1
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Rivoire O. A role for conformational changes in enzyme catalysis. Biophys J 2024; 123:1563-1578. [PMID: 38704639 PMCID: PMC11213973 DOI: 10.1016/j.bpj.2024.04.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 04/15/2024] [Accepted: 04/29/2024] [Indexed: 05/06/2024] Open
Abstract
The role played by conformational changes in enzyme catalysis is controversial. In addition to examining specific enzymes, studying formal models can help identify the conditions under which conformational changes promote catalysis. Here, we present a model demonstrating how conformational changes can break a generic trade-off due to the conflicting requirements of successive steps in catalytic cycles, namely high specificity for the transition state to accelerate the chemical transformation and low affinity for the products to favor their release. The mechanism by which the trade-off is broken is a transition between conformations with different affinities for the substrate. The role of the effector that induces the transition is played by a substrate "handle," a part of the substrate that is not chemically transformed but whose interaction with the enzyme is nevertheless essential to rapidly complete the catalytic cycle. A key element of the model is the formalization of the constraints causing the trade-off that the presence of multiple states breaks, which we attribute to the strong chemical similarity between successive reaction states-substrates, transition states, and products. For the sake of clarity, we present our model for irreversible one-step unimolecular reactions. In this context, we demonstrate how the different forms that chemical similarities between reaction states can take impose limits on the overall catalytic turnover. We first analyze catalysts without internal degrees of freedom and then show how two-state catalysts can overcome their limitations. Our results recapitulate previous proposals concerning the role of conformational changes and substrate handles in a formalism that makes explicit the constraints that elicit these features. In addition, our approach establishes links with studies in the field of heterogeneous catalysis, where the same trade-offs are observed and where overcoming them is a well-recognized challenge.
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2
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Alnajjar K, Wang K, Alvarado-Cruz I, Chavira C, Negahbani A, Nakhjiri M, Minard C, Garcia-Barboza B, Kashemirov BA, McKenna CE, Goodman MF, Sweasy JB. Modifying the Basicity of the dNTP Leaving Group Modulates Precatalytic Conformational Changes of DNA Polymerase β. Biochemistry 2024; 63:1412-1422. [PMID: 38780930 PMCID: PMC11155676 DOI: 10.1021/acs.biochem.4c00065] [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: 02/03/2024] [Revised: 05/15/2024] [Accepted: 05/16/2024] [Indexed: 05/25/2024]
Abstract
The catalytic function of DNA polymerase β (pol β) fulfills the gap-filling requirement of the base excision DNA repair pathway by incorporating a single nucleotide into a gapped DNA substrate resulting from the removal of damaged DNA bases. Most importantly, pol β can select the correct nucleotide from a pool of similarly structured nucleotides to incorporate into DNA in order to prevent the accumulation of mutations in the genome. Pol β is likely to employ various mechanisms for substrate selection. Here, we use dCTP analogues that have been modified at the β,γ-bridging group of the triphosphate moiety to monitor the effect of leaving group basicity of the incoming nucleotide on precatalytic conformational changes, which are important for catalysis and selectivity. It has been previously shown that there is a linear free energy relationship between leaving group pKa and the chemical transition state. Our results indicate that there is a similar relationship with the rate of a precatalytic conformational change, specifically, the closing of the fingers subdomain of pol β. In addition, by utilizing analogue β,γ-CHX stereoisomers, we identified that the orientation of the β,γ-bridging group relative to R183 is important for the rate of fingers closing, which directly influences chemistry.
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Affiliation(s)
- Khadijeh
S. Alnajjar
- Department
of Cellular and Molecular Medicine, University
of Arizona Cancer Center, University of Arizona, Tucson, Arizona 85724, United States
| | - Katarina Wang
- Therapeutic
Radiology Department, Yale University, New Haven, Connecticut 06520, United States
| | - Isabel Alvarado-Cruz
- Department
of Cellular and Molecular Medicine, University
of Arizona Cancer Center, University of Arizona, Tucson, Arizona 85724, United States
| | - Cristian Chavira
- Fred
and Pamela Buffett Cancer Center and Eppley Institute for Cancer Research, Omaha, Nebraska 68198, United States
- Department
of Cellular and Molecular Medicine, University
of Arizona Cancer Center, University of Arizona, Tucson, Arizona 85724, United States
| | - Amirsoheil Negahbani
- Department
of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Maryam Nakhjiri
- Department
of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Corinne Minard
- Department
of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Beatriz Garcia-Barboza
- Department
of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Boris A. Kashemirov
- Department
of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Charles E. McKenna
- Department
of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Myron F. Goodman
- Department
of Chemistry, University of Southern California, Los Angeles, California 90089, United States
- Department
of Biological Sciences, University of Southern
California, Los Angeles, California 90089, United States
| | - Joann B. Sweasy
- Fred
and Pamela Buffett Cancer Center and Eppley Institute for Cancer Research, Omaha, Nebraska 68198, United States
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3
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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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4
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Chamberlain AR, Huynh L, Huang W, Taylor DJ, Harris ME. The specificity landscape of bacterial ribonuclease P. J Biol Chem 2024; 300:105498. [PMID: 38013087 PMCID: PMC10731613 DOI: 10.1016/j.jbc.2023.105498] [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] [Received: 07/24/2023] [Revised: 11/14/2023] [Accepted: 11/17/2023] [Indexed: 11/29/2023] Open
Abstract
Developing quantitative models of substrate specificity for RNA processing enzymes is a key step toward understanding their biology and guiding applications in biotechnology and biomedicine. Optimally, models to predict relative rate constants for alternative substrates should integrate an understanding of structures of the enzyme bound to "fast" and "slow" substrates, large datasets of rate constants for alternative substrates, and transcriptomic data identifying in vivo processing sites. Such data are either available or emerging for bacterial ribonucleoprotein RNase P a widespread and essential tRNA 5' processing endonuclease, thus making it a valuable model system for investigating principles of biological specificity. Indeed, the well-established structure and kinetics of bacterial RNase P enabled the development of high throughput measurements of rate constants for tRNA variants and provided the necessary framework for quantitative specificity modeling. Several studies document the importance of conformational changes in the precursor tRNA substrate as well as the RNA and protein subunits of bacterial RNase P during binding, although the functional roles and dynamics are still being resolved. Recently, results from cryo-EM studies of E. coli RNase P with alternative precursor tRNAs are revealing prospective mechanistic relationships between conformational changes and substrate specificity. Yet, extensive uncharted territory remains, including leveraging these advances for drug discovery, achieving a complete accounting of RNase P substrates, and understanding how the cellular context contributes to RNA processing specificity in vivo.
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Affiliation(s)
| | - Loc Huynh
- Department of Chemistry, University of Florida, Gainesville, Florida, USA
| | - Wei Huang
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Derek J Taylor
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Michael E Harris
- Department of Chemistry, University of Florida, Gainesville, Florida, USA.
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5
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Dangerfield TL, Johnson KA. Design and interpretation of experiments to establish enzyme pathway and define the role of conformational changes in enzyme specificity. Methods Enzymol 2023; 685:461-492. [PMID: 37245912 DOI: 10.1016/bs.mie.2023.03.018] [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
We describe the experimental methods and analysis to define the role of enzyme conformational changes in specificity based on published studies using DNA polymerases as an ideal model system. Rather than give details of how to perform transient-state and single-turnover kinetic experiments, we focus on the rationale of the experimental design and interpretation. We show how initial experiments to measure kcat and kcat/Km can accurately quantify specificity but do not define its underlying mechanistic basis. We describe methods to fluorescently label enzymes to monitor conformational changes and to correlate fluorescence signals with rapid-chemical-quench flow assays to define the steps in the pathway. Measurements of the rate of product release and of the kinetics of the reverse reaction complete the kinetic and thermodynamic description of the full reaction pathway. This analysis showed that the substrate-induced change in enzyme structure from an open to a closed state was much faster than rate-limiting chemical bond formation. However, because the reverse of the conformational change was much slower than chemistry, specificity is governed solely by the product of the binding constant for the initial weak substrate binding and the rate constant for the conformational change (kcat/Km=K1k2) so that the specificity constant does not include kcat. The enzyme conformational change leads to a closed complex in which the substrate is bound tightly and is committed to the forward reaction. In contrast, an incorrect substrate is bound weakly, and the rate of chemistry is slow, so the mismatch is released from the enzyme rapidly. Thus, the substrate-induced-fit is the major determinant of specificity. The methods outlined here should be applicable to other enzyme systems.
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Affiliation(s)
- Tyler L Dangerfield
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, United States
| | - Kenneth A Johnson
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, United States.
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6
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Structural and mechanistic basis for recognition of alternative tRNA precursor substrates by bacterial ribonuclease P. Nat Commun 2022; 13:5120. [PMID: 36045135 PMCID: PMC9433436 DOI: 10.1038/s41467-022-32843-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 08/19/2022] [Indexed: 11/25/2022] Open
Abstract
Binding of precursor tRNAs (ptRNAs) by bacterial ribonuclease P (RNase P) involves an encounter complex (ES) that isomerizes to a catalytic conformation (ES*). However, the structures of intermediates and the conformational changes that occur during binding are poorly understood. Here, we show that pairing between the 5′ leader and 3′RCCA extending the acceptor stem of ptRNA inhibits ES* formation. Cryo-electron microscopy single particle analysis reveals a dynamic enzyme that becomes ordered upon formation of ES* in which extended acceptor stem pairing is unwound. Comparisons of structures with alternative ptRNAs reveals that once unwinding is completed RNase P primarily uses stacking interactions and shape complementarity to accommodate alternative sequences at its cleavage site. Our study reveals active site interactions and conformational changes that drive molecular recognition by RNase P and lays the foundation for understanding how binding interactions are linked to helix unwinding and catalysis. Ribonuclease P efficiently processes all tRNA precursors despite sequence variation at the site of cleavage. Here, authors use high-throughput enzymology and cryoEM to reveal conformational changes that drive recognition by bacterial RNase P.
