1
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Cristobal J, Hegazy R, Richard JP. Glycerol 3-Phosphate Dehydrogenase: Role of the Protein Conformational Change in Activation of a Readily Reversible Enzyme-Catalyzed Hydride Transfer Reaction. Biochemistry 2024; 63:1016-1025. [PMID: 38546289 PMCID: PMC11025551 DOI: 10.1021/acs.biochem.3c00702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 02/26/2024] [Accepted: 03/13/2024] [Indexed: 04/17/2024]
Abstract
Kinetic parameters are reported for glycerol 3-phosphate dehydrogenase (GPDH)-catalyzed hydride transfer from the whole substrate glycerol 3-phosphate (G3P) or truncated substrate ethylene glycol (EtG) to NAD, and for activation of the hydride transfer reaction of EtG by phosphite dianion. These kinetic parameters were combined with parameters for enzyme-catalyzed hydride transfer in the microscopic reverse direction to give the reaction equilibrium constants Keq. Hydride transfer from G3P is favored in comparison to EtG because the carbonyl product of the former reaction is stabilized by hyperconjugative electron donation from the -CH2R keto substituent. The kinetic data show that the phosphite dianion provides the same 7.6 ± 0.1 kcal/mol stabilization of the transition states for enzyme-catalyzed reactions in the forward [reduction of NAD by EtG] and reverse [oxidation of NADH by glycolaldehyde] directions. The experimental evidence that supports a role for phosphite dianion in stabilizing the active closed form of the GPDH (EC) relative to the ca. 6 kcal/mol more unstable open form (EO) is summarized.
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Affiliation(s)
- Judith
R. Cristobal
- Department
of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
| | - Rania Hegazy
- Department
of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
| | - John P. Richard
- Department
of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
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2
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Liu X, Brooks Iii CL. Enhanced Sampling of Buried Charges in Free Energy Calculations Using Replica Exchange with Charge Tempering. J Chem Theory Comput 2024; 20:1051-1061. [PMID: 38232295 PMCID: PMC11275198 DOI: 10.1021/acs.jctc.3c00993] [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] [Indexed: 01/19/2024]
Abstract
Buried ionizable groups in proteins often play important structural and functional roles. However, it is generally challenging to study the detailed molecular mechanisms solely based on experimental measurements. Free energy calculations using atomistic simulations, on the other hand, complement experimental studies and can provide high temporal and spatial resolution information that can lead to mechanistic insights. Nevertheless, it is also well recognized that sufficient sampling of such atomistic simulations can be challenging, considering that structural changes related to the buried charges may be very slow. In the present study, we describe a simple but effective enhanced sampling technique called replica exchange with charge tempering (REChgT) with a novel free energy method, multisite λ dynamics (MSλD), to study two systems containing buried charges, pKa prediction of a small molecule, orotate, in complex with the dihydroorotate dehydrogenase, and relative stability of a Glu-Lys pair buried in the hydrophobic core of two variants of Staphylococcal nuclease. Compared to the original MSλD simulations, the usage of REChgT dramatically increases sampling in both conformational and alchemical spaces, which directly translates into a significant reduction of wall time to converge the free energy calculations. This study highlights the importance of sufficient sampling toward developing improved free energy methods.
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Affiliation(s)
- Xiaorong Liu
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Charles L Brooks Iii
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
- Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, United States
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3
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Perrin CL, Agranat I, Bagno A, Braslavsky SE, Fernandes PA, Gal JF, Lloyd-Jones GC, Mayr H, Murdoch JR, Nudelman NS, Radom L, Rappoport Z, Ruasse MF, Siehl HU, Takeuchi Y, Tidwell TT, Uggerud E, Williams IH. Glossary of terms used in physical organic chemistry (IUPAC Recommendations 2021). PURE APPL CHEM 2022. [DOI: 10.1515/pac-2018-1010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Abstract
This Glossary contains definitions, explanatory notes, and sources for terms used in physical organic chemistry. Its aim is to provide guidance on the terminology of physical organic chemistry, with a view to achieving a consensus on the meaning and applicability of useful terms and the abandonment of unsatisfactory ones. Owing to the substantial progress in the field, this 2021 revision of the Glossary is much expanded relative to the previous edition, and it includes terms from cognate fields.
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Affiliation(s)
- Charles L. Perrin
- Department of Chemistry , University of California , San Diego , La Jolla , CA , USA
| | | | - Alessandro Bagno
- University of Padova Faculty of Mathematics Physics and Natural Sciences , Padova , Veneto , Italy
| | - Silvia E. Braslavsky
- Max Planck Institute for Chemical Energy Conversion , Muelheim an der Ruhr , Germany
| | | | | | | | - Herbert Mayr
- Department Chemie , Ludwig-Maximilians-Universität München , München , Germany
| | | | | | - Leo Radom
- School of Chemistry, University of Sydney , Sydney , NSW , Australia
| | - Zvi Rappoport
- Organic Chemistry, The Hebrew University , Jerusalem , Israel
| | | | | | | | - Thomas T. Tidwell
- Department of Chemistry , University of Toronto , Toronto , ON , Canada
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4
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Benkovic SJ. From Bioorganic Models to Cells. Annu Rev Biochem 2021; 90:57-76. [PMID: 34153218 DOI: 10.1146/annurev-biochem-062320-062929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
I endeavor to share how various choices-some deliberate, some unconscious-and the unmistakable influence of many others shaped my scientific pursuits. I am fascinated by how two long-term, major streams of my research, DNA replication and purine biosynthesis, have merged with unexpected interconnections. If I have imparted to many of the talented individuals who have passed through my lab a degree of my passion for uncloaking the mysteries hidden in scientific research and an understanding of the honesty and rigor it demands and its impact on the world community, then my mentorship has been successful.
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Affiliation(s)
- Stephen J Benkovic
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA;
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5
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Enzyme free energy profiles: Can substrate binding be nonspontaneous? Can ground state interactions enhance catalysis? Biophys Chem 2021; 274:106606. [PMID: 33945990 DOI: 10.1016/j.bpc.2021.106606] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/23/2021] [Accepted: 04/25/2021] [Indexed: 11/21/2022]
Abstract
Two influential enzymological theories were proposed in the late 1970s - that catalytic power stems only from transition state stabilization, while ground state interactions are either irrelevant or inhibitory; and enzyme substrate binding is nonspontaneous at low substrate concentrations ([S]0 << Km). I show here that ground state destabilization can be a very effective source of catalytic power, especially at high substrate concentrations, and enzyme-substrate binding thermodynamics are independent of initial substrate concentration. Binding free energy ranges from negative (spontaneous) under pre-steady state conditions up to a maximum of zero at steady state. Nonspontaneous binding can only occur under standard state conditions when c° is defined to be less than Km.
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6
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Silverstein TP. How enzymes harness highly unfavorable proton transfer reactions. Protein Sci 2021; 30:735-744. [PMID: 33554401 DOI: 10.1002/pro.4037] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 02/01/2021] [Accepted: 02/05/2021] [Indexed: 11/12/2022]
Abstract
Acid-base reactions that are exceedingly unfavorable under standard conditions can be catalytically important at enzyme active sites. For example, in triose phosphate isomerase, a glutamate side chain (nominal pKa ≈ 4 in solution) can in fact deprotonate a CH group that is vicinal to a carbonyl (pKa ≈ 18 in solution). This is true because of three distinct interactions: (a) ground state pKa shifts due to environment polarity and electrostatics; (b) dramatic increases in effective molarity due to optimization of proximity and orientation; and (c) transition state pKa shifts due to binding interactions and the formation of strong low barrier hydrogen bonds. In this report, we review the literature showing that the sum of these three effects supplies more than enough free energy to push forward proton transfer reactions that under standard conditions are exceedingly nonspontaneous and slow.
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7
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Mukherjee P, Chandra Singh P. Experimental insight into enzyme catalysis and dynamics: A review on applications of state of art spectroscopic methods. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2021; 122:33-62. [PMID: 32951815 DOI: 10.1016/bs.apcsb.2020.06.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Enzymes are dynamic in nature and understanding their activity depends on exploring their overall structural fluctuation as well as transformation at the active site in free state as well as turnover conditions. In this chapter, the application of several different spectroscopy techniques viz. single molecule spectroscopy, ultrafast spectroscopy and Raman spectroscopy in the context of enzyme dynamics and catalysis are discussed. The importance of such studies are significant in the understanding of new discoveries of drugs, cure for some lethal diseases, gene modification as well as in industrial applications.
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Affiliation(s)
- Puspal Mukherjee
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata, West Bengal, India
| | - Prashant Chandra Singh
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata, West Bengal, India
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8
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Britton S, Alber M, Cannon WR. Enzyme activities predicted by metabolite concentrations and solvent capacity in the cell. J R Soc Interface 2020; 17:20200656. [PMID: 33050777 PMCID: PMC7653389 DOI: 10.1098/rsif.2020.0656] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 09/17/2020] [Indexed: 12/23/2022] Open
Abstract
Experimental measurements or computational model predictions of the post-translational regulation of enzymes needed in a metabolic pathway is a difficult problem. Consequently, regulation is mostly known only for well-studied reactions of central metabolism in various model organisms. In this study, we use two approaches to predict enzyme regulation policies and investigate the hypothesis that regulation is driven by the need to maintain the solvent capacity in the cell. The first predictive method uses a statistical thermodynamics and metabolic control theory framework while the second method is performed using a hybrid optimization-reinforcement learning approach. Efficient regulation schemes were learned from experimental data that either agree with theoretical calculations or result in a higher cell fitness using maximum useful work as a metric. As previously hypothesized, regulation is herein shown to control the concentrations of both immediate and downstream product concentrations at physiological levels. Model predictions provide the following two novel general principles: (1) the regulation itself causes the reactions to be much further from equilibrium instead of the common assumption that highly non-equilibrium reactions are the targets for regulation; and (2) the minimal regulation needed to maintain metabolite levels at physiological concentrations maximizes the free energy dissipation rate instead of preserving a specific energy charge. The resulting energy dissipation rate is an emergent property of regulation which may be represented by a high value of the adenylate energy charge. In addition, the predictions demonstrate that the amount of regulation needed can be minimized if it is applied at the beginning or branch point of a pathway, in agreement with common notions. The approach is demonstrated for three pathways in the central metabolism of E. coli (gluconeogenesis, glycolysis-tricarboxylic acid (TCA) and pentose phosphate-TCA) that each require different regulation schemes. It is shown quantitatively that hexokinase, glucose 6-phosphate dehydrogenase and glyceraldehyde phosphate dehydrogenase, all branch points of pathways, play the largest roles in regulating central metabolism.
