301
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Abstract
Isomerization reactions are fundamental in biology, and isomers usually differ in their biological role and pharmacological effects. In this study, we have cataloged the isomerization reactions known to occur in biology using a combination of manual and computational approaches. This method provides a robust basis for comparison and clustering of the reactions into classes. Comparing our results with the Enzyme Commission (EC) classification, the standard approach to represent enzyme function on the basis of the overall chemistry of the catalyzed reaction, expands our understanding of the biochemistry of isomerization. The grouping of reactions involving stereoisomerism is straightforward with two distinct types (racemases/epimerases and cis-trans isomerases), but reactions entailing structural isomerism are diverse and challenging to classify using a hierarchical approach. This study provides an overview of which isomerases occur in nature, how we should describe and classify them, and their diversity.
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302
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Mangel WF, McGrath WJ, Xiong K, Graziano V, Blainey PC. Molecular sled is an eleven-amino acid vehicle facilitating biochemical interactions via sliding components along DNA. Nat Commun 2016; 7:10202. [PMID: 26831565 PMCID: PMC4740752 DOI: 10.1038/ncomms10202] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 11/13/2015] [Indexed: 01/27/2023] Open
Abstract
Recently, we showed the adenovirus proteinase interacts productively with its protein substrates in vitro and in vivo in nascent virus particles via one-dimensional diffusion along the viral DNA. The mechanism by which this occurs has heretofore been unknown. We show sliding of these proteins along DNA occurs on a new vehicle in molecular biology, a 'molecular sled' named pVIc. This 11-amino acid viral peptide binds to DNA independent of sequence. pVIc slides on DNA, exhibiting the fastest one-dimensional diffusion constant, 26±1.8 × 10(6) (bp)(2) s(-1). pVIc is a 'molecular sled,' because it can slide heterologous cargos along DNA, for example, a streptavidin tetramer. Similar peptides, for example, from the C terminus of β-actin or NLSIII of the p53 protein, slide along DNA. Characteristics of the 'molecular sled' in its milieu (virion, nucleus) have implications for how proteins in the nucleus of cells interact and imply a new form of biochemistry, one-dimensional biochemistry.
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Affiliation(s)
- Walter F. Mangel
- Department of Biology, Brookhaven National Laboratory, 50 Bell Avenue, Upton, New York 11973, USA
| | - William J. McGrath
- Department of Biology, Brookhaven National Laboratory, 50 Bell Avenue, Upton, New York 11973, USA
| | - Kan Xiong
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Vito Graziano
- Department of Biology, Brookhaven National Laboratory, 50 Bell Avenue, Upton, New York 11973, USA
| | - Paul C. Blainey
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
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303
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Bourne Y, Sharpless KB, Taylor P, Marchot P. Steric and Dynamic Parameters Influencing In Situ Cycloadditions to Form Triazole Inhibitors with Crystalline Acetylcholinesterase. J Am Chem Soc 2016; 138:1611-21. [PMID: 26731630 DOI: 10.1021/jacs.5b11384] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ligand binding sites on acetylcholinesterase (AChE) comprise an active center, at the base of a deep and narrow gorge lined by aromatic residues, and a peripheral site at the gorge entry. These features launched AChE as a reaction vessel for in situ click-chemistry synthesis of high-affinity TZ2PA6 and TZ2PA5 inhibitors, forming a syn-triazole upon cycloaddition within the gorge from alkyne and azide reactants bound at the two sites, respectively. Subsequent crystallographic analyses of AChE complexes with the TZ2PA6 regioisomers demonstrated that syn product association is accompanied by side chain reorganization within the gorge, freezing-in-frame a conformation distinct from an unbound state or anti complex. To correlate inhibitor dimensions with reactivity and explore whether in situ cycloaddition could be accelerated in a concentrated, crystalline template, we developed crystal-soaking procedures and solved structures of AChE complexes with the TZ2PA5 regioisomers and their TZ2/PA5 precursors (2.1-2.7 Å resolution). The structures reveal motions of residue His447 in the active site and, unprecedentedly, residue Tyr341 at the gorge mouth, associated with TZ2 binding and coordinated with other side chain motions in the gorge that may guide AChE toward a transient state favoring syn-triazole formation. Despite precursor binding to crystalline AChE, coupling of rapid electric field fluctuations in the gorge with proper alignments of the azide and alkyne reactants to form the triazole remains a likely limiting step. These observations point to a prime requirement for AChE to interconvert dynamically between sequential conformations to promote favorable electrostatic factors enabling a productive apposition of the reactants for reactivity.