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7
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Dangerfield TL, Kirmizialtin S, Johnson KA. Conformational dynamics during misincorporation and mismatch extension defined using a DNA polymerase with a fluorescent artificial amino acid. J Biol Chem 2021; 298:101451. [PMID: 34838820 PMCID: PMC8715121 DOI: 10.1016/j.jbc.2021.101451] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 09/09/2021] [Accepted: 11/23/2021] [Indexed: 11/29/2022] Open
Abstract
High-fidelity DNA polymerases select the correct nucleotide over the structurally similar incorrect nucleotides with extremely high specificity while maintaining fast rates of incorporation. Previous analysis revealed the conformational dynamics and complete kinetic pathway governing correct nucleotide incorporation using a high-fidelity DNA polymerase variant containing a fluorescent unnatural amino acid. Here we extend this analysis to investigate the kinetics of nucleotide misincorporation and mismatch extension. We report the specificity constants for all possible misincorporations and characterize the conformational dynamics of the enzyme during misincorporation and mismatch extension. We present free energy profiles based on the kinetic measurements and discuss the effect of different steps on specificity. During mismatch incorporation and subsequent extension with the correct nucleotide, the rates of the conformational change and chemistry are both greatly reduced. The nucleotide dissociation rate, however, increases to exceed the rate of chemistry. To investigate the structural basis for discrimination against mismatched nucleotides, we performed all atom molecular dynamics simulations on complexes with either the correct or mismatched nucleotide bound at the polymerase active site. The simulations suggest that the closed form of the enzyme with a mismatch bound is greatly destabilized due to weaker interactions with active site residues, nonideal base pairing, and a large increase in the distance from the 3'-OH group of the primer strand to the α-phosphate of the incoming nucleotide, explaining the reduced rates of misincorporation. The observed kinetic and structural mechanisms governing nucleotide misincorporation reveal the general principles likely applicable to other high-fidelity DNA polymerases.
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Affiliation(s)
- Tyler L Dangerfield
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas, Austin, Texas, USA
| | - Serdal Kirmizialtin
- Chemistry Program, Division of Science, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Kenneth A Johnson
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas, Austin, Texas, USA.
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8
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Kassab SE, Mowafy S. Structural Basis of Selective Human Indoleamine-2,3-dioxygenase 1 (hIDO1) Inhibition. ChemMedChem 2021; 16:3149-3164. [PMID: 34174026 DOI: 10.1002/cmdc.202100253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 06/23/2021] [Indexed: 11/08/2022]
Abstract
hIDO1 is a heme-dioxygenase overexpressed in the tumor microenvironment and is implicated in the survival of cancer cells. Metabolism of tryptophan to N-formyl-kynurenine by hIDO1 leads to immune suppression to result in cancer cell immune escape. In this article, we discuss the discovery of selective hIDO1 inhibitors for therapeutic intervention that have been promoted to clinical trials and for which crystallographic structural information is available for the respective inhibitor-enzyme complex. The structural insights are based on the complex crystal structures and the relative biological data profiles. The structural basis of selective hIDO1 inhibition, as discussed herein, opens new avenues to the discovery of novel inhibitors with improved activity profiles, selectivity, and distinct structure frameworks.
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Affiliation(s)
- Shaymaa Emam Kassab
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Damanhour University, Damanhour, El-Buhaira, 22516, Egypt
| | - Samar Mowafy
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Misr International University, Cairo, 11431, Egypt.,Department of Chemistry, University of Washington, Seattle, Washington, 98195, United States of America
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9
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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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10
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Abstract
In this chapter we consider the catalytic approaches used by aminoacyl-tRNA synthetase (AARS) enzymes to synthesize aminoacyl-tRNA from cognate amino acid and tRNA. This ligase reaction proceeds through an activated aminoacyl-adenylate (aa-AMP). Common themes among AARSs include use of induced fit to drive catalysis and transition state stabilization by class-conserved sequence and structure motifs. Active site metal ions contribute to the amino acid activation step, while amino acid transfer to tRNA is generally a substrate-assisted concerted mechanism. A distinction between classes is the rate-limiting step for aminoacylation. We present some examples for each aspect of aminoacylation catalysis, including the experimental approaches developed to address questions of AARS chemistry.
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11
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Kirst C, Zoller F, Bräuniger T, Mayer P, Fattakhova-Rohlfing D, Karaghiosoff K. Investigation of Structural Changes of Cu(I) and Ag(I) Complexes Utilizing a Flexible, Yet Sterically Demanding Multidentate Phosphine Oxide Ligand. Inorg Chem 2021; 60:2437-2445. [PMID: 33534576 DOI: 10.1021/acs.inorgchem.0c03334] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The syntheses of a sterically demanding, multidentate bis(quinaldinyl)phenylphosphine oxide ligand and some Cu(I) and Ag(I) complexes thereof are described. By introducing a methylene group between the quinoline unit and phosphorus, the phosphine oxide ligand gains additional flexibility. This specific ligand design induces not only a versatile coordination chemistry but also a rarely observed and investigated behavior in solution. The flexibility of the birdlike ligand offers the unexpected opportunity of open-wing and closed-wing coordination to the metal. In fact, the determined crystal structures of these complexes show both orientations. Investigations of the ligand in solution show a strong dependency of the chemical shift of the CH2 protons on the solvent used. Variable-temperature, multinuclear NMR spectroscopy was carried out, and an interesting dynamic behavior of the complexes is observed. Due to the introduced flexibility, the quinaldinyl substituents change their arrangements from open-wing to closed-wing upon cooling, while still staying coordinated to the metal. This change in conformation is completely reversible when warming up the sample. Based on 2D NMR spectra measured at -80 °C, an assignment of the signals corresponding to the different arrangements was possible. Additionally, the copper(I) complex shows reversible redox activity in solution. The combination of structural flexibility of a multidentate ligand and the positive redox properties of the resulting complexes comprises key factors for a possible application of such compounds in transition-metal catalysis. Via a reorganization of the ligand, occurring transition states could be stabilized, and selectivity might be enhanced.
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Affiliation(s)
- Christin Kirst
- Department of Chemistry, Ludwig Maximilian University of Munich, Butenandtstraße 5-13, DE 81377 Munich, Germany
| | - Florian Zoller
- Department of Chemistry, Ludwig Maximilian University of Munich, Butenandtstraße 5-13, DE 81377 Munich, Germany.,Institute of Energy and Climate Research (IEK-1): Materials Synthesis and Processing, Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Straße, 52425 Jülich, Germany.,Faculty of Engineering and Center for Nanointegration Duisburg-Essen (CENIDE), Universität Duisburg-Essen, Lotharstraße 1, 47057 Duisburg, Germany
| | - Thomas Bräuniger
- Department of Chemistry, Ludwig Maximilian University of Munich, Butenandtstraße 5-13, DE 81377 Munich, Germany
| | - Peter Mayer
- Department of Chemistry, Ludwig Maximilian University of Munich, Butenandtstraße 5-13, DE 81377 Munich, Germany
| | - Dina Fattakhova-Rohlfing
- Institute of Energy and Climate Research (IEK-1): Materials Synthesis and Processing, Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Straße, 52425 Jülich, Germany.,Faculty of Engineering and Center for Nanointegration Duisburg-Essen (CENIDE), Universität Duisburg-Essen, Lotharstraße 1, 47057 Duisburg, Germany
| | - Konstantin Karaghiosoff
- Department of Chemistry, Ludwig Maximilian University of Munich, Butenandtstraße 5-13, DE 81377 Munich, Germany
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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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Egawa T, Callender R. General mathematical formula for near equilibrium relaxation kinetics of basic enzyme reactions and its applications to find conformational selection steps. Math Biosci 2019; 313:61-70. [PMID: 30935841 DOI: 10.1016/j.mbs.2019.03.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 03/27/2019] [Accepted: 03/27/2019] [Indexed: 10/27/2022]
Abstract
A general mathematical formula of basic enzyme reactions was derived with nearly no dependence on conditions nor assumptions on relaxation kinetic processes near equilibrium in a simple single-substrate-single-product enzyme reaction. The new formula gives precise relationships between the rate constants of the elementary reaction steps and the apparent relaxation rate constant, rather than the initial velocity that is generally used to determine enzymatic parameters according to the Michaelis-Menten theory. The present formula is shown to be complementary to the Michaelis-Menten formulae in a sense that the initial velocity and the relaxation rate constant data together could determine the enzyme-substrate dissociation constant KES, which has been usually conditionally approximated by the Michaelis constant KM within the framework of the Michaelis-Menten formulae. We also describe relaxation kinetics of enzyme reactions that include the conformational selection processes, in which only one enzymatic conformer among a conformational ensemble can bind with either the substrate or product. The present mathematical approaches, together with numerical computation analyses, suggested that the presence of conformational selection steps in enzymatic reactions can be experimentally detected simply by enzymatic assays with catalytic amounts of enzyme.
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Affiliation(s)
- Tsuyoshi Egawa
- Department of Biochemistry, Albert Einstein College of Medicine, United States.
| | - Robert Callender
- Department of Biochemistry, Albert Einstein College of Medicine, United States.