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Affiliation(s)
- Samuel Britton
- Department of Mathematics, University of California Riverside, Riverside, CA 92505, USA
- Center for Quantitative Modeling in Biology, University of California Riverside, Riverside, CA 92505, USA
| | - Mark Alber
- Department of Mathematics, University of California Riverside, Riverside, CA 92505, USA
- Center for Quantitative Modeling in Biology, University of California Riverside, Riverside, CA 92505, USA
| | - William R. Cannon
- Department of Mathematics, University of California Riverside, Riverside, CA 92505, USA
- Center for Quantitative Modeling in Biology, University of California Riverside, Riverside, CA 92505, USA
- Physical and Computational Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
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9
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Yunoki T, Kimura Y, Fujimori A. Maintenance Properties of Enzyme Molecule Stereostructure at High Temperature by Adsorption on Organo-Modified Magnetic Nanoparticle Layer Template. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2019. [DOI: 10.1246/bcsj.20190102] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Takeru Yunoki
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Yusuke Kimura
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Atsuhiro Fujimori
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-okubo, Sakura-ku, Saitama 338-8570, Japan
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10
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Moghadamchargari Z, Huddleston J, Shirzadeh M, Zheng X, Clemmer DE, M Raushel F, Russell DH, Laganowsky A. Intrinsic GTPase Activity of K-RAS Monitored by Native Mass Spectrometry. Biochemistry 2019; 58:3396-3405. [PMID: 31306575 DOI: 10.1021/acs.biochem.9b00532] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Mutations in RAS are associated with many different cancers and have been a therapeutic target for more than three decades. RAS cycles from an active to inactive state by both intrinsic and GTPase-activating protein (GAP)-stimulated hydrolysis. The activated enzyme interacts with downstream effectors, leading to tumor proliferation. Mutations in RAS associated with cancer are insensitive to GAP, and the rate of inactivation is limited to their intrinsic hydrolysis rate. Here, we use high-resolution native mass spectrometry (MS) to determine the kinetics and transition state thermodynamics of intrinsic hydrolysis for K-RAS and its oncogenic mutants. MS data reveal heterogeneity where both 2'-deoxy and 2'-hydroxy forms of GDP (guanosine diphosphate) and GTP (guanosine triphosphate) are bound to the recombinant enzyme. Intrinsic GTPase activity is directly monitored by the loss in mass of K-RAS bound to GTP, which corresponds to the release of phosphate. The rates determined from MS are in direct agreement with those measured using an established solution-based assay. Our results show that the transition state thermodynamics for the intrinsic GTPase activity of K-RAS is both enthalpically and entropically unfavorable. The oncogenic mutants G12C, Q61H, and G13D unexpectedly exhibit a 2'-deoxy GTP intrinsic hydrolysis rate higher than that for GTP.
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Affiliation(s)
- Zahra Moghadamchargari
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
| | - Jamison Huddleston
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
| | - Mehdi Shirzadeh
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
| | - Xueyun Zheng
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
| | - David E Clemmer
- Department of Chemistry , Indiana University , Bloomington , Indiana , 47405 , United States
| | - Frank M Raushel
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
| | - David H Russell
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
| | - Arthur Laganowsky
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
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11
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Calixto AR, Moreira C, Pabis A, Kötting C, Gerwert K, Rudack T, Kamerlin SCL. GTP Hydrolysis Without an Active Site Base: A Unifying Mechanism for Ras and Related GTPases. J Am Chem Soc 2019; 141:10684-10701. [PMID: 31199130 DOI: 10.1021/jacs.9b03193] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
GTP hydrolysis is a biologically crucial reaction, being involved in regulating almost all cellular processes. As a result, the enzymes that catalyze this reaction are among the most important drug targets. Despite their vital importance and decades of substantial research effort, the fundamental mechanism of enzyme-catalyzed GTP hydrolysis by GTPases remains highly controversial. Specifically, how do these regulatory proteins hydrolyze GTP without an obvious general base in the active site to activate the water molecule for nucleophilic attack? To answer this question, we perform empirical valence bond simulations of GTPase-catalyzed GTP hydrolysis, comparing solvent- and substrate-assisted pathways in three distinct GTPases, Ras, Rab, and the Gαi subunit of a heterotrimeric G-protein, both in the presence and in the absence of the corresponding GTPase activating proteins. Our results demonstrate that a general base is not needed in the active site, as the preferred mechanism for GTP hydrolysis is a conserved solvent-assisted pathway. This pathway involves the rate-limiting nucleophilic attack of a water molecule, leading to a short-lived intermediate that tautomerizes to form H2PO4- and GDP as the final products. Our fundamental biochemical insight into the enzymatic regulation of GTP hydrolysis not only resolves a decades-old mechanistic controversy but also has high relevance for drug discovery efforts. That is, revisiting the role of oncogenic mutants with respect to our mechanistic findings would pave the way for a new starting point to discover drugs for (so far) "undruggable" GTPases like Ras.
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Affiliation(s)
- Ana R Calixto
- Department of Chemistry-BMC , Uppsala University , Box 576, S-751 23 Uppsala , Sweden
| | - Cátia Moreira
- Department of Chemistry-BMC , Uppsala University , Box 576, S-751 23 Uppsala , Sweden
| | - Anna Pabis
- Department of Cell and Molecular Biology , Uppsala University , BMC Box 596, S-751 24 , Uppsala , Sweden
| | - Carsten Kötting
- Department of Biophysics , Ruhr University Bochum , 44801 Bochum , Germany
| | - Klaus Gerwert
- Department of Biophysics , Ruhr University Bochum , 44801 Bochum , Germany
| | - Till Rudack
- Department of Biophysics , Ruhr University Bochum , 44801 Bochum , Germany
| | - Shina C L Kamerlin
- Department of Chemistry-BMC , Uppsala University , Box 576, S-751 23 Uppsala , Sweden
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12
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Abstract
![]()
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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13
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Biava H, Schreiber T, Katz S, Völler JS, Stolarski M, Schulz C, Michael N, Budisa N, Kozuch J, Utesch T, Hildebrandt P. Long-Range Modulations of Electric Fields in Proteins. J Phys Chem B 2018; 122:8330-8342. [PMID: 30109934 DOI: 10.1021/acs.jpcb.8b03870] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Electrostatic interactions are essential for controlling the protein structure and function. Whereas so far experimental and theoretical efforts focused on the effect of local electrostatics, this work aims at elucidating the long-range modulation of electric fields in proteins upon binding to charged surfaces. The study is based on cytochrome c (Cytc) variants carrying nitrile reporters for the vibrational Stark effect that are incorporated into the protein via genetic engineering and chemical modification. The Cytc variants were thoroughly characterized with respect to possible structural perturbations due to labeling. For the proteins in solution, the relative hydrogen bond occupancy and the calculated electric fields, both obtained from molecular dynamics (MD) simulations, and the experimental nitrile stretching frequencies were used to develop a relationship for separating hydrogen-bonding and non-hydrogen-bonding electric field effects. This relationship provides an excellent description for the stable Cytc variants in solution. For the proteins bound to Au electrodes coated with charged self-assembled monolayers (SAMs), the underlying MD simulations can only account for the electric field changes Δ Eads due to the formation of the electrostatic SAM-Cytc complexes but not for the additional contribution, Δ Eint, representing the consequences of the potential drops over the electrode/SAM/protein interfaces. Both Δ Eads and Δ Eint, determined at distances between 20 and 30 Å with respect to the SAM surface, are comparable in magnitude to the non-hydrogen-bonding electric field in the unbound protein. This long-range modulation of the internal electric field may be of functional relevance for proteins in complexes with partner proteins (Δ Eads) and attached to membranes (Δ Eads + Δ Eint).