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Affiliation(s)
- Yves Bourne
- Aix-Marseille Université, laboratory Architecture et Fonction des Macromolécules Biologiques, Faculté des Sciences de Luminy , 13288 Marseille cedex 09, France.,Centre National de la Recherche Scientifique, laboratory Architecture et Fonction des Macromolécules Biologiques, Faculté des Sciences de Luminy , 13288 Marseille cedex 09, France
| | - K Barry Sharpless
- Department of Chemistry, The Skaggs Institute for Chemical Biology, The Scripps Research Institute , La Jolla, California 92037, United States
| | - Palmer Taylor
- Department of Pharmacology, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego , La Jolla, California 92093-0650, United States
| | - Pascale Marchot
- Aix-Marseille Université, laboratory Architecture et Fonction des Macromolécules Biologiques, Faculté des Sciences de Luminy , 13288 Marseille cedex 09, France.,Centre National de la Recherche Scientifique, laboratory Architecture et Fonction des Macromolécules Biologiques, Faculté des Sciences de Luminy , 13288 Marseille cedex 09, France
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304
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Wei Y, Wang X, Wang X, Tao Z, Cui Y, Yang M. A theoretical study of the activation of nitromethane under applied electric fields. RSC Adv 2016. [DOI: 10.1039/c6ra00724d] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
C–N activation is the key step of nitromethane decomposition.
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Affiliation(s)
- Yuan Wei
- Institute of Atomic and Molecular Physics
- Key Laboratory of High Energy Density
- Physics and Technology of Ministry of Education
- Sichuan University
- Chengdu
| | - Xinqin Wang
- Institute of Atomic and Molecular Physics
- Key Laboratory of High Energy Density
- Physics and Technology of Ministry of Education
- Sichuan University
- Chengdu
| | - Xin Wang
- College of Chemistry
- Sichuan University
- Chengdu
- China
| | - Zhiqiang Tao
- College of Chemistry
- Sichuan University
- Chengdu
- China
| | - Yingqi Cui
- Institute of Atomic and Molecular Physics
- Key Laboratory of High Energy Density
- Physics and Technology of Ministry of Education
- Sichuan University
- Chengdu
| | - Mingli Yang
- Institute of Atomic and Molecular Physics
- Key Laboratory of High Energy Density
- Physics and Technology of Ministry of Education
- Sichuan University
- Chengdu
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305
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Abstract
David Craig (1919–2015) left us with a lasting legacy concerning basic understanding of chemical spectroscopy and bonding. This is expressed in terms of some of the recent achievements of my own research career, with a focus on integration of Craig’s theories with those of Noel Hush to solve fundamental problems in photosynthesis, molecular electronics (particularly in regard to the molecules synthesized by Maxwell Crossley), and self-assembled monolayer structure and function. Reviewed in particular is the relation of Craig’s legacy to: the 50-year struggle to assign the visible absorption spectrum of arguably the world’s most significant chromophore, chlorophyll; general theories for chemical bonding and structure extending Hush’s adiabatic theory of electron-transfer processes; inelastic electron-tunnelling spectroscopy (IETS); chemical quantum entanglement and the Penrose–Hameroff model for quantum consciousness; synthetic design strategies for NMR quantum computing; Gibbs free-energy measurements and calculations for formation and polymorphism of organic self-assembled monolayers on graphite surfaces from organic solution; and understanding the basic chemical processes involved in the formation of gold surfaces and nanoparticles protected by sulfur-bound ligands, ligands whose form is that of Au0-thiyl rather than its commonly believed AuI-thiolate tautomer.
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306
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List NH, Olsen JMH, Kongsted J. Excited states in large molecular systems through polarizable embedding. Phys Chem Chem Phys 2016; 18:20234-50. [DOI: 10.1039/c6cp03834d] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Using the polarizable embedding model enables rational design of light-sensitive functional biological materials.
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Affiliation(s)
- Nanna Holmgaard List
- Department of Physics, Chemistry and Pharmacy
- University of Southern Denmark
- 5230 Odense M
- Denmark
| | | | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy
- University of Southern Denmark
- 5230 Odense M
- Denmark
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307
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Wu Y, Fried SD, Boxer SG. Dissecting Proton Delocalization in an Enzyme's Hydrogen Bond Network with Unnatural Amino Acids. Biochemistry 2015; 54:7110-9. [PMID: 26571340 DOI: 10.1021/acs.biochem.5b00958] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Extended hydrogen bond networks are a common structural motif of enzymes. A recent analysis proposed quantum delocalization of protons as a feature present in the hydrogen bond network spanning a triad of tyrosines (Y(16), Y(32), and Y(57)) in the active site of ketosteroid isomerase (KSI), contributing to its unusual acidity and large isotope shift. In this study, we utilized amber suppression to substitute each tyrosine residue with 3-chlorotyrosine to test the delocalization model and the proton affinity balance in the triad. X-ray crystal structures of each variant demonstrated that the structure, notably the O-O distances within the triad, was unaffected by 3-chlorotyrosine substitutions. The changes in the cluster's acidity and the acidity's isotope dependence in these variants were assessed via UV-vis spectroscopy and the proton sharing pattern among individual residues with (13)C nuclear magnetic resonance. Our data show pKa detuning at each triad residue alters the proton delocalization behavior in the H-bond network. The extra stabilization energy necessary for the unusual acidity mainly comes from the strong interactions between Y(57) and Y(16). This is further enabled by Y(32), which maintains the right geometry and matched proton affinity in the triad. This study provides a rich picture of the energetics of the hydrogen bond network in enzymes for further model refinement.
