toward reduction of glycolaldehyde (GA), or activation of
this reaction by 30 mM HPO32–. We report
the unprecedented self-assembly of R269A hlGPDH,
dianions (X2– = FPO32–, HPO32–, or SO42–), Gua+ and GA into a functioning catalyst of the reduction
of GA, and fourth-order reaction rate constants kcat/KGAKXKGua. The linear logarithmic correlation
(slope = 1.0) between values of kcat/KGAKX for dianion
activation of wildtype hlGPDH-catalyzed reduction
of GA and kcat/KGAKXKGua shows that the electrostatic interaction between exogenous dianions
and the side chain of R269 is not significantly perturbed by cutting hlGPDH into R269A and Gua+ pieces. The advantage
for connection of hlGPDH (R269A mutant + Gua+) and substrate pieces (GA + HPi) pieces, (ΔGS‡)HPi+E+Gua = 5.6 kcal/mol, is nearly equal to the sum
of the advantage to connection of the substrate pieces, (ΔGS‡)GA+HPi = 3.3 kcal/mol, for wildtype hlGPDH-catalyzed reaction of GA + HPi, and for connection
of the enzyme pieces, (ΔGS‡)E+Gua = 2.4
kcal/mol, for Gua+ activation of the R269A hlGPDH-catalyzed reaction of DHAP.
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Affiliation(s)
- Archie C Reyes
- Department of Chemistry, University at Buffalo, SUNY , Buffalo, New York 14260-3000, United States
| | - Tina L Amyes
- Department of Chemistry, University at Buffalo, SUNY , Buffalo, New York 14260-3000, United States
| | - John P Richard
- Department of Chemistry, University at Buffalo, SUNY , Buffalo, New York 14260-3000, United States
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39
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Abstract
The results of studies on the structure and reactivity of spiro[5.2]oct-5,7-diene-4yl carbocation [phenonium ion] have had a significant impact on the course of discussion about the distinction between classical and nonclassical carbocations. This minireview will present a brief overview of the structure, bonding and reactivity of ring substituted phenonium ions (X-4+), with an emphasis on work completed since 2004. The discussion will focus on the development of new experimental protocol for determination of the selectivity for addition of nucleophilic anions to X-4+ in aqueous solution. The existing relationships between carbocation lifetime and nucleophilic selectivity, and the known lifetime of ca 140 sec for spiro[2.5]oct-4,7-diene-6-one provide rough estimates of the lifetimes for 4-Me-X-4+ and 4-MeO-X-4+ in aqueous solution. Evidence is presented that nucleophile addition to X-4+ proceeds through an "exploded" transition state, with relatively weak bonding the nucleophile and leaving group, and the development of significant positive charge at the reacting primary cyclopropyl carbon.
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Affiliation(s)
- Yutaka Tsuji
- Department of Biochemistry and Applied Chemistry, Kurume National College of Technology, Komorinomachi, Kurume 830-8555, Japan
| | - John P. Richard
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, NY 14260, USA
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40
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Reyes AC, Amyes TL, Richard JP. Structure-Reactivity Effects on Intrinsic Primary Kinetic Isotope Effects for Hydride Transfer Catalyzed by Glycerol-3-phosphate Dehydrogenase. J Am Chem Soc 2016; 138:14526-14529. [PMID: 27769116 PMCID: PMC5105681 DOI: 10.1021/jacs.6b07028] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
![]()
Primary deuterium
kinetic isotope effects (1°DKIE) on (kcat/KGA, M–1 s–1) for dianion (X2–) activated
hydride transfer from NADL to glycolaldehyde (GA) catalyzed by glycerol-3-phosphate
dehydrogenase were determined over a 2100-fold range of enzyme reactivity:
(X2–, 1°DKIE); FPO32–, 2.8 ± 0.1; HPO32–, 2.5 ±
0.1; SO42–, 2.8 ± 0.2; HOPO32–, 2.5 ± 0.1; S2O32–, 2.9 ± 0.1; unactivated; 2.4 ± 0.2.