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Affiliation(s)
- Hernan Biava
- Institut für Chemie , Technische Universität Berlin , Sekr. L1, Müller-Breslau-Straße 10 , D-10623 Berlin , Germany
| | - Toni Schreiber
- Institut für Chemie , Technische Universität Berlin , Sekr. PC14, Straße des 17. Juni 135 , D-10623 Berlin , Germany
| | - Sagie Katz
- Institut für Chemie , Technische Universität Berlin , Sekr. PC14, Straße des 17. Juni 135 , D-10623 Berlin , Germany
| | - Jan-Stefan Völler
- Institut für Chemie , Technische Universität Berlin , Sekr. L1, Müller-Breslau-Straße 10 , D-10623 Berlin , Germany
| | - Michael Stolarski
- Institut für Chemie , Technische Universität Berlin , Sekr. PC14, Straße des 17. Juni 135 , D-10623 Berlin , Germany
| | - Claudia Schulz
- Institut für Chemie , Technische Universität Berlin , Sekr. PC14, Straße des 17. Juni 135 , D-10623 Berlin , Germany
| | - Norbert Michael
- Institut für Chemie , Technische Universität Berlin , Sekr. PC14, Straße des 17. Juni 135 , D-10623 Berlin , Germany
| | - Nediljko Budisa
- Institut für Chemie , Technische Universität Berlin , Sekr. L1, Müller-Breslau-Straße 10 , D-10623 Berlin , Germany
| | - Jacek Kozuch
- Institut für Chemie , Technische Universität Berlin , Sekr. PC14, Straße des 17. Juni 135 , D-10623 Berlin , Germany
| | - Tillmann Utesch
- Institut für Chemie , Technische Universität Berlin , Sekr. PC14, Straße des 17. Juni 135 , D-10623 Berlin , Germany
| | - Peter Hildebrandt
- Institut für Chemie , Technische Universität Berlin , Sekr. PC14, Straße des 17. Juni 135 , D-10623 Berlin , Germany
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14
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He R, Reyes AC, Amyes TL, Richard JP. Enzyme Architecture: The Role of a Flexible Loop in Activation of Glycerol-3-phosphate Dehydrogenase for Catalysis of Hydride Transfer. Biochemistry 2018; 57:3227-3236. [PMID: 29337541 PMCID: PMC6001809 DOI: 10.1021/acs.biochem.7b01282] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
![]()
The side chain of Q295 of glycerol-3-phosphate
dehydrogenase from
human liver (hlGPDH) lies in a flexible loop, that
folds over the phosphodianion of substrate dihydroxyacetone phosphate
(DHAP). Q295 interacts with the side-chain cation from R269, which
is ion-paired to the substrate phosphodianion. Kinetic parameters kcat/Km (M–1 s–1) and kcat/KGAKHPi (M–2 s–1) were determined, respectively, for catalysis
of the reduction of DHAP and for dianion activation of catalysis of
reduction of glycolaldehyde (GA) catalyzed by wild-type, Q295G, Q295S,
Q295A, and Q295N mutants of hlGPDH. These mutations
result in up to a 150-fold decrease in (kcat/Km)DHAP and up to a 2.7 kcal/mol
decrease in the intrinsic phosphodianion binding energy. The data
define a linear correlation with slope 1.1, between the intrinsic
phosphodianion binding energy and the intrinsic phosphite dianion
binding energy for activation of hlGPDH-catalyzed
reduction of GA, that demonstrates a role for Q295 in optimizing this
dianion binding energy. The R269A mutation of wild-type GPDH results
in a 9.1 kcal/mol destabilization of the transition state for reduction
of DHAP, but the same R269A mutation of N270A and Q295A mutants result
in smaller 5.9 and 4.9 kcal/mol transition-state destabilization.
Similarly, the N270A or Q295A mutations of R269A GPDH each result
in large falloffs in the efficiency of rescue of the R269A mutant
by guanidine cation. We conclude that N270, which interacts for the
substrate phosphodianion and Q295, which interacts with the guanidine
side chain of R269, function to optimize the apparent
transition-state stabilization provided by the cationic side chain
of R269.
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Affiliation(s)
- Rui He
- Department of Chemistry , University at Buffalo, SUNY , Buffalo , New York 14260-3000 , United States
| | - Archie C Reyes
- Department of Chemistry , University at Buffalo, SUNY , Buffalo , New York 14260-3000 , United States
| | - Tina L Amyes
- Department of Chemistry , University at Buffalo, SUNY , Buffalo , New York 14260-3000 , United States
| | - John P Richard
- Department of Chemistry , University at Buffalo, SUNY , Buffalo , New York 14260-3000 , United States
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15
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Substrate binding interferes with active site conformational dynamics in endoglucanase Cel5A from Thermobifida fusca. Biochem Biophys Res Commun 2017; 491:236-240. [DOI: 10.1016/j.bbrc.2017.07.086] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 07/14/2017] [Indexed: 11/16/2022]
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16
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Norris V, Krylov SN, Agarwal PK, White GJ. Synthetic, Switchable Enzymes. J Mol Microbiol Biotechnol 2017; 27:117-127. [PMID: 28448969 DOI: 10.1159/000464443] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The construction of switchable, radiation-controlled, aptameric enzymes - "swenzymes" - is, in principle, feasible. We propose a strategy to make such catalysts from 2 (or more) aptamers each selected to bind specifically to one of the substrates in, for example, a 2-substrate reaction. Construction of a combinatorial library of candidate swenzymes entails selecting a set of a million aptamers that bind one substrate and a second set of a million aptamers that bind the second substrate; the aptamers in these sets are then linked pairwise by a linker, thus bringing together the substrates. In the presence of the substrates, some linked aptamer pairs catalyze the reaction when exposed to external energy in the form of a specific frequency of low-intensity, nonionizing electromagnetic or acoustic radiation. Such swenzymes are detected via a separate product-capturing aptamer that changes conformation on capturing the product; this altered conformation allows it (1) to bind to every potential swenzyme in its vicinity (thereby giving a higher probability of capture to the swenzymes that generate the product) and (2) to bind to a sequence on a magnetic bead (thereby permitting purification of the swenzyme plus product-capturing aptamer by precipitation). Attempts to implement the swenzyme strategy may help elucidate fundamental problems in enzyme catalysis.
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Affiliation(s)
- Vic Norris
- Theoretical Biology Unit, EA 4312, Department of Biology, University of Rouen, Mont Saint Aignan, France
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17
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Pathak AK. Effect of a buried ion pair in the hydrophobic core of a protein: An insight from constant pH molecular dynamics study. Biopolymers 2016; 103:148-57. [PMID: 25363335 DOI: 10.1002/bip.22577] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Revised: 10/07/2014] [Accepted: 10/09/2014] [Indexed: 01/18/2023]
Abstract
Constant pH molecular dynamics (CpHMD) is a commonly used sampling method, which incorporates the coupling of conformational flexibility and protonation state of a protein during the simulation by using pH as an external parameter. The effects on the structure and stability of a hyperstable variant of staphylococcal nuclease (Δ+PHS) protein of an artificial charge pair buried in its hydrophobic core are investigated by applying both CpHMD and accelerated molecular dynamics coupled with constant pH (CpHaMD) methods. Generalized Born electrostatics is used to model the solvent water. Two sets of starting coordinates of V23E/L36K variant of Δ+PHS, namely, Maestro generated coordinates from Δ+PHS and crystal structure coordinates of the same are considered for detail investigations. On the basis of root mean square displacement (RMSD) and root mean square fluctuations (RMSF) calculations, it is observed that this variant is stable over a wide range of pH. The calculated pKa values for aspartate and glutamate residues based on both CpHMD and CpHaMD simulations are consistent with the reported experimental values (within ± 0.5 to ± 1.5 pH unit), which clearly indicates that the local chemical environment of the carboxylic acids in V23E/L36K variant are comparable to the parent form. The strong salt bridge interaction between the mutated pair, E23/K36 and additional hydrogen bonds formed in the V23E/L36K variant, may help to compensate for the unfavorable self-energy experienced by the burial of these residues in the hydrophobic core. However, from RMSD, RMSF, and pKa analysis, no significant change in the global conformation of V23E/L36K variant with respect to the parent form, Δ+PHS is noticed.
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Affiliation(s)
- Arup K Pathak
- Theoretical Chemistry Section, Bhabha Atomic Research Centre, Mumbai, 400085, India
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18
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Chen D, Savidge T. BIOPHYSICS. Comment on "Extreme electric fields power catalysis in the active site of ketosteroid isomerase". Science 2015; 349:936. [PMID: 26315427 DOI: 10.1126/science.aab0095] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 07/24/2015] [Indexed: 11/02/2022]
Abstract
Fried et al. (Reports, 19 December 2014, p. 1510) demonstrate electric field-dependent acceleration of biological catalysis using ketosteroid isomerase as a prototypic example. These findings were not extended to aqueous solution because water by itself has field fluctuations that are too large and fast to provide a catalytic effect. Given physiological context, when water electrostatic interactions are considered, electric fields play a less important role in the catalysis.
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Affiliation(s)
- Deliang Chen
- Jiangxi Key Laboratory of Organo-Pharmaceutical Chemistry, Gannan Normal University, Jiangxi 341000, China
| | - Tor Savidge
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030, USA. Department of Pathology, Texas Children's Hospital, Houston, TX 77030, USA.
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19
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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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20
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Pathak AK. Constant pH molecular dynamics study on the doubly mutated staphylococcal nuclease: capturing the microenvironment. RSC Adv 2015. [DOI: 10.1039/c5ra17983a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Small rearrangements of residues in the microenvironment of V23E/L36K variant of staphylococcal nuclease can effectively be captured by CpHMD method.
