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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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] [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] [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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Corbella M, Pinto GP, Kamerlin SCL. Loop dynamics and the evolution of enzyme activity. Nat Rev Chem 2023; 7:536-547. [PMID: 37225920 DOI: 10.1038/s41570-023-00495-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/06/2023] [Indexed: 05/26/2023]
Abstract
In the early 2000s, Tawfik presented his 'New View' on enzyme evolution, highlighting the role of conformational plasticity in expanding the functional diversity of limited repertoires of sequences. This view is gaining increasing traction with increasing evidence of the importance of conformational dynamics in both natural and laboratory evolution of enzymes. The past years have seen several elegant examples of harnessing conformational (particularly loop) dynamics to successfully manipulate protein function. This Review revisits flexible loops as critical participants in regulating enzyme activity. We showcase several systems of particular interest: triosephosphate isomerase barrel proteins, protein tyrosine phosphatases and β-lactamases, while briefly discussing other systems in which loop dynamics are important for selectivity and turnover. We then discuss the implications for engineering, presenting examples of successful loop manipulation in either improving catalytic efficiency, or changing selectivity completely. Overall, it is becoming clearer that mimicking nature by manipulating the conformational dynamics of key protein loops is a powerful method of tailoring enzyme activity, without needing to target active-site residues.
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Affiliation(s)
- Marina Corbella
- Department of Chemistry, Uppsala University, Uppsala, Sweden
| | - Gaspar P Pinto
- Department of Chemistry, Uppsala University, Uppsala, Sweden
- Cortex Discovery GmbH, Regensburg, Germany
| | - Shina C L Kamerlin
- Department of Chemistry, Uppsala University, Uppsala, Sweden.
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA.
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5
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Veeramachineni VM, Ubayawardhana ST, Murkin AS. Kinetic characterization of methylthio-d-ribose-1-phosphate isomerase. Methods Enzymol 2023; 685:279-318. [PMID: 37245905 DOI: 10.1016/bs.mie.2023.03.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Methylthio-d-ribose-1-phosphate (MTR1P) isomerase (MtnA) catalyzes the reversible isomerization of the aldose MTR1P into the ketose methylthio-d-ribulose 1-phosphate. It serves as a member of the methionine salvage pathway that many organisms require for recycling methylthio-d-adenosine, a byproduct of S-adenosylmethionine metabolism, back to methionine. MtnA is of mechanistic interest because unlike most other aldose-ketose isomerases, its substrate exists as an anomeric phosphate ester and therefore cannot equilibrate with a ring-opened aldehyde that is otherwise required to promote isomerization. To investigate the mechanism of MtnA, it is necessary to establish reliable methods for determining the concentration of MTR1P and to measure enzyme activity in a continuous assay. This chapter describes several such protocols needed to perform steady-state kinetics measurements. It additionally outlines the preparation of [32P]MTR1P, its use in radioactively labeling the enzyme, and the characterization of the resulting phosphoryl adduct.
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Affiliation(s)
- Vamsee M Veeramachineni
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, NY, United States
| | - Subashi T Ubayawardhana
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, NY, United States
| | - Andrew S Murkin
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, NY, United States.
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6
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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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7
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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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8
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Romero-Rivera A, Corbella M, Parracino A, Patrick WM, Kamerlin SCL. Complex Loop Dynamics Underpin Activity, Specificity, and Evolvability in the (βα) 8 Barrel Enzymes of Histidine and Tryptophan Biosynthesis. JACS AU 2022; 2:943-960. [PMID: 35557756 PMCID: PMC9088769 DOI: 10.1021/jacsau.2c00063] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 03/16/2022] [Accepted: 03/18/2022] [Indexed: 05/16/2023]
Abstract
Enzymes are conformationally dynamic, and their dynamical properties play an important role in regulating their specificity and evolvability. In this context, substantial attention has been paid to the role of ligand-gated conformational changes in enzyme catalysis; however, such studies have focused on tremendously proficient enzymes such as triosephosphate isomerase and orotidine 5'-monophosphate decarboxylase, where the rapid (μs timescale) motion of a single loop dominates the transition between catalytically inactive and active conformations. In contrast, the (βα)8-barrels of tryptophan and histidine biosynthesis, such as the specialist isomerase enzymes HisA and TrpF, and the bifunctional isomerase PriA, are decorated by multiple long loops that undergo conformational transitions on the ms (or slower) timescale. Studying the interdependent motions of multiple slow loops, and their role in catalysis, poses a significant computational challenge. This work combines conventional and enhanced molecular dynamics simulations with empirical valence bond simulations to provide rich details of the conformational behavior of the catalytic loops in HisA, PriA, and TrpF, and the role of their plasticity in facilitating bifunctionality in PriA and evolved HisA variants. In addition, we demonstrate that, similar to other enzymes activated by ligand-gated conformational changes, loops 3 and 4 of HisA and PriA act as gripper loops, facilitating the isomerization of the large bulky substrate ProFAR, albeit now on much slower timescales. This hints at convergent evolution on these different (βα)8-barrel scaffolds. Finally, our work reemphasizes the potential of engineering loop dynamics as a tool to artificially manipulate the catalytic repertoire of TIM-barrel proteins.