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14
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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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15
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Johnson KA. New standards for collecting and fitting steady state kinetic data. Beilstein J Org Chem 2019; 15:16-29. [PMID: 30680035 PMCID: PMC6334795 DOI: 10.3762/bjoc.15.2] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 12/04/2018] [Indexed: 11/23/2022] Open
Abstract
The Michaelis-Menten equation is usually expressed in terms of k cat and K m values: v = k cat[S]/(K m + [S]). However, it is impossible to interpret K m in the absence of additional information, while the ratio of k cat/K m provides a measure of enzyme specificity and is proportional to enzyme efficiency and proficiency. Moreover, k cat/K m provides a lower limit on the second order rate constant for substrate binding. For these reasons it is better to redefine the Michaelis-Menten equation in terms of k cat and k cat/K m values: v = k SP[S]/(1 + k SP[S]/k cat), where the specificity constant, k SP = k cat/K m. In this short review, the rationale for this assertion is explained and it is shown that more accurate measurements of k cat/K m can be derived directly using the modified form of the Michaelis-Menten equation rather than calculated from the ratio of k cat and K m values measured separately. Even greater accuracy is achieved with fitting the raw data directly by numerical integration of the rate equations rather than using analytically derived equations. The importance of fitting to derive k cat and k cat/K m is illustrated by considering the role of conformational changes in enzyme specificity where k cat and k cat/K m can reflect different steps in the pathway. This highlights the pitfalls in attempting to interpret K m, which is best understood as the ratio of k cat divided by k cat/K m.
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Affiliation(s)
- Kenneth A Johnson
- Department of Molecular Biosciences, The University of Texas, Austin, TX 78735, USA
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16
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Peracchi A. The Limits of Enzyme Specificity and the Evolution of Metabolism. Trends Biochem Sci 2018; 43:984-996. [DOI: 10.1016/j.tibs.2018.09.015] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Revised: 09/16/2018] [Accepted: 09/19/2018] [Indexed: 12/23/2022]
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17
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Richard JP, Amyes TL, Reyes AC. Orotidine 5'-Monophosphate Decarboxylase: Probing the Limits of the Possible for Enzyme Catalysis. Acc Chem Res 2018; 51:960-969. [PMID: 29595949 PMCID: PMC6016548 DOI: 10.1021/acs.accounts.8b00059] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
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The mystery associated with catalysis by what were once regarded
as protein black boxes, diminished with the X-ray crystallographic
determination of the three-dimensional structures of enzyme–substrate
complexes. The report that several high-resolution X-ray crystal structures
of orotidine 5′-monophosphate decarboxylase (OMPDC) failed
to provide a consensus mechanism for enzyme-catalyzed decarboxylation
of OMP to form uridine 5′-monophosphate, therefore, provoked
a flurry of controversy. This controversy was fueled by the enormous
1023-fold rate acceleration for this enzyme, which had
“jolted many biochemists’ assumptions about
the catalytic potential of enzymes.” Our studies on
the mechanism of action of OMPDC provide strong evidence that catalysis
by this enzyme is not fundamentally different from less proficient
catalysts, while highlighting important architectural elements that
enable a peak level of performance. Many enzymes undergo substrate-induced
protein conformational changes that trap their substrates in solvent
occluded protein cages, but the conformational change induced by ligand
binding to OMPDC is incredibly complex, as required to enable the
development of 22 kcal/mol of stabilizing binding interactions with
the phosphodianion and ribosyl substrate fragments of OMP. The binding
energy from these fragments is utilized to activate OMPDC for catalysis
of decarboxylation at the orotate fragment of OMP, through the creation
of a tight, catalytically active, protein cage from the floppy, open,
unliganded form of OMPDC. Such utilization of binding energy for ligand-driven
conformational changes provides a general mechanism to obtain specificity
in transition state binding. The rate enhancement that results from
the binding of carbon acid substrates to enzymes is partly due to
a reduction in the carbon acid pKa that
is associated with ligand binding. The binding of UMP to OMPDC results
in an unusually large >12 unit decrease in the pKa = 29 for abstraction of the C-6 substrate hydrogen,
due to stabilization of an enzyme-bound vinyl carbanion, which is
also an intermediate of OMPDC-catalyzed decarboxylation. The protein–ligand
interactions operate to stabilize the vinyl carbanion at the enzyme
active site compared to aqueous solution, rather than to stabilize
the transition state for the concerted electrophilic displacement
of CO2 by H+ that avoids formation of this reaction
intermediate. There is evidence that OMPDC induces strain into the
bound substrate. The interaction between the amide side chain of Gln-215
from the phosphodianion gripper loop and the hydroxymethylene side
chain of Ser-154 from the pyrimidine umbrella of ScOMPDC position the amide side chain to interact with the phosphodianion
of OMP. There are no direct stabilizing interactions between dianion
gripper protein side chains Gln-215, Tyr-217, and Arg-235 and the
pyrimidine ring at the decarboxylation transition state. Rather these
side chains function solely to hold OMPDC in the catalytically active
closed conformation. The hydrophobic side chains that line the active
site of OMPDC in the region of the departing CO2 product
may function to stabilize the decarboxylation transition state by
providing hydrophobic solvation of this product.
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Affiliation(s)
- John P. Richard
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
| | - Tina L. Amyes
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
| | - Archie C. Reyes
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
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18
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Kulkarni YS, Liao Q, Byléhn F, Amyes TL, Richard JP, Kamerlin SCL. Role of Ligand-Driven Conformational Changes in Enzyme Catalysis: Modeling the Reactivity of the Catalytic Cage of Triosephosphate Isomerase. J Am Chem Soc 2018. [PMID: 29516737 PMCID: PMC5867644 DOI: 10.1021/jacs.8b00251] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
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We have previously performed empirical
valence bond calculations
of the kinetic activation barriers, ΔG‡calc, for the deprotonation of complexes
between TIM and the whole substrate glyceraldehyde-3-phosphate (GAP, Kulkarni et al.2017, 139, 10514–1052528683550). We now extend
this work to also study the deprotonation of the substrate pieces
glycolaldehyde (GA) and GA·HPi [HPi = phosphite
dianion]. Our combined calculations provide activation barriers, ΔG‡calc, for the TIM-catalyzed
deprotonation of GAP (12.9 ± 0.8 kcal·mol–1), of the substrate piece GA (15.0 ± 2.4 kcal·mol–1), and of the pieces GA·HPi (15.5 ± 3.5 kcal·mol–1). The effect of bound dianion on ΔG‡calc is small (≤2.6 kcal·mol–1), in comparison to the much larger 12.0 and 5.8 kcal·mol–1 intrinsic phosphodianion and phosphite dianion binding
energy utilized to stabilize the transition states for TIM-catalyzed
deprotonation of GAP and GA·HPi, respectively. This
shows that the dianion binding energy is essentially fully expressed
at our protein model for the Michaelis complex, where it is utilized
to drive an activating change in enzyme conformation. The results
represent an example of the synergistic use of results from experiments
and calculations to advance our understanding of enzymatic reaction
mechanisms.
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Affiliation(s)
- Yashraj S Kulkarni
- Science for Life Laboratory, Department of Cell and Molecular Biology , Uppsala University , BMC Box 596, S-751 24 Uppsala , Sweden
| | - Qinghua Liao
- Science for Life Laboratory, Department of Cell and Molecular Biology , Uppsala University , BMC Box 596, S-751 24 Uppsala , Sweden
| | - Fabian Byléhn
- Science for Life Laboratory, Department of Cell and Molecular Biology , Uppsala University , BMC Box 596, S-751 24 Uppsala , Sweden.,Department of Chemical Engineering , University College London , Torrington Place , London WC1E 7JE , United Kingdom
| | - Tina L Amyes
- Department of Chemistry , University at Buffalo, SUNY , Buffalo , New York 14260-3000 , United States
| | - John P Richard
- Department of Chemistry , University at Buffalo, SUNY , Buffalo , New York 14260-3000 , United States
| | - Shina C L Kamerlin
- Science for Life Laboratory, Department of Cell and Molecular Biology , Uppsala University , BMC Box 596, S-751 24 Uppsala , Sweden
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19
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Endrizzi JA, Beernink PT. Charge neutralization in the active site of the catalytic trimer of aspartate transcarbamoylase promotes diverse structural changes. Protein Sci 2017; 26:2221-2228. [PMID: 28833948 DOI: 10.1002/pro.3277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 08/14/2017] [Indexed: 11/05/2022]
Abstract
A classical model for allosteric regulation of enzyme activity posits an equilibrium between inactive and active conformations. An alternative view is that allosteric activation is achieved by increasing the potential for conformational changes that are essential for catalysis. In the present study, substitution of a basic residue in the active site of the catalytic (C) trimer of aspartate transcarbamoylase with a non-polar residue results in large interdomain hinge changes in the three chains of the trimer. One conformation is more open than the chains in both the wild-type C trimer and the catalytic chains in the holoenzyme, the second is closed similar to the bisubstrate-analog bound conformation and the third hinge angle is intermediate to the other two. The active-site 240s loop conformation is very different between the most open and closed chains, and is disordered in the third chain, as in the holoenzyme. We hypothesize that binding of anionic substrates may promote similar structural changes. Further, the ability of the three catalytic chains in the trimer to access the open and closed active-site conformations simultaneously suggests a cyclic catalytic mechanism, in which at least one of the chains is in an open conformation suitable for substrate binding whereas another chain is closed for catalytic turnover. Based on the many conformations observed for the chains in the isolated catalytic trimer to date, we propose that allosteric activation of the holoenzyme occurs by release of quaternary constraint into an ensemble of active-site conformations.