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Affiliation(s)
- Arup Kumar Pathak
- Theoretical Chemistry Section
- Bhabha Atomic Reserch Centre
- Mumbai-400085
- India
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21
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Pallotta MT, Fallarino F, Matino D, Macchiarulo A, Orabona C. AhR-Mediated, Non-Genomic Modulation of IDO1 Function. Front Immunol 2014; 5:497. [PMID: 25360135 PMCID: PMC4197771 DOI: 10.3389/fimmu.2014.00497] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 09/24/2014] [Indexed: 01/01/2023] Open
Abstract
The evolutionary process has conferred a dual – enzymatic and signaling – function on the ancestral metabolic enzyme indoleamine 2,3-dioxygenase 1 (IDO1), which has long been known for converting the essential amino acid tryptophan (TRP) into neuroactive and immunoactive catabolites (kynurenines). In addition to TRP catabolic activity, phosphorylated immunoreceptor tyrosine-based inhibitory motifs, present in the IDO1 protein, act as docking sites for different molecular partners, which activate positive (transcriptional) or negative (post-translational) modulation of IDO1 protein. The ligand-operated transcription factor aryl hydrocarbon receptor (AhR) contributes to Ido1 transcription, and it can be operated by both exogenous and endogenous ligands, including l-kynurenine itself, the first byproduct of TRP catabolism. Ligand-bound AhR is also a component of a ubiquitin ligase complex responsible for regulatory proteolysis of different target proteins. Because IDO1 half-life is controlled by the ubiquitin–proteasome system, we here discuss the possibility that AhR, in addition to enhancing Ido1 transcription, contributes to IDO1 regulation by a non-genomic mechanism affecting the protein’s half-life.
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Affiliation(s)
- Maria Teresa Pallotta
- Pharmacology Section, Department of Experimental Medicine, University of Perugia , Perugia , Italy
| | - Francesca Fallarino
- Pharmacology Section, Department of Experimental Medicine, University of Perugia , Perugia , Italy
| | - Davide Matino
- Pharmacology Section, Department of Experimental Medicine, University of Perugia , Perugia , Italy
| | - Antonio Macchiarulo
- Department of Pharmaceutical Sciences, University of Perugia , Perugia , Italy
| | - Ciriana Orabona
- Pharmacology Section, Department of Experimental Medicine, University of Perugia , Perugia , Italy
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22
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Structural and thermodynamic consequences of burial of an artificial ion pair in the hydrophobic interior of a protein. Proc Natl Acad Sci U S A 2014; 111:11685-90. [PMID: 25074910 DOI: 10.1073/pnas.1402900111] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An artificial charge pair buried in the hydrophobic core of staphylococcal nuclease was engineered by making the V23E and L36K substitutions. Buried individually, Glu-23 and Lys-36 both titrate with pKa values near 7. When buried together their pKa values appear to be normal. The ionizable moieties of the buried Glu-Lys pair are 2.6 Å apart. The interaction between them at pH 7 is worth 5 kcal/mol. Despite this strong interaction, the buried Glu-Lys pair destabilizes the protein significantly because the apparent Coulomb interaction is sufficient to offset the dehydration of only one of the two buried charges. Save for minor reorganization of dipoles and water penetration consistent with the relatively high dielectric constant reported by the buried ion pair, there is no evidence that the presence of two charges in the hydrophobic interior of the protein induces any significant structural reorganization. The successful engineering of an artificial ion pair in a highly hydrophobic environment suggests that buried Glu-Lys pairs in dehydrated environments can be charged and that it is possible to engineer charge clusters that loosely resemble catalytic sites in a scaffold protein with high thermodynamic stability, without the need for specialized structural adaptations.
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23
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Zhai X, Malabanan MM, Amyes TL, Richard JP. Mechanistic Imperatives for Deprotonation of Carbon Catalyzed by Triosephosphate Isomerase: Enzyme-Activation by Phosphite Dianion. J PHYS ORG CHEM 2014; 27:269-276. [PMID: 24729658 PMCID: PMC3979633 DOI: 10.1002/poc.3195] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The mechanistic imperatives for catalysis of deprotonation of α-carbonyl carbon by triosephosphate isomerase (TIM) are discussed. There is a strong imperative to reduce the large thermodynamic barrier for deprotonation of carbon to form an enediolate reaction intermediate; and, a strong imperative for specificity in the expression of the intrinsic phosphodianion binding energy at the transition state for the enzyme-catalyzed reaction. Binding energies of 2 and 6 kcal/mol, respectively, have been determined for formation of phosphite dianion complexes to TIM and to the transition state for TIM-catalyzed deprotonation of the truncated substrate glycolaldehyde [T. L. Amyes, J. P. Richard, Biochemistry2007, 46, 5841]. We propose that the phosphite dianion binding energy, which is specifically expressed at the transition state complex, is utilized to stabilize a rare catalytically active loop-closed form of TIM. The results of experiments to probe the role of the side chains of Ile172 and Leu232 in activating the loop-closed form of TIM for catalysis of substrate deprotonation are discussed. Evidence is presented that the hydrophobic side chain of Ile172 assists in activating TIM for catalysis of substrate deprotonation through an enhancement of the basicity of the carboxylate side-chain of Glu167. Our experiments link the two imperatives for TIM-catalyzed deprotonation of carbon by providing evidence that the phosphodianion binding energy is utilized to drive an enzyme conformational change, which results in a reduction in the thermodynamic barrier to deprotonation of the carbon acid substrate at TIM compared with the barrier for deprotonation in water. The effects of a P168A mutation on the kinetic parameters for the reactions of whole and truncated substrates are discussed.
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Affiliation(s)
- Xiang Zhai
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, NY 14260, USA
| | - M Merced Malabanan
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, NY 14260, USA
| | - Tina L Amyes
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, NY 14260, USA
| | - John P Richard
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, NY 14260, USA
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24
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Bhojane PP, Duff MR, Patel HC, Vogt ME, Howell EE. Investigation of osmolyte effects on FolM: comparison with other dihydrofolate reductases. Biochemistry 2014; 53:1330-41. [PMID: 24517487 DOI: 10.1021/bi4014165] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A weak association between osmolytes and dihydrofolate (DHF) decreases the affinity of the substrate for the Escherichia coli chromosomal and R67 plasmid dihydrofolate reductase (DHFR) enzymes. To test whether the osmolyte-DHF association also interferes with binding of DHF to FolM, an E. coli enzyme that possesses weak DHFR activity, ligand binding was monitored in the presence of osmolytes. The affinity of FolM for DHF, measured by kcat/Km(DHF), was decreased by the addition of an osmolyte. Additionally, binding of the antifolate drug, methotrexate, to FolM was weakened by the addition of an osmolyte. The changes in ligand binding with water activity were unique for each osmolyte, indicating preferential interaction between the osmolyte and folate and its derivatives; however, additional evidence provided support for further interactions between FolM and osmolytes. Binding of the reduced nicotinamide adenine dinucleotide phosphate (NADPH) cofactor to FolM was monitored by isothermal titration calorimetry as a control for protein-osmolyte association. In the presence of betaine (proposed to be the osmolyte most excluded from protein surfaces), the NADPH Kd decreased, consistent with dehydration effects. However, other osmolytes did not tighten binding to the cofactor. Rather, dimethyl sulfoxide (DMSO) had no effect on the NADPH Kd, while ethylene glycol and polyethylene glycol 400 weakened cofactor binding. Differential scanning calorimetry of FolM in the presence of osmolytes showed that both DMSO and ethylene glycol decreased the stability of FolM, while betaine increased the stability of the protein. These results suggest that some osmolytes can destabilize FolM by preferentially interacting with the protein. Further, these weak attractions can impede ligand binding. These various contributions have to be considered when interpreting osmotic pressure results.
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Affiliation(s)
- Purva P Bhojane
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee , Knoxville, Tennessee 37996-0840, United States
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25
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Goryanova B, Goldman LM, Amyes TL, Gerlt JA, Richard JP. Role of a guanidinium cation-phosphodianion pair in stabilizing the vinyl carbanion intermediate of orotidine 5'-phosphate decarboxylase-catalyzed reactions. Biochemistry 2013; 52:7500-11. [PMID: 24053466 DOI: 10.1021/bi401117y] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The side chain cation of Arg235 provides a 5.6 and 2.6 kcal/mol stabilization of the transition states for orotidine 5'-monophosphate (OMP) decarboxylase (OMPDC) from Saccharomyces cerevisiae catalyzed reactions of OMP and 5-fluoroorotidine 5'-monophosphate (FOMP), respectively, a 7.2 kcal/mol stabilization of the vinyl carbanion-like transition state for enzyme-catalyzed exchange of the C-6 proton of 5-fluorouridine 5'-monophosphate (FUMP), but no stabilization of the transition states for enzyme-catalyzed decarboxylation of truncated substrates 1-(β-d-erythrofuranosyl)orotic acid and 1-(β-d-erythrofuranosyl) 5-fluorouracil. These observations show that the transition state stabilization results from formation of a protein cation-phosphodianion pair, and that there is no detectable stabilization from an interaction between the side chain and the pyrimidine ring of substrate. The 5.6 kcal/mol side chain interaction with the transition state for the decarboxylation reaction is 50% of the total 11.2 kcal/mol transition state stabilization by interactions with the phosphodianion of OMP, whereas the 7.2 kcal/mol side chain interaction with the transition state for the deuterium exchange reaction is a larger 78% of the total 9.2 kcal/mol transition state stabilization by interactions with the phosphodianion of FUMP. The effect of the R235A mutation on the enzyme-catalyzed deuterium exchange is expressed predominantly as a change in the turnover number kex, whereas the effect on the enzyme-catalyzed decarboxylation of OMP is expressed predominantly as a change in the Michaelis constant Km. These results are rationalized by a mechanism in which the binding of OMP, compared with that for FUMP, provides a larger driving force for conversion of OMPDC from an inactive open conformation to a productive, active, closed conformation.
