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Planeta Kepp K. Bioinorganic Chemistry of Zinc in Relation to the Immune System. Chembiochem 2021; 23:e202100554. [PMID: 34889510 DOI: 10.1002/cbic.202100554] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 12/09/2021] [Indexed: 01/18/2023]
Abstract
Zinc is well-known to have a central role in human inflammation and immunity and is itself an anti-inflammatory and antiviral agent. Despite its massively documented role in such processes, the underlying chemistry of zinc in relation to specific proteins and pathways of the immune system has not received much focus. This short review provides an overview of this topic, with emphasis on the structures of key proteins, zinc coordination chemistry, and probable mechanisms involved in zinc-based immunity, with some focus points for future chemical and biological research.
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Affiliation(s)
- Kasper Planeta Kepp
- DTU Chemistry, Technical University of Denmark, Building 206, 2800, Kongens Lyngby, Denmark
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2
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Khalili Arjomandi O, Kavoosi M, Adibi H. Synthesis and investigation of inhibitory activities of imidazole derivatives against the metallo-β-lactamase IMP-1. Bioorg Chem 2019; 92:103277. [PMID: 31539743 DOI: 10.1016/j.bioorg.2019.103277] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Revised: 09/03/2019] [Accepted: 09/11/2019] [Indexed: 12/21/2022]
Abstract
Mutations in bacteria can result in antibiotic resistance due to the overuse or abuse of β-lactam antibiotics. One strategy which bacteria can become resistance toward antibiotics is secreting of metallo β-lactamase enzymes that can open the lactam ring of the β-lactam antibiotic and inactivate them. This issue is a threat for human health and one strategy to overcome this situation is co-administration of β-lactam antibiotics with an inhibitor. So far, no clinically available inhibitors of metallo β-lactamases (MBLs) reported and the clinically inhibitors of serine β-lactamase are useless for MBLs. Accordingly, finding a potent inhibitor of the MBLs being very important. In this study, imidazole derivatives primarily were synthesized and their inhibitory activity were measured. Later in silico binding model was used to predict the configuration and conformation of the ligands into the active site of enzyme. Two molecules demonstrated with IC50 of 39 µM and 46 µM against MBL (IMP-1).
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Affiliation(s)
- Omid Khalili Arjomandi
- The University of Queensland, School of Chemistry and Molecular Biosciences, Brisbane, Qld 4072, Australia; Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran.
| | - Mahboubeh Kavoosi
- Department of Biochemistry, Pasteur Institute of Iran, Tehran, Iran.
| | - Hadi Adibi
- Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran.
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3
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Khalili Arjomandi O, Kavoosi M, Adibi H. Synthesis and enzyme-based evaluation of analogues L-tyrosine thiol carboxylic acid inhibitor of metallo-β-lactamase IMP-1. J Enzyme Inhib Med Chem 2019; 34:1414-1425. [PMID: 31401901 PMCID: PMC8853707 DOI: 10.1080/14756366.2019.1651314] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
The emergence of drug-resistant pathogenic bacteria is occurring due to the global overuse and misuse of β-lactam antibiotics. Infections caused by some bacteria which secrete metallo-β-lactamases (enzymes that inactivate β-lactam antibiotics) are increasingly prevalent and have become a major worldwide threat to human health. These bacteria are resistant to β-lactam antibiotics and MBL-inhibitor/β-lactam antibiotic combination therapy can be a strategy to overcome this problem. So far, no clinically available inhibitors of metallo-β-lactamases (MBLs) have been reported. In this study, L-benzyl tyrosine thiol carboxylic acid analogues (2a–2k) were synthesized after the study of computational simulation by adding of methyl, chloro, bromo and nitro groups to the benzyl ring for investigation of SAR analysis. Although the synthesized molecules 2a–k shows the potent inhibitory effects against metallo-β-lactamase (IMP-1) with the range of Kic values of 1.04–4.77 µM, they are not as potent as the candidate inhibitor.