Similar 1°DKIEs were determined for kcat. The observed 1°DKIEs are essentially independent of changes
in enzyme reactivity with changing dianion activator. The results
are consistent with (i) fast and reversible ligand binding; (ii) the
conclusion that the observed 1°DKIEs are equal to the intrinsic
1°DKIE on hydride transfer from NADL to GA; (iii) similar intrinsic
1°DKIEs on GPDH-catalyzed reduction of the substrate pieces and
the whole physiological substrate dihydroxyacetone phosphate. The
ground-state binding interactions for different X2– are similar, but there are large differences in the transition state
interactions for different X2–. The changes in transition
state binding interactions are expressed as changes in kcat and are proposed to represent changes in stabilization
of the active closed form of GPDH. The 1°DKIEs are much smaller
than observed for enzyme-catalyzed hydrogen transfer that occurs mainly
by quantum-mechanical tunneling.
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Affiliation(s)
- Archie C Reyes
- Department of Chemistry, University at Buffalo, SUNY , Buffalo, New York 14260-3000, United States
| | - Tina L Amyes
- Department of Chemistry, University at Buffalo, SUNY , Buffalo, New York 14260-3000, United States
| | - John P Richard
- Department of Chemistry, University at Buffalo, SUNY , Buffalo, New York 14260-3000, United States
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41
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Richard JP, Amyes TL, Malabanan MM, Zhai X, Kim KJ, Reinhardt CJ, Wierenga RK, Drake EJ, Gulick AM. Structure-Function Studies of Hydrophobic Residues That Clamp a Basic Glutamate Side Chain during Catalysis by Triosephosphate Isomerase. Biochemistry 2016; 55:3036-47. [PMID: 27149328 PMCID: PMC4934371 DOI: 10.1021/acs.biochem.6b00311] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Kinetic
parameters are reported for the reactions of whole substrates
(kcat/Km,
M–1 s–1) (R)-glyceraldehyde
3-phosphate (GAP) and
dihydroxyacetone phosphate (DHAP) and for the substrate pieces [(kcat/Km)E·HPi/Kd, M–2 s–1] glycolaldehyde (GA) and phosphite dianion
(HPi) catalyzed by the I172A/L232A mutant of triosephosphate
isomerase
from Trypanosoma brucei brucei (TbbTIM). A comparison with the corresponding parameters for wild-type,
I172A, and L232A TbbTIM-catalyzed reactions shows
that the effect of I172A and L232A mutations on ΔG⧧ for the wild-type TbbTIM-catalyzed
reactions of the substrate pieces is nearly the same
as the effect of the same mutations on TbbTIM previously
mutated at the second side chain. This provides strong evidence that
mutation of the first hydrophobic side chain does not affect the functioning
of the second side chain in catalysis of the reactions of the substrate
pieces. By contrast, the effects of I172A and L232A mutations on ΔG⧧ for wild-type TbbTIM-catalyzed
reactions of the whole substrate are different from
the effect of the same mutations on TbbTIM previously
mutated at the second side chain. This is due to the change in the
rate-determining step that determines the barrier to the isomerization
reaction. X-ray crystal structures are reported for I172A, L232A,
and I172A/L232A TIMs and for the complexes of these mutants to the
intermediate analogue phosphoglycolate (PGA). The structures of the
PGA complexes with wild-type and mutant enzymes are nearly superimposable,
except that the space opened by replacement of the hydrophobic side
chain is occupied by a water molecule that lies ∼3.5 Å
from the basic side chain of Glu167. The new water at I172A mutant TbbTIM provides a simple rationalization for the increase
in the activation barrier ΔG⧧ observed for mutant enzyme-catalyzed
reactions of the whole substrate and substrate pieces. By contrast,
the new water at the L232A mutant does not predict the decrease in
ΔG⧧ observed for the mutant
enzyme-catalyzed
reactions of the substrate piece GA.