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Affiliation(s)
- Bogdana Goryanova
- Department of Chemistry, University at Buffalo , Buffalo, New York 14260, United States
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26
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Wang Z, Sapienza PJ, Abeysinghe T, Luzum C, Lee AL, Finer-Moore JS, Stroud RM, Kohen A. Mg2+ binds to the surface of thymidylate synthase and affects hydride transfer at the interior active site. J Am Chem Soc 2013; 135:7583-92. [PMID: 23611499 PMCID: PMC3674108 DOI: 10.1021/ja400761x] [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] [Indexed: 01/02/2023]
Abstract
Thymidylate synthase (TSase) produces the sole intracellular de novo source of thymidine (i.e., the DNA base T) and thus is a common target for antibiotic and anticancer drugs. Mg(2+) has been reported to affect TSase activity, but the mechanism of this interaction has not been investigated. Here we show that Mg(2+) binds to the surface of Escherichia coli TSase and affects the kinetics of hydride transfer at the interior active site (16 Å away). Examination of the crystal structures identifies a Mg(2+) near the glutamyl moiety of the folate cofactor, providing the first structural evidence for Mg(2+) binding to TSase. The kinetics and NMR relaxation experiments suggest that the weak binding of Mg(2+) to the protein surface stabilizes the closed conformation of the ternary enzyme complex and reduces the entropy of activation on the hydride transfer step. Mg(2+) accelerates the hydride transfer by ~7-fold but does not affect the magnitude or temperature dependence of the intrinsic kinetic isotope effect. These results suggest that Mg(2+) facilitates the protein motions that bring the hydride donor and acceptor together, but it does not change the tunneling ready state of the hydride transfer. These findings highlight how variations in cellular Mg(2+) concentration can modulate enzyme activity through long-range interactions in the protein, rather than binding at the active site. The interaction of Mg(2+) with the glutamyl tail of the folate cofactor and nonconserved residues of bacterial TSase may assist in designing antifolates with polyglutamyl substitutes as species-specific antibiotic drugs.
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Affiliation(s)
- Zhen Wang
- Department of Chemistry, University of Iowa, Iowa City, IA 52242, USA
| | - Paul J. Sapienza
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Thelma Abeysinghe
- Department of Chemistry, University of Iowa, Iowa City, IA 52242, USA
| | - Calvin Luzum
- Department of Chemistry, University of Iowa, Iowa City, IA 52242, USA
| | - Andrew L. Lee
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Janet S. Finer-Moore
- Department of Biochemistry & Biophysics, University of California, San Francisco, CA 94158, USA
| | - Robert M. Stroud
- Department of Biochemistry & Biophysics, University of California, San Francisco, CA 94158, USA
| | - Amnon Kohen
- Department of Chemistry, University of Iowa, Iowa City, IA 52242, USA
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27
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Linder M. Computational Enzyme Design: Advances, hurdles and possible ways forward. Comput Struct Biotechnol J 2012; 2:e201209009. [PMID: 24688650 PMCID: PMC3962231 DOI: 10.5936/csbj.201209009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Revised: 09/30/2012] [Accepted: 10/12/2012] [Indexed: 12/13/2022] Open
Abstract
This mini review addresses recent developments in computational enzyme design. Successful protocols as well as known issues and limitations are discussed from an energetic perspective. It will be argued that improved results can be obtained by including a dynamic treatment in the design protocol. Finally, a molecular dynamics-based approach for evaluating and refining computational designs is presented.
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Affiliation(s)
- Mats Linder
- Applied Physical Chemistry, KTH Royal Institute of Technology, Teknikringen 30, SE-100 44, Stockholm, Sweden
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28
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Wang Z, Abeysinghe T, Finer-Moore JS, Stroud RM, Kohen A. A remote mutation affects the hydride transfer by disrupting concerted protein motions in thymidylate synthase. J Am Chem Soc 2012; 134:17722-30. [PMID: 23034004 DOI: 10.1021/ja307859m] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The role of protein flexibility in enzyme-catalyzed activation of chemical bonds is an evolving perspective in enzymology. Here we examine the role of protein motions in the hydride transfer reaction catalyzed by thymidylate synthase (TSase). Being remote from the chemical reaction site, the Y209W mutation of Escherichia coli TSase significantly reduces the protein activity, despite the remarkable similarity between the crystal structures of the wild-type and mutant enzymes with ligands representing their Michaelis complexes. The most conspicuous difference between these two crystal structures is in the anisotropic B-factors, which indicate disruption of the correlated atomic vibrations of protein residues in the mutant. This dynamically altered mutant allows a variety of small thiols to compete for the reaction intermediate that precedes the hydride transfer, indicating disruption of motions that preorganize the protein environment for this chemical step. Although the mutation causes higher enthalpy of activation of the hydride transfer, it only shows a small effect on the temperature dependence of the intrinsic KIE, suggesting marginal changes in the geometry and dynamics of the H-donor and -acceptor at the tunneling ready state. These observations suggest that the mutation disrupts the concerted motions that bring the H-donor and -acceptor together during the pre- and re-organization of the protein environment. The integrated structural and kinetic data allow us to probe the impact of protein motions on different time scales of the hydride transfer reaction within a complex enzymatic mechanism.
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Affiliation(s)
- Zhen Wang
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242-1727, USA
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29
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Linder M, Johansson AJ, Olsson TSG, Liebeschuetz J, Brinck T. Computational design of a Diels-Alderase from a thermophilic esterase: the importance of dynamics. J Comput Aided Mol Des 2012; 26:1079-95. [PMID: 22983490 DOI: 10.1007/s10822-012-9601-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Accepted: 09/03/2012] [Indexed: 12/01/2022]
Abstract
A novel computational Diels-Alderase design, based on a relatively rare form of carboxylesterase from Geobacillus stearothermophilus, is presented and theoretically evaluated. The structure was found by mining the PDB for a suitable oxyanion hole-containing structure, followed by a combinatorial approach to find suitable substrates and rational mutations. Four lead designs were selected and thoroughly modeled to obtain realistic estimates of substrate binding and prearrangement. Molecular dynamics simulations and DFT calculations were used to optimize and estimate binding affinity and activation energies. A large quantum chemical model was used to capture the salient interactions in the crucial transition state (TS). Our quantitative estimation of kinetic parameters was validated against four experimentally characterized Diels-Alderases with good results. The final designs in this work are predicted to have rate enhancements of ≈ 10(3)-10(6) and high predicted proficiencies. This work emphasizes the importance of considering protein dynamics in the design approach, and provides a quantitative estimate of the how the TS stabilization observed in most de novo and redesigned enzymes is decreased compared to a minimal, 'ideal' model. The presented design is highly interesting for further optimization and applications since it is based on a thermophilic enzyme (T (opt) = 70 °C).
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Affiliation(s)
- Mats Linder
- Applied Physical Chemistry, KTH Royal Institute of Technology, Teknikringen 30, 100 44, Stockholm, Sweden
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30
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Ferrer S, Ruiz-Pernía J, Martí S, Moliner V, Tuñón I, Bertrán J, Andrés J. Hybrid schemes based on quantum mechanics/molecular mechanics simulations goals to success, problems, and perspectives. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2012; 85:81-142. [PMID: 21920322 DOI: 10.1016/b978-0-12-386485-7.00003-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The development of characterization techniques, advanced synthesis methods, as well as molecular modeling has transformed the study of systems in a well-established research field. The current research challenges in biocatalysis and biotransformation evolve around enzyme discovery, design, and optimization. How can we find or create enzymes that catalyze important synthetic reactions, even reactions that may not exist in nature? What is the source of enzyme catalytic power? To answer these and other related questions, the standard strategies have evolved from trial-and-error methodologies based on chemical knowledge, accumulated experience, and common sense into a clearly multidisciplinary science that allows one to reach the molecular design of tailor-made enzyme catalysts. This is even more so when one refers to enzyme catalysts, for which the detailed structure and composition are known and can be manipulated to introduce well-defined residues which can be implicated in the chemical rearrangements taking place in the active site. The methods and techniques of theoretical and computational chemistry are becoming more and more important in both understanding the fundamental biological roles of enzymes and facilitating their utilization in biotechnology. Improvement of the catalytic function of enzymes is important from scientific and industrial viewpoints, and to put this fact in the actual perspective as well as the potentialities, we recommend the very recent report of Sanderson [Sanderson, K. (2011). Chemistry: enzyme expertise. Nature 471, 397.]. Great fundamental advances have been made toward the ab initio design of enzyme catalysts based on molecular modeling. This has been based on the molecular mechanistic knowledge of the reactions to be catalyzed, together with the development of advanced synthesis and characterization techniques. The corresponding molecular mechanism can be studied by means of powerful quantum chemical calculations. The catalytic active site can be optimized to improve the transition state analogues (TSA) and to enhance the catalytic activity, even improve the active site to favor a desired direction of some promiscuous enzymes. In this chapter, we give a brief introduction, the state of the art, and future prospects and implications of enzyme design. Current computational tools to assist experimentalists for the design and engineering of proteins with desired catalytic properties are described. The interplay between enzyme design, molecular simulations, and experiments will be presented to emphasize the interdisciplinary nature of this research field. This text highlights the recent advances and examples selected from our laboratory are shown, of how the applications of these tools are a first attempt to de novo design of protein active sites. Identification of neutral/advantageous/deleterious mutation platforms can be exploited to penetrate some of Nature's closely guarded secrets of chemical reactivity. In this chapter, we give a brief introduction, the state of the art, and future prospects and implications of enzyme design. The first part describes briefly how the molecular modeling is carried out. Then, we discuss the requirements of hybrid quantum mechanical/molecular mechanics molecular dynamics (QM/MM MD) simulations, analyzing what are the basis of these theoretical methodologies, how we can use them with a view to its application in the study of enzyme catalysis, and what are the best methodologies for assessing its catalytic potential. In the second part, we focus on some selected examples, taking as a common guide the chorismate to prephenate rearrangement, studying the corresponding molecular mechanism in vacuo, in solution and in an enzyme environment. In addition, examples involving catalytic antibodies (CAs) and promiscuous enzymes will be presented. Finally, a special emphasis is made to provide some hints about the logical evolution that can be anticipated in this research field. Moreover, it helps in understanding the open directions in this area of knowledge and highlights the importance of computational approaches in discovering specific drugs and the impact on the rational design of tailor-made enzymes.
