1
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Rama GR, Saraiva Macedo Timmers LF, Volken de Souza CF. In Silico Strategies to Predict Anti-aging Features of Whey Peptides. Mol Biotechnol 2024; 66:2426-2440. [PMID: 37737930 DOI: 10.1007/s12033-023-00887-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 09/01/2023] [Indexed: 09/23/2023]
Abstract
We have analysed the in silico potential of bioactive peptides from cheese whey, the most relevant by-product from the dairy industry, to bind into the active site of collagenase and elastase. The peptides generated from the hydrolysis of bovine β-lactoglobulin with three proteases (trypsin, chymotrypsin, and subtilisin) were docked onto collagenase and elastase by molecular docking. The interaction models were ranked according to their free binding energy using molecular dynamics simulations, which showed that most complexes presented favourable interactions. Interactions with elastase had significantly lower binding energies than those with collagenase. Regarding the interaction site, it was found that four bioactive peptides were positioned in collagenase's active site, while six were found in elastase's active site. Among these, the most we have found one promising collagen-binding peptide produced by chymotrypsin and two for elastase, produced by subtilisin and chymotrypsin. These in silico results can be used as a tool for designing further experiments aiming at testing the in vitro potential of the peptides found in this work.
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Affiliation(s)
- Gabriela Rabaioli Rama
- Graduate Program in Biotechnology, University of Vale do Taquari-Univates, Av. Avelino Tallini, 171, Lajeado, RS, 95914-014, Brazil
| | | | - Claucia Fernanda Volken de Souza
- Graduate Program in Biotechnology, University of Vale do Taquari-Univates, Av. Avelino Tallini, 171, Lajeado, RS, 95914-014, Brazil.
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2
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Tupikina EY, Sigalov MV, Alkhuder O, Tolstoy PM. Charge Relay Without Proton Transfer: Coupling of Two Short Hydrogen Bonds via Imidazole in Models of Catalytic Triad of Serine Protease Active Site. Chemphyschem 2024; 25:e202300970. [PMID: 38563616 DOI: 10.1002/cphc.202300970] [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: 12/15/2023] [Revised: 03/01/2024] [Accepted: 03/27/2024] [Indexed: 04/04/2024]
Abstract
A homologous series of 20 substituted alcohol-imidazole-acetate model complexes imitating the charge relay system in Ser-His-Asp catalytic triad of serine proteases is considered quantum-chemically. We show qualitatively that the geometries of alcohol-imidazole and imidazole-acetate short hydrogen bonds are strongly coupled via the central imidazole and such complexes are capable of effectively relaying the charge from acetate to alcohol moiety upon relatively small concerted proton displacements. We hypothesize an alternative catalytic mechanism of serine proteases that does not require two complete proton transfers or hydrogen bond breakage between Ser and His residues.
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Affiliation(s)
- Elena Yu Tupikina
- Institute of Chemistry, St. Petersburg State University, St. Petersburg, Russia
| | - Mark V Sigalov
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Omar Alkhuder
- Institute of Chemistry, St. Petersburg State University, St. Petersburg, Russia
| | - Peter M Tolstoy
- Institute of Chemistry, St. Petersburg State University, St. Petersburg, Russia
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3
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Zheng C, Schneider M, Marion A, Antes I. The Q41R mutation in the HCV-protease enhances the reactivity towards MAVS by suppressing non-reactive pathways. Phys Chem Chem Phys 2022; 24:2126-2138. [PMID: 35029245 DOI: 10.1039/d1cp05002h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Recent experimental findings pointed out a new mutation in the HCV protease, Q41R, responsible for a significant enhancement of the enzyme's reactivity towards the mitochondrial antiviral-signaling protein (MAVS). The Q41R mutation is located rather far from the active site, and its involvement in the overall reaction mechanism is thus unclear. We used classical molecular dynamics and QM/MM to study the acylation reaction of HCV NS3/4A protease variants bound to MAVS and the NS4A/4B substrate and uncovered the indirect mechanism by which the Q41R mutation plays a critical role in the efficient cleavage of the substrate. Our simulations reveal that there are two major conformations of the MAVS H1'(p) residue for the wild type protease and only one conformation for the Q41R mutant. The conformational space of H1'(p) is restricted by the Q41R mutation due to a π-π stacking between H1'(p) and R41 as well as a strong hydrogen bond between the backbone of H57 and the side chain of R41. Further QM/MM calculations indicate that the complex with the conformation ruled out by the Q41R substitution is a non-reactive species due to its higher free energy barrier for the acylation reaction. Based on our calculations, we propose a kinetic mechanism that explains experimental data showing an increase of apparent rate constants for MAVS cleavage in Q41R mutants. Our model predicts that the non-reactive conformation of the enzyme-substrate complex modulates reaction kinetics like an uncompetitive inhibitor.
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Affiliation(s)
- Chen Zheng
- Technische Universität München (TUM), TUM School of Life Sciences, Freising 85354, Germany. .,Technische Universität München (TUM), TUM Center for Functional Protein Assemblies, Garching 85747, Germany
| | - Markus Schneider
- Technische Universität München (TUM), TUM School of Life Sciences, Freising 85354, Germany. .,Technische Universität München (TUM), TUM Center for Functional Protein Assemblies, Garching 85747, Germany
| | - Antoine Marion
- Technische Universität München (TUM), TUM School of Life Sciences, Freising 85354, Germany. .,Middle East Technical University, Department of Chemistry, Ankara 06800, Turkey.
| | - Iris Antes
- Technische Universität München (TUM), TUM School of Life Sciences, Freising 85354, Germany. .,Technische Universität München (TUM), TUM Center for Functional Protein Assemblies, Garching 85747, Germany
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4
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Steinert RM, Kasireddy C, Heikes ME, Mitchell-Koch KR. Newly identified C–H⋯O hydrogen bond in histidine. Phys Chem Chem Phys 2022; 24:19233-19251. [DOI: 10.1039/d2cp02048c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Histidine C–H bonds observed in protein structures include (clockwise from top left): myoglobin, β-lactamase, and photoactive yellow protein; calculations indicate that tautomeric/protonation state influences H-bonding ability (bottom left).
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Affiliation(s)
- Ryan M. Steinert
- Department of Chemistry and Biochemistry, Wichita State University, 1845 Fairmount Street, Wichita, KS 67260-0051, USA
| | - Chandana Kasireddy
- Department of Chemistry and Biochemistry, Wichita State University, 1845 Fairmount Street, Wichita, KS 67260-0051, USA
| | - Micah E. Heikes
- Department of Chemistry and Biochemistry, Wichita State University, 1845 Fairmount Street, Wichita, KS 67260-0051, USA
| | - Katie R. Mitchell-Koch
- Department of Chemistry and Biochemistry, Wichita State University, 1845 Fairmount Street, Wichita, KS 67260-0051, USA
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5
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Elsässer B, Goettig P. Mechanisms of Proteolytic Enzymes and Their Inhibition in QM/MM Studies. Int J Mol Sci 2021; 22:3232. [PMID: 33810118 PMCID: PMC8004986 DOI: 10.3390/ijms22063232] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/24/2021] [Accepted: 02/26/2021] [Indexed: 12/11/2022] Open
Abstract
Experimental evidence for enzymatic mechanisms is often scarce, and in many cases inadvertently biased by the employed methods. Thus, apparently contradictory model mechanisms can result in decade long discussions about the correct interpretation of data and the true theory behind it. However, often such opposing views turn out to be special cases of a more comprehensive and superior concept. Molecular dynamics (MD) and the more advanced molecular mechanical and quantum mechanical approach (QM/MM) provide a relatively consistent framework to treat enzymatic mechanisms, in particular, the activity of proteolytic enzymes. In line with this, computational chemistry based on experimental structures came up with studies on all major protease classes in recent years; examples of aspartic, metallo-, cysteine, serine, and threonine protease mechanisms are well founded on corresponding standards. In addition, experimental evidence from enzyme kinetics, structural research, and various other methods supports the described calculated mechanisms. One step beyond is the application of this information to the design of new and powerful inhibitors of disease-related enzymes, such as the HIV protease. In this overview, a few examples demonstrate the high potential of the QM/MM approach for sophisticated pharmaceutical compound design and supporting functions in the analysis of biomolecular structures.