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Affiliation(s)
- John P Richard
- Department of Chemistry, University at Buffalo, State University of New York , Buffalo, New York 14260, United States
| | - Tina L Amyes
- Department of Chemistry, University at Buffalo, State University of New York , Buffalo, New York 14260, United States
| | - M Merced Malabanan
- Department of Chemistry, University at Buffalo, State University of New York , Buffalo, New York 14260, United States
| | - Xiang Zhai
- Department of Chemistry, University at Buffalo, State University of New York , Buffalo, New York 14260, United States
| | - Kalvin J Kim
- Department of Chemistry, University at Buffalo, State University of New York , Buffalo, New York 14260, United States
| | - Christopher J Reinhardt
- Department of Chemistry, University at Buffalo, State University of New York , Buffalo, New York 14260, United States
| | - Rik K Wierenga
- Department of Biochemistry and Biocenter, University of Oulu , P.O. Box 3000, FIN-90014 Oulu, Finland
| | - Eric J Drake
- Hauptman-Woodward Institute , 700 Ellicott Street, Buffalo, New York 14203, United States.,Department of Structural Biology, University at Buffalo, State University of New York , Buffalo, New York 14203, United States
| | - Andrew M Gulick
- Hauptman-Woodward Institute , 700 Ellicott Street, Buffalo, New York 14203, United States.,Department of Structural Biology, University at Buffalo, State University of New York , Buffalo, New York 14203, United States
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42
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Abstract
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The
side chains of R269 and N270 interact with the phosphodianion
of dihydroxyacetone phosphate (DHAP) bound to glycerol 3-phosphate
dehydrogenase (GPDH). The R269A, N270A, and R269A/N270A mutations
of GPDH result in 9.1, 5.6, and 11.5 kcal/mol destabilization, respectively,
of the transition state for GPDH-catalyzed reduction of DHAP by the
reduced form of nicotinamide adenine dinucleotide. The N270A mutation
results in a 7.7 kcal/mol decrease in the intrinsic phosphodianion
binding energy, which is larger than the 5.6 kcal/mol effect of the
mutation on the stability of the transition state for reduction of
DHAP; a 2.2 kcal/mol stabilization of the transition state for unactivated
hydride transfer to the truncated substrate glycolaldehyde (GA); and
a change in the effect of phosphite dianion on GPDH-catalyzed reduction
of GA, from strongly activating to inhibiting. The N270A mutation
breaks the network of hydrogen bonding side chains, Asn270, Thr264,
Asn205, Lys204, Asp260, and Lys120, which connect the dianion activation
and catalytic sites of GPDH. We propose that this disruption dramatically
alters the performance of GPDH at these sites.
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Affiliation(s)
- Archie C Reyes
- Department of Chemistry, University at Buffalo , Buffalo, New York 14260-3000, United States
| | - Tina L Amyes
- Department of Chemistry, University at Buffalo , Buffalo, New York 14260-3000, United States
| | - John P Richard
- Department of Chemistry, University at Buffalo , Buffalo, New York 14260-3000, United States
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43
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Abstract
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The side chains of
Y208 and S211 from loop 7 of triosephosphate
isomerase (TIM) form hydrogen bonds to backbone amides and carbonyls
from loop 6 to stabilize the caged enzyme–substrate complex.
