1
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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] [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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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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3
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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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4
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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] [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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5
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Zhang Z, Yao Y, He L, Hong T, Li S, Huang F, Stang PJ. Coordination-driven self-assembly of dibenzo-18-crown-6 functionalized Pt(II) metallacycles. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.05.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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6
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Heimhalt M, Mukherjee P, Grainger RA, Szabla R, Brown C, Turner R, Junop MS, Berti PJ. An Inhibitor-in-Pieces Approach to DAHP Synthase Inhibition: Potent Enzyme and Bacterial Growth Inhibition. ACS Infect Dis 2021; 7:3292-3302. [PMID: 34761906 DOI: 10.1021/acsinfecdis.1c00462] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
3-Deoxy-d-arabinoheptulosonate-7-phosphate (DAHP) synthase catalyzes the first step in the shikimate biosynthetic pathway and is an antimicrobial target. We used an inhibitor-in-pieces approach, based on the previously reported inhibitor DAHP oxime, to screen inhibitor fragments in the presence and absence of glycerol 3-phosphate to occupy the distal end of the active site. This led to DAHP hydrazone, the most potent inhibitor to date, Ki = 10 ± 1 nM. Three trifluoropyruvate (TFP)-based inhibitor fragments were efficient inhibitors with ligand efficiencies of up to 0.7 kcal mol-1/atom compared with 0.2 kcal mol-1/atom for a typical good inhibitor. The crystal structures showed the TFP-based inhibitors binding upside down in the active site relative to DAHP oxime, providing new avenues for inhibitor development. The ethyl esters of TFP oxime and TFP semicarbazone prevented E. coli growth in culture with IC50 = 0.21 ± 0.01 and 0.77 ± 0.08 mg mL-1, respectively. Overexpressing DAHP synthase relieved growth inhibition, demonstrating that DAHP synthase was the target. Growth inhibition occurred in media containing aromatic amino acids, suggesting that growth inhibition was due to depletion of some other product(s) of the shikimate pathway, possibly folate.
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Affiliation(s)
| | | | - Ryan A. Grainger
- Department of Biochemistry, Molecular Biology Lab, Western University, London, Ontario N6A 5C1, Canada
| | - Robert Szabla
- Department of Biochemistry, Molecular Biology Lab, Western University, London, Ontario N6A 5C1, Canada
| | - Christopher Brown
- Department of Biochemistry, Molecular Biology Lab, Western University, London, Ontario N6A 5C1, Canada
| | | | - Murray S. Junop
- Department of Biochemistry, Molecular Biology Lab, Western University, London, Ontario N6A 5C1, Canada
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7
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Richard JP, Cristobal JR, Amyes TL. Linear Free Energy Relationships for Enzymatic Reactions: Fresh Insight from a Venerable Probe. Acc Chem Res 2021; 54:2532-2542. [PMID: 33939414 PMCID: PMC8157535 DOI: 10.1021/acs.accounts.1c00147] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
![]()
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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8
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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] [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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9
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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] [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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10
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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] [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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11
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Costa CHSD, Bichara TW, Gomes GC, Dos Santos AM, da Costa KS, Lima AHLE, Alves CN, Lameira J. Unraveling the conformational dynamics of glycerol 3-phosphate dehydrogenase, a nicotinamide adenine dinucleotide-dependent enzyme of Leishmania mexicana. J Biomol Struct Dyn 2020; 39:2044-2055. [PMID: 32174264 DOI: 10.1080/07391102.2020.1742206] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Allosteric changes modulate the enzymatic activity, leading to activation or inhibition of the molecular target. Understanding the induced fit accommodation mechanism of a ligand in its lowest-free energy state and the subsequent conformational changes induced in the protein are important questions for drug design. In the present study, molecular dynamics (MD) simulations, binding free energy calculations, and principal component analysis (PCA) were applied to analyze the glycerol-3-phosphate dehydrogenase of Leishmania mexicana (LmGPDH) conformational changes induced by its cofactor and substrate binding. GPDH is a nicotinamide adenine dinucleotide (NAD)-dependent enzyme, which has been reported as an interesting target for drug discovery and development against leishmaniasis. Despite its relevance for glycolysis and pentose phosphate pathways, the structural flexibility and conformational motions of LmGPDH in complex with NADH and dihydroxyacetone phosphate (DHAP) remain unexplored. Here, we analyzed the conformational dynamics of the enzyme-NADH complex (cofactor), and the enzyme-NADH-DHAP complex (adduct), mapped the hydrogen-bond interactions for the complexes and pointed some structural determinants of the enzyme that emerge from these contacts to NADH and DHAP. Finally, we proposed a consistent mechanism for the conformational changes on the first step of the reversible redox conversion of dihydroxyacetone phosphate to glycerol 3-phosphate, indicating key residues and interactions that could be further explored in drug discovery.