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Affiliation(s)
| | - Peter Goettig
- Structural Biology Group, Department of Biosciences, University of Salzburg, Billrothstrasse 11, 5020 Salzburg, Austria;
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6
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The novel mutation p.Asp315Tyr causes severe hemophilia B by impairing coagulation factor IX expression. Thromb Res 2020; 198:23-25. [PMID: 33249248 DOI: 10.1016/j.thromres.2020.11.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 11/03/2020] [Accepted: 11/17/2020] [Indexed: 11/21/2022]
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7
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Stuttgen GM, Grosskopf JD, Berger CR, May JF, Bhattacharyya B, Weaver TM. Closed fumarase C active‐site structures reveal SS Loop residue contribution in catalysis. FEBS Lett 2019; 594:337-357. [DOI: 10.1002/1873-3468.13603] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 08/26/2019] [Accepted: 09/05/2019] [Indexed: 12/23/2022]
Affiliation(s)
- Gage M. Stuttgen
- Department of Chemistry and Biochemistry University Wisconsin – La Crosse WI USA
| | - Julian D. Grosskopf
- Department of Chemistry and Biochemistry University Wisconsin – La Crosse WI USA
| | - Colton R. Berger
- Department of Chemistry and Biochemistry University Wisconsin – La Crosse WI USA
| | - John F. May
- Department of Chemistry and Biochemistry University Wisconsin – La Crosse WI USA
| | | | - Todd M. Weaver
- Department of Chemistry and Biochemistry University Wisconsin – La Crosse WI USA
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8
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Wan Y, Liu C, Ma Q. Structural analysis of a Vibrio phospholipase reveals an unusual Ser-His-chloride catalytic triad. J Biol Chem 2019; 294:11391-11401. [PMID: 31073025 DOI: 10.1074/jbc.ra119.008280] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 04/30/2019] [Indexed: 12/22/2022] Open
Abstract
Phospholipases can disrupt host membranes and are important virulence factors in many pathogens. VvPlpA is a phospholipase A2 secreted by Vibrio vulnificus and essential for virulence. Its homologs, termed thermolabile hemolysins (TLHs), are widely distributed in Vibrio bacteria, but no structural information for this virulence factor class is available. Herein, we report the crystal structure of VvPlpA to 1.4-Å resolution, revealing that VvPlpA contains an N-terminal domain of unknown function and a C-terminal phospholipase domain and that these two domains are packed closely together. The phospholipase domain adopts a typical SGNH hydrolase fold, containing the four conserved catalytic residues Ser, Gly, Asn, and His. Interestingly, the structure also disclosed that the phospholipase domain accommodates a chloride ion near the catalytic His residue. The chloride is five-coordinated in a distorted bipyramid geometry, accepting hydrogen bonds from a water molecule and the amino groups of surrounding residues. This chloride substitutes for the most common Asp/Glu residue and forms an unusual Ser-His-chloride catalytic triad in VvPlpA. The chloride may orient the catalytic His and stabilize the charge on its imidazole ring during catalysis. Indeed, VvPlpA activity depended on chloride concentration, confirming the important role of chloride in catalysis. The VvPlpA structure also revealed a large hydrophobic substrate-binding pocket that is capable of accommodating a long-chain acyl group. Our results provide the first structure of the TLH family and uncover an unusual Ser-His-chloride catalytic triad, expanding our knowledge on the biological role of chloride.
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Affiliation(s)
- Ye Wan
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Changshui Liu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Qingjun Ma
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China .,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
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9
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Ishida T. Computational analysis of carbohydrate recognition based on hybrid QM/MM modeling: a case study of norovirus capsid protein in complex with Lewis antigen. Phys Chem Chem Phys 2018; 20:4652-4665. [PMID: 29372731 DOI: 10.1039/c7cp07701g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Norovirus is a major pathogen of nonbacterial acute gastroenteritis in humans and animals. Carbohydrate recognition between norovirus capsid proteins and Lewis antigens is considered to play a critical role in initiating infection of eukaryotic cells. In this article, we first report a detailed atomistic simulation study of the norovirus capsid protein in complex with the Lewis antigen based on ab initio QM/MM combined with MD-FEP simulations. To understand the mechanistic details of ligand binding, we analyzed and compared the carbohydrate recognition mechanism of the wild-type P domain protein with a mutant protein. Small structural differences between two capsid proteins are observed on the weak interaction site of residue 389, which is located on the solvent exposed surface of the P domain. To further clarify affinity differences in ligand binding, we directly evaluated free energy changes of the ligand binding process. Although the mutant protein loses its interaction energy with the Lewis antigen, this small amount of energy penalty is compensated for by an increase in the solvation stability, which is induced by structural reorganization at the ligand binding site on the protein surface. As a sum of these opposite energy components, the mutant P domain obtains a slightly enhanced binding affinity for the Lewis antigen. The present computational study clearly demonstrated that a detailed free energy balance of the interaction energy between the capsid protein and the surrounding aqueous solvent is the mechanistic basis of carbohydrate recognition in the norovirus capsid protein.
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Affiliation(s)
- Toyokazu Ishida
- Research Center for Computational Design of Advanced Functional Materials (CD-FMat), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 2, 1-1-1 Umezono, Tsukuba, 305-8568, Japan.
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10
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Masuda Y, Yoshida T, Yamaotsu N, Hirono S. Linear Discriminant Analysis for the <i>in Silico</i> Discovery of Mechanism-Based Reversible Covalent Inhibitors of a Serine Protease: Application of Hydration Thermodynamics Analysis and Semi-empirical Molecular Orbital Calculation. Chem Pharm Bull (Tokyo) 2018; 66:399-409. [DOI: 10.1248/cpb.c17-00854] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Yosuke Masuda
- School of Pharmaceutical Sciences, Kitasato University
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11
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Effects of Glycosylation on the Enzymatic Activity and Mechanisms of Proteases. Int J Mol Sci 2016; 17:ijms17121969. [PMID: 27898009 PMCID: PMC5187769 DOI: 10.3390/ijms17121969] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Revised: 11/07/2016] [Accepted: 11/10/2016] [Indexed: 02/06/2023] Open
Abstract
Posttranslational modifications are an important feature of most proteases in higher organisms, such as the conversion of inactive zymogens into active proteases. To date, little information is available on the role of glycosylation and functional implications for secreted proteases. Besides a stabilizing effect and protection against proteolysis, several proteases show a significant influence of glycosylation on the catalytic activity. Glycans can alter the substrate recognition, the specificity and binding affinity, as well as the turnover rates. However, there is currently no known general pattern, since glycosylation can have both stimulating and inhibiting effects on activity. Thus, a comparative analysis of individual cases with sufficient enzyme kinetic and structural data is a first approach to describe mechanistic principles that govern the effects of glycosylation on the function of proteases. The understanding of glycan functions becomes highly significant in proteomic and glycomic studies, which demonstrated that cancer-associated proteases, such as kallikrein-related peptidase 3, exhibit strongly altered glycosylation patterns in pathological cases. Such findings can contribute to a variety of future biomedical applications.
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12
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Zhou Y, Xie D, Zhang Y. Amide Rotation Hindrance Predicts Proteolytic Resistance of Cystine-Knot Peptides. J Phys Chem Lett 2016; 7:1138-42. [PMID: 26958702 PMCID: PMC4824663 DOI: 10.1021/acs.jpclett.6b00373] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Cystine-knot peptides have remarkable stability against protease degradation and are attractive scaffolds for peptide-based therapeutic and diagnostic agents. In this work, by studying the hydrolysis reaction of a cystine-knot inhibitor MCTI-A and its variants with ab initio QM/MM molecular dynamics simulations, we have elucidated an amide rotation hindrance mechanism for proteolysis resistance: The proteolysis of MCTI-A is retarded due to the higher free energy cost during the rotation of NH group around scissile peptide bond at the tetrahedral intermediate of acylation, and covalent constraint provided by disulfide bonds is the key factor to hinder this rotation. A nearly linear correlation has been revealed between free energy barriers of the peptide hydrolysis reaction and the amide rotation free energy changes at the protease-peptide Michaelis complex state. This suggests that amide rotation hindrance could be one useful feature to estimate peptide proteolysis stability.