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Affiliation(s)
- Yufan Wu
- Department of Chemistry, Stanford University , Stanford, California 94305-5012, United States
| | - Stephen D Fried
- Department of Chemistry, Stanford University , Stanford, California 94305-5012, United States
| | - Steven G Boxer
- Department of Chemistry, Stanford University , Stanford, California 94305-5012, United States
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308
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Onwukwe GU, Koski MK, Pihko P, Schmitz W, Wierenga RK. Structures of yeast peroxisomal Δ(3),Δ(2)-enoyl-CoA isomerase complexed with acyl-CoA substrate analogues: the importance of hydrogen-bond networks for the reactivity of the catalytic base and the oxyanion hole. ACTA ACUST UNITED AC 2015; 71:2178-91. [PMID: 26527136 DOI: 10.1107/s139900471501559x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 08/19/2015] [Indexed: 11/10/2022]
Abstract
Δ(3),Δ(2)-Enoyl-CoA isomerases (ECIs) catalyze the shift of a double bond from 3Z- or 3E-enoyl-CoA to 2E-enoyl-CoA. ECIs are members of the crotonase superfamily. The crotonase framework is used by many enzymes to catalyze a wide range of reactions on acyl-CoA thioesters. The thioester O atom is bound in a conserved oxyanion hole. Here, the mode of binding of acyl-CoA substrate analogues to peroxisomal Saccharomyces cerevisiae ECI (ScECI2) is described. The best defined part of the bound acyl-CoA molecules is the 3',5'-diphosphate-adenosine moiety, which interacts with residues of loop 1 and loop 2, whereas the pantetheine part is the least well defined. The catalytic base, Glu158, is hydrogen-bonded to the Asn101 side chain and is further hydrogen-bonded to the side chain of Arg100 in the apo structure. Arg100 is completely buried in the apo structure and a conformational change of the Arg100 side chain appears to be important for substrate binding and catalysis. The oxyanion hole is formed by the NH groups of Ala70 (loop 2) and Leu126 (helix 3). The O atoms of the corresponding peptide units, Gly69 O and Gly125 O, are both part of extensive hydrogen-bond networks. These hydrogen-bond networks are a conserved feature of the crotonase oxyanion hole and their importance for catalysis is discussed.
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Affiliation(s)
- Goodluck U Onwukwe
- Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - M Kristian Koski
- Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Petri Pihko
- Department of Chemistry, University of Jyväskylä, Jyväskylä, Finland
| | - Werner Schmitz
- Department of Biochemistry and Molecular Biology, University of Würzburg, Biozentrum, Am Hubland, 97074 Würzburg, Germany
| | - Rik K Wierenga
- Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
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309
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Shi Y, Acerson MJ, Shuford KL, Shaw BF. Voltage-Induced Misfolding of Zinc-Replete ALS Mutant Superoxide Dismutase-1. ACS Chem Neurosci 2015. [PMID: 26207449 DOI: 10.1021/acschemneuro.5b00146] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The monomerization of Cu, Zn superoxide dismutase (SOD1) is an early step along pathways of misfolding linked to amyotrophic lateral sclerosis (ALS). Monomerization requires the reversal of two post-translational modifications that are thermodynamically favorable: (i) dissociation of active-site metal ions and (ii) reduction of intramolecular disulfide bonds. This study found, using amide hydrogen/deuterium (H/D) exchange, capillary electrophoresis, and lysine-acetyl protein charge ladders, that ALS-linked A4V SOD1 rapidly monomerizes and partially unfolds in an external electric field (of physiological strength), without loss of metal ions, exposure to disulfide-reducing agents, or Joule heating. Voltage-induced monomerization was not observed for metal-free A4V SOD1, metal-free WT SOD1, or metal-loaded WT SOD1. Computational modeling suggested a mechanism for this counterintuitive effect: subunit macrodipoles of dimeric SOD1 are antiparallel and amplified 2-fold by metal coordination, which increases torque at the dimer interface as subunits rotate to align with the electric field.