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Affiliation(s)
- Silvia Ferrer
- Departamento de Química Física y Analítica, Universitat Jaume I, Castellón, Spain
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Evolutionarily conserved linkage between enzyme fold, flexibility, and catalysis. PLoS Biol 2011; 9:e1001193. [PMID: 22087074 PMCID: PMC3210774 DOI: 10.1371/journal.pbio.1001193] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Accepted: 09/27/2011] [Indexed: 11/19/2022] Open
Abstract
Proteins are intrinsically flexible molecules. The role of internal motions in a protein's designated function is widely debated. The role of protein structure in enzyme catalysis is well established, and conservation of structural features provides vital clues to their role in function. Recently, it has been proposed that the protein function may involve multiple conformations: the observed deviations are not random thermodynamic fluctuations; rather, flexibility may be closely linked to protein function, including enzyme catalysis. We hypothesize that the argument of conservation of important structural features can also be extended to identification of protein flexibility in interconnection with enzyme function. Three classes of enzymes (prolyl-peptidyl isomerase, oxidoreductase, and nuclease) that catalyze diverse chemical reactions have been examined using detailed computational modeling. For each class, the identification and characterization of the internal protein motions coupled to the chemical step in enzyme mechanisms in multiple species show identical enzyme conformational fluctuations. In addition to the active-site residues, motions of protein surface loop regions (>10 Å away) are observed to be identical across species, and networks of conserved interactions/residues connect these highly flexible surface regions to the active-site residues that make direct contact with substrates. More interestingly, examination of reaction-coupled motions in non-homologous enzyme systems (with no structural or sequence similarity) that catalyze the same biochemical reaction shows motions that induce remarkably similar changes in the enzyme–substrate interactions during catalysis. The results indicate that the reaction-coupled flexibility is a conserved aspect of the enzyme molecular architecture. Protein motions in distal areas of homologous and non-homologous enzyme systems mediate similar changes in the active-site enzyme–substrate interactions, thereby impacting the mechanism of catalyzed chemistry. These results have implications for understanding the mechanism of allostery, and for protein engineering and drug design.
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Direct measurement of the protein response to an electrostatic perturbation that mimics the catalytic cycle in ketosteroid isomerase. Proc Natl Acad Sci U S A 2011; 108:16612-7. [PMID: 21949360 DOI: 10.1073/pnas.1113874108] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Understanding how electric fields and their fluctuations in the active site of enzymes affect efficient catalysis represents a critical objective of biochemical research. We have directly measured the dynamics of the electric field in the active site of a highly proficient enzyme, Δ(5)-3-ketosteroid isomerase (KSI), in response to a sudden electrostatic perturbation that simulates the charge displacement that occurs along the KSI catalytic reaction coordinate. Photoexcitation of a fluorescent analog (coumarin 183) of the reaction intermediate mimics the change in charge distribution that occurs between the reactant and intermediate state in the steroid substrate of KSI. We measured the electrostatic response and angular dynamics of four probe dipoles in the enzyme active site by monitoring the time-resolved changes in the vibrational absorbance (IR) spectrum of a spectator thiocyanate moiety (a quantitative sensor of changes in electric field) placed at four different locations in and around the active site, using polarization-dependent transient vibrational Stark spectroscopy. The four different dipoles in the active site remain immobile and do not align to the changes in the substrate electric field. These results indicate that the active site of KSI is preorganized with respect to functionally relevant changes in electric fields.
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Warshel A, Dryga A. Simulating electrostatic energies in proteins: perspectives and some recent studies of pKas, redox, and other crucial functional properties. Proteins 2011; 79:3469-84. [PMID: 21910139 DOI: 10.1002/prot.23125] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2011] [Revised: 05/09/2011] [Accepted: 06/09/2011] [Indexed: 01/30/2023]
Abstract
Electrostatic energies provide what is arguably the most effective tool for structure-function correlation of biological molecules. Here, we provide an overview of the current state-of-the-art simulations of electrostatic energies in macromolecules, emphasizing the microscopic perspective but also relating it to macroscopic approaches. We comment on the convergence issue and other problems of the microscopic models and the ways of keeping the microscopic physics while moving to semi-macroscopic directions. We discuss the nature of the protein dielectric "constants" reiterating our long-standing point that the dielectric "constants" in semi-macroscopic models depend on the definition and the specific treatment. The advances and the challenges in the field are illustrated considering different functional properties including pK(a)'s, redox potentials, ion and proton channels, enzyme catalysis, ligand binding, and protein stability. We emphasize the microscopic overcharging approach for studying pK(a) 's of internal groups in proteins and give a demonstration of power of this approach. We also emphasize recent advances in coarse grained models with a physically based electrostatic treatment and provide some examples including further directions in treating voltage activated ion channels.
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Affiliation(s)
- Arieh Warshel
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-1062, USA.
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Bar-Even A, Noor E, Savir Y, Liebermeister W, Davidi D, Tawfik DS, Milo R. The Moderately Efficient Enzyme: Evolutionary and Physicochemical Trends Shaping Enzyme Parameters. Biochemistry 2011; 50:4402-10. [DOI: 10.1021/bi2002289] [Citation(s) in RCA: 649] [Impact Index Per Article: 49.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Arren Bar-Even
- Department of Plant Sciences, ‡Department of Physics of Complex Systems, and §Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Elad Noor
- Department of Plant Sciences, ‡Department of Physics of Complex Systems, and §Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yonatan Savir
- Department of Plant Sciences, ‡Department of Physics of Complex Systems, and §Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Wolfram Liebermeister
- Department of Plant Sciences, ‡Department of Physics of Complex Systems, and §Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Dan Davidi
- Department of Plant Sciences, ‡Department of Physics of Complex Systems, and §Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Dan S. Tawfik
- Department of Plant Sciences, ‡Department of Physics of Complex Systems, and §Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ron Milo
- Department of Plant Sciences, ‡Department of Physics of Complex Systems, and §Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
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Ramanathan A, Savol AJ, Langmead CJ, Agarwal PK, Chennubhotla CS. Discovering conformational sub-states relevant to protein function. PLoS One 2011; 6:e15827. [PMID: 21297978 PMCID: PMC3030567 DOI: 10.1371/journal.pone.0015827] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2010] [Accepted: 11/25/2010] [Indexed: 11/23/2022] Open
Abstract
Background Internal motions enable proteins to explore a range of conformations, even in the vicinity of native state. The role of conformational fluctuations in the designated function of a protein is widely debated. Emerging evidence suggests that sub-groups within the range of conformations (or sub-states) contain properties that may be functionally relevant. However, low populations in these sub-states and the transient nature of conformational transitions between these sub-states present significant challenges for their identification and characterization. Methods and Findings To overcome these challenges we have developed a new computational technique, quasi-anharmonic analysis (QAA). QAA utilizes higher-order statistics of protein motions to identify sub-states in the conformational landscape. Further, the focus on anharmonicity allows identification of conformational fluctuations that enable transitions between sub-states. QAA applied to equilibrium simulations of human ubiquitin and T4 lysozyme reveals functionally relevant sub-states and protein motions involved in molecular recognition. In combination with a reaction pathway sampling method, QAA characterizes conformational sub-states associated with cis/trans peptidyl-prolyl isomerization catalyzed by the enzyme cyclophilin A. In these three proteins, QAA allows identification of conformational sub-states, with critical structural and dynamical features relevant to protein function. Conclusions Overall, QAA provides a novel framework to intuitively understand the biophysical basis of conformational diversity and its relevance to protein function.
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Affiliation(s)
- Arvind Ramanathan
- Computational Biology Institute and Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- Lane Center for Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Andrej J. Savol
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Joint Carnegie Mellon University–University of Pittsburgh Ph.D. Program in Computational Biology, Pittsburgh, Pennsylvania, United States of America
| | - Christopher J. Langmead
- Computer Science Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
- Lane Center for Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Pratul K. Agarwal
- Computational Biology Institute and Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- * E-mail: (PKA); (CSC)
| | - Chakra S. Chennubhotla
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- * E-mail: (PKA); (CSC)
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Ballester P, Vidal-Ferran A, van Leeuwen PW. Modern Strategies in Supramolecular Catalysis. ADVANCES IN CATALYSIS 2011. [DOI: 10.1016/b978-0-12-387772-7.00002-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
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Go MK, Amyes TL, Richard JP. Rescue of K12G triosephosphate isomerase by ammonium cations: the reaction of an enzyme in pieces. J Am Chem Soc 2010; 132:13525-32. [PMID: 20822141 DOI: 10.1021/ja106104h] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The K12G mutation at yeast triosephosphate isomerase (TIM) results in a 5.5 × 10(5)-fold decrease in k(cat)/K(m) for isomerization of glyceraldehyde 3-phosphate, and the activity of this mutant can be successfully "rescued" by NH(4)(+) and primary alkylammonium cations. The transition state for the K12G mutant TIM-catalyzed reaction is stabilized by 1.5 kcal/mol by interaction with NH(4)(+). The larger 3.9 kcal/mol stabilization by CH(3)CH(2)CH(2)CH(2)NH(3)(+) is due to hydrophobic interactions between the mutant enzyme and the butyl side chain of the cation activator. There is no significant transfer of a proton from alkylammonium cations to GAP at the transition state for the K12G mutant TIM-catalyzed reaction, because activation by a series of RNH(3)(+) shows little or no dependence on the pK(a) of RNH(3)(+). A comparison of k(cat)/K(m) = 6.6 × 10(6) M(-1) s(-1) for the wildtype TIM-catalyzed isomerization of GAP and the third-order rate constant of 150 M(-2) s(-1) for activation by NH(4)(+) of the K12G mutant TIM-catalyzed isomerization shows that stabilization of the bound transition state by the effectively intramolecular interaction of the cationic side chain of Lys-12 at wildtype TIM is 6.3 kcal/mol greater than that for the corresponding intermolecular interaction of NH(4)(+) at K12G mutant TIM.