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Affiliation(s)
- Yanzi Zhou
- Laboratory of Mesoscopic Chemistry, Collaborative Innovation Center of Chemistry for Life Sciences, Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
- Corresponding Author: 1) , 2)
| | - Daiqian Xie
- Laboratory of Mesoscopic Chemistry, Collaborative Innovation Center of Chemistry for Life Sciences, Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Yingkai Zhang
- Department of Chemistry, New York University, New York, NY 10003 USA
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
- Corresponding Author: 1) , 2)
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13
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Martı́nez-González JÁ, González M, Masgrau L, Martı́nez R. Theoretical Study of the Free Energy Surface and Kinetics of the Hepatitis C Virus NS3/NS4A Serine Protease Reaction with the NS5A/5B Substrate. Does the Generally Accepted Tetrahedral Intermediate Really Exist? ACS Catal 2014. [DOI: 10.1021/cs5011162] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - Miguel González
- Departament
de Quı́mica Fı́sica i IQTC, Universitat de Barcelona, C/Martı́ i Franquès, 1, 08028 Barcelona, Spain
| | - Laura Masgrau
- Institut
de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Rodrigo Martı́nez
- Departamento
de Quı́mica, Universidad de La Rioja, C/Madre de
Dios, 51, 26006 Logroño, Spain
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14
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Mashima A, Kurahashi M, Sasahara K, Yoshida T, Chuman H. Connecting Classical QSAR and LERE Analyses Using Modern Molecular Calculations, LERE-QSAR (VI): Hydrolysis of Substituted Hippuric Acid Phenyl Esters by Trypsin. Mol Inform 2014; 33:802-14. [PMID: 27485426 DOI: 10.1002/minf.201400099] [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: 07/14/2014] [Accepted: 09/14/2014] [Indexed: 11/08/2022]
Abstract
The reaction mechanism of trypsin was studied by applying DFT and ab initio molecular orbital (MO) calculations to complexes of trypsin with a congeneric series of eight para-substituted hippuric acid phenyl esters, for which a previous quantitative structureactivity relationship (QSAR) study revealed nice linearity of Hammett substitution constant σ(-) with logarithmic values of the MichaelisMenten and catalytic rate constants. Based on the LERE procedure, we performed QSAR analyses on each elementary reaction step during the acylation process. The present calculations showed that the rate-determining step during the acylation process is the transition state (TS) between the enzymesubstrate complex (ES) and tetrahedral intermediate (TET), and that the proton transfer occurs from Ser195 to His57, not between His57 and Asp102. The LERE-QSAR analysis statistically suggested that the variation of overall free-energy changes leading to formation of TS is governed mostly by that of activation energies required to form TS from ES. In spite of a very limited number of congeneric ligands in the current work, it is critically essential to clarify and verify physicochemical meanings of a typical QSAR/Chemoinformatics parameter, Hammett σ(-) based on quantum chemical calculations on the proteinligand kinetics; how Hammett σ(-) behaves in terms of proteinligand interaction energies.
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Affiliation(s)
- Akira Mashima
- Institute of Health Biosciences, The University of Tokushima Graduate School, 1-78 Shomachi, Tokushima 770-8505, Japan phone/fax: +81-88-633-7257/+81-88-633-9508
| | - Masahiro Kurahashi
- Institute of Health Biosciences, The University of Tokushima Graduate School, 1-78 Shomachi, Tokushima 770-8505, Japan phone/fax: +81-88-633-7257/+81-88-633-9508
| | - Katsunori Sasahara
- Institute of Health Biosciences, The University of Tokushima Graduate School, 1-78 Shomachi, Tokushima 770-8505, Japan phone/fax: +81-88-633-7257/+81-88-633-9508
| | - Tatsusada Yoshida
- Institute of Health Biosciences, The University of Tokushima Graduate School, 1-78 Shomachi, Tokushima 770-8505, Japan phone/fax: +81-88-633-7257/+81-88-633-9508
| | - Hiroshi Chuman
- Institute of Health Biosciences, The University of Tokushima Graduate School, 1-78 Shomachi, Tokushima 770-8505, Japan phone/fax: +81-88-633-7257/+81-88-633-9508.
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15
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Hediger MR, De Vico L, Rannes JB, Jäckel C, Besenmatter W, Svendsen A, Jensen JH. In silico screening of 393 mutants facilitates enzyme engineering of amidase activity in CalB. PeerJ 2013; 1:e145. [PMID: 24010022 PMCID: PMC3757469 DOI: 10.7717/peerj.145] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 08/06/2013] [Indexed: 11/25/2022] Open
Abstract
Our previously presented method for high throughput computational screening of mutant activity (Hediger et al., 2012) is benchmarked against experimentally measured amidase activity for 22 mutants of Candida antarctica lipase B (CalB). Using an appropriate cutoff criterion for the computed barriers, the qualitative activity of 15 out of 22 mutants is correctly predicted. The method identifies four of the six most active mutants with ≥3-fold wild type activity and seven out of the eight least active mutants with ≤0.5-fold wild type activity. The method is further used to screen all sterically possible (386) double-, triple- and quadruple-mutants constructed from the most active single mutants. Based on the benchmark test at least 20 new promising mutants are identified.
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Affiliation(s)
- Martin R Hediger
- Department of Chemistry, University of Copenhagen , Copenhagen , Denmark
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16
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Uritsky N, Shokhen M, Albeck A. The Catalytic Machinery of Rhomboid Proteases: Combined MD and QM Simulations. J Chem Theory Comput 2012; 8:4663-71. [DOI: 10.1021/ct3003767] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Neta Uritsky
- The Julius
Spokojny Bioorganic Chemistry Laboratory,
Department of Chemistry, Bar Ilan University, Ramat Gan 52900, Israel
| | - Michael Shokhen
- The Julius
Spokojny Bioorganic Chemistry Laboratory,
Department of Chemistry, Bar Ilan University, Ramat Gan 52900, Israel
| | - Amnon Albeck
- The Julius
Spokojny Bioorganic Chemistry Laboratory,
Department of Chemistry, Bar Ilan University, Ramat Gan 52900, Israel
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17
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Conformational dynamics of threonine 195 and the S1 subsite in functional trypsin variants. J Mol Model 2012; 18:4941-54. [DOI: 10.1007/s00894-012-1541-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Accepted: 07/16/2012] [Indexed: 12/25/2022]
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18
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Janowski T, Wolinski K, Pulay P. Ultrafast Quantum Mechanics/Molecular Mechanics Monte Carlo simulations using generalized multipole polarizabilities. Chem Phys Lett 2012. [DOI: 10.1016/j.cplett.2012.01.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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19
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Lundberg M. Understanding cross-boundary events in ONIOM QM:QM' calculations. J Comput Chem 2011; 33:406-15. [DOI: 10.1002/jcc.21982] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Revised: 09/18/2011] [Accepted: 10/05/2011] [Indexed: 12/31/2022]
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20
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Uesugi Y, Usuki H, Arima J, Iwabuchi M, Hatanaka T. Molecular dissection of Streptomyces trypsin on substrate recognition. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1814:1295-304. [PMID: 21767670 DOI: 10.1016/j.bbapap.2011.06.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2010] [Revised: 06/09/2011] [Accepted: 06/14/2011] [Indexed: 10/18/2022]
Abstract
We recently identified residue 71 of two homologous serine proteases from Streptomyces omiyaensis (SOT) and Streptomyces griseus (SGT) as a crucial residue for differences in their topological specificities, i.e. recognition of a distinct three-dimensional structure. To study the role of this key residue in substrate recognition, we used surface plasmon resonance analysis to evaluate the affinities of inactive mutants, in which residues 71 of SOT and SGT were substituted respectively with Leu and Tyr, toward different types of collagens. We identified another amino acid residue involved in the interaction with collagens from analyses of inactive chimeras between SOT and SGT using an in vivo DNA shuffling system. Results showed that residue 72 contributes to collagen binding. By substituting Leu71 and Gln72 with Tyr and Arg, respectively, SGT mutant showed a change in topological specificity and high hydrolytic activity toward type IV collagen comparable to SOT. We demonstrated that the neighboring residues 71 and 72 in the N-terminal β-barrel domain of the enzyme synergistically play an important role in substrate recognition.