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Affiliation(s)
| | - Peter T Beernink
- Children's Hospital Oakland Research Institute, UCSF Benioff Children's Hospital, Oakland, California.,Department of Pediatrics, School of Medicine, University of California, San Francisco, San Francisco, California
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20
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Han H, Huang Q, Liu H, Zhang J. Highly Efficient Cofactors of Cu 2+
-Dependent Deoxyribozymes. ChemistrySelect 2017. [DOI: 10.1002/slct.201700424] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Haiyan Han
- School of Pharmacy; East China University of Science and Technology; No. 130 Meilong Road, Xuhui District Shanghai 200237 P. R. China
| | - Qiping Huang
- School of Pharmacy; East China University of Science and Technology; No. 130 Meilong Road, Xuhui District Shanghai 200237 P. R. China
| | - Hui Liu
- School of Pharmacy; East China University of Science and Technology; No. 130 Meilong Road, Xuhui District Shanghai 200237 P. R. China
| | - Jingyan Zhang
- School of Pharmacy; East China University of Science and Technology; No. 130 Meilong Road, Xuhui District Shanghai 200237 P. R. China
- Department of Biochemistry, Molecular Biology, and Biophysics, and the Center for Metals in Biocatalysis; University of Minnesota; Minneapolis, MN 55455 USA
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21
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Lehmann J. Induced fit of the peptidyl-transferase center of the ribosome and conformational freedom of the esterified amino acids. RNA (NEW YORK, N.Y.) 2017; 23:229-239. [PMID: 27879432 PMCID: PMC5238797 DOI: 10.1261/rna.057273.116] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 11/18/2016] [Indexed: 06/06/2023]
Abstract
The catalytic site of most enzymes can efficiently handle only one substrate. In contrast, the ribosome is capable of polymerizing at a similar rate at least 20 different kinds of amino acids from aminoacyl-tRNA carriers while using just one catalytic site, the peptidyl-transferase center (PTC). An induced-fit mechanism has been uncovered in the PTC, but a possible connection between this mechanism and the uniform handling of the substrates has not been investigated. We present an analysis of published ribosome structures supporting the hypothesis that the induced fit eliminates unreactive rotamers predominantly populated for some A-site aminoacyl esters before induction. We show that this hypothesis is fully consistent with the wealth of kinetic data obtained with these substrates. Our analysis reveals that induction constrains the amino acids into a reactive conformation in a side-chain independent manner. It allows us to highlight the rationale of the PTC structural organization, which confers to the ribosome the very unusual ability to handle large as well as small substrates.
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Affiliation(s)
- Jean Lehmann
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Campus Paris-Saclay, 91198 Gif-sur-Yvette, France
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22
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Bisaria N, Jarmoskaite I, Herschlag D. Lessons from Enzyme Kinetics Reveal Specificity Principles for RNA-Guided Nucleases in RNA Interference and CRISPR-Based Genome Editing. Cell Syst 2017; 4:21-29. [PMID: 28125791 PMCID: PMC5308874 DOI: 10.1016/j.cels.2016.12.010] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 09/15/2016] [Accepted: 12/09/2016] [Indexed: 12/26/2022]
Abstract
RNA-guided nucleases (RGNs) provide sequence-specific gene regulation through base-pairing interactions between a small RNA guide and target RNA or DNA. RGN systems, which include CRISPR-Cas9 and RNA interference (RNAi), hold tremendous promise as programmable tools for engineering and therapeutic purposes. However, pervasive targeting of sequences that closely resemble the intended target has remained a major challenge, limiting the reliability and interpretation of RGN activity and the range of possible applications. Efforts to reduce off-target activity and enhance RGN specificity have led to a collection of empirically derived rules, which often paradoxically include decreased binding affinity of the RNA-guided nuclease to its target. We consider the kinetics of these reactions and show that basic kinetic properties can explain the specificities observed in the literature and the changes in these specificities in engineered systems. The kinetic models described provide a foundation for understanding RGN targeting and a necessary conceptual framework for their rational engineering.
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Affiliation(s)
- Namita Bisaria
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - Inga Jarmoskaite
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - Daniel Herschlag
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA; Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA; Department of Chemistry, Stanford University, Stanford, CA 94305, USA; Stanford ChEM-H, Stanford University, Stanford, CA 94305, USA.
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23
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Metrano A, Abascal NC, Mercado BQ, Paulson EK, Hurtley AE, Miller SJ. Diversity of Secondary Structure in Catalytic Peptides with β-Turn-Biased Sequences. J Am Chem Soc 2017; 139:492-516. [PMID: 28029251 PMCID: PMC5312972 DOI: 10.1021/jacs.6b11348] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Indexed: 11/30/2022]
Abstract
X-ray crystallography has been applied to the structural analysis of a series of tetrapeptides that were previously assessed for catalytic activity in an atroposelective bromination reaction. Common to the series is a central Pro-Xaa sequence, where Pro is either l- or d-proline, which was chosen to favor nucleation of canonical β-turn secondary structures. Crystallographic analysis of 35 different peptide sequences revealed a range of conformational states. The observed differences appear not only in cases where the Pro-Xaa loop-region is altered, but also when seemingly subtle alterations to the flanking residues are introduced. In many instances, distinct conformers of the same sequence were observed, either as symmetry-independent molecules within the same unit cell or as polymorphs. Computational studies using DFT provided additional insight into the analysis of solid-state structural features. Select X-ray crystal structures were compared to the corresponding solution structures derived from measured proton chemical shifts, 3J-values, and 1H-1H-NOESY contacts. These findings imply that the conformational space available to simple peptide-based catalysts is more diverse than precedent might suggest. The direct observation of multiple ground state conformations for peptides of this family, as well as the dynamic processes associated with conformational equilibria, underscore not only the challenge of designing peptide-based catalysts, but also the difficulty in predicting their accessible transition states. These findings implicate the advantages of low-barrier interconversions between conformations of peptide-based catalysts for multistep, enantioselective reactions.
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Affiliation(s)
- Anthony
J. Metrano
- Department of Chemistry, Yale University, P.O.
Box 208107, New Haven, Connecticut 06520-8107, United States
| | - Nadia C. Abascal
- Department of Chemistry, Yale University, P.O.
Box 208107, New Haven, Connecticut 06520-8107, United States
| | - Brandon Q. Mercado
- Department of Chemistry, Yale University, P.O.
Box 208107, New Haven, Connecticut 06520-8107, United States
| | - Eric K. Paulson
- Department of Chemistry, Yale University, P.O.
Box 208107, New Haven, Connecticut 06520-8107, United States
| | - Anna E. Hurtley
- Department of Chemistry, Yale University, P.O.
Box 208107, New Haven, Connecticut 06520-8107, United States
| | - Scott J. Miller
- Department of Chemistry, Yale University, P.O.
Box 208107, New Haven, Connecticut 06520-8107, United States
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24
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Shears SB, Baughman BM, Gu C, Nair VS, Wang H. The significance of the 1-kinase/1-phosphatase activities of the PPIP5K family. Adv Biol Regul 2016; 63:98-106. [PMID: 27776974 DOI: 10.1016/j.jbior.2016.10.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2016] [Revised: 10/13/2016] [Accepted: 10/15/2016] [Indexed: 01/29/2023]
Abstract
The inositol pyrophosphates (diphosphoinositol polyphosphates), which include 1-InsP7, 5-InsP7, and InsP8, are highly 'energetic' signaling molecules that play important roles in many cellular processes, particularly with regards to phosphate and bioenergetic homeostasis. Two classes of kinases synthesize the PP-InsPs: IP6Ks and PPIP5Ks. The significance of the IP6Ks - and their 5-InsP7 product - has been widely reported. However, relatively little is known about the biological significance of the PPIP5Ks. The purpose of this review is to provide an update on developments in our understanding of key features of the PPIP5Ks, which we believe strengthens the hypothesis that their catalytic activities serve important cellular functions. Central to this discussion is the recent discovery that the PPIP5K is a rare example of a single protein that catalyzes a kinase/phosphatase futile cycle.
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Affiliation(s)
- Stephen B Shears
- Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, National Institutes of Health, 101 T.W. Alexander Drive, Research Triangle Park, NC, 27709, USA.
| | - Brandi M Baughman
- Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, National Institutes of Health, 101 T.W. Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Chunfang Gu
- Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, National Institutes of Health, 101 T.W. Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Vasudha S Nair
- Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, National Institutes of Health, 101 T.W. Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Huanchen Wang
- Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, National Institutes of Health, 101 T.W. Alexander Drive, Research Triangle Park, NC, 27709, USA
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25
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Niland CN, Zhao J, Lin HC, Anderson DR, Jankowsky E, Harris ME. Determination of the Specificity Landscape for Ribonuclease P Processing of Precursor tRNA 5' Leader Sequences. ACS Chem Biol 2016; 11:2285-92. [PMID: 27336323 DOI: 10.1021/acschembio.6b00275] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Maturation of tRNA depends on a single endonuclease, ribonuclease P (RNase P), to remove highly variable 5' leader sequences from precursor tRNA transcripts. Here, we use high-throughput enzymology to report multiple-turnover and single-turnover kinetics for Escherichia coli RNase P processing of all possible 5' leader sequences, including nucleotides contacting both the RNA and protein subunits of RNase P. The results reveal that the identity of N(-2) and N(-3) relative to the cleavage site at N(1) primarily control alternative substrate selection and act at the level of association not the cleavage step. As a consequence, the specificity for N(-1), which contacts the active site and contributes to catalysis, is suppressed. This study demonstrates high-throughput RNA enzymology as a means to globally determine RNA specificity landscapes and reveals the mechanism of substrate discrimination by a widespread and essential RNA-processing enzyme.