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Affiliation(s)
- Adrian Romero-Rivera
- Department
of Chemistry—BMC, Uppsala University, BMC Box 576, S-751 23 Uppsala, Sweden
| | - Marina Corbella
- 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
| | - Wayne M. Patrick
- Centre
for Biodiscovery, School of Biological Sciences, Victoria University of Wellington, 6012 Wellington, New Zealand
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9
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Zhang H, Wen B, Liu Y, Du G, Wei X, Imam KMSU, Zhou H, Fan S, Wang F, Wang Y, Xin F. A reverse catalytic triad Asp containing loop shaping a wide substrate binding pocket of a feruloyl esterase from Lactobacillus plantarum. Int J Biol Macromol 2021; 184:92-100. [PMID: 34116094 DOI: 10.1016/j.ijbiomac.2021.06.033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 05/08/2021] [Accepted: 06/06/2021] [Indexed: 11/18/2022]
Abstract
Feruloyl esterase is an indispensable biocatalyst in food processing, pesticide and pharmaceutical industries, catalyzing the cleavage of the ester bond cross-linked between the polysaccharide side chain of hemicellulose and ferulic acid in plant cell walls. LP_0796 from Lactobacillus plantarum was identified as a feruloyl esterase that may have potential applications in the food industry, but the lack of the substrate recognition and catalytic mechanisms limits its application. Here, LP_0796 showed the highest activity towards methyl caffeate at pH 6.6 and 40 °C. The crystal structure of LP_0796 was determined at 2.5 Å resolution and featured a catalytic triad Asp195-containing loop facing the opposite direction, thus forming a wider substrate binding pocket. Molecular docking simulation and site-directed mutagenesis studies further demonstrated that in addition to the catalytic triad (Ser94, Asp195, His225), Arg125 and Val128 played essential roles in the function of the active site. Our data also showed that Asp mutation of Ala23 and Ile198 increased the catalytic efficiency to 4- and 5-fold, respectively. Collectively, this work provided a better understanding of the substrate recognition and catalytic mechanisms of LP_0796 and may facilitate the future protein design of this important feruloyl esterase.
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Affiliation(s)
- Haowen Zhang
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Boting Wen
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yusi Liu
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Guoming Du
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xue Wei
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Khandaker Md Sharif Uddin Imam
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Huan Zhou
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, China
| | - Shilong Fan
- Key Laboratory of Ministry of Education for Protein Science, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Fengzhong Wang
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yulu Wang
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Fengjiao Xin
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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10
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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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11
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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] [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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12
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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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13
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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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14
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Yildiz I, Sizirici Yildiz B. Computational mechanistic study of human liver glycerol 3‐phosphate dehydrogenase using ONIOM method. J PHYS ORG CHEM 2020. [DOI: 10.1002/poc.4104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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15
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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
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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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16
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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
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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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17
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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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18
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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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19
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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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20
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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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21
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Liao Q, Kulkarni Y, Sengupta U, Petrović D, Mulholland AJ, van der Kamp MW, Strodel B, Kamerlin SCL. Loop Motion in Triosephosphate Isomerase Is Not a Simple Open and Shut Case. J Am Chem Soc 2018; 140:15889-15903. [PMID: 30362343 DOI: 10.1021/jacs.8b09378] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Conformational changes are crucial for the catalytic action of many enzymes. A prototypical and well-studied example is loop opening and closure in triosephosphate isomerase (TIM), which is thought to determine the rate of catalytic turnover in many circumstances. Specifically, TIM loop 6 "grips" the phosphodianion of the substrate and, together with a change in loop 7, sets up the TIM active site for efficient catalysis. Crystal structures of TIM typically show an open or a closed conformation of loop 6, with the tip of the loop moving ∼7 Å between conformations. Many studies have interpreted this motion as a two-state, rigid-body transition. Here, we use extensive molecular dynamics simulations, with both conventional and enhanced sampling techniques, to analyze loop motion in apo and substrate-bound TIM in detail, using five crystal structures of the dimeric TIM from Saccharomyces cerevisiae. We find that loop 6 is highly flexible and samples multiple conformational states. Empirical valence bond simulations of the first reaction step show that slight displacements away from the fully closed-loop conformation can be sufficient to abolish most of the catalytic activity; full closure is required for efficient reaction. The conformational change of the loops in TIM is thus not a simple "open and shut" case and is crucial for its catalytic action. Our detailed analysis of loop motion in a highly efficient enzyme highlights the complexity of loop conformational changes and their role in biological catalysis.
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Affiliation(s)
- Qinghua Liao
- Department of Chemistry - BMC , Uppsala University , BMC Box 576, 751 23 Uppsala , Sweden
| | - Yashraj Kulkarni
- Department of Chemistry - BMC , Uppsala University , BMC Box 576, 751 23 Uppsala , Sweden
| | - Ushnish Sengupta
- Institute of Complex Systems: Structural Biochemistry (ICS-6) , Forschungszentrum Jülich , 52425 Jülich , Germany.,German Research School for Simulation Sciences , RWTH Aachen University , 52062 Aachen , Germany
| | - Dušan Petrović
- Department of Chemistry - BMC , Uppsala University , BMC Box 576, 751 23 Uppsala , Sweden.,Institute of Complex Systems: Structural Biochemistry (ICS-6) , Forschungszentrum Jülich , 52425 Jülich , Germany
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry , University of Bristol , Cantock's Close , BS8 1TS Bristol , United Kingdom
| | - Marc W van der Kamp
- Centre for Computational Chemistry, School of Chemistry , University of Bristol , Cantock's Close , BS8 1TS Bristol , United Kingdom.,School of Biochemistry , University of Bristol , University Walk , BS8 1TD Bristol , United Kingdom
| | - Birgit Strodel
- Institute of Complex Systems: Structural Biochemistry (ICS-6) , Forschungszentrum Jülich , 52425 Jülich , Germany.,Institute of Theoretical and Computational Chemistry , Heinrich Heine University Düsseldorf , 40225 Düsseldorf , Germany
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22
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Jimenez-Rosales A, Flores-Merino MV. Tailoring Proteins to Re-Evolve Nature: A Short Review. Mol Biotechnol 2018; 60:946-974. [DOI: 10.1007/s12033-018-0122-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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