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Affiliation(s)
- Yoshiko Uesugi
- Research Institute for Biological Sciences, Okayama, Japan
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21
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Zhou Y, Zhang Y. Serine protease acylation proceeds with a subtle re-orientation of the histidine ring at the tetrahedral intermediate. Chem Commun (Camb) 2010; 47:1577-9. [PMID: 21116528 DOI: 10.1039/c0cc04112b] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The acylation mechanism of a prototypical serine protease trypsin and its complete free energy reaction profile have been determined by Born-Oppenheimer ab initio QM/MM molecular dynamics simulations with umbrella sampling.
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Affiliation(s)
- Yanzi Zhou
- Department of Chemistry, New York University, New York, NY 10003, USA
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22
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Khan MN. Can a Typical Protein Assist the Rate of its Own Aqueous Cleavage? PROGRESS IN REACTION KINETICS AND MECHANISM 2010. [DOI: 10.3184/146867810x12700573609126] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A recent finding of a large rate enhancement in the intramolecular secondary amide group-assisted cleavage of an adjacent tertiary amide bond predicts the possibility of the cleavage of the peptide bond of a protein through a similar reaction mechanism. Based upon enzymatic partial model reactions, the usual proton-switch mechanism has been suggested for the acylation step of the chymotrypsin–catalysed cleavage of the peptide bond which does not favour a His57-shift mechanism - an essential component of the classical charge relay mechanism. Also, the proton-switch mechanism does not necessarily require the two proton-transfer of the classical charge relay mechanism. The unique structural feature of the imidazole moiety of His57 is concluded to be essential in decreasing the rate of collapse of the proposed reactive tetrahedral intermediate back to the reactants. The proposed intramolecular intimate ion-pair formation between anionic Asp102 and cationic His57 is attributed to the energetically preferred location of the proton at Nδ1 of the imidazole moiety of His57. Thus, the analysis described in this review does not favour the necessary requirements of a two proton-transfer and His57-shift as proposed in the classical charge relay mechanism as well as the relatively recently proposed His57-flip mechanism.
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Affiliation(s)
- Mohammad Niyaz Khan
- Department of Chemistry, University of Malaya, Faculty of Science, 50603 Kuala Lumpur, Malaysia
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23
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Ishida T. Computational modeling of carbohydrate-recognition process in E-selectin complex: structural mapping of sialyl Lewis X onto ab initio QM/MM free energy surface. J Phys Chem B 2010; 114:3950-64. [PMID: 20078087 DOI: 10.1021/jp905872t] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
To advance our knowledge of carbohydrate recognition by lectins, we propose a systematic computational modeling strategy to identify complex sugar-chain conformations on the reduced free energy surface (FES). We selected the complex of E-selectin with sialyl Lewis X (denoted E-selectin/SLe(x) complex) as a first target molecule. First, we introduced the reduced 2D-FES that characterizes conformational changes in carbohydrate structure as well as the degree of solvation stability of the carbohydrate ligand, and evaluated the overall free energy profile by classical molecular dynamics simulation combined with ab initio QM/MM energy corrections. Second, we mapped flexible carbohydrate structures onto the reduced QM/MM 2D-FES, and identified the details of molecular interactions between each monosaccharide component and the amino acid residues at the carbohydrate-recognition domain. Finally, we confirmed the validity of our modeling strategy by evaluating the chemical shielding tensor by ab initio QM/MM-GIAO computations for several QM/MM-refined geometries sampled from the minimum free energy region in the 2D-FES, and compared this theoretical averaging data with the experimental 1D-NMR profile. The model clearly shows that the binding geometries of the E-selectin/SLe(x) complex are determined not by one single, rigid carbohydrate structure but rather by the sum of averaged conformations fluctuating around the minimum free energy region. For the E-selectin/SLe(x) complex, the major molecular interactions are hydrogen bonds between Fuc and the Ca(2+) binding site in the carbohydrate-recognition domain, and Gal is important in determining the ligand specificity.
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Affiliation(s)
- Toyokazu Ishida
- Research Institute for Computational Sciences, 1-1-1 Umezono, Tsukuba, 305-8568, Japan.
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24
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Rodríguez A, Oliva C, González M. A comparative QM/MM study of the reaction mechanism of the Hepatitis C virus NS3/NS4A protease with the three main natural substrates NS5A/5B, NS4B/5A and NS4A/4B. Phys Chem Chem Phys 2010; 12:8001-15. [PMID: 20520921 DOI: 10.1039/c002116d] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The reaction mechanism of the NS3/NS4A protease with the NS4B/5A and NS4A/4B natural substrates has been investigated using the QM/MM (quantum mechanics/molecular mechanics) approach, and some calculations have been performed on the reaction with the NS5A/5B natural substrate. This study widely extends a previous contribution of our group on the reaction mechanism with the NS5A/5B substrate, the main goal here being to understand the differences found between the reaction mechanism of each natural substrate and the role played by the enzymatic residues in the catalytic cycle. This knowledge will ultimately help in developing new NS3/NS4A protease inhibitors. The two first steps of the mechanism have been considered: Acylation and breaking of the peptide bond, with emphasis on the former one (rate limiting process). Energy and free energy profiles for both steps have been calculated at the AM1/MM level and corrected by means of MP2 ab initio calculations, being evident the importance of correlation energy. Acylation is the rate limiting step in all cases and occurs through a tetracoordinated intermediate, as previously suggested for other serine proteases. Specificities in the NS4B/5A mechanism can be attributed to the presence of a Proline residue in the substrate P2 position. The analysis of structures and energies confirm the importance of the oxyanion hole in the electrostatic stabilization of the tetracoordinated intermediate. Finally, the role of other residues, e.g., Arg-155 and Asp-79, has been explained, and the viability of Arg-155 mutants and its resistance to some protease inhibitors has been understood thanks to virtual mutation studies.
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Affiliation(s)
- Alejandro Rodríguez
- Departament de Química Física i IQTC, Universitat de Barcelona, C/Martí i Franquès 1, 08028 Barcelona, Spain
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25
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Ishida T. Effects of Point Mutation on Enzymatic Activity: Correlation between Protein Electronic Structure and Motion in Chorismate Mutase Reaction. J Am Chem Soc 2010; 132:7104-18. [DOI: 10.1021/ja100744h] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Toyokazu Ishida
- Research Institute for Computational Sciences (RICS), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 2, 1-1-1 Umezono, Tsukuba 305-8568, Japan
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26
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Bellucci L, Laino T, Tafi A, Botta M. Metadynamics Simulations of Enantioselective Acylation Give Insights into the Catalytic Mechanism of Burkholderia cepacia Lipase. J Chem Theory Comput 2010. [DOI: 10.1021/ct900636w] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Luca Bellucci
- Dipartimento Farmaco Chimico Tecnologico, Università degli Studi di Siena, Via Aldo Moro 2, I-53100 Siena, Italy, Physikalisch Chemisches Institut, Universität Zürich, Winterthurerstrasse 190, CH-8057 Zürich Switzerland, and IBM Zurich Research Laboratory, Säumerstrasse 4, CH-8803 Rüschlikon Switzerland
| | - Teodoro Laino
- Dipartimento Farmaco Chimico Tecnologico, Università degli Studi di Siena, Via Aldo Moro 2, I-53100 Siena, Italy, Physikalisch Chemisches Institut, Universität Zürich, Winterthurerstrasse 190, CH-8057 Zürich Switzerland, and IBM Zurich Research Laboratory, Säumerstrasse 4, CH-8803 Rüschlikon Switzerland
| | - Andrea Tafi
- Dipartimento Farmaco Chimico Tecnologico, Università degli Studi di Siena, Via Aldo Moro 2, I-53100 Siena, Italy, Physikalisch Chemisches Institut, Universität Zürich, Winterthurerstrasse 190, CH-8057 Zürich Switzerland, and IBM Zurich Research Laboratory, Säumerstrasse 4, CH-8803 Rüschlikon Switzerland
| | - Maurizio Botta
- Dipartimento Farmaco Chimico Tecnologico, Università degli Studi di Siena, Via Aldo Moro 2, I-53100 Siena, Italy, Physikalisch Chemisches Institut, Universität Zürich, Winterthurerstrasse 190, CH-8057 Zürich Switzerland, and IBM Zurich Research Laboratory, Säumerstrasse 4, CH-8803 Rüschlikon Switzerland
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27
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Zhang R, Lev B, Cuervo JE, Noskov SY, Salahub DR. A Guide to QM/MM Methodology and Applications. ADVANCES IN QUANTUM CHEMISTRY 2010. [DOI: 10.1016/s0065-3276(10)59010-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
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28
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Srinivasan A, Giri AP, Gupta VS. Structural and functional diversities in lepidopteran serine proteases. Cell Mol Biol Lett 2009; 11:132-54. [PMID: 16847755 PMCID: PMC6275901 DOI: 10.2478/s11658-006-0012-8] [Citation(s) in RCA: 138] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2006] [Accepted: 02/16/2006] [Indexed: 12/02/2022] Open
Abstract
Primary protein-digestion in Lepidopteran larvae relies on serine proteases like trypsin and chymotrypsin. Efforts toward the classification and characterization of digestive proteases have unraveled a considerable diversity in the specificity and mechanistic classes of gut proteases. Though the evolutionary significance of mutations that lead to structural diversity in serine proteases has been well characterized, detailing the resultant functional diversity has continually posed a challenge to researchers. Functional diversity can be correlated to the adaptation of insects to various host-plants as well as to exposure of insects to naturally occurring antagonistic biomolecules such as plant-derived protease inhibitors (PIs) and lectins. Current research is focused on deciphering the changes in protease specificities and activities arising from altered amino acids at the active site, specificity-determining pockets and other regions, which influence activity. Some insight has been gained through in silico modeling and simulation experiments, aided by the limited availability of characterized proteases. We examine the structurally and functionally diverse Lepidopteran serine proteases, and assess their influence on larval digestive processes and on overall insect physiology.