The effect of seven mutations [Y208T, Y208S, Y208A, Y208F, S211G,
S211A, Y208T/S211G] on the kinetic parameters for TIM catalyzed reactions
of the whole substrates dihydroxyacetone phosphate and d-glyceraldehyde
3-phosphate [(kcat/Km)GAP and (kcat/Km)DHAP] and of the substrate pieces
glycolaldehyde and phosphite dianion (kcat/KHPiKGA)
are reported. The linear logarithmic correlation between these kinetic
parameters, with slope of 1.04 ± 0.03, shows that most mutations
of TIM result in an identical change in the activation barriers for
the catalyzed reactions of whole substrate and substrate pieces, so
that the transition states for these reactions are stabilized by similar
interactions with the protein catalyst. The second linear logarithmic
correlation [slope = 0.53 ± 0.16] between kcat for isomerization of GAP and Kd⧧ for phosphite dianion binding to the transition
state for wildtype and many mutant TIM-catalyzed reactions of substrate
pieces shows that ca. 50% of the wildtype TIM dianion binding energy,
eliminated by these mutations, is expressed at the wildtype Michaelis
complex, and ca. 50% is only expressed at the wildtype transition
state. Negative deviations from this correlation are observed when
the mutation results in a decrease in enzyme reactivity at the catalytic
site. The main effect of Y208T, Y208S, and Y208A mutations is to cause
a reduction in the total intrinsic dianion binding energy, but the
effect of Y208F extends to the catalytic site.
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Affiliation(s)
- Xiang Zhai
- Department of Chemistry, University at Buffalo, SUNY , Buffalo, New York 14260-3000, United States
| | - Tina L Amyes
- Department of Chemistry, University at Buffalo, SUNY , Buffalo, New York 14260-3000, United States
| | - John P Richard
- Department of Chemistry, University at Buffalo, SUNY , Buffalo, New York 14260-3000, United States
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Goryanova B, Goldman L, Ming S, Amyes TL, Gerlt JA, Richard JP. Rate and Equilibrium Constants for an Enzyme Conformational Change during Catalysis by Orotidine 5'-Monophosphate Decarboxylase. Biochemistry 2015; 54:4555-64. [PMID: 26135041 PMCID: PMC4520626 DOI: 10.1021/acs.biochem.5b00591] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 07/01/2015] [Indexed: 11/29/2022]
Abstract
The caged complex between orotidine 5'-monophosphate decarboxylase (ScOMPDC) and 5-fluoroorotidine 5'-monophosphate (FOMP) undergoes decarboxylation ∼300 times faster than the caged complex between ScOMPDC and the physiological substrate, orotidine 5'-monophosphate (OMP). Consequently, the enzyme conformational changes required to lock FOMP at a protein cage and release product 5-fluorouridine 5'-monophosphate (FUMP) are kinetically significant steps. The caged form of ScOMPDC is stabilized by interactions between the side chains from Gln215, Tyr217, and Arg235 and the substrate phosphodianion. The control of these interactions over the barrier to the binding of FOMP and the release of FUMP was probed by determining the effect of all combinations of single, double, and triple Q215A, Y217F, and R235A mutations on kcat/Km and kcat for turnover of FOMP by wild-type ScOMPDC; its values are limited by the rates of substrate binding and product release, respectively. The Q215A and Y217F mutations each result in an increase in kcat and a decrease in kcat/Km, due to a weakening of the protein-phosphodianion interactions that favor fast product release and slow substrate binding. The Q215A/R235A mutation causes a large decrease in the kinetic parameters for ScOMPDC-catalyzed decarboxylation of OMP, which are limited by the rate of the decarboxylation step, but much smaller decreases in the kinetic parameters for ScOMPDC-catalyzed decarboxylation of FOMP, which are limited by the rate of enzyme conformational changes. By contrast, the Y217A mutation results in large decreases in kcat/Km for ScOMPDC-catalyzed decarboxylation of both OMP and FOMP, because of the comparable effects of this mutation on rate-determining decarboxylation of enzyme-bound OMP and on the rate-determining enzyme conformational change for decarboxylation of FOMP. We propose that kcat = 8.2 s(-1) for decarboxylation of FOMP by the Y217A mutant is equal to the rate constant for cage formation from the complex between FOMP and the open enzyme, that the tyrosyl phenol group stabilizes the closed form of ScOMPDC by hydrogen bonding to the substrate phosphodianion, and that the phenyl group of Y217 and F217 facilitates formation of the transition state for the rate-limiting conformational change. An analysis of kinetic data for mutant enzyme-catalyzed decarboxylation of OMP and FOMP provides estimates for the rate and equilibrium constants for the conformational change that traps FOMP at the enzyme active site.