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Affiliation(s)
- Courtney N. Niland
- Department
of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, United States
| | - Jing Zhao
- Department
of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, United States
| | - Hsuan-Chun Lin
- Department
of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, United States
| | - David R. Anderson
- School
of Business, CUNY Baruch College, New York, New York 10010, United States
| | - Eckhard Jankowsky
- Center
for RNA Molecular Biology, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, United States
| | - Michael E. Harris
- Department
of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, United States
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26
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Niland CN, Jankowsky E, Harris ME. Optimization of high-throughput sequencing kinetics for determining enzymatic rate constants of thousands of RNA substrates. Anal Biochem 2016; 510:1-10. [PMID: 27296633 DOI: 10.1016/j.ab.2016.06.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 06/03/2016] [Indexed: 12/12/2022]
Abstract
Quantification of the specificity of RNA binding proteins and RNA processing enzymes is essential to understanding their fundamental roles in biological processes. High-throughput sequencing kinetics (HTS-Kin) uses high-throughput sequencing and internal competition kinetics to simultaneously monitor the processing rate constants of thousands of substrates by RNA processing enzymes. This technique has provided unprecedented insight into the substrate specificity of the tRNA processing endonuclease ribonuclease P. Here, we investigated the accuracy and robustness of measurements associated with each step of the HTS-Kin procedure. We examine the effect of substrate concentration on the observed rate constant, determine the optimal kinetic parameters, and provide guidelines for reducing error in amplification of the substrate population. Importantly, we found that high-throughput sequencing and experimental reproducibility contribute to error, and these are the main sources of imprecision in the quantified results when otherwise optimized guidelines are followed.
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Affiliation(s)
- Courtney N Niland
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Eckhard Jankowsky
- Center for RNA Molecular Biology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Michael E Harris
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.
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27
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Measuring specificity in multi-substrate/product systems as a tool to investigate selectivity in vivo. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1864:70-6. [PMID: 26321598 DOI: 10.1016/j.bbapap.2015.08.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2015] [Revised: 08/07/2015] [Accepted: 08/25/2015] [Indexed: 01/24/2023]
Abstract
Multiple substrate enzymes present a particular challenge when it comes to understanding their activity in a complex system. Although a single target may be easy to model, it does not always present an accurate representation of what that enzyme will do in the presence of multiple substrates simultaneously. Therefore, there is a need to find better ways to both study these enzymes in complicated systems, as well as accurately describe the interactions through kinetic parameters. This review looks at different methods for studying multiple substrate enzymes, as well as explores options on how to most accurately describe an enzyme's activity within these multi-substrate systems. Identifying and defining this enzymatic activity should help clear the way to using in vitro systems to accurately predicting the behavior of multi-substrate enzymes in vivo. This article is part of a Special Issue entitled: Physiological Enzymology and Protein Functions.
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28
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Anderson VE. Multiple alternative substrate kinetics. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1729-36. [PMID: 26051088 DOI: 10.1016/j.bbapap.2015.05.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Revised: 05/18/2015] [Accepted: 05/26/2015] [Indexed: 11/29/2022]
Abstract
The specificity of enzymes for their respective substrates has been a focal point of enzyme kinetics since the initial characterization of metabolic chemistry. Various processes to quantify an enzyme's specificity using kinetics have been utilized over the decades. Fersht's definition of the ratio kcat/Km for two different substrates as the "specificity constant" (ref [7]), based on the premise that the important specificity existed when the substrates were competing in the same reaction, has become a consensus standard for enzymes obeying Michaelis-Menten kinetics. The expansion of the theory for the determination of the relative specificity constants for a very large number of competing substrates, e.g. those present in a combinatorial library, in a single reaction mixture has been developed in this contribution. The ratio of kcat/Km for isotopologs has also become a standard in mechanistic enzymology where kinetic isotope effects have been measured by the development of internal competition experiments with extreme precision. This contribution extends the theory of kinetic isotope effects to internal competition between three isotopologs present at non-tracer concentrations in the same reaction mix. This article is part of a special issue titled: Enzyme Transition States from Theory and Experiment.
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29
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Kellerman DL, Simmons KS, Pedraza M, Piccirilli JA, York DM, Harris ME. Determination of hepatitis delta virus ribozyme N(-1) nucleobase and functional group specificity using internal competition kinetics. Anal Biochem 2015; 483:12-20. [PMID: 25937290 DOI: 10.1016/j.ab.2015.04.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Revised: 04/17/2015] [Accepted: 04/23/2015] [Indexed: 12/16/2022]
Abstract
Biological catalysis involves interactions distant from the site of chemistry that can position the substrate for reaction. Catalysis of RNA 2'-O-transphosphorylation by the hepatitis delta virus (HDV) ribozyme is sensitive to the identity of the N(-1) nucleotide flanking the reactive phosphoryl group. However, the interactions that affect the conformation of this position, and in turn the 2'O nucleophile, are unclear. Here, we describe the application of multiple substrate internal competition kinetic analyses to understand how the N(-1) nucleobase contributes to HDV catalysis and test the utility of this approach for RNA structure-function studies. Internal competition reactions containing all four substrate sequence variants at the N(-1) position in reactions using ribozyme active site mutations at A77 and A78 were used to test a proposed base-pairing interaction. Mutants A78U, A78G, and A79G retain significant catalytic activity but do not alter the specificity for the N(-1) nucleobase. Effects of nucleobase analog substitutions at N(-1) indicate that U is preferred due to the ability to donate an H-bond in the Watson-Crick face and avoid minor groove steric clash. The results provide information essential for evaluating models of the HDV active site and illustrate multiple substrate kinetic analyses as a practical approach for characterizing structure-function relationships in RNA reactions.
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Affiliation(s)
- Daniel L Kellerman
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Kandice S Simmons
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Mayra Pedraza
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Joseph A Piccirilli
- Department of Chemistry and Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Darrin M York
- Center for Integrative Proteomics Research, BioMaPS Institute for Quantitative Biology and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Michael E Harris
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.
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30
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Sunden F, Peck A, Salzman J, Ressl S, Herschlag D. Extensive site-directed mutagenesis reveals interconnected functional units in the alkaline phosphatase active site. eLife 2015; 4. [PMID: 25902402 PMCID: PMC4438272 DOI: 10.7554/elife.06181] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Accepted: 04/22/2015] [Indexed: 01/30/2023] Open
Abstract
Enzymes enable life by accelerating reaction rates to biological timescales. Conventional studies have focused on identifying the residues that have a direct involvement in an enzymatic reaction, but these so-called 'catalytic residues' are embedded in extensive interaction networks. Although fundamental to our understanding of enzyme function, evolution, and engineering, the properties of these networks have yet to be quantitatively and systematically explored. We dissected an interaction network of five residues in the active site of Escherichia coli alkaline phosphatase. Analysis of the complex catalytic interdependence of specific residues identified three energetically independent but structurally interconnected functional units with distinct modes of cooperativity. From an evolutionary perspective, this network is orders of magnitude more probable to arise than a fully cooperative network. From a functional perspective, new catalytic insights emerge. Further, such comprehensive energetic characterization will be necessary to benchmark the algorithms required to rationally engineer highly efficient enzymes.
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Affiliation(s)
- Fanny Sunden
- Department of Biochemistry, Beckman Center, Stanford University, Stanford, United States
| | - Ariana Peck
- Department of Biochemistry, Beckman Center, Stanford University, Stanford, United States
| | - Julia Salzman
- Department of Biochemistry, Beckman Center, Stanford University, Stanford, United States
| | - Susanne Ressl
- Molecular and Cellular Biochemistry Department, Indiana University Bloomington, Bloomington, United States
| | - Daniel Herschlag
- Department of Biochemistry, Beckman Center, Stanford University, Stanford, United States
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31
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Reyes A, Zhai X, Morgan KT, Reinhardt CJ, Amyes TL, Richard JP. The activating oxydianion binding domain for enzyme-catalyzed proton transfer, hydride transfer, and decarboxylation: specificity and enzyme architecture. J Am Chem Soc 2015; 137:1372-82. [PMID: 25555107 PMCID: PMC4311969 DOI: 10.1021/ja5123842] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Indexed: 11/29/2022]
Abstract
The kinetic parameters for activation of yeast triosephosphate isomerase (ScTIM), yeast orotidine monophosphate decarboxylase (ScOMPDC), and human liver glycerol 3-phosphate dehydrogenase (hlGPDH) for catalysis of reactions of their respective phosphodianion truncated substrates are reported for the following oxydianions: HPO3(2-), FPO3(2-), S2O3(2-), SO4(2-) and HOPO3(2-). Oxydianions bind weakly to these unliganded enzymes and tightly to the transition state complex (E·S(‡)), with intrinsic oxydianion Gibbs binding free energies that range from -8.4 kcal/mol for activation of hlGPDH-catalyzed reduction of glycolaldehyde by FPO3(2-) to -3.0 kcal/mol for activation of ScOMPDC-catalyzed decarboxylation of 1-β-d-erythrofuranosyl)orotic acid by HOPO3(2-). Small differences in the specificity of the different oxydianion binding domains are observed. We propose that the large -8.4 kcal/mol and small -3.8 kcal/mol intrinsic oxydianion binding energy for activation of hlGPDH by FPO3(2-) and S2O3(2-), respectively, compared with activation of ScTIM and ScOMPDC reflect stabilizing and destabilizing interactions between the oxydianion -F and -S with the cationic side chain of R269 for hlGPDH. These results are consistent with a cryptic function for the similarly structured oxydianion binding domains of ScTIM, ScOMPDC and hlGPDH. Each enzyme utilizes the interactions with tetrahedral inorganic oxydianions to drive a conformational change that locks the substrate in a caged Michaelis complex that provides optimal stabilization of the different enzymatic transition states. The observation of dianion activation by stabilization of active caged Michaelis complexes may be generalized to the many other enzymes that utilize substrate binding energy to drive changes in enzyme conformation, which induce tight substrate fits.