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Affiliation(s)
- Ajay Srinivasan
- Plant Molecular Biology Group, Division of Biochemical Sciences, National Chemical Laboratory, Pune, 411008 India
| | - Ashok P. Giri
- Plant Molecular Biology Group, Division of Biochemical Sciences, National Chemical Laboratory, Pune, 411008 India
| | - Vidya S. Gupta
- Plant Molecular Biology Group, Division of Biochemical Sciences, National Chemical Laboratory, Pune, 411008 India
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29
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Huang HH, Arscott LD, Ballou DP, Williams CH. Function of Glu-469' in the acid-base catalysis of thioredoxin reductase from Drosophila melanogaster. Biochemistry 2009; 47:12769-76. [PMID: 18991392 DOI: 10.1021/bi801449h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Thioredoxin reductase (TrxR) catalyzes the reduction of thioredoxin (Trx) by NADPH. Because dipteran insects such as Drosophila melanogaster lack glutathione reductase, their TrxRs are particularly important for antioxidant protection; reduced Trx reacts nonenzymatically with oxidized glutathione to maintain a high glutathione/glutathione disulfide ratio. Like other members of the pyridine nucleotide-disulfide oxidoreductase family, TrxR is a homodimer; in the enzyme from D. melanogaster (DmTrxR), each catalytically active unit consists of three redox centers: FAD and an N-terminal Cys-57-Cys-62 redox-active disulfide from one monomer and a Cys-489'-Cys-490' C-terminal redox-active disulfide from the second monomer. A dyad of His-464' and Glu-469' in TrxR acts as the acid-base catalyst of the dithiol-disulfide interchange reactions required in catalysis [Huang, H.-H., et al. (2008) Biochemistry 47, 1721-1731]. In this investigation, the role of Glu-469' in catalysis by DmTrxR has been studied. The E469'A and E469'Q DmTrxR variants retain 28 and 35% of the wild-type activity, respectively, indicating that this glutamate residue is important but not critical to catalysis. The pH dependence of V(max) for both glutamate variants yields pK(a) values of 6.0 and 8.7, compared to those in the wild-type enzyme of 6.4 and 9.3, respectively, indicating that the basicity of His-464' in TrxR in complex with its substrate, DmTrx-2, is significantly lower in the glutamate variants than in wild-type enzyme. The rates of some steps in the reductive half-reactions in both glutamate variants are much slower than those of the wild-type enzyme. On the basis of our observations, it is proposed that the function of Glu-469' is to facilitate the positioning of His-464' toward the interchange thiol, Cys-57, as suggested for the analogous residue in glutathione reductase.
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Affiliation(s)
- Hsin-Hung Huang
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109-0606, USA
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30
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Bergfeld AK, Claus H, Lorenzen NK, Spielmann F, Vogel U, Mu Hlenhoff M. The polysialic acid-specific O-acetyltransferase OatC from Neisseria meningitidis serogroup C evolved apart from other bacterial sialate O-acetyltransferases. J Biol Chem 2008; 284:6-16. [PMID: 18986988 DOI: 10.1074/jbc.m807518200] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Neisseria meningitidis serogroup C is a major cause of bacterial meningitis and septicaemia. This human pathogen is protected by a capsule composed of alpha2,9-linked polysialic acid that represents an important virulence factor. In the majority of strains, the capsular polysaccharide is modified by O-acetylation at C-7 or C-8 of the sialic acid residues. The gene encoding the capsule modifying O-acetyltransferase is part of the capsule gene complex and shares no sequence similarities with other proteins. Here, we describe the purification and biochemical characterization of recombinant OatC. The enzyme was found as a homodimer, with the first 34 amino acids forming an efficient oligomerization domain that worked even in a different protein context. Using acetyl-CoA as donor substrate, OatC transferred acetyl groups exclusively onto polysialic acid joined by alpha2,9-linkages and did not act on free or CMP-activated sialic acid. Motif scanning revealed a nucleophile elbow motif (GXS286XGG), which is a hallmark of alpha/beta-hydrolase fold enzymes. In a comprehensive site-directed mutagenesis study, we identified a catalytic triad composed of Ser-286, Asp-376, and His-399. Consistent with a double-displacement mechanism common to alpha/beta-hydrolase fold enzymes, a covalent acetylenzyme intermediate was found. Together with secondary structure prediction highlighting an alpha/beta-hydrolase fold topology, our data provide strong evidence that OatC belongs to the alpha/beta-hydrolase fold family. This clearly distinguishes OatC from all other bacterial sialate O-acetyltransferases known so far because these are members of the hexapeptide repeat family, a class of acyltransferases that adopt a left-handed beta-helix fold and assemble into catalytic trimers.
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Affiliation(s)
- Anne K Bergfeld
- Department of Cellular Chemistry, Medical School Hannover, 30623 Hannover, Germany and the Institute for Hygiene and Microbiology, University of Wu¨rzburg, 97080 Wu¨rzburg, Germany
| | - Heike Claus
- Department of Cellular Chemistry, Medical School Hannover, 30623 Hannover, Germany and the Institute for Hygiene and Microbiology, University of Wu¨rzburg, 97080 Wu¨rzburg, Germany
| | - Nina K Lorenzen
- Department of Cellular Chemistry, Medical School Hannover, 30623 Hannover, Germany and the Institute for Hygiene and Microbiology, University of Wu¨rzburg, 97080 Wu¨rzburg, Germany
| | - Fabian Spielmann
- Department of Cellular Chemistry, Medical School Hannover, 30623 Hannover, Germany and the Institute for Hygiene and Microbiology, University of Wu¨rzburg, 97080 Wu¨rzburg, Germany
| | - Ulrich Vogel
- Department of Cellular Chemistry, Medical School Hannover, 30623 Hannover, Germany and the Institute for Hygiene and Microbiology, University of Wu¨rzburg, 97080 Wu¨rzburg, Germany
| | - Martina Mu Hlenhoff
- Department of Cellular Chemistry, Medical School Hannover, 30623 Hannover, Germany and the Institute for Hygiene and Microbiology, University of Wu¨rzburg, 97080 Wu¨rzburg, Germany.