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Affiliation(s)
- Yunhua Shi
- Department
of Chemistry and
Biochemistry, Baylor University, Waco, Texas 76706, United States
| | - Mark J. Acerson
- Department
of Chemistry and
Biochemistry, Baylor University, Waco, Texas 76706, United States
| | - Kevin L. Shuford
- Department
of Chemistry and
Biochemistry, Baylor University, Waco, Texas 76706, United States
| | - Bryan F. Shaw
- Department
of Chemistry and
Biochemistry, Baylor University, Waco, Texas 76706, United States
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310
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Ritchie AW, Webb LJ. Understanding and Manipulating Electrostatic Fields at the Protein-Protein Interface Using Vibrational Spectroscopy and Continuum Electrostatics Calculations. J Phys Chem B 2015; 119:13945-57. [PMID: 26375183 DOI: 10.1021/acs.jpcb.5b06888] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Biological function emerges in large part from the interactions of biomacromolecules in the complex and dynamic environment of the living cell. For this reason, macromolecular interactions in biological systems are now a major focus of interest throughout the biochemical and biophysical communities. The affinity and specificity of macromolecular interactions are the result of both structural and electrostatic factors. Significant advances have been made in characterizing structural features of stable protein-protein interfaces through the techniques of modern structural biology, but much less is understood about how electrostatic factors promote and stabilize specific functional macromolecular interactions over all possible choices presented to a given molecule in a crowded environment. In this Feature Article, we describe how vibrational Stark effect (VSE) spectroscopy is being applied to measure electrostatic fields at protein-protein interfaces, focusing on measurements of guanosine triphosphate (GTP)-binding proteins of the Ras superfamily binding with structurally related but functionally distinct downstream effector proteins. In VSE spectroscopy, spectral shifts of a probe oscillator's energy are related directly to that probe's local electrostatic environment. By performing this experiment repeatedly throughout a protein-protein interface, an experimental map of measured electrostatic fields generated at that interface is determined. These data can be used to rationalize selective binding of similarly structured proteins in both in vitro and in vivo environments. Furthermore, these data can be used to compare to computational predictions of electrostatic fields to explore the level of simulation detail that is necessary to accurately predict our experimental findings.
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Affiliation(s)
- Andrew W Ritchie
- Department of Chemistry, Center for Nano- and Molecular Science and Technology, and Institute for Cell and Molecular Biology, The University of Texas at Austin , 105 East 24th Street STOP A5300, Austin, Texas 78712, United States
| | - Lauren J Webb
- Department of Chemistry, Center for Nano- and Molecular Science and Technology, and Institute for Cell and Molecular Biology, The University of Texas at Austin , 105 East 24th Street STOP A5300, Austin, Texas 78712, United States
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311
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Pokorný J, Pokorný J, Foletti A, Kobilková J, Vrba J, Vrba J. Mitochondrial Dysfunction and Disturbed Coherence: Gate to Cancer. Pharmaceuticals (Basel) 2015; 8:675-95. [PMID: 26437417 PMCID: PMC4695805 DOI: 10.3390/ph8040675] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 09/06/2015] [Accepted: 09/11/2015] [Indexed: 12/21/2022] Open
Abstract
Continuous energy supply, a necessary condition for life, excites a state far from thermodynamic equilibrium, in particular coherent electric polar vibrations depending on water ordering in the cell. Disturbances in oxidative metabolism and coherence are a central issue in cancer development. Oxidative metabolism may be impaired by decreased pyruvate transfer to the mitochondrial matrix, either by parasitic consumption and/or mitochondrial dysfunction. This can in turn lead to disturbance in water molecules’ ordering, diminished power, and coherence of the electromagnetic field. In tumors with the Warburg (reverse Warburg) effect, mitochondrial dysfunction affects cancer cells (fibroblasts associated with cancer cells), and the electromagnetic field generated by microtubules in cancer cells has low power (high power due to transport of energy-rich metabolites from fibroblasts), disturbed coherence, and a shifted frequency spectrum according to changed power. Therapeutic strategies restoring mitochondrial function may trigger apoptosis in treated cells; yet, before this step is performed, induction (inhibition) of pyruvate dehydrogenase kinases (phosphatases) may restore the cancer state. In tumor tissues with the reverse Warburg effect, Caveolin-1 levels should be restored and the transport of energy-rich metabolites interrupted to cancer cells. In both cancer phenotypes, achieving permanently reversed mitochondrial dysfunction with metabolic-modulating drugs may be an effective, specific anti-cancer strategy.
