1
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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] [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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2
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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] [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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3
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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] [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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4
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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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5
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Pfeiffer M, Crean RM, Moreira C, Parracino A, Oberdorfer G, Brecker L, Hammerschmidt F, Kamerlin SCL, Nidetzky B. Essential Functional Interplay of the Catalytic Groups in Acid Phosphatase. ACS Catal 2022; 12:3357-3370. [PMID: 35356705 PMCID: PMC8938923 DOI: 10.1021/acscatal.1c05656] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/31/2022] [Indexed: 01/15/2023]
Abstract
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The cooperative interplay
between the functional devices of a preorganized
active site is fundamental to enzyme catalysis. An in-depth understanding
of this phenomenon is central to elucidating the remarkable efficiency
of natural enzymes and provides an essential benchmark for enzyme
design and engineering. Here, we study the functional interconnectedness
of the catalytic nucleophile (His18) in an acid phosphatase by analyzing
the consequences of its replacement with aspartate. We present crystallographic,
biochemical, and computational evidence for a conserved mechanistic
pathway via a phospho-enzyme intermediate on Asp18. Linear free-energy
relationships for phosphoryl transfer from phosphomonoester substrates
to His18/Asp18 provide evidence for the cooperative interplay between
the nucleophilic and general-acid catalytic groups in the wild-type
enzyme, and its substantial loss in the H18D variant. As an isolated
factor of phosphatase efficiency, the advantage of a histidine compared
to an aspartate nucleophile is ∼104-fold. Cooperativity
with the catalytic acid adds ≥102-fold to that advantage.
Empirical valence bond simulations of phosphoryl transfer from glucose
1-phosphate to His and Asp in the enzyme explain the loss of activity
of the Asp18 enzyme through a combination of impaired substrate positioning
in the Michaelis complex, as well as a shift from early to late protonation
of the leaving group in the H18D variant. The evidence presented furthermore
suggests that the cooperative nature of catalysis distinguishes the
enzymatic reaction from the corresponding reaction in solution and
is enabled by the electrostatic preorganization of the active site.
Our results reveal sophisticated discrimination in multifunctional
catalysis of a highly proficient phosphatase active site.
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Affiliation(s)
- Martin Pfeiffer
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 12/I, 8010 Graz, Austria.,Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010 Graz, Austria
| | - Rory M Crean
- Department of Chemistry-BMC, Uppsala University, BMC Box 576, S-751 23 Uppsala, Sweden
| | - Catia Moreira
- Department of Chemistry-BMC, Uppsala University, BMC Box 576, S-751 23 Uppsala, Sweden
| | - Antonietta Parracino
- Department of Chemistry-BMC, Uppsala University, BMC Box 576, S-751 23 Uppsala, Sweden
| | - Gustav Oberdorfer
- Institute of Biochemistry, Graz University of Technology, NAWI Graz, Petersgasse 12/II, 8010 Graz, Austria
| | - Lothar Brecker
- Department of Organic Chemistry, University of Vienna, Währingerstraße 38, 1090 Vienna, Austria
| | - Friedrich Hammerschmidt
- Department of Organic Chemistry, University of Vienna, Währingerstraße 38, 1090 Vienna, Austria
| | | | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 12/I, 8010 Graz, Austria.,Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010 Graz, Austria
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6
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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] [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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7
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Di Cera E. Mechanisms of ligand binding. BIOPHYSICS REVIEWS 2020; 1:011303. [PMID: 33313600 PMCID: PMC7714259 DOI: 10.1063/5.0020997] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 09/09/2020] [Indexed: 12/25/2022]
Abstract
Many processes in chemistry and biology involve interactions of a ligand with its molecular target. Interest in the mechanism governing such interactions has dominated theoretical and experimental analysis for over a century. The interpretation of molecular recognition has evolved from a simple rigid body association of the ligand with its target to appreciation of the key role played by conformational transitions. Two conceptually distinct descriptions have had a profound impact on our understanding of mechanisms of ligand binding. The first description, referred to as induced fit, assumes that conformational changes follow the initial binding step to optimize the complex between the ligand and its target. The second description, referred to as conformational selection, assumes that the free target exists in multiple conformations in equilibrium and that the ligand selects the optimal one for binding. Both descriptions can be merged into more complex reaction schemes that better describe the functional repertoire of macromolecular systems. This review deals with basic mechanisms of ligand binding, with special emphasis on induced fit, conformational selection, and their mathematical foundations to provide rigorous context for the analysis and interpretation of experimental data. We show that conformational selection is a surprisingly versatile mechanism that includes induced fit as a mathematical special case and even captures kinetic properties of more complex reaction schemes. These features make conformational selection a dominant mechanism of molecular recognition in biology, consistent with the rich conformational landscape accessible to biological macromolecules being unraveled by structural biology.
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Affiliation(s)
- Enrico Di Cera
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri 63104, USA
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8
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Brandão TAS, Richard JP. Orotidine 5'-Monophosphate Decarboxylase: The Operation of Active Site Chains Within and Across Protein Subunits. Biochemistry 2020; 59:2032-2040. [PMID: 32374983 PMCID: PMC7476526 DOI: 10.1021/acs.biochem.0c00241] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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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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9
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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] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
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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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10
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Horovitz A, Fleisher RC, Mondal T. Double-mutant cycles: new directions and applications. Curr Opin Struct Biol 2019; 58:10-17. [PMID: 31029859 DOI: 10.1016/j.sbi.2019.03.025] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Accepted: 03/20/2019] [Indexed: 11/17/2022]
Abstract
Double-mutant cycle (DMC) analysis is a powerful approach for detecting and quantifying the energetics of both direct and long-range interactions in proteins and other chemical systems. It can also be used to unravel higher-order interactions (e.g. three-body effects) that lead to cooperativity in protein folding and function. In this review, we describe new applications of DMC analysis based on advances in native mass spectrometry and high-throughput methods such as next generation sequencing and protein complementation assays. These developments have facilitated carrying out high-throughput DMC analysis, which can be used to characterize increasingly higher-order interactions and very large interaction networks in proteins. Such studies have provided insights into the extent of cooperativity (epistasis) in protein structures. High-throughput DMC studies have also been used to validate correlated mutation analysis and can provide restraints for protein docking.
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Affiliation(s)
- Amnon Horovitz
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Rachel C Fleisher
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Tridib Mondal
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
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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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