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Affiliation(s)
- Archie
C. Reyes
- Department
of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
| | - Xiang Zhai
- Department
of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
| | - Kelsey T. Morgan
- Department
of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
| | - Christopher J. Reinhardt
- Department
of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
| | - Tina L. Amyes
- Department
of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
| | - John P. Richard
- Department
of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
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32
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Lin HC, Yandek LE, Gjermeni I, Harris ME. Determination of relative rate constants for in vitro RNA processing reactions by internal competition. Anal Biochem 2014; 467:54-61. [PMID: 25173512 DOI: 10.1016/j.ab.2014.08.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Revised: 08/08/2014] [Accepted: 08/20/2014] [Indexed: 12/21/2022]
Abstract
Studies of RNA recognition and catalysis typically involve measurement of rate constants for reactions of individual RNA sequence variants by fitting changes in substrate or product concentration to exponential or linear functions. A complementary approach is determination of relative rate constants by internal competition, which involves quantifying the time-dependent changes in substrate or product ratios in reactions containing multiple substrates. Here, we review approaches for determining relative rate constants by analysis of both substrate and product ratios and illustrate their application using the in vitro processing of precursor transfer RNA (tRNA) by ribonuclease P as a model system. The presence of inactive substrate populations is a common complicating factor in analysis of reactions involving RNA substrates, and approaches for quantitative correction of observed rate constants for these effects are illustrated. These results, together with recent applications in the literature, indicate that internal competition offers an alternate method for analyzing RNA processing kinetics using standard molecular biology methods that directly quantifies substrate specificity and may be extended to a range of applications.
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Affiliation(s)
- Hsuan-Chun Lin
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Lindsay E Yandek
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Ino Gjermeni
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Michael E Harris
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.
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33
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Wang H, Godage HY, Riley AM, Weaver JD, Shears SB, Potter BVL. Synthetic inositol phosphate analogs reveal that PPIP5K2 has a surface-mounted substrate capture site that is a target for drug discovery. ACTA ACUST UNITED AC 2014; 21:689-99. [PMID: 24768307 PMCID: PMC4085797 DOI: 10.1016/j.chembiol.2014.03.009] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 02/28/2014] [Accepted: 03/17/2014] [Indexed: 11/17/2022]
Abstract
Diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2) is one of the mammalian PPIP5K isoforms responsible for synthesis of diphosphoinositol polyphosphates (inositol pyrophosphates; PP-InsPs), regulatory molecules that function at the interface of cell signaling and organismic homeostasis. The development of drugs that inhibit PPIP5K2 could have both experimental and therapeutic applications. Here, we describe a synthetic strategy for producing naturally occurring 5-PP-InsP4, as well as several inositol polyphosphate analogs, and we study their interactions with PPIP5K2 using biochemical and structural approaches. These experiments uncover an additional ligand-binding site on the surface of PPIP5K2, adjacent to the catalytic pocket. This site facilitates substrate capture from the bulk phase, prior to transfer into the catalytic pocket. In addition to demonstrating a “catch-and-pass” reaction mechanism in a small molecule kinase, we demonstrate that binding of our analogs to the substrate capture site inhibits PPIP5K2. This work suggests that the substrate-binding site offers new opportunities for targeted drug design. Chemical synthesis of 5-PP-InsP4 and a diphosphorylated analog Chemical synthesis of inositol polyphosphate analogs with hydrophobic groups An inositol pyrophosphate kinase has a surface-mounted, substrate capture site Structural and biochemical characterization of a catch-and-pass catalytic cycle
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Affiliation(s)
- Huanchen Wang
- Inositol Signaling Group, Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Himali Y Godage
- Wolfson Laboratory of Medicinal Chemistry, Department of Pharmacy and Pharmacology, University of Bath, Bath, Somerset BA2 7AY, UK
| | - Andrew M Riley
- Wolfson Laboratory of Medicinal Chemistry, Department of Pharmacy and Pharmacology, University of Bath, Bath, Somerset BA2 7AY, UK
| | - Jeremy D Weaver
- Inositol Signaling Group, Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Stephen B Shears
- Inositol Signaling Group, Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA.
| | - Barry V L Potter
- Wolfson Laboratory of Medicinal Chemistry, Department of Pharmacy and Pharmacology, University of Bath, Bath, Somerset BA2 7AY, UK.
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34
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Jamshidi S, Jalili S, Rafii-Tabar H. Study of orotidine 5'-monophosphate decarboxylase in complex with the top three OMP, BMP, and PMP ligands by molecular dynamics simulation. J Biomol Struct Dyn 2014; 33:404-17. [PMID: 24559040 DOI: 10.1080/07391102.2014.881303] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Catalytic mechanism of orotidine 5'-monophosphate decarboxylase (OMPDC), one of the nature most proficient enzymes which provides large rate enhancement, has not been fully understood yet. A series of 30 ns molecular dynamics (MD) simulations were run on X-ray structure of the OMPDC from Saccharomyces cerevisiae in its free form as well as in complex with different ligands, namely 1-(5'-phospho-D-ribofuranosyl) barbituric acid (BMP), orotidine 5'-monophosphate (OMP), and 6-phosphonouridine 5'-monophosphate (PMP). The importance of this biological system is justified both by its high rate enhancement and its potential use as a target in chemotherapy. This work focuses on comparing two physicochemical states of the enzyme (protonated and deprotonated Asp91) and three ligands (substrate OMP, inhibitor, and transition state analog BMP and substrate analog PMP). Detailed analysis of the active site geometry and its interactions is properly put in context by extensive comparison with relevant experimental works. Our overall results show that in terms of hydrogen bond occupancy, electrostatic interactions, dihedral angles, active site configuration, and movement of loops, notable differences among different complexes are observed. Comparison of the results obtained from these simulations provides some detailed structural data for the complexes, the enzyme, and the ligands, as well as useful insights into the inhibition mechanism of the OMPDC enzyme. Furthermore, these simulations are applied to clarify the ambiguous mechanism of the OMPDC enzyme, and imply that the substrate destabilization and transition state stabilization contribute to the mechanism of action of the most proficient enzyme, OMPDC.
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Affiliation(s)
- Shirin Jamshidi
- a Faculty of Medicine, Department of Medical Physics and Biomedical Engineering , Shahid Beheshti University of Medical Sciences , Evin, Tehran , Iran
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35
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Durola F, Heitz V, Reviriego F, Roche C, Sauvage JP, Sour A, Trolez Y. Cyclic [4]rotaxanes containing two parallel porphyrinic plates: toward switchable molecular receptors and compressors. Acc Chem Res 2014; 47:633-45. [PMID: 24428574 DOI: 10.1021/ar4002153] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Twenty years ago, researchers considered the synthesis of simple rotaxanes a challenging task, but with the rapid development of this field, chemists now view these interlocking molecules as accessible synthetic targets. In a major advance for the field, researchers have developed transition metals or organic molecules as templating structures, making it easier to construct these molecular systems. In addition, chemists have found ways to introduce new functional groups, which have given these compounds new properties. Today researchers can also construct multirotaxanes consisting of several individual components, but the synthesis of the most complex structures remains challenging. This Account primarily discusses the cyclic [4]rotaxanes incorporating porphyrins that the Strasbourg group has synthesized and studied during the past few years. These cyclic [4]rotaxanes consist of two rigid rods threaded through the four rings of two molecules of a bis-macrocycle, and the synthetic strategy used for making them relies on the copper(I)-driven "gathering-and-threading" reaction. The formation of the threaded precursors was mostly quantitative, and the quadruple stoppering reaction leading to the target compound produces high yields because of the efficient copper-catalyzed azide-alkyne cycloaddition (CuAAC) or click chemistry reaction. These rotaxanes behave as receptors for various ditopic guests. We prepared and studied two types of molecules: (i) a rigid compound whose copper(I) complex has a well-defined shape, with high selectivity for the guest geometry and (ii) a much more flexible [4]rotaxane host that could act as a distensible receptor. The rigid [4]rotaxane was crystallized, affording a spectacular X-ray structure that matched the expected chemical structure. In addition, metalation or demetalation of the rigid [4]rotaxane induces a drastic geometric rearrangement. The metal-free compound is flat without a binding pocket, while the copper-complexed species forms a rectangle-like structure. The removal of copper(I) also expels any complexed guest molecule, and this process is reversible, making the rigid porphyrinic [4]rotaxane a switchable receptor. The rigid [4]rotaxane was highly selective for short, ditopic guests in its copper(I)-complexed form, but the flexible copper(I)-complexed [4]rotaxane proved to be a versatile receptor. Its conformation can adjust to the size of the guest molecule similar to the induced fit mechanism that some enzymes employ with substrates.