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Affiliation(s)
- Bogdana Goryanova
- Department
of Chemistry, University at Buffalo, State
University of New York, Buffalo, New York 14260-3000, United States
| | - Lawrence
M. Goldman
- Department
of Chemistry, University at Buffalo, State
University of New York, Buffalo, New York 14260-3000, United States
| | - Shonoi Ming
- Department
of Chemistry, University at Buffalo, State
University of New York, Buffalo, New York 14260-3000, United States
| | - Tina L. Amyes
- Department
of Chemistry, University at Buffalo, State
University of New York, Buffalo, New York 14260-3000, United States
| | - John A. Gerlt
- Departments
of Biochemistry and Chemistry, University
of Illinois, Urbana, Illinois 61801, United
States
| | - John P. Richard
- Department
of Chemistry, University at Buffalo, State
University of New York, Buffalo, New York 14260-3000, United States
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45
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Reyes AC, Koudelka AP, Amyes TL, Richard JP. Enzyme architecture: optimization of transition state stabilization from a cation-phosphodianion pair. J Am Chem Soc 2015; 137:5312-5. [PMID: 25884759 PMCID: PMC4416717 DOI: 10.1021/jacs.5b02202] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
![]()
The
side chain cation of R269 lies at the surface of l-glycerol
3-phosphate dehydrogenase (GPDH) and forms an ion pair
to the phosphodianion of substrate dihydroxyacetone phosphate (DHAP),
which is buried at the nonpolar protein interior. The R269A mutation
of GPDH results in a 110-fold increase in Km (2.8 kcal/mol effect) and a 41 000-fold decrease in kcat (6.3 kcal/mol effect), which corresponds
to a 9.1 kcal/mol destabilization of the transition state for GPDH-catalyzed
reduction of DHAP by NADH. There is a 6.7 kcal/mol stabilization of
the transition state for the R269A mutant GPDH-catalyzed reaction
by 1.0 M guanidinium ion, and the transition state for the reaction
of the substrate pieces is stabilized by an additional 2.4 kcal/mol
by their covalent attachment at wildtype GPDH. These results provide
strong support for the proposal that GPDH invests the 11 kcal/mol
intrinsic phosphodianion binding energy of DHAP in trapping the substrate
at a nonpolar active site, where strong electrostatic interactions
are favored, and obtains a 9 kcal/mol return from stabilizing interactions
between the side chain cation and transition state trianion. We propose
a wide propagation for the catalytic motif examined in this work,
which enables strong transition state stabilization from enzyme–phosphodianion
pairs.
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Affiliation(s)
- Archie C Reyes
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
| | - Astrid P Koudelka
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
| | - Tina L Amyes
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
| | - John P Richard
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
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Reyes A, Zhai X, Morgan KT, Reinhardt CJ, Amyes TL, Richard JP. The activating oxydianion binding domain for enzyme-catalyzed proton transfer, hydride transfer, and decarboxylation: specificity and enzyme architecture. J Am Chem Soc 2015; 137:1372-82. [PMID: 25555107 PMCID: PMC4311969 DOI: 10.1021/ja5123842] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Indexed: 11/29/2022]
Abstract
The kinetic parameters for activation of yeast triosephosphate isomerase (ScTIM), yeast orotidine monophosphate decarboxylase (ScOMPDC), and human liver glycerol 3-phosphate dehydrogenase (hlGPDH) for catalysis of reactions of their respective phosphodianion truncated substrates are reported for the following oxydianions: HPO3(2-), FPO3(2-), S2O3(2-), SO4(2-) and HOPO3(2-). Oxydianions bind weakly to these unliganded enzymes and tightly to the transition state complex (E·S(‡)), with intrinsic oxydianion Gibbs binding free energies that range from -8.4 kcal/mol for activation of hlGPDH-catalyzed reduction of glycolaldehyde by FPO3(2-) to -3.0 kcal/mol for activation of ScOMPDC-catalyzed decarboxylation of 1-β-d-erythrofuranosyl)orotic acid by HOPO3(2-). Small differences in the specificity of the different oxydianion binding domains are observed. We propose that the large -8.4 kcal/mol and small -3.8 kcal/mol intrinsic oxydianion binding energy for activation of hlGPDH by FPO3(2-) and S2O3(2-), respectively, compared with activation of ScTIM and ScOMPDC reflect stabilizing and destabilizing interactions between the oxydianion -F and -S with the cationic side chain of R269 for hlGPDH. These results are consistent with a cryptic function for the similarly structured oxydianion binding domains of ScTIM, ScOMPDC and hlGPDH. Each enzyme utilizes the interactions with tetrahedral inorganic oxydianions to drive a conformational change that locks the substrate in a caged Michaelis complex that provides optimal stabilization of the different enzymatic transition states. The observation of dianion activation by stabilization of active caged Michaelis complexes may be generalized to the many other enzymes that utilize substrate binding energy to drive changes in enzyme conformation, which induce tight substrate fits.