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Affiliation(s)
- Omid Khalili Arjomandi
- Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
- The University of Queensland, School of Chemistry and Molecular Biosciences, Brisbane, Australia
| | | | - Hadi Adibi
- Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
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4
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de Arruda EGR, Rocha BA, Barrionuevo MVF, Aðalsteinsson HM, Galdino FE, Loh W, Lima FA, Abbehausen C. The influence of ZnII coordination sphere and chemical structure over the reactivity of metallo-β-lactamase model compounds. Dalton Trans 2019; 48:2900-2916. [DOI: 10.1039/c8dt03905d] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The first coordination sphere influences the reactivity of metallo-β-lactamase monozinc model complexes.
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5
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Anaya J, Grande M, Monleón LM, Sánchez RM. Synthesis and reactivity against Cp2TiCl of 4-isoprenyl-β-lactams. Trapping of N-titanoimidoyl radicals from cyanoformyl-2-azetidinones. Tetrahedron 2018. [DOI: 10.1016/j.tet.2018.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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6
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Khrenova MG, Nemukhin AV. Modeling the Transient Kinetics of the L1 Metallo-β-Lactamase. J Phys Chem B 2018; 122:1378-1386. [DOI: 10.1021/acs.jpcb.7b10188] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Maria G. Khrenova
- Department
of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Alexander V. Nemukhin
- Department
of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
- Emanuel
Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, 119334, Russia
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7
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Vidossich P, Magistrato A. QM/MM molecular dynamics studies of metal binding proteins. Biomolecules 2014; 4:616-45. [PMID: 25006697 PMCID: PMC4192665 DOI: 10.3390/biom4030616] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 06/05/2014] [Accepted: 06/06/2014] [Indexed: 11/16/2022] Open
Abstract
Mixed quantum-classical (quantum mechanical/molecular mechanical (QM/MM)) simulations have strongly contributed to providing insights into the understanding of several structural and mechanistic aspects of biological molecules. They played a particularly important role in metal binding proteins, where the electronic effects of transition metals have to be explicitly taken into account for the correct representation of the underlying biochemical process. In this review, after a brief description of the basic concepts of the QM/MM method, we provide an overview of its capabilities using selected examples taken from our work. Specifically, we will focus on heme peroxidases, metallo-β-lactamases, α-synuclein and ligase ribozymes to show how this approach is capable of describing the catalytic and/or structural role played by transition (Fe, Zn or Cu) and main group (Mg) metals. Applications will reveal how metal ions influence the formation and reduction of high redox intermediates in catalytic cycles and enhance drug metabolism, amyloidogenic aggregate formation and nucleic acid synthesis. In turn, it will become manifest that the protein frame directs and modulates the properties and reactivity of the metal ions.
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Affiliation(s)
- Pietro Vidossich
- Department of Chemistry, Autonomous University of Barcelona, 08193 Cerdanyola del Vallés, Spain.
| | - Alessandra Magistrato
- CNR-IOM-Democritos National Simulation Center c/o, International School for Advanced Studies (SISSA/ISAS), via Bonomea 265, 34165 Trieste, Italy.
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8
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Daumann LJ, Schenk G, Gahan LR. Metallo-β-lactamases and Their Biomimetic Complexes. Eur J Inorg Chem 2014. [DOI: 10.1002/ejic.201402203] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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10
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Zhu K, Lu J, Liang Z, Kong X, Ye F, Jin L, Geng H, Chen Y, Zheng M, Jiang H, Li JQ, Luo C. A quantum mechanics/molecular mechanics study on the hydrolysis mechanism of New Delhi metallo-β-lactamase-1. J Comput Aided Mol Des 2013; 27:247-56. [DOI: 10.1007/s10822-012-9630-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2012] [Accepted: 12/28/2012] [Indexed: 10/27/2022]
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11
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Monlen LM, Grande M, Anaya J. Synthesis of polycyclic ?-lactams. Evolution of tertiary radicals generated by Cp2TiCl from 1,5- and 1,6-epoxynitriles. Tetrahedron 2012. [DOI: 10.1016/j.tet.2011.11.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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12