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31
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Ishida T. Probing protein environment in an enzymatic process: All-electron quantum chemical analysis combined with ab initio quantum mechanical/molecular mechanical modeling of chorismate mutase. J Chem Phys 2008; 129:125105. [DOI: 10.1063/1.2977458] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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32
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Scheiner S. Analysis of catalytic mechanism of serine proteases. Viability of the ring-flip hypothesis. J Phys Chem B 2008; 112:6837-46. [PMID: 18461994 DOI: 10.1021/jp710617w] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Quantum calculations are applied to the active site of serine proteases, including four specific residues and a water molecule, as well as a substrate and proton donors in the oxyanion hole. Residues are tethered to the protein backbone of an X-ray structure but otherwise allowed to move freely to their lowest energy positions. The viability of the ring-flip hypothesis, which proposes that a 180 degrees rotation of the His-57 imidazole ring facilitates the catalysis, is assessed by comparison of energies of configurations both before and after such a flip. Specifically considered is the contribution to catalysis of the Ser-214 residue and a water molecule that is observed in the active site. The calculations provide detailed information concerning the nature, geometry, and strength of hydrogen bonds that are formed within the active site at each stage of the enzymatic mechanism.
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Affiliation(s)
- Steve Scheiner
- Department of Chemistry & Biochemistry, Utah State University, Logan, Utah 84322-0300, USA.
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33
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Rational design of a new one-step purification strategy for Candida antarctica lipase B by ion-exchange chromatography. J Chromatogr A 2008; 1179:161-7. [DOI: 10.1016/j.chroma.2007.11.108] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2007] [Revised: 11/20/2007] [Accepted: 11/22/2007] [Indexed: 11/19/2022]
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34
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Rodríguez A, Oliva C, González M, van der Kamp M, Mulholland AJ. Comparison of different quantum mechanical/molecular mechanics boundary treatments in the reaction of the hepatitis C virus NS3 protease with the NS5A/5B substrate. J Phys Chem B 2007; 111:12909-15. [PMID: 17935316 DOI: 10.1021/jp0743469] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The link atom (LA) and the generalized hybrid orbital (GHO) quantum mechanical/molecular mechanics (QM/MM) boundary treatment methods are compared, in the context of the acylation process (the rate-limiting step) involving the NS3/NS4A HCV serine protease and its NS5A/5B natural substrate. The potential energy surface was calculated, and the free energy along the selected reaction coordinate was obtained from umbrella sampling molecular dynamics simulations, at the AM1/CHARMM27 level. The LA and GHO methods, when properly applied, lead to similar chemical behavior, although the agreement is not quantitative. The choice of QM/MM partitioning is dictated to some extent by the nature of the two different methods, and this influences the results. The free energy profiles obtained by umbrella sampling suggest that the GHO approach is better suited for this system, because it provides a consistent description of the reaction in both the forward and backward directions. This is probably a consequence of the different QM/MM partitioning required by the two different methods (i.e., different numbers of atoms have to be included in the QM region). This finding is therefore likely to be system dependent, so careful testing should be considered for each enzyme application.
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Affiliation(s)
- Alejandro Rodríguez
- Departament de Química Física i Centre de Recerca en Química Teòrica, Universitat de Barcelona i Parc Científic de Barcelona, C/Martí i Franquès 1, 08028 Barcelona, Spain
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35
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Dormeyer W, Mohammed S, Breukelen BV, Krijgsveld J, Heck AJR. Targeted analysis of protein termini. J Proteome Res 2007; 6:4634-45. [PMID: 17927228 DOI: 10.1021/pr070375k] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We describe a targeted analysis of protein isoforms by selective enrichment and identification of in vivo acetylated protein N-termini and protein C-termini. Our method allows the characterization of these protein termini regardless of their annotation in protein databases and requires no chemical derivatization. Using an iterative database search strategy that takes account of the enrichment protocol, 263 IPI annotated and 87 unpredicted acetylated N-termini were identified in the crude membrane fraction of human embryonic carcinoma cells. The N-acetylated peptides conform to the reported criteria for in vivo modification. In addition, 168 IPI annotated and 193 unpredicted C-termini were identified. Additionally, and for the first time, we also report on in vivo N-terminal propionylation. The significant number of unknown protein N- and C-termini suggests a high degree of novel transcription independent of annotated gene boundaries and/or specific protein processing. Biological relevance of several of these unpredicted protein termini could be curated from the literature, adding further weight to the argument to go beyond routine database search strategies. Our method will improve the correct annotation of genes and proteins in databases.
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Affiliation(s)
- Wilma Dormeyer
- Department of Biomolecular Mass Spectrometry, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, the Netherlands
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36
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Shokhen M, Khazanov N, Albeck A. Screening of the active site from water by the incoming ligand triggers catalysis and inhibition in serine proteases. Proteins 2007; 70:1578-87. [PMID: 17912756 DOI: 10.1002/prot.21727] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The pKa of the catalytic His57 N(epsilon)H in the tetrahedral complex (TC) of chymotrypsin with trifluoromethyl ketone inhibitors is 4-5 units higher relative to the free enzyme (FE). Such stable TC's, formed with transition state (TS) analog inhibitors, are topologically similar to the catalytic TS. Thus, analysis of this pKa shift may shed light on the role of water solvation in the general base catalysis by histidine. We applied our QM/SCRF(VS) approach to study this shift. The method enables explicit quantum mechanical DFT calculations of large molecular clusters that simulate chemical reactions at the active site (AS) of water solvated enzymes. We derived an analytical expression for the pKa dependence on the degree of water exposure of the ionizable group, and on the total charge in the enzyme AS, Q(A) and Q(B), when the target ionizable functional group (His57 in this study) is in the acidic (A) and basic (B) forms, respectively. Q2(B) > Q2(A) both in the FE and in the TC of chymotrypsin. Therefore, water solvation decreases the relative stability of the protonated histidine in both. Ligand binding reduces the degree of water solvation of the imidazole ring, and consequently elevates the histidine pKa. Thus, the binding of the ligand plays a triggering role that switches on the cascade of catalytic reactions in serine proteases.
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Affiliation(s)
- Michael Shokhen
- Julius Spokojny Bioorganic Chemistry Laboratory, Department of Chemistry, Bar Ilan University, Ramat Gan 52900, Israel.
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37
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Anderson VE, Ruszczycky MW, Harris ME. Activation of oxygen nucleophiles in enzyme catalysis. Chem Rev 2007; 106:3236-51. [PMID: 16895326 DOI: 10.1021/cr050281z] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Vernon E Anderson
- Department of Biochemistry and the Center for RNA Molecular Biology, Case Western Reserve University, School of Medicine, Cleveland, Ohio 44106, USA.
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38
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Shokhen M, Khazanov N, Albeck A. The Cooperative Effect Between Active Site Ionized Groups and Water Desolvation Controls the Alteration of Acid/Base Catalysis in Serine Proteases. Chembiochem 2007; 8:1416-21. [PMID: 17600794 DOI: 10.1002/cbic.200700241] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
What is the driving force that alters the catalytic function of His57 in serine proteases between general base and general acid in each step along the enzymatic reaction? The stable tetrahedral complexes (TC) of chymotrypsin with trifluoromethyl ketone transition state analogue inhibitors are topologically similar to the catalytic transition state. Therefore, they can serve as a good model to study the enzyme catalytic reaction. We used DFT quantum mechanical calculations to analyze the effect of solvation and of polar factors in the active site of chymotrypsin on the pKa of the catalytic histidine in FE (the free enzyme), EI (the noncovalent enzyme inhibitor complex), and TC. We demonstrated that the acid/base alteration is controlled by the charged groups in the active site--the catalytic Asp102 carboxylate and the oxyanion. The effect of these groups on the catalytic His is modulated by water solvation of the active site.
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Affiliation(s)
- Michael Shokhen
- The Julius Spokojny Bioorganic Chemistry Laboratory, Department of Chemistry, Bar Ilan University, Ramat Gan 52900, Israel.