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Affiliation(s)
- Jiří Pokorný
- Institute of Photonics and Electronics, Czech Academy of Sciences, Chaberská 57, 182 51 Prague 8, Czech Republic.
| | - Jan Pokorný
- Institute of Physics, Czech Academy of Sciences, Na Slovance 2, 182 21 Prague 8, Czech Republic.
| | - Alberto Foletti
- Institute of Translational Pharmacology, National Research Council-CNR, Via Fosso del Cavaliere 100, Rome 00133, Italy.
- Clinical Biophysics International Research Group, via Maggio 21, Lugano 6900, Switzerland.
| | - Jitka Kobilková
- Department of Obstetrics and Gynaecology, 1st Faculty of Medicine, Charles University in Prague, Apolinářská 18, 128 00 Prague 2, Czech Republic.
| | - Jan Vrba
- Faculty of Electrical Engineering, Czech Technical University in Prague, Technická 2, 166 27 Prague 6, Czech Republic.
| | - Jan Vrba
- Faculty of Biomedical Engineering, Czech Technical University in Kladno, Sitná Square 3105, 272 01 Kladno, Czech Republic.
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312
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Natarajan A, Yabukarski F, Lamba V, Schwans JP, Sunden F, Herschlag D. BIOPHYSICS. Comment on "Extreme electric fields power catalysis in the active site of ketosteroid isomerase". Science 2015; 349:936. [PMID: 26315426 DOI: 10.1126/science.aab1584] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 07/24/2015] [Indexed: 11/02/2022]
Abstract
Fried et al. (Reports, 19 December 2014, p. 1510) demonstrated a strong correlation between reaction rate and the carbonyl stretching frequency of a product analog bound to ketosteroid isomerase oxyanion hole mutants and concluded that the active-site electric field provides 70% of catalysis. Alternative comparisons suggest a smaller contribution, relative to the corresponding solution reaction, and highlight the importance of atomic-level descriptions.
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Affiliation(s)
- Aditya Natarajan
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Filip Yabukarski
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Vandana Lamba
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jason P Schwans
- Department of Chemistry and Biochemistry, California State University Long Beach, Long Beach, CA 90840, USA
| | - Fanny Sunden
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Daniel Herschlag
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA.
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313
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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: 8] [Impact Index Per Article: 0.9] [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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314
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Fried SD, Boxer SG. BIOPHYSICS. Response to Comments on "Extreme electric fields power catalysis in the active site of ketosteroid isomerase". Science 2015; 349:936. [PMID: 26315428 DOI: 10.1126/science.aab1627] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 07/24/2015] [Indexed: 01/28/2023]
Abstract
Natarajan et al. and Chen and Savidge comment that comparing the electric field in ketosteroid isomerase's (KSI's) active site to zero overestimates the catalytic effect of KSI's electric field because the reference reaction occurs in water, which itself exerts a sizable electrostatic field. To compensate, Natarajan et al. argue that additional catalytic weight arises from positioning of the general base, whereas Chen and Savidge propose a separate contribution from desolvation of the general base. We note that the former claim is not well supported by published results, and the latter claim is intriguing but lacks experimental basis. We also take the opportunity to clarify some of the more conceptually subtle aspects of electrostatic catalysis.
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Affiliation(s)
- Stephen D Fried
- Department of Chemistry, Stanford University, Stanford, CA 94305-5080, USA
| | - Steven G Boxer
- Department of Chemistry, Stanford University, Stanford, CA 94305-5080, USA.
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315
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Long- and Short-Range Electrostatic Fields in GFP Mutants: Implications for Spectral Tuning. Sci Rep 2015; 5:13223. [PMID: 26286372 PMCID: PMC4541067 DOI: 10.1038/srep13223] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 07/20/2015] [Indexed: 12/27/2022] Open
Abstract
The majority of protein functions are governed by their internal local electrostatics. Quantitative information about these interactions can shed light on how proteins work and allow for improving/altering their performance. Green fluorescent protein (GFP) and its mutation variants provide unique optical windows for interrogation of internal electric fields, thanks to the intrinsic fluorophore group formed inside them. Here we use an all-optical method, based on the independent measurements of transition frequency and one- and two-photon absorption cross sections in a number of GFP mutants to evaluate these internal electric fields. Two physical models based on the quadratic Stark effect, either with or without taking into account structural (bond-length) changes of the chromophore in varying field, allow us to separately evaluate the long-range and the total effective (short- and long-range) fields. Both types of the field quantitatively agree with the results of independent molecular dynamic simulations, justifying our method of measurement.