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Affiliation(s)
- Fabien Durola
- Laboratoire de Chimie Organo-Minérale, Institut de Chimie, Université de Strasbourg-CNRS/UMR7177, 4 rue Blaise Pascal, 67070 Strasbourg Cedex, France
| | - Valérie Heitz
- Laboratoire de Chimie Organo-Minérale, Institut de Chimie, Université de Strasbourg-CNRS/UMR7177, 4 rue Blaise Pascal, 67070 Strasbourg Cedex, France
| | - Felipe Reviriego
- Laboratoire de Chimie Organo-Minérale, Institut de Chimie, Université de Strasbourg-CNRS/UMR7177, 4 rue Blaise Pascal, 67070 Strasbourg Cedex, France
| | - Cécile Roche
- Laboratoire de Chimie Organo-Minérale, Institut de Chimie, Université de Strasbourg-CNRS/UMR7177, 4 rue Blaise Pascal, 67070 Strasbourg Cedex, France
| | - Jean-Pierre Sauvage
- Laboratoire de Chimie Organo-Minérale, Institut de Chimie, Université de Strasbourg-CNRS/UMR7177, 4 rue Blaise Pascal, 67070 Strasbourg Cedex, France
| | - Angélique Sour
- Laboratoire de Chimie Organo-Minérale, Institut de Chimie, Université de Strasbourg-CNRS/UMR7177, 4 rue Blaise Pascal, 67070 Strasbourg Cedex, France
| | - Yann Trolez
- Laboratoire de Chimie Organo-Minérale, Institut de Chimie, Université de Strasbourg-CNRS/UMR7177, 4 rue Blaise Pascal, 67070 Strasbourg Cedex, France
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36
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Idili A, Plaxco KW, Vallée-Bélisle A, Ricci F. Thermodynamic basis for engineering high-affinity, high-specificity binding-induced DNA clamp nanoswitches. ACS NANO 2013; 7:10863-9. [PMID: 24219761 PMCID: PMC4281346 DOI: 10.1021/nn404305e] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Naturally occurring chemoreceptors almost invariably employ structure-switching mechanisms, an observation that has inspired the use of biomolecular switches in a wide range of artificial technologies in the areas of diagnostics, imaging, and synthetic biology. In one mechanism for generating such behavior, clamp-based switching, binding occurs via the clamplike embrace of two recognition elements onto a single target molecule. In addition to coupling recognition with a large conformational change, this mechanism offers a second advantage: it improves both affinity and specificity simultaneously. To explore the physics of such switches we have dissected here the thermodynamics of a clamp-switch that recognizes a target DNA sequence through both Watson-Crick base pairing and triplex-forming Hoogsteen interactions. When compared to the equivalent linear DNA probe (which relies solely on Watson-Crick interactions), the extra Hoogsteen interactions in the DNA clamp-switch increase the probe's affinity for its target by ∼0.29 ± 0.02 kcal/mol/base. The Hoogsteen interactions of the clamp-switch likewise provide an additional specificity check that increases the discrimination efficiency toward a single-base mismatch by 1.2 ± 0.2 kcal/mol. This, in turn, leads to a 10-fold improvement in the width of the "specificity window" of this probe relative to that of the equivalent linear probe. Given these attributes, clamp-switches should be of utility not only for sensing applications but also, in the specific field of DNA nanotechnology, for applications calling for a better control over the building of nanostructures and nanomachines.
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Affiliation(s)
- Andrea Idili
- Dipartimento di Scienze e Tecnologie Chimiche, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
- Consorzio Interuniversitario Biostrutture e Biosistemi “INBB”, Rome, Italy
| | - Kevin W. Plaxco
- Center for Bioengineering & Department of Chemistry and Biochemistry, University of California, Santa Barbara CA 93106 USA
- Interdepartmental Program in Biomolecular Science and Engineering, University of California, Santa Barbara CA 93106 USA
| | - Alexis Vallée-Bélisle
- Laboratory of Biosensors and Nanomachines, Département de Chimie, Université de Montréal, Québec, Canada
| | - Francesco Ricci
- Dipartimento di Scienze e Tecnologie Chimiche, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
- Consorzio Interuniversitario Biostrutture e Biosistemi “INBB”, Rome, Italy
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37
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Blomberg R, Kries H, Pinkas DM, Mittl PRE, Grütter MG, Privett HK, Mayo SL, Hilvert D. Precision is essential for efficient catalysis in an evolved Kemp eliminase. Nature 2013; 503:418-21. [DOI: 10.1038/nature12623] [Citation(s) in RCA: 235] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 08/30/2013] [Indexed: 11/09/2022]
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38
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Guenther UP, Yandek LE, Niland CN, Campbell FE, Anderson D, Anderson VE, Harris ME, Jankowsky E. Hidden specificity in an apparently nonspecific RNA-binding protein. Nature 2013; 502:385-8. [PMID: 24056935 PMCID: PMC3800043 DOI: 10.1038/nature12543] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Accepted: 08/14/2013] [Indexed: 12/27/2022]
Abstract
Nucleic-acid-binding proteins are generally viewed as either specific or nonspecific, depending on characteristics of their binding sites in DNA or RNA. Most studies have focused on specific proteins, which identify cognate sites by binding with highest affinities to regions with defined signatures in sequence, structure or both. Proteins that bind to sites devoid of defined sequence or structure signatures are considered nonspecific. Substrate binding by these proteins is poorly understood, and it is not known to what extent seemingly nonspecific proteins discriminate between different binding sites, aside from those sequestered by nucleic acid structures. Here we systematically examine substrate binding by the apparently nonspecific RNA-binding protein C5, and find clear discrimination between different binding site variants. C5 is the protein subunit of the transfer RNA processing ribonucleoprotein enzyme RNase P from Escherichia coli. The protein binds 5' leaders of precursor tRNAs at a site without sequence or structure signatures. We measure functional binding of C5 to all possible sequence variants in its substrate binding site, using a high-throughput sequencing kinetics approach (HITS-KIN) that simultaneously follows processing of thousands of RNA species. C5 binds different substrate variants with affinities varying by orders of magnitude. The distribution of functional affinities of C5 for all substrate variants resembles affinity distributions of highly specific nucleic acid binding proteins. Unlike these specific proteins, C5 does not bind its physiological RNA targets with the highest affinity, but with affinities near the median of the distribution, a region that is not associated with a sequence signature. We delineate defined rules governing substrate recognition by C5, which reveal specificity that is hidden in cellular substrates for RNase P. Our findings suggest that apparently nonspecific and specific RNA-binding modes may not differ fundamentally, but represent distinct parts of common affinity distributions.
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Affiliation(s)
- Ulf-Peter Guenther
- Center for RNA Molecular Biology, Case Western Reserve University, Cleveland, Ohio 44106, USA
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39
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Wilson C, Ramai D, Serjanov D, Lama N, Levinger L, Chang EJ. Tethered domains and flexible regions in tRNase Z(L), the long form of tRNase Z. PLoS One 2013; 8:e66942. [PMID: 23874404 PMCID: PMC3714273 DOI: 10.1371/journal.pone.0066942] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Accepted: 05/13/2013] [Indexed: 11/30/2022] Open
Abstract
tRNase Z, a member of the metallo-β-lactamase family, endonucleolytically removes the pre-tRNA 3′ trailer in a step central to tRNA maturation. The short form (tRNase ZS) is the only one found in bacteria and archaebacteria and is also present in some eukaryotes. The homologous long form (tRNase ZL), exclusively found in eukaryotes, consists of related amino- and carboxy-domains, suggesting that tRNase ZL arose from a tandem duplication of tRNase ZS followed by interdependent divergence of the domains. X-ray crystallographic structures of tRNase ZS reveal a flexible arm (FA) extruded from the body of tRNase Z remote from the active site that binds tRNA far from the scissile bond. No tRNase ZL structures have been solved; alternative biophysical studies are therefore needed to illuminate its functional characteristics. Structural analyses of tRNase ZL performed by limited proteolysis, two dimensional gel electrophoresis and mass spectrometry establish stability of the amino and carboxy domains and flexibility of the FA and inter-domain tether, with implications for tRNase ZL function.
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Affiliation(s)
- Christopher Wilson
- Department of Biology, York College of The City University of New York, Jamaica, New York, United States of America
| | - Daryl Ramai
- Department of Chemistry, York College of The City University of New York, Jamaica, New York, United States of America
| | - Dmitri Serjanov
- Department of Biology, York College of The City University of New York, Jamaica, New York, United States of America
| | - Neema Lama
- Department of Chemistry, York College of The City University of New York, Jamaica, New York, United States of America
| | - Louis Levinger
- Department of Biology, York College of The City University of New York, Jamaica, New York, United States of America
| | - Emmanuel J. Chang
- Department of Chemistry, York College of The City University of New York, Jamaica, New York, United States of America
- * E-mail:
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41
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The Ribosome as an Optimal Decoder: A Lesson in Molecular Recognition. Cell 2013; 153:471-9. [DOI: 10.1016/j.cell.2013.03.032] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Revised: 10/03/2012] [Accepted: 03/22/2013] [Indexed: 11/24/2022]
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42
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Herschlag D, Natarajan A. Fundamental challenges in mechanistic enzymology: progress toward understanding the rate enhancements of enzymes. Biochemistry 2013; 52:2050-67. [PMID: 23488725 DOI: 10.1021/bi4000113] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Enzymes are remarkable catalysts that lie at the heart of biology, accelerating chemical reactions to an astounding extent with extraordinary specificity. Enormous progress in understanding the chemical basis of enzymatic transformations and the basic mechanisms underlying rate enhancements over the past decades is apparent. Nevertheless, it has been difficult to achieve a quantitative understanding of how the underlying mechanisms account for the energetics of catalysis, because of the complexity of enzyme systems and the absence of underlying energetic additivity. We review case studies from our own work that illustrate the power of precisely defined and clearly articulated questions when dealing with such complex and multifaceted systems, and we also use this approach to evaluate our current ability to design enzymes. We close by highlighting a series of questions that help frame some of what remains to be understood, and we encourage the reader to define additional questions and directions that will deepen and broaden our understanding of enzymes and their catalysis.
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Affiliation(s)
- Daniel Herschlag
- Department of Biochemistry, Stanford University School of Medicine , Stanford, California 94305, United States
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43
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Yandek LE, Lin HC, Harris ME. Alternative substrate kinetics of Escherichia coli ribonuclease P: determination of relative rate constants by internal competition. J Biol Chem 2013; 288:8342-8354. [PMID: 23362254 DOI: 10.1074/jbc.m112.435420] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
A single enzyme, ribonuclease P (RNase P), processes the 5' ends of tRNA precursors (ptRNA) in cells and organelles that carry out tRNA biosynthesis. This substrate population includes over 80 different competing ptRNAs in Escherichia coli. Although the reaction kinetics and molecular recognition of a few individual model substrates of bacterial RNase P have been well described, the competitive substrate kinetics of the enzyme are comparatively unexplored. To understand the factors that determine how different ptRNA substrates compete for processing by E. coli RNase P, we compared the steady state reaction kinetics of two ptRNAs that differ at sequences that are contacted by the enzyme. For both ptRNAs, substrate cleavage is fast relative to dissociation. As a consequence, V/K, the rate constant for the reaction at limiting substrate concentrations, reflects the substrate association step for both ptRNAs. Reactions containing two or more ptRNAs follow simple competitive alternative substrate kinetics in which the relative rates of processing are determined by ptRNA concentration and their V/K. The relative V/K values for eight different ptRNAs, which were selected to represent the range of structure variation at sites contacted by RNase P, were determined by internal competition in reactions in which all eight substrates were present simultaneously. The results reveal a relatively narrow range of V/K values, suggesting that rates of ptRNA processing by RNase P are tuned for uniform specificity and consequently optimal coupling to precursor biosynthesis.