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39
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Oliva C, Rodríguez A, González M, Yang W. A quantum mechanics/molecular mechanics study of the reaction mechanism of the hepatitis C virus NS3 protease with the NS5A/5B substrate. Proteins 2007; 66:444-55. [PMID: 17094110 DOI: 10.1002/prot.21190] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Combined quantum mechanics and molecular mechanics (QM/MM) calculations were carried out to characterize the reaction mechanism of the NS3 protease with its preferred substrate (NS5A/5B). The main purpose of this study was to locate the barrier states and intermediates along the distinguished coordinate path (DCP) involved in this process. These structures, and in particular the one corresponding to the first barrier state and intermediate (B1 and I1), could be a starting point for the synthesis of inhibitors of this protease, which could be used to treat hepatitis C. The two first steps of the reaction mechanism were studied, i.e., the acylation step and the breaking of the peptide bond. The first step takes place through a tetracoordinated intermediate, as suggested from previous works on other Serine proteases. The importance of the different amino acid residues was also considered (perturbation study where the MM charges of each residue were set to zero independently). The residues of the oxyanion hole were confirmed as the most important for the electrostatic stabilization of the tetracoordinate intermediate. Moreover, the role of other residues, e.g., Arg-155 and Asp-79, was also explained.
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Affiliation(s)
- Carolina Oliva
- Departament de Química Física i Centre de Recerca en Química Teòrica, Universitat de Barcelona i Parc Científic de Barcelona, C/ Martí i Franquès 1, 08028 Barcelona, Spain.
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40
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Wang C, Xu D, Zhang L, Xie D, Guo H. Molecular Dynamics and Density Functional Studies of Substrate Binding and Catalysis of Arginine Deiminase. J Phys Chem B 2007; 111:3267-73. [PMID: 17388453 DOI: 10.1021/jp067541g] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The active-site dynamics of arginine deiminase (ADI) complexed with the arginine substrate are investigated with ns molecular dynamics for the wildtype ADI and several mutants. It is shown that the substrate is held in the active site by an extensive hydrogen bond network, which may be weakened by substitution of active-site residues. In addition, the initial step of the catalysis is explored in several truncated active-site models with density functional theory. Evidence is presented in support of the hypothesis that the nucleophilic attack of the ADI Cys thiol at the guanidino carbon of the substrate is initiated by substrate-mediated proton transfer to a His residue in the catalytic triad (Cys-His-Glu). In addition, the active-site residues are found to strongly influence the reaction profile, consistent with their important role in catalysis.
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Affiliation(s)
- Canhui Wang
- Department of Chemistry, University of New Mexico, Albuquerque, New Mexico 87131, USA
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41
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Bruylants G, Redfield C, Bartik K. Developments in the Characterisation of the Catalytic Triad of α-Chymotrypsin: Effect of the Protonation State of Asp102 on the1H NMR Signals of His57. Chembiochem 2007; 8:51-4. [PMID: 17121406 DOI: 10.1002/cbic.200600433] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Gilles Bruylants
- Ingénierie Moléculaire et Biomoléculaire (CP 164/65), Ecole Polytechnique, Université Libre de Bruxelles, 50 Avenue F. D. Roosevelt, 1050 Bruxelles, Belgium
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42
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Solá RJ, Griebenow K. Influence of modulated structural dynamics on the kinetics of alpha-chymotrypsin catalysis. Insights through chemical glycosylation, molecular dynamics and domain motion analysis. FEBS J 2006; 273:5303-19. [PMID: 17076704 DOI: 10.1111/j.1742-4658.2006.05524.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Although the chemical nature of the catalytic mechanism of the serine protease alpha-chymotrypsin (alpha-CT) is largely understood, the influence of the enzyme's structural dynamics on its catalysis remains uncertain. Here we investigate whether alpha-CT's structural dynamics directly influence the kinetics of enzyme catalysis. Chemical glycosylation [Solá RJ & Griebenow K (2006) FEBS Lett 580, 1685-1690] was used to generate a series of glycosylated alpha-CT conjugates with reduced structural dynamics, as determined from amide hydrogen/deuterium exchange kinetics (k(HX)). Determination of their catalytic behavior (K(S), k(2), and k(3)) for the hydrolysis of N-succinyl-Ala-Ala-Pro-Phe p-nitroanilide (Suc-Ala-Ala-Pro-Phe-pNA) revealed decreased kinetics for the catalytic steps (k(2) and k(3)) without affecting substrate binding (K(S)) at increasing glycosylation levels. Statistical correlation analysis between the catalytic (DeltaG( not equal)k(i)) and structurally dynamic (DeltaG(HX)) parameters determined revealed that the enzyme acylation and deacylation steps are directly influenced by the changes in protein structural dynamics. Molecular modelling of the alpha-CT glycoconjugates coupled with molecular dynamics simulations and domain motion analysis employing the Gaussian network model revealed structural insights into the relation between the protein's surface glycosylation, the resulting structural dynamic changes, and the influence of these on the enzyme's collective dynamics and catalytic residues. The experimental and theoretical results presented here not only provide fundamental insights concerning the influence of glycosylation on the protein biophysical properties but also support the hypothesis that for alpha-CT the global structural dynamics directly influence the kinetics of enzyme catalysis via mechanochemical coupling between domain motions and active site chemical groups.
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Affiliation(s)
- Ricardo J Solá
- Laboratory for Applied Biochemistry and Biotechnology, Department of Chemistry, University of Puerto Rico, Río Piedras Campus, San Juan, PR 00931
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43
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Hopmann KH, Himo F. Theoretical Study of the Full Reaction Mechanism of Human Soluble Epoxide Hydrolase. Chemistry 2006; 12:6898-909. [PMID: 16856182 DOI: 10.1002/chem.200501519] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The complete reaction mechanism of soluble epoxide hydrolase (sEH) has been investigated by using the B3LYP density functional theory method. Epoxide hydrolases catalyze the conversion of epoxides to their corresponding vicinal diols. In our theoretical study, the sEH active site is represented by quantum-chemical models that are based on the X-ray crystal structure of human soluble epoxide hydrolase. The trans-substituted epoxide (1S,2S)-beta-methylstyrene oxide has been used as a substrate in the theoretical investigation of the sEH reaction mechanism. Both the alkylation and the hydrolytic half-reactions have been studied in detail. We present the energetics of the reaction mechanism as well as the optimized intermediates and transition-state structures. Full potential energy curves for the reactions involving nucleophilic attack at either the benzylic or the homo-benzylic carbon atom of (1S,2S)-beta-methylstyrene oxide have been computed. The regioselectivity of epoxide opening has been addressed for the two substrates (1S,2S)-beta-methylstyrene oxide and (S)-styrene oxide.
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Affiliation(s)
- Kathrin H Hopmann
- Department of Theoretical Chemistry, School of Biotechnology, Royal Institute of Technology, Albanova University Center, SE-106 91 Stockholm, Sweden
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44
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Cavalli A, Carloni P, Recanatini M. Target-Related Applications of First Principles Quantum Chemical Methods in Drug Design. Chem Rev 2006; 106:3497-519. [PMID: 16967914 DOI: 10.1021/cr050579p] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Andrea Cavalli
- Department of Pharmaceutical Sciences, University of Bologna, Via Belmeloro 6, I-40126 Bologna, Italy
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45
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Ishida T. Low-barrier hydrogen bond hypothesis in the catalytic triad residue of serine proteases: correlation between structural rearrangement and chemical shifts in the acylation process. Biochemistry 2006; 45:5413-20. [PMID: 16634622 DOI: 10.1021/bi051515b] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To elucidate the catalytic advantage of the low-barrier hydrogen bond (LBHB), we analyze the hydrogen bonding network of the catalytic triad (His57-Asp102-Ser195) of serine protease trypsin, one of the best examples of the LBHB reaction mechanism. Especially, we focus on the correlation between the change of the chemical shifts and the structural rearrangement of the active site in the acylation process. To clarify LBHB, we evaluate the two complementary properties. First, we calculate the NMR chemical shifts of the imidazole ring of His57 by the gauge-including atomic orbital (GIAO) approach within the ab initio QM/MM framework. Second, the free energy profile of the proton transfer from His57 to Asp102 in the tetrahedral intermediate is obtained by ab initio QM/MM calculations combined with molecular dynamics free energy perturbation (MD-FEP) simulations. The present analyses reveal that the calculated shifts reasonably reproduce the observed values for (1)H chemical shift of H(epsilon)(1) and H(delta)(1) in His57. The (15)N and (13)C chemical shifts are also consistent with the experiments. It is also shown that the proton between His57 and Asp102 is localized at the His57 side. This largely downfield chemical shift is originated from the strong electrostatic interaction, not a covalent-like bonding character between His57 and Asp102. Also, it is proved that a slight downfield character of H(epsilon)(1) is originated from a electrostatic interaction between His57 and the backbone carbonyl group of Val213 and Ser214. These downfield chemical shifts are observed only when the tetrahedral intermediate is formed in the acylation process.