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Affiliation(s)
- Maybelle K Go
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, USA
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Go MK, Koudelka A, Amyes TL, Richard JP. Role of Lys-12 in catalysis by triosephosphate isomerase: a two-part substrate approach. Biochemistry 2010; 49:5377-89. [PMID: 20481463 DOI: 10.1021/bi100538b] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report that the K12G mutation in triosephosphate isomerase (TIM) from Saccharomyces cerevisiae results in (1) a approximately 50-fold increase in K(m) for the substrate glyceraldehyde 3-phosphate (GAP) and a 60-fold increase in K(i) for competitive inhibition by the intermediate analogue 2-phosphoglycolate, resulting from the loss of stabilizing ground state interactions between the alkylammonium side chain of Lys-12 and the ligand phosphodianion group; (2) a 12000-fold decrease in k(cat) for isomerization of GAP, suggesting a tightening of interactions between the side chain of Lys-12 and the substrate on proceeding from the Michaelis complex to the transition state; and (3) a 6 x 10(5)-fold decrease in k(cat)/K(m), corresponding to a total 7.8 kcal/mol stabilization of the transition state by the cationic side chain of Lys-12. The yields of the four products of the K12G TIM-catalyzed isomerization of GAP in D(2)O were quantified as dihydroxyacetone phosphate (DHAP) (27%), [1(R)-(2)H]DHAP (23%), [2(R)-(2)H]GAP (31%), and methylglyoxal (18%) from an enzyme-catalyzed elimination reaction. The K12G mutation has only a small effect on the relative yields of the three products of the transfer of a proton to the TIM-bound enediol(ate) intermediate in D(2)O, but it strongly favors catalysis of the elimination reaction to give methylglyoxal. The K12G mutation also results in a >or=14-fold decrease in k(cat)/K(m) for isomerization of bound glycolaldehyde (GA), although the dominant observed product of the mutant enzyme-catalyzed reaction of [1-(13)C]GA in D(2)O is [1-(13)C,2,2-di-(2)H]GA from a nonspecific protein-catalyzed reaction. The observation that the K12G mutation results in a large decrease in k(cat)/K(m) for the reactions of both GAP and the neutral truncated substrate [1-(13)C]GA provides evidence for a stabilizing interaction between the cationic side chain of Lys-12 and the negative charge that develops at the enolate-like oxygen in the transition state for deprotonation of the sugar substrate "piece".
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Affiliation(s)
- Maybelle K Go
- Department of Chemistry, University at Buffalo, State University of New York, Buffalo, New York 14260-3000, USA
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Childs W, Boxer SG. Solvation response along the reaction coordinate in the active site of ketosteroid isomerase. J Am Chem Soc 2010; 132:6474-80. [PMID: 20397697 PMCID: PMC2871671 DOI: 10.1021/ja1007849] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A light-activated reaction analog has been developed to mimic the catalytic reaction cycle of Delta(5)-3-ketosteroid isomerase to probe the functionally relevant protein solvation response to the catalytic charge transfer. Delta(5)-3-ketosteroid isomerase from Pseudomonas putida catalyzes a C-H bond cleavage and formation through an enolate intermediate. Conversion of the ketone substrate to the enolate intermediate is simulated by a photoacid bound to the active site oxyanion hole. In the ground state, the photoacid electrostatically resembles the enolate intermediate while the low pK(a) excited state resembles the ketone starting material. Time-resolved fluorescence experiments with photoacids coumarin 183 and equilenin show the active site of Delta(5)-3-ketosteroid isomerase to be largely unperturbed by the light-activated reaction. The small solvation response for the photoacid at the active site as compared with a simple solvent suggests the active site does not significantly change its electrostatic environment during the catalytic cycle. Instead, the reaction takes place in an electrostatically preorganized environment.
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Affiliation(s)
- William Childs
- Department of Chemistry, Stanford University, Stanford, California 94305-5080, USA
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40
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Bren U, Lah J, Bren M, Martínek V, Florián J. DNA duplex stability: the role of preorganized electrostatics. J Phys Chem B 2010; 114:2876-85. [PMID: 20131770 PMCID: PMC2841231 DOI: 10.1021/jp9064246] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The insertion of a DNA base moiety at the end of a DNA duplex to form a Watson-Crick or wobble pair during DNA annealing or replication is a step of fundamental biological importance. Therefore, we investigated the energetics of a formation of the terminal G x C, G x T, and G x A base pairs in DNA containing a 5'-dangling G adjacent to the base insertion point using differential scanning calorimetry and computer simulations. The energies calculated along classical molecular dynamics trajectories in aqueous solution were analyzed in the framework of linear-response approximation (LRA) to obtain relative free energies for the base insertion and their electrostatic, van der Waals, and preorganization components. Using the generic set of LRA parameters, the calculated free energies disfavored the mispair formation by 2.5 (G x C --> G x T) and 1.7 (G x C --> G x A) kcal/mol, in reasonable agreement with the experimental free energy differences of 1.8 and 1.4 kcal/mol, respectively. The calculated preorganization components of these free energies of 0.6 (G x C --> G x T) and -0.1 (G x C --> G x A) kcal/mol show that electrostatic preorganization, which is an important source of DNA replication fidelity, plays a lesser role in the mispair destabilization in the absence of DNA polymerase.
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Affiliation(s)
- Urban Bren
- National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia
| | - Jurij Lah
- University of Ljubljana, Faculty of Chemistry and Chemical Technology, Aškerčeva 5, 1000 Ljubljana, Slovenia
| | - Matevž Bren
- Institute of Mathematics, Physics and Mechanics, Jadranska 19, 1000 Ljubljana, Slovenia
| | - Václav Martínek
- Department of Chemistry, Loyola University Chicago, Chicago, IL 60626, USA
| | - Jan Florián
- Department of Chemistry, Loyola University Chicago, Chicago, IL 60626, USA
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Yang K, Hsieh YH, Kim CK, Zhang H, Wolfe S. Hydration of acetone in the gas phase and in water solvent. CAN J CHEM 2010. [DOI: 10.1139/v09-135] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In water solvent, the hydration of acetone proceeds by a cyclic (cooperative) process in which concurrent C–O bond formation and proton transfer to oxygen take place through a solvent and (or) catalyst bridge. Reactivity is determined primarily by the concentration of a reactant complex and not the barrier from this complex. This situation is reversed in the gas phase; although the concentrations of reactive complexes are much higher than in solution, the barriers are also higher and dominant in determining reactivity. Calculations of isotope effects suggest that multiple hydron transfers are synchronous in the gas phase to avoid zwitterionic transition states. In solution, such transition states are stabilized by solvation and hydron transfers can be asynchronous.
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Affiliation(s)
- Kiyull Yang
- Department of Chemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
- On leave from Department of Chemistry Education, Gyeongsang National University, Jinju 660-701, Korea
- On leave from Department of Chemistry, Inha University, Incheon 402-751, Korea
| | - Yih-Huang Hsieh
- Department of Chemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
- On leave from Department of Chemistry Education, Gyeongsang National University, Jinju 660-701, Korea
- On leave from Department of Chemistry, Inha University, Incheon 402-751, Korea
| | - Chan-Kyung Kim
- Department of Chemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
- On leave from Department of Chemistry Education, Gyeongsang National University, Jinju 660-701, Korea
- On leave from Department of Chemistry, Inha University, Incheon 402-751, Korea
| | - Hui Zhang
- Department of Chemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
- On leave from Department of Chemistry Education, Gyeongsang National University, Jinju 660-701, Korea
- On leave from Department of Chemistry, Inha University, Incheon 402-751, Korea
| | - Saul Wolfe
- Department of Chemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
- On leave from Department of Chemistry Education, Gyeongsang National University, Jinju 660-701, Korea
- On leave from Department of Chemistry, Inha University, Incheon 402-751, Korea
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Ramanathan A, Agarwal PK. Computational identification of slow conformational fluctuations in proteins. J Phys Chem B 2009; 113:16669-80. [PMID: 19908896 PMCID: PMC2872677 DOI: 10.1021/jp9077213] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Conformational flexibility of proteins has been linked to their designated functions. Slow conformational fluctuations occurring at the microsecond to millisecond time scale, in particular, have recently attracted considerable interest in connection to the mechanism of enzyme catalysis. Computational methods are providing valuable insights into the connection between protein structure, flexibility, and function. In this report, we present studies on identification and characterization of microsecond flexibility of ubiquitin, based on quasi-harmonic analysis (QHA) and normal-mode analysis (NMA). The results indicate that the slowest 10 QHA modes, computed from the 0.5 mus molecular dynamics ensemble, contribute over 78% of all motions. The identified slow movements show over 75% similarity with the conformational fluctuations observed in nuclear magnetic resonance ensemble and also agree with displacements in the set of X-ray structures. The slowest modes show high flexibility in the beta1-beta2, alpha1-beta3, and beta3-beta4 loop regions, with functional implications in the mechanism of binding other proteins. NMA of ubiquitin structures was not able to reproduce the long time scale fluctuations, as they were found to strongly depend on the reference structures. Further, conformational fluctuations coupled to the cis/trans isomerization reaction catalyzed by the enzyme cyclophilin A (CypA), occurring at the microsecond to millisecond time scale, have also been identified and characterized on the basis of QHA of conformations sampled along the reaction pathway. The results indicate that QHA covers the same conformational landscape as the experimentally observed CypA flexibility. Overall, the identified slow conformational fluctuations in ubiquitin and CypA indicate that the intrinsic flexibility of these proteins is closely linked to their designated functions.