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Affiliation(s)
| | | | | | | | | | | | - Cláudio Nahum Alves
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Universidade Federal do Pará, Belém, PA, Brazil
| | - Jerônimo Lameira
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Universidade Federal do Pará, Belém, PA, Brazil
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12
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The role of ligand-gated conformational changes in enzyme catalysis. Biochem Soc Trans 2020; 47:1449-1460. [PMID: 31657438 PMCID: PMC6824834 DOI: 10.1042/bst20190298] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 10/03/2019] [Accepted: 10/07/2019] [Indexed: 11/17/2022]
Abstract
Structural and biochemical studies on diverse enzymes have highlighted the importance of ligand-gated conformational changes in enzyme catalysis, where the intrinsic binding energy of the common phosphoryl group of their substrates is used to drive energetically unfavorable conformational changes in catalytic loops, from inactive open to catalytically competent closed conformations. However, computational studies have historically been unable to capture the activating role of these conformational changes. Here, we discuss recent experimental and computational studies, which can remarkably pinpoint the role of ligand-gated conformational changes in enzyme catalysis, even when not modeling the loop dynamics explicitly. Finally, through our joint analyses of these data, we demonstrate how the synergy between theory and experiment is crucial for furthering our understanding of enzyme catalysis.
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13
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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
![]()
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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14
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Antony N, Unnikrishnan L, Mohanty S, Nayak SK. The imperative role of polymers in enzymatic cholesterol biosensors- an overview. POLYM-PLAST TECH MAT 2019. [DOI: 10.1080/25740881.2019.1576197] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Neethu Antony
- Laboratory for Advanced Research in Polymeric Materials, Central Institute of Plastics Engineering and Technology, Bhubaneswar, Odisha, India
| | - Lakshmi Unnikrishnan
- Laboratory for Advanced Research in Polymeric Materials, Central Institute of Plastics Engineering and Technology, Bhubaneswar, Odisha, India
| | - Smita Mohanty
- Laboratory for Advanced Research in Polymeric Materials, Central Institute of Plastics Engineering and Technology, Bhubaneswar, Odisha, India
| | - Sanjay K. Nayak
- Laboratory for Advanced Research in Polymeric Materials, Central Institute of Plastics Engineering and Technology, Bhubaneswar, Odisha, India
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15
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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] [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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16
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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] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
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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17
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Reyes AC, Amyes TL, Richard JP. A reevaluation of the origin of the rate acceleration for enzyme-catalyzed hydride transfer. Org Biomol Chem 2018; 15:8856-8866. [PMID: 28956050 DOI: 10.1039/c7ob01652b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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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18
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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] [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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19
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Lamba V, Yabukarski F, Herschlag D. An Activator-Blocker Pair Provides a Controllable On-Off Switch for a Ketosteroid Isomerase Active Site Mutant. J Am Chem Soc 2017; 139:11089-11095. [PMID: 28719738 DOI: 10.1021/jacs.7b03547] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Control of enzyme activity is fundamental to biology and represents a long-term goal in bioengineering and precision therapeutics. While several powerful molecular strategies have been developed, limitations remain in their generalizability and dynamic range. We demonstrate a control mechanism via separate small molecules that turn on the enzyme (activator) and turn off the activation (blocker). We show that a pocket created near the active site base of the enzyme ketosteriod isomerase (KSI) allows efficient and saturable base rescue when the enzyme's natural general base is removed. Binding a small molecule with similar properties but lacking general-base capability in this pocket shuts off rescue. The ability of small molecules to directly participate in and directly block catalysis may afford a broad controllable dynamic range. This approach may be amenable to numerous enzymes and to engineering and screening approaches to identify activators and blockers with strong, specific binding for engineering and therapeutic applications.
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Affiliation(s)
- Vandana Lamba
- Department of Biochemistry, ‡Department of Chemistry, §Department of Chemical Engineering, and ∥Stanford ChEM-H, Stanford University , Stanford, California 94305, United States
| | - Filip Yabukarski
- Department of Biochemistry, ‡Department of Chemistry, §Department of Chemical Engineering, and ∥Stanford ChEM-H, Stanford University , Stanford, California 94305, United States
| | - Daniel Herschlag
- Department of Biochemistry, ‡Department of Chemistry, §Department of Chemical Engineering, and ∥Stanford ChEM-H, Stanford University , Stanford, California 94305, United States
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20
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Balachandran N, To F, Berti PJ. Linear Free Energy Relationship Analysis of Transition State Mimicry by 3-Deoxy-d-arabino-heptulosonate-7-phosphate (DAHP) Oxime, a DAHP Synthase Inhibitor and Phosphate Mimic. Biochemistry 2017; 56:592-601. [PMID: 28045507 DOI: 10.1021/acs.biochem.6b01211] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Naresh Balachandran
- Department of Chemistry & Chemical Biology and ‡Department of Biochemistry & Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4M1, Canada
| | - Frederick To
- Department of Chemistry & Chemical Biology and ‡Department of Biochemistry & Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4M1, Canada
| | - Paul J. Berti
- Department of Chemistry & Chemical Biology and ‡Department of Biochemistry & Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4M1, Canada
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