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Affiliation(s)
- Lindsay E Yandek
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106
| | - Hsuan-Chun Lin
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106
| | - Michael E Harris
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106.
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44
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Shears SB, Weaver JD, Wang H. Structural insight into inositol pyrophosphate turnover. Adv Biol Regul 2013; 53:19-27. [PMID: 23107997 PMCID: PMC3570603 DOI: 10.1016/j.jbior.2012.10.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Accepted: 10/04/2012] [Indexed: 11/28/2022]
Abstract
The diphosphoinositol polyphosphates ("inositol pyrophosphates"; PP-InsPs) regulate many cellular processes in eukaryotes, including stress responses, apoptosis, vesicle trafficking, cytoskeletal dynamics, exocytosis, telomere maintenance, insulin signaling and neutrophil activation. Thus, the enzymes that control the metabolism of the PP-InsPs serve important cell signaling roles. In order to fully characterize how these enzymes are regulated, we need to determine the atomic-level architecture of their active sites. Only then can we fully appreciate reaction mechanisms and their modes of regulation. In this review, we summarize published information obtained from the structural analysis of a human diphosphoinositol polyphosphate phosphohydrolase (DIPP), and a human diphosphoinositol polyphosphate kinase (PPIP5K). This work includes the analysis of crystal complexes with substrates, products, transition state analogs, and a novel phosphonoacetate substrate analog.
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Affiliation(s)
- Stephen B Shears
- Inositol Signaling Group, Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, PO Box 12233, NC 27709, USA.
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Carroll MP, Guiry PJ, Brown JM. Meta-analysis in asymmetric catalysis. Influence of chelate geometry on the roles of PN chelating ligands. Org Biomol Chem 2013; 11:4591-601. [DOI: 10.1039/c3ob40360b] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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2-nitrobenzoate 2-nitroreductase (NbaA) switches its substrate specificity from 2-nitrobenzoic acid to 2,4-dinitrobenzoic acid under oxidizing conditions. J Bacteriol 2012; 195:180-92. [PMID: 23123905 DOI: 10.1128/jb.02016-12] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
2-Nitrobenzoate 2-nitroreductase (NbaA) of Pseudomonas fluorescens strain KU-7 is a unique enzyme, transforming 2-nitrobenzoic acid (2-NBA) and 2,4-dinitrobenzoic acid (2,4-DNBA) to the 2-hydroxylamine compounds. Sequence comparison reveals that NbaA contains a conserved cysteine residue at position 141 and two variable regions at amino acids 65 to 74 and 193 to 216. The truncated mutant Δ65-74 exhibited markedly reduced activity toward 2,4-DNBA, but its 2-NBA reduction activity was unaffected; however, both activities were abolished in the Δ193-216 mutant, suggesting that these regions are necessary for the catalysis and specificity of NbaA. NbaA showed different lag times for the reduction of 2-NBA and 2,4-DNBA with NADPH, and the reduction of 2,4-DNBA, but not 2-NBA, failed in the presence of 1 mM dithiothreitol or under anaerobic conditions, indicating oxidative modification of the enzyme for 2,4-DNBA. The enzyme was irreversibly inhibited by 5,5'-dithio-bis-(2-nitrobenzoic acid) and ZnCl(2), which bind to reactive thiol/thiolate groups, and was eventually inactivated during the formation of higher-order oligomers at high pH, high temperature, or in the presence of H(2)O(2). SDS-PAGE and mass spectrometry revealed the formation of intermolecular disulfide bonds by involvement of the two cysteines at positions 141 and 194. Site-directed mutagenesis indicated that the cysteines at positions 39, 103, 141, and 194 played a role in changing the enzyme activity and specificity toward 2-NBA and 2,4-DNBA. This study suggests that oxidative modifications of NbaA are responsible for the differential specificity for the two substrates and further enzyme inactivation through the formation of disulfide bonds under oxidizing conditions.
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Roche C, Sour A, Sauvage J. A Flexible Copper(I)‐Complexed [4]Rotaxane Containing Two Face‐to‐Face Porphyrinic Plates that Behaves as a Distensible Receptor. Chemistry 2012; 18:8366-76. [DOI: 10.1002/chem.201200389] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2012] [Indexed: 11/10/2022]
Affiliation(s)
- Cécile Roche
- Laboratoire de Chimie Organo‐Minérale, Institut de Chimie, Université de Strasbourg‐CNRS/UMR7177, 4 rue Blaise Pascal, 67070 Strasbourg Cedex (France), Fax: (+33) 368851637
| | - Angélique Sour
- Laboratoire de Chimie Organo‐Minérale, Institut de Chimie, Université de Strasbourg‐CNRS/UMR7177, 4 rue Blaise Pascal, 67070 Strasbourg Cedex (France), Fax: (+33) 368851637
| | - Jean‐Pierre Sauvage
- Laboratoire de Chimie Organo‐Minérale, Institut de Chimie, Université de Strasbourg‐CNRS/UMR7177, 4 rue Blaise Pascal, 67070 Strasbourg Cedex (France), Fax: (+33) 368851637
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Wang H, Falck JR, Hall TMT, Shears SB. Structural basis for an inositol pyrophosphate kinase surmounting phosphate crowding. Nat Chem Biol 2011; 8:111-6. [PMID: 22119861 PMCID: PMC3923263 DOI: 10.1038/nchembio.733] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2011] [Accepted: 08/30/2011] [Indexed: 01/16/2023]
Abstract
Inositol pyrophosphates (such as IP7 and IP8) are multifunctional signaling molecules that regulate diverse cellular activities. Inositol pyrophosphates have 'high-energy' phosphoanhydride bonds, so their enzymatic synthesis requires that a substantial energy barrier to the transition state be overcome. Additionally, inositol pyrophosphate kinases can show stringent ligand specificity, despite the need to accommodate the steric bulk and intense electronegativity of nature's most concentrated three-dimensional array of phosphate groups. Here we examine how these catalytic challenges are met by describing the structure and reaction cycle of an inositol pyrophosphate kinase at the atomic level. We obtained crystal structures of the kinase domain of human PPIP5K2 complexed with nucleotide cofactors and either substrates, product or a MgF(3)(-) transition-state mimic. We describe the enzyme's conformational dynamics, its unprecedented topological presentation of nucleotide and inositol phosphate, and the charge balance that facilitates partly associative in-line phosphoryl transfer.
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Affiliation(s)
- Huanchen Wang
- Inositol Signaling Group, Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA.
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Cooperativity in monomeric enzymes with single ligand-binding sites. Bioorg Chem 2011; 43:44-50. [PMID: 22137502 DOI: 10.1016/j.bioorg.2011.11.001] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Revised: 11/04/2011] [Accepted: 11/05/2011] [Indexed: 11/21/2022]
Abstract
Cooperativity is widespread in biology. It empowers a variety of regulatory mechanisms and impacts both the kinetic and thermodynamic properties of macromolecular systems. Traditionally, cooperativity is viewed as requiring the participation of multiple, spatially distinct binding sites that communicate via ligand-induced structural rearrangements; however, cooperativity requires neither multiple ligand binding events nor multimeric assemblies. An underappreciated manifestation of cooperativity has been observed in the non-Michaelis-Menten kinetic response of certain monomeric enzymes that possess only a single ligand-binding site. In this review, we present an overview of kinetic cooperativity in monomeric enzymes. We discuss the primary mechanisms postulated to give rise to monomeric cooperativity and highlight modern experimental methods that could offer new insights into the nature of this phenomenon. We conclude with an updated list of single subunit enzymes that are suspected of displaying cooperativity, and a discussion of the biological significance of this unique kinetic response.
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Ram Prasad B, Warshel A. Prechemistry versus preorganization in DNA replication fidelity. Proteins 2011; 79:2900-19. [PMID: 21905114 DOI: 10.1002/prot.23128] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2011] [Revised: 06/30/2011] [Accepted: 07/05/2011] [Indexed: 01/30/2023]
Abstract
The molecular origin of nucleotide insertion catalysis and fidelity of DNA polymerases is explored by means of computational simulations. Special attention is paid to the examination of the validity of proposals that invoke prechemistry effects, checkpoints concepts, and dynamical effects. The simulations reproduce the observed fidelity in Pol β, starting with the relevant observed X-ray structures of the complex with the right (R) and wrong (W) nucleotides. The generation of free energy surfaces for the R and W systems also allowed us to analyze different proposals about the origin of the fidelity and to reach several important conclusions. It is found that the potential of mean force (PMF) obtained by proper sampling does not support QM/MM-based proposals of a large barrier before the prechemistry state. Furthermore, examination of dynamical proposals by the renormalization approach indicates that the motions from open to close configurations do not contribute to catalysis or fidelity. Finally we discuss and analyze the induced fit concept and show that, despite its importance, it does not explain fidelity. That is, the fidelity is apparently due to the change in the preorganization of the chemical site, as a result of the relaxation of the binding site upon binding of the incorrect nucleotide. Finally and importantly, since the issue is the barrier associated with the enzyme-substrate (ES)/DNA complex at the chemical transition state and not the path to this complex formation (unless this path involves rate determining steps), it is also not useful to invoke checkpoints while discussing fidelity.
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Affiliation(s)
- B Ram Prasad
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
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