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Affiliation(s)
- Toyokazu Ishida
- Research Institute for Computational Science, National Institute of Advanced Industrial Science and Technology, Tsukuba Central 2, 1-1-1 Umezono, Tsukuba, 305-8568, Japan.
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46
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Rod TH, Rydberg P, Ryde U. Implicit versus explicit solvent in free energy calculations of enzyme catalysis: Methyl transfer catalyzed by catechol O-methyltransferase. J Chem Phys 2006; 124:174503. [PMID: 16689579 DOI: 10.1063/1.2186635] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We compare free energy calculations for the methyl transfer reaction catalyzed by catechol O-methyltransferase using the quantum mechanical/molecular mechanical free energy method with implicit and explicit solvents. An analogous methylation reaction in a solution is also studied. For the explicit solvent model, we use the three-point transferable intermolecular potential model, and for the implicit model, we use the generalized Born molecular volume model as implemented in CHARMM. We find that activation and reaction free energies calculated with the two models are very similar, despite some structural differences that exist. A significant change in the polarization of the environment occurs as the reaction proceeds. This is more pronounced for the reaction in a solution than for the enzymatic reaction. For the enzymatic reaction, most of the changes take place in the protein rather than in the solvent, and, hence, the benefit of having an instantaneous relaxation of the solvent degrees of freedom is less pronounced for the enzymatic reaction than for the reaction in a solution. This is a likely reason why energies of the enzyme reaction are less sensitive to the choice of atomic radii than are energies of the reaction in a solution.
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Affiliation(s)
- Thomas H Rod
- Department of Theoretical Chemistry, Chemical Center, Lund University, P.O. Box 124, S-22100 Lund, Sweden.
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47
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Pacios LF, Gómez PC, Gálvez O. Variation of atomic charges on proton transfer in strong hydrogen bonds: The case of anionic and neutral imidazole–acetate complexes. J Comput Chem 2006; 27:1650-61. [PMID: 16900495 DOI: 10.1002/jcc.20476] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The variation of atomic charges upon proton transfer in hydrogen bonding complexes of 4-methylimidazole, in both neutral and protonated cationic forms, and acetate anion, is investigated. These complexes model the histidine (neutral and protonated)-aspartate pair present in active sites of proteases where strong N--H...O hydrogen bonds are formed. Three procedures (Merz-Kollman scheme, Natural Population Analysis, and Atoms in Molecules Method) are used to compute atomic charges and explore their variation upon H-transfer in the gas phase and in the presence of two continuum media with dielectric constants 5 (protein interiors) and 78.39 (water). The effect of electron correlation was also studied by comparing Hartree-Fock and MP2 results for both complexes in the gas phase. Greater net charge interchanged upon H-transfer is observed in the anionic complex with respect to the neutral complex. Raising the polarity of the medium increases the amount of net charge transfer in both complexes, although the neutral system exhibits a larger sensitivity to the presence of solvent. Charge transfer associated to N--H...O and N...H--O bonds reveal the ionic contribution to the interaction depending on the number of charged subunits but the presence of solvent affects little this quantity. The lack of electron correlation overestimates all the charges as well as their variations and so uncorrelated calculations should be avoided.
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Affiliation(s)
- Luis F Pacios
- Departamento de Biotecnología, Unidad de Química y Bioquímica, E.T.S.I. Montes, Universidad Politécnica de Madrid, 28040 Madrid, Spain.
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48
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Ishida T, Fedorov DG, Kitaura K. All Electron Quantum Chemical Calculation of the Entire Enzyme System Confirms a Collective Catalytic Device in the Chorismate Mutase Reaction. J Phys Chem B 2005; 110:1457-63. [PMID: 16471697 DOI: 10.1021/jp0557159] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To elucidate the catalytic power of enzymes, we analyzed the reaction profile of Claisen rearrangement of Bacillus subtilis chorismate mutase (BsCM) by all electron quantum chemical calculations using the fragment molecular orbital (FMO) method. To the best of our knowledge, this is the first report of ab initio-based quantum chemical calculations of the entire enzyme system, where we provide a detailed analysis of the catalytic factors that accomplish transition-state stabilization (TSS). FMO calculations deliver an ab initio-level estimate of the intermolecular interaction between the substrate and the amino acid residues of the enzyme. To clarify the catalytic role of Arg90, we calculated the reaction profile of the wild-type BsCM as well as Lys90 and Cit90 mutant BsCMs. Structural refinement and the reaction path determination were performed at the ab initio QM/MM level, and FMO calculations were applied to the QM/MM refined structures. Comparison between three types of reactions established two collective catalytic factors in the BsCM reaction: (1) the hydrogen bonds connecting the Glu78-Arg90-substrate cooperatively control the stability of TS relative to the ES complex and (2) the positive charge on Arg90 polarizes the substrate in the TS region to gain more electrostatic stabilization.
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Affiliation(s)
- Toyokazu Ishida
- Research Institute for Computational Science (RICS), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 2, 1-1-1 Umezono, Tsukuba, 305-8568, Japan.
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49
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Hudáky P, Perczel A. A self-stabilized model of the chymotrypsin catalytic pocket. The energy profile of the overall catalytic cycle. Proteins 2005; 62:749-59. [PMID: 16358328 DOI: 10.1002/prot.20827] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
A model of the catalytic triad of chymotrypsin is built assuring the arrangement and properties as they are within the complete enzyme. The model contains 18 amino acid residues of chymotrypsin and its substrate. A total of 135 atoms (including 70 heavy atoms) were subjected to full ab initio geometry optimizations through 127 individual steps along the reaction coordinate of the complete catalytic mechanism. It was shown that the described model of the catalytic apparatus forms a self-stabilized molecule ensemble without the rest of the enzyme and substrate. According to the calculations, the formations of the first and second tetrahedral intermediates in the model have 20.3 and 15.7 kcal/mol activation energy barriers, respectively. Removing elements of the catalytic apparatus such as the (1) catalytic aspartate or (2) the anion hole, as well as (3) inserting a water molecule "early" in the catalytic process, or (4) introducing conformational rigidity of the substrate, results in an increase of the above energy barrier of the first catalytic step in the model by 6.4, 13.7, 3.7, and 4.1 kcal/mol, respectively. Based on the calculated process one can conclude that the catalytic reaction in this model is much more similar to the reaction in the enzyme than to the reference reaction. To our knowledge, this is the first model system that mimics the complete catalytic mechanism.
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Affiliation(s)
- Péter Hudáky
- Department of Theoretical Chemistry, Eötvös Loránd University, Budapest 112, Hungary
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50
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Gutteridge A, Thornton JM. Understanding nature's catalytic toolkit. Trends Biochem Sci 2005; 30:622-9. [PMID: 16214343 DOI: 10.1016/j.tibs.2005.09.006] [Citation(s) in RCA: 128] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2005] [Revised: 08/24/2005] [Accepted: 09/15/2005] [Indexed: 11/25/2022]
Abstract
Enzymes catalyse numerous reactions in nature, often causing spectacular accelerations in the catalysis rate. One aspect of understanding how enzymes achieve these feats is to explore how they use the limited set of residue side chains that form their 'catalytic toolkit'. Combinations of different residues form 'catalytic units' that are found repeatedly in different unrelated enzymes. Most catalytic units facilitate rapid catalysis in the enzyme active site either by providing charged groups to polarize substrates and to stabilize transition states, or by modifying the pKa values of other residues to provide more effective acids and bases. Given recent efforts to design novel enzymes, the rise of structural genomics and subsequent efforts to predict the function of enzymes from their structure, these units provide a simple framework to describe how nature uses the tools at her disposal, and might help to improve techniques for designing and predicting enzyme function.
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Affiliation(s)
- Alex Gutteridge
- EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
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