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Affiliation(s)
- Archie
C. Reyes
- Department
of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
| | - Xiang Zhai
- Department
of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
| | - Kelsey T. Morgan
- Department
of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
| | - Christopher J. Reinhardt
- Department
of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
| | - Tina L. Amyes
- Department
of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
| | - John P. Richard
- Department
of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
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47
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Affiliation(s)
- John P Richard
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, NY 14260-3000, United States.
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48
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Abstract
The products of the reactions of 2-(4-methoxyphenyl)ethyl tosylate (MeO-1-Ts) and 2-(4-methyphenyl)ethyl tosylate (Me-1-Ts) with nucleophilic anions were determined for reactions in 50/50 (v/v) trifluoroethanol/water at 25°C. In many cases the nucleophile selectivity kNu/ks (M-1) for reactions of nucleophile and solvent, calculated from the ratio of product yields, depends upon [Nu-]. This demonstrates the existence of competing reaction pathways, which show different selectivities for reactions with nucleophiles. A carbon-13 NMR analysis of the products of the reactions of substrate enriched with carbon-13 at the α-carbon, X-1-[α-13C]Ts, (X = -OCH3, -Me) with nucleophilic anions in 50/50 (v/v) trifluoroethanol/water at 25°C shows the formation of X-1-[β-13C]OH, X-1-[β-13C]OCH2CF3 and X-1-[β-13C]Nu (Nu = Br, Cl, CH3CO2, Cl2CHCO2) from the trapping of symmetrical 4-substituted phenonium ion reaction intermediates X-2+ . The observation of excess label in the α-position, [α-13C]/[β-13C] > 1.0, for both the water and nucleophile adducts, shows that water and anionic nucleophiles also react by direct substitution at X-1-[α-13C]Ts. The ratios of product yields, [α-13C]/[β-13C], and observed nucleophile selectivity (kNu/ks)obs were used to dissect the contribution of direct nucleophile addition at Me-1-Ts and trapping of X-2+ to the product yields. The product yields from partitioning of the intermediate gave the nucleophile selectivity kNu/ks (M-1) for X-2+ . Swain-Scott plots of log (kNu/ks) are correlated by slopes of s = 0.78 and s = 0.73 for reactions of MeO-2+ and Me-2+ , respectively. This shows that the sensitivity of bimolecular substitution at X-2+ to changes in nucleophile reactivity is smaller than for nucleophilic substitution at the methyl iodide. Evidence is presented that nucleophile addition to X-2+ proceeds through an "exploded" transition state.