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316
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Ross MR, White AM, Yu F, King JT, Pecoraro VL, Kubarych KJ. Histidine Orientation Modulates the Structure and Dynamics of a de Novo Metalloenzyme Active Site. J Am Chem Soc 2015; 137:10164-76. [PMID: 26247178 PMCID: PMC5250509 DOI: 10.1021/jacs.5b02840] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The ultrafast dynamics of a de novo metalloenzyme active site is monitored using two-dimensional infrared spectroscopy. The homotrimer of parallel, coiled coil α-helices contains a His3-Cu(I) metal site where CO is bound and serves as a vibrational probe of the hydrophobic interior of the self-assembled complex. The ultrafast spectral dynamics of Cu-CO reveals unprecedented ultrafast (2 ps) nonequilibrium structural rearrangements launched by vibrational excitation of CO. This initial rapid phase is followed by much slower ∼40 ps vibrational relaxation typical of metal-CO vibrations in natural proteins. To identify the hidden coupled coordinate, small molecule analogues and the full peptide were studied by QM and QM/MM calculations, respectively. The calculations show that variation of the histidines' dihedral angles in coordinating Cu controls the coupling between the CO stretch and the Cu-C-O bending coordinates. Analysis of different optimized structures with significantly different electrostatic field magnitudes at the CO ligand site indicates that the origin of the stretch-bend coupling is not directly due to through-space electrostatics. Instead, the large, ∼3.6 D dipole moments of the histidine side chains effectively transduce the electrostatic environment to the local metal coordination orientation. The sensitivity of the first coordination sphere to the protein electrostatics and its role in altering the potential energy surface of the bound ligands suggests that long-range electrostatics can be leveraged to fine-tune function through enzyme design.
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Affiliation(s)
| | | | | | | | - Vincent L. Pecoraro
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Kevin J. Kubarych
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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317
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Barrozo A, Duarte F, Bauer P, Carvalho ATP, Kamerlin SCL. Cooperative Electrostatic Interactions Drive Functional Evolution in the Alkaline Phosphatase Superfamily. J Am Chem Soc 2015; 137:9061-76. [PMID: 26091851 PMCID: PMC4513756 DOI: 10.1021/jacs.5b03945] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
It is becoming widely accepted that catalytic promiscuity, i.e., the ability of a single enzyme to catalyze the turnover of multiple, chemically distinct substrates, plays a key role in the evolution of new enzyme functions. In this context, the members of the alkaline phosphatase superfamily have been extensively studied as model systems in order to understand the phenomenon of enzyme multifunctionality. In the present work, we model the selectivity of two multiply promiscuous members of this superfamily, namely the phosphonate monoester hydrolases from Burkholderia caryophylli and Rhizobium leguminosarum. We have performed extensive simulations of the enzymatic reaction of both wild-type enzymes and several experimentally characterized mutants. Our computational models are in agreement with key experimental observables, such as the observed activities of the wild-type enzymes, qualitative interpretations of experimental pH-rate profiles, and activity trends among several active site mutants. In all cases the substrates of interest bind to the enzyme in similar conformations, with largely unperturbed transition states from their corresponding analogues in aqueous solution. Examination of transition-state geometries and the contribution of individual residues to the calculated activation barriers suggest that the broad promiscuity of these enzymes arises from cooperative electrostatic interactions in the active site, allowing each enzyme to adapt to the electrostatic needs of different substrates. By comparing the structural and electrostatic features of several alkaline phosphatases, we suggest that this phenomenon is a generalized feature driving selectivity and promiscuity within this superfamily and can be in turn used for artificial enzyme design.
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Affiliation(s)
- Alexandre Barrozo
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, SE-751 24, Uppsala, Sweden
| | - Fernanda Duarte
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, SE-751 24, Uppsala, Sweden
| | - Paul Bauer
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, SE-751 24, Uppsala, Sweden
| | - Alexandra T P Carvalho
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, SE-751 24, Uppsala, Sweden
| | - Shina C L Kamerlin
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, SE-751 24, Uppsala, Sweden
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318
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Klinska M, Smith LM, Gryn'ova G, Banwell MG, Coote ML. Experimental demonstration of pH-dependent electrostatic catalysis of radical reactions. Chem Sci 2015; 6:5623-5627. [PMID: 29861899 PMCID: PMC5949849 DOI: 10.1039/c5sc01307k] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2015] [Accepted: 06/20/2015] [Indexed: 01/05/2023] Open
Abstract
Fluorescence spectroscopy demonstrated pH-dependent electrostatic effects on the kinetics and thermodynamics of hydrogen atom transfer between 1-hydroxy-2,2,6,6-tetramethyl-4-piperidinecarboxylic acid and {2,2,6,6-tetramethyl-4-[(7-nitro-2,1,3-benzoxadiazol-4-yl)amino]-1-piperidinyl}oxidanyl radical in dichloromethane.