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Affiliation(s)
- Arvind Ramanathan
- Joint Carnegie Mellon University-University of Pittsburgh Ph.D. Program in Computational Biology, Lane Center for Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213
- Computational Biology Institute, and Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge National Laboratory, Oak Ridge, TN 37831
| | - Pratul K. Agarwal
- Computational Biology Institute, and Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge National Laboratory, Oak Ridge, TN 37831
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43
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Monti D, Riva S. Natural and Artificial Microenzymes: Is It Possible to have Small and Efficient Biocatalysts? BIOCATAL BIOTRANSFOR 2009. [DOI: 10.3109/10242420109003643] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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44
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Hu H, Yang W. Development and application of ab initio QM/MM methods for mechanistic simulation of reactions in solution and in enzymes. ACTA ACUST UNITED AC 2009; 898:17-30. [PMID: 24146439 DOI: 10.1016/j.theochem.2008.12.025] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Determining the free energies and mechanisms of chemical reactions in solution and enzymes is a major challenge. For such complex reaction processes, combined quantum mechanics/molecular mechanics (QM/MM) method is the most effective simulation method to provide an accurate and efficient theoretical description of the molecular system. The computational costs of ab initio QM methods, however, have limited the application of ab initio QM/MM methods. Recent advances in ab initio QM/MM methods allowed the accurate simulation of the free energies for reactions in solution and in enzymes and thus paved the way for broader application of the ab initio QM/MM methods. We review here the theoretical developments and applications of the ab initio QM/MM methods, focusing on the determination of reaction path and the free energies of the reaction processes in solution and enzymes.
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Affiliation(s)
- Hao Hu
- Department of Chemistry, Duke University, Durham, NC 27708, USA
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Abstract
A major issue for organisms living at extreme temperatures is to preserve both stability and activity of their enzymes. Cold-adapted enzymes generally have a reduced thermal stability, to counteract freezing, and show a lower enthalpy and a more negative entropy of activation compared to mesophilic and thermophilic homologues. Such a balance of thermodynamic activation parameters can make the reaction rate decrease more linearly, rather than exponentially, as the temperature is lowered, but the structural basis for rate optimization toward low working temperatures remains unclear. In order to computationally address this problem, it is clear that reaction simulations rather than standard molecular dynamics calculations are needed. We have thus carried out extensive computer simulations of the keto-enol(ate) isomerization steps in differently adapted citrate synthases to explore the structure-function relationships behind catalytic rate adaptation to different temperatures. The calculations reproduce the absolute rates of the psychrophilic and mesophilic enzymes at 300 K, as well as the lower enthalpy and more negative entropy of activation of the cold-adapted enzyme, where the latter simulation result is obtained from high-precision Arrhenius plots. The overall catalytic effect originates from electrostatic stabilization of the transition state and enolate and the reduction of reorganization free energy. The simulations, however, show psychrophilic, mesophilic, and hyperthermophilic citrate synthases to have increasingly stronger electrostatic stabilization of the transition state, while the energetic penalty in terms of internal protein interactions follows the reverse order with the cold-adapted enzyme having the most favorable energy term. The lower activation enthalpy and more negative activation entropy observed for cold-adapted enzymes are found to be associated with a decreased protein stiffness. The origin of this effect is, however, not localized to the active site but to other regions of the protein structure.
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Affiliation(s)
- Sinisa Bjelic
- Department of Cell and Molecular Biology, Uppsala University Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden
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46
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Abriata LA, González LJ, Llarrull LI, Tomatis PE, Myers WK, Costello AL, Tierney DL, Vila AJ. Engineered mononuclear variants in Bacillus cereus metallo-beta-lactamase BcII are inactive. Biochemistry 2008; 47:8590-9. [PMID: 18652482 PMCID: PMC2565585 DOI: 10.1021/bi8006912] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Metallo-beta-lactamases (MbetaLs) are zinc enzymes able to hydrolyze almost all beta-lactam antibiotics, rendering them inactive, at the same time endowing bacteria high levels of resistance. The design of inhibitors active against all classes of MbetaLs has been hampered by their structural diversity and by the heterogeneity in metal content in enzymes from different sources. BcII is the metallo-beta-lactamase from Bacillus cereus, which is found in both the mononuclear and dinuclear forms. Despite extensive studies, there is still controversy about the nature of the active BcII species. Here we have designed two mutant enzymes in which each one of the metal binding sites was selectively removed. Both mutants were almost inactive, despite preserving most of the structural features of each metal site. These results reveal that neither site isolated in the MbetaL scaffold is sufficient to render a fully active enzyme. This suggests that only the dinuclear species is active or that the mononuclear variants can be active only if aided by other residues that would be metal ligands in the dinuclear species.
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Affiliation(s)
| | | | | | | | | | | | | | - Alejandro J. Vila
- To whom correspondence should be addressed. Phone: +54−341−4350661, ext. 108. Fax: +54−341−4390465. E-mail:
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47
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Tsang WY, Amyes TL, Richard JP. A substrate in pieces: allosteric activation of glycerol 3-phosphate dehydrogenase (NAD+) by phosphite dianion. Biochemistry 2008; 47:4575-82. [PMID: 18376850 DOI: 10.1021/bi8001743] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The ratio of the second-order rate constants for reduction of dihydroxyacetone phosphate (DHAP) and of the neutral truncated substrate glycolaldehyde (GLY) by glycerol 3-phosphate dehydrogenase (NAD (+), GPDH) saturated with NADH is (1.0 x 10 (6) M (-1) s (-1))/(8.7 x 10 (-3) M (-1) s (-1)) = 1.1 x 10 (8), which was used to calculate an intrinsic phosphate binding energy of at least 11.0 kcal/mol. Phosphite dianion binds very weakly to GPDH ( K d > 0.1 M), but the bound dianion strongly activates GLY toward enzyme-catalyzed reduction by NADH. Thus, the large intrinsic phosphite binding energy is expressed only at the transition state for the GPDH-catalyzed reaction. The ratio of rate constants for the phosphite-activated and the unactivated GPDH-catalyzed reduction of GLY by NADH is (4300 M (-2) s (-1))/(8.7 x 10 (-3) M (-1) s (-1)) = 5 x 10 (5) M (-1), which was used to calculate an intrinsic phosphite binding energy of -7.7 kcal/mol for the association of phosphite dianion with the transition state complex for the GPDH-catalyzed reduction of GLY. Phosphite dianion has now been shown to activate bound substrates for enzyme-catalyzed proton transfer, decarboxylation, hydride transfer, and phosphoryl transfer reactions. Structural data provide strong evidence that enzymic activation by the binding of phosphite dianion occurs at a modular active site featuring (1) a binding pocket complementary to the reactive substrate fragment which contains all the active site residues needed to catalyze the reaction of the substrate piece or of the whole substrate and (2) a phosphate/phosphite dianion binding pocket that is completed by the movement of flexible protein loop(s) to surround the nonreacting oxydianion. We propose that loop motion and associated protein conformational changes that accompany the binding of phosphite dianion and/or phosphodianion substrates lead to encapsulation of the substrate and/or its pieces in the protein interior, and to placement of the active site residues in positions where they provide optimal stabilization of the transition state for the catalyzed reaction.
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Affiliation(s)
- Wing-Yin Tsang
- Department of Chemistry, University at Buffalo, State University of New York, Buffalo, NY 14260-3000, USA
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48
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Determination of Electrostatic Interaction Energies and Protonation State Populations in Enzyme Active Sites. J Mol Biol 2008; 376:269-87. [DOI: 10.1016/j.jmb.2007.09.070] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2007] [Revised: 09/17/2007] [Accepted: 09/25/2007] [Indexed: 11/21/2022]
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49
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Taran O, Medrano F, Yatsimirsky AK. Rapid hydrolysis of model phosphate diesters by alkaline-earth cations in aqueous DMSO: speciation and kinetics. Dalton Trans 2008:6609-18. [DOI: 10.1039/b807030j] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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50
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Hu H, Yang W. Free energies of chemical reactions in solution and in enzymes with ab initio quantum mechanics/molecular mechanics methods. Annu Rev Phys Chem 2008; 59:573-601. [PMID: 18393679 PMCID: PMC3727228 DOI: 10.1146/annurev.physchem.59.032607.093618] [Citation(s) in RCA: 349] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Combined quantum mechanics/molecular mechanics (QM/MM) methods provide an accurate and efficient energetic description of complex chemical and biological systems, leading to significant advances in the understanding of chemical reactions in solution and in enzymes. Here we review progress in QM/MM methodology and applications, focusing on ab initio QM-based approaches. Ab initio QM/MM methods capitalize on the accuracy and reliability of the associated quantum-mechanical approaches, however, at a much higher computational cost compared with semiempirical quantum-mechanical approaches. Thus reaction-path and activation free-energy calculations based on ab initio QM/MM methods encounter unique challenges in simulation timescales and phase-space sampling. This review features recent developments overcoming these challenges and enabling accurate free-energy determination for reaction processes in solution and in enzymes, along with applications.
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Affiliation(s)
- Hao Hu
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA.
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