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Affiliation(s)
- Yutaka Tsuji
- Department of Biochemistry and Applied Chemistry, Kurume National College of Technology, Komorinomachi, Kurume 830-8555, Japan
| | - John P. Richard
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, NY 14260, USA
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Goldman L, Amyes TL, Goryanova B, Gerlt JA, Richard JP. Enzyme architecture: deconstruction of the enzyme-activating phosphodianion interactions of orotidine 5'-monophosphate decarboxylase. J Am Chem Soc 2014; 136:10156-65. [PMID: 24958125 PMCID: PMC4227808 DOI: 10.1021/ja505037v] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Indexed: 12/12/2022]
Abstract
The mechanism for activation of orotidine 5'-monophosphate decarboxylase (OMPDC) by interactions of side chains from Gln215 and Try217 at a gripper loop and R235, adjacent to this loop, with the phosphodianion of OMP was probed by determining the kinetic parameters k(cat) and K(m) for all combinations of single, double, and triple Q215A, Y217F, and R235A mutations. The 12 kcal/mol intrinsic binding energy of the phosphodianion is shown to be equal to the sum of the binding energies of the side chains of R235 (6 kcal/mol), Q215 (2 kcal/mol), Y217 (2 kcal/mol), and hydrogen bonds to the G234 and R235 backbone amides (2 kcal/mol). Analysis of a triple mutant cube shows small (ca. 1 kcal/mol) interactions between phosphodianion gripper side chains, which are consistent with steric crowding of the side chains around the phosphodianion at wild-type OMPDC. These mutations result in the same change in the activation barrier to the OMPDC-catalyzed reactions of the whole substrate OMP and the substrate pieces (1-β-D-erythrofuranosyl)orotic acid (EO) and phosphite dianion. This shows that the transition states for these reactions are stabilized by similar interactions with the protein catalyst. The 12 kcal/mol intrinsic phosphodianion binding energy of OMP is divided between the 8 kcal/mol of binding energy, which is utilized to drive a thermodynamically unfavorable conformational change of the free enzyme, resulting in an increase in (k(cat))(obs) for OMPDC-catalyzed decarboxylation of OMP, and the 4 kcal/mol of binding energy, which is utilized to stabilize the Michaelis complex, resulting in a decrease in (K(m))(obs).
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Affiliation(s)
- Lawrence
M. Goldman
- Department
of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
| | - Tina L. Amyes
- Department
of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
| | - Bogdana Goryanova
- Department
of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
| | - John A. Gerlt
- Departments
of Biochemistry and Chemistry, University
of Illinois, Urbana, Illinois 61801, United
States
| | - John P. Richard
- Department
of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
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Richard JP, Zhai X, Malabanan MM. Reflections on the catalytic power of a TIM-barrel. Bioorg Chem 2014; 57:206-212. [PMID: 25092608 DOI: 10.1016/j.bioorg.2014.07.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2014] [Revised: 07/03/2014] [Accepted: 07/04/2014] [Indexed: 12/14/2022]
Abstract
The TIM-barrel fold is described and its propagation throughout the enzyme universe noted. The functions of the individual front loops of the eponymous TIM-barrel of triosephosphate isomerase are presented in a discussion of: (a) electrophilic catalysis, by amino acid side chains from loops 1 and 4, of abstraction of an α-carbonyl hydrogen from substrate dihydroxyacetone phosphate (DHAP) or d-glyceraldehyde 3-phosphate (DGAP). (b) The engineering of loop 3 to give the monomeric variant monoTIM and the structure and catalytic properties of this monomer. (c) The interaction between loops 6, 7 and 8 and the phosphodianion of DHAP or DGAP. (d) The mechanism by which a ligand-gated conformational change, dominated by motion of loops 6 and 7, activates TIM for catalysis of deprotonation of DHAP or DGAP. (e) The conformational plasticity of TIM, and the utilization of substrate binding energy to "mold" the distorted active site loops of TIM mutants into catalytically active enzymes. The features of the TIM-barrel fold that favor effective protein catalysis are discussed.
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Affiliation(s)
- John P Richard
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, NY 14260, United States.
| | - Xiang Zhai
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, NY 14260, United States
| | - M Merced Malabanan
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, NY 14260, United States
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