Time-dependent fluorescence spectroscopy has been used to demonstrate significant pH-dependent electrostatic effects on the kinetics and thermodynamics of hydrogen atom transfer between 1-hydroxy-2,2,6,6-tetramethyl-4-piperidinecarboxylic acid (4-CT-H) and the profluorescent nitroxide {2,2,6,6-tetramethyl-4-[(7-nitro-2,1,3-benzoxadiazol-4-yl)amino]-1-piperidinyl}oxidanyl radical (PFN) in dichloromethane. This pH switching does not occur when 4-CT-H is replaced with a structurally analogous hydroxylamine that lacks an acid-base group, or when the polarity of the solvent is increased. These findings validate our recent theoretical predictions that electrostatic stabilisation of delocalised radicals is of functional significance in low polarity environments.
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Affiliation(s)
- Marta Klinska
- Research School of Chemistry , Australian National University , Canberra ACT 2601 , Australia .
| | - Leesa M Smith
- Research School of Chemistry , Australian National University , Canberra ACT 2601 , Australia .
| | - Ganna Gryn'ova
- Research School of Chemistry , Australian National University , Canberra ACT 2601 , Australia .
| | - Martin G Banwell
- Research School of Chemistry , Australian National University , Canberra ACT 2601 , Australia .
| | - Michelle L Coote
- Research School of Chemistry , Australian National University , Canberra ACT 2601 , Australia . .,ARC Centre of Excellence for Electromaterials Science , Australia
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319
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Brodkin HR, DeLateur NA, Somarowthu S, Mills CL, Novak WR, Beuning PJ, Ringe D, Ondrechen MJ. Prediction of distal residue participation in enzyme catalysis. Protein Sci 2015; 24:762-78. [PMID: 25627867 PMCID: PMC4420525 DOI: 10.1002/pro.2648] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Revised: 01/10/2015] [Accepted: 01/26/2015] [Indexed: 11/09/2022]
Abstract
A scoring method for the prediction of catalytically important residues in enzyme structures is presented and used to examine the participation of distal residues in enzyme catalysis. Scores are based on the Partial Order Optimum Likelihood (POOL) machine learning method, using computed electrostatic properties, surface geometric features, and information obtained from the phylogenetic tree as input features. Predictions of distal residue participation in catalysis are compared with experimental kinetics data from the literature on variants of the featured enzymes; some additional kinetics measurements are reported for variants of Pseudomonas putida nitrile hydratase (ppNH) and for Escherichia coli alkaline phosphatase (AP). The multilayer active sites of P. putida nitrile hydratase and of human phosphoglucose isomerase are predicted by the POOL log ZP scores, as is the single-layer active site of P. putida ketosteroid isomerase. The log ZP score cutoff utilized here results in over-prediction of distal residue involvement in E. coli alkaline phosphatase. While fewer experimental data points are available for P. putida mandelate racemase and for human carbonic anhydrase II, the POOL log ZP scores properly predict the previously reported participation of distal residues.
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Affiliation(s)
- Heather R Brodkin
- Department of Chemistry and Chemical Biology, Northeastern UniversityBoston, Massachusetts, 02115
- Department of Biochemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis UniversityWaltham, Massachusetts, 02454–9110
- Department of Chemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis UniversityWaltham, Massachusetts, 02454–9110
| | - Nicholas A DeLateur
- Department of Chemistry and Chemical Biology, Northeastern UniversityBoston, Massachusetts, 02115
| | - Srinivas Somarowthu
- Department of Chemistry and Chemical Biology, Northeastern UniversityBoston, Massachusetts, 02115
| | - Caitlyn L Mills
- Department of Chemistry and Chemical Biology, Northeastern UniversityBoston, Massachusetts, 02115
| | - Walter R Novak
- Department of Biochemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis UniversityWaltham, Massachusetts, 02454–9110
- Department of Chemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis UniversityWaltham, Massachusetts, 02454–9110
| | - Penny J Beuning
- Department of Chemistry and Chemical Biology, Northeastern UniversityBoston, Massachusetts, 02115
| | - Dagmar Ringe
- Department of Biochemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis UniversityWaltham, Massachusetts, 02454–9110
- Department of Chemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis UniversityWaltham, Massachusetts, 02454–9110
| | - Mary Jo Ondrechen
- Department of Chemistry and Chemical Biology, Northeastern UniversityBoston, Massachusetts, 02115
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320
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Reyes AC, Koudelka AP, Amyes TL, Richard JP. Enzyme architecture: optimization of transition state stabilization from a cation-phosphodianion pair. J Am Chem Soc 2015; 137:5312-5. [PMID: 25884759 PMCID: PMC4416717 DOI: 10.1021/jacs.5b02202] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
![]()
The
side chain cation of R269 lies at the surface of l-glycerol
3-phosphate dehydrogenase (GPDH) and forms an ion pair
to the phosphodianion of substrate dihydroxyacetone phosphate (DHAP),
which is buried at the nonpolar protein interior. The R269A mutation
of GPDH results in a 110-fold increase in Km (2.8 kcal/mol effect) and a 41 000-fold decrease in kcat (6.3 kcal/mol effect), which corresponds
to a 9.1 kcal/mol destabilization of the transition state for GPDH-catalyzed
reduction of DHAP by NADH. There is a 6.7 kcal/mol stabilization of
the transition state for the R269A mutant GPDH-catalyzed reaction
by 1.0 M guanidinium ion, and the transition state for the reaction
of the substrate pieces is stabilized by an additional 2.4 kcal/mol
by their covalent attachment at wildtype GPDH. These results provide
strong support for the proposal that GPDH invests the 11 kcal/mol
intrinsic phosphodianion binding energy of DHAP in trapping the substrate
at a nonpolar active site, where strong electrostatic interactions
are favored, and obtains a 9 kcal/mol return from stabilizing interactions
between the side chain cation and transition state trianion. We propose
a wide propagation for the catalytic motif examined in this work,
which enables strong transition state stabilization from enzyme–phosphodianion
pairs.
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Affiliation(s)
- Archie C Reyes
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
| | - Astrid P Koudelka
- 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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321
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Fried SD, Boxer SG. Measuring electric fields and noncovalent interactions using the vibrational stark effect. Acc Chem Res 2015; 48:998-1006. [PMID: 25799082 DOI: 10.1021/ar500464j] [Citation(s) in RCA: 318] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Over the past decade, we have developed a spectroscopic approach to measure electric fields inside matter with high spatial (<1 Å) and field (<1 MV/cm) resolution. The approach hinges on exploiting a physical phenomenon known as the vibrational Stark effect (VSE), which ultimately provides a direct mapping between observed vibrational frequencies and electric fields. Therefore, the frequency of a vibrational probe encodes information about the local electric field in the vicinity around the probe. The VSE method has enabled us to understand in great detail the underlying physical nature of several important biomolecular phenomena, such as drug-receptor selectivity in tyrosine kinases, catalysis by the enzyme ketosteroid isomerase, and unidirectional electron transfer in the photosynthetic reaction center. Beyond these specific examples, the VSE has provided a conceptual foundation for how to model intermolecular (noncovalent) interactions in a quantitative, consistent, and general manner. The starting point for research in this area is to choose (or design) a vibrational probe to interrogate the particular system of interest. Vibrational probes are sometimes intrinsic to the system in question, but we have also devised ways to build them into the system (extrinsic probes), often with minimal perturbation. With modern instruments, vibrational frequencies can increasingly be recorded with very high spatial, temporal, and frequency resolution, affording electric field maps correspondingly resolved in space, time, and field magnitude. In this Account, we set out to explain the VSE in broad strokes to make its relevance accessible to chemists of all specialties. Our intention is not to provide an encyclopedic review of published work but rather to motivate the underlying framework of the methodology and to describe how we make and interpret the measurements. Using certain vibrational probes, benchmarked against computer models, it is possible to use the VSE to measure absolute electric fields in arbitrary environments. The VSE approach provides an organizing framework for thinking generally about intermolecular interactions in a quantitative way and may serve as a useful conceptual tool for molecular design.
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Affiliation(s)
- Stephen D. Fried
- Department
of Chemistry; Stanford University, Stanford, California 94305-5080, United States
| | - Steven G. Boxer
- Department
of Chemistry; Stanford University, Stanford, California 94305-5080, United States
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322
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A simplified electrostatic model for hydrolase catalysis. Int J Biol Macromol 2015; 78:257-65. [PMID: 25881958 DOI: 10.1016/j.ijbiomac.2015.04.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 03/31/2015] [Accepted: 04/01/2015] [Indexed: 11/23/2022]
Abstract
Toward the development of an electrostatic model for enzyme catalysis, the active site of the enzyme is represented by a cavity whose surface (and beyond) is populated by electric charges as determined by pH and the enzyme's structure. The electric field in the cavity is obtained from electrostatics and a suitable computer program. The key chemical bond in the substrate, at its ends, has partial charges with opposite signs determined from published force-field parameters. The electric field attracts one end of the bond and repels the other, causing bond tension. If that tension exceeds the attractive force between the atoms, the bond breaks; the enzyme is then a successful catalyst. To illustrate this very simple model, based on numerous assumptions, some results are presented for three hydrolases: hen-egg white lysozyme, bovine trypsin and bovine ribonuclease. Attention is given to the effect of pH.
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323
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Affiliation(s)
- Peter Hildebrandt
- Technische Universität Berlin, Institut für Chemie, 10623 Berlin, Germany.
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