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Valdez CE, Sparta M, Alexandrova AN. The Role of the Flexible L43-S54 Protein Loop in the CcrA Metallo-β-lactamase in Binding Structurally Dissimilar β-Lactam Antibiotics. J Chem Theory Comput 2012; 9:730-7. [DOI: 10.1021/ct300712j] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Crystal E. Valdez
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, Los Angeles, California 90095-1569, United
States
| | - Manuel Sparta
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, Los Angeles, California 90095-1569, United
States
| | - Anastassia N. Alexandrova
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, Los Angeles, California 90095-1569, United
States
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13
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Valdez CE, Alexandrova AN. Why Urease Is a Di-Nickel Enzyme whereas the CcrA β-Lactamase Is a Di-Zinc Enzyme. J Phys Chem B 2012; 116:10649-56. [DOI: 10.1021/jp302771n] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Crystal E. Valdez
- Department of Chemistry
and Biochemistry, University of California, Los Angeles, Los Angeles,
California 90095-1569, United States
| | - Anastassia N. Alexandrova
- Department of Chemistry
and Biochemistry, University of California, Los Angeles, Los Angeles,
California 90095-1569, United States
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14
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Zack LN, Sun M, Bucchino MP, Clouthier DJ, Ziurys LM. Gas-Phase Synthesis and Structure of Monomeric ZnOH: A Model Species for Metalloenzymes and Catalytic Surfaces. J Phys Chem A 2012; 116:1542-50. [DOI: 10.1021/jp209875a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Lindsay N. Zack
- Department
of Chemistry, Department
of Astronomy and Steward Observatory, University of Arizona, 933 North Cherry Avenue, Tucson, Arizona 85721, United States
| | - Ming Sun
- Department
of Chemistry, Department
of Astronomy and Steward Observatory, University of Arizona, 933 North Cherry Avenue, Tucson, Arizona 85721, United States
| | - Matthew P. Bucchino
- Department
of Chemistry, Department
of Astronomy and Steward Observatory, University of Arizona, 933 North Cherry Avenue, Tucson, Arizona 85721, United States
| | - Dennis J. Clouthier
- Department of Chemistry, University of Kentucky, 125 Chemistry-Physics Building,
Lexington, Kentucky 40506, United States
| | - Lucy M. Ziurys
- Department
of Chemistry, Department
of Astronomy and Steward Observatory, University of Arizona, 933 North Cherry Avenue, Tucson, Arizona 85721, United States
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15
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GU WEI, ZHU JIANG, LIU HAIYAN. DIFFERENT PROTONATION STATES OF THE BACILLUS CEREUS BINUCLEAR ZINC METALLO-β-LACTAMASE ACTIVE SITE STUDIED BY COMBINED QUANTUM MECHANICAL AND MOLECULAR MECHANICAL SIMULATIONS. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2012. [DOI: 10.1142/s0219633602000038] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Three different protonation states of the active site of the Bacillus cereus zinc-β-lactamase in its binuclear form are studied using combined quantum mechanics/molecular mechanics molecular dynamics simulations. The reliability of the quantum mechanical model, the self-consistent-charge density-functional-based tight binding method, in describing the zinc centers are tested through comparisons with ab initio quantum mechanical results. We found that this model gave relatively accurate results for structures and performed much better than the MNDO type semi-empirical method for the particular systems. The enzyme simulations suggested that when the overall charge of the active site is +1, i.e., both Asp90 and Wat1 (a water molecule coordinated with the first zinc ion) deprotonated, the second zinc ion is coordinated with Asp90 and Wat1, and a second water molecule cannot coordinate with the second zinc ion. When the overall charge is +2, i.e., either Asp90 or Wat1 protonated, Asp90 and Wat1 form a stable hydrogen bond. Depending on the proton being on Asp90 or on Wat1, the active site structure produced by the simulations is either similar to molecule A or to molecule B, both contained in the same crystal structure that has two enzyme molecules in a single asymmetric unit. The simulations of the +2 charge states also reproduced the experimentally observed "loose" coordination around the second zinc for the Bacillus Cereus enzyme. Based on the simulations and a gas phase potential energy surface scanning using ab initio model, we argue that the penta-coordination around the second zinc ion is not a stable arrangement. Mechanistic implications of these results are discussed.
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Affiliation(s)
- WEI GU
- School of Life Science, University of Science and Technology of China (USTC), Laboratory of Structural Biology, Chinese Academy of Science (CAS), USTC, Hefei, Anhui, 230026, China
| | - JIANG ZHU
- School of Life Science, University of Science and Technology of China (USTC), Laboratory of Structural Biology, Chinese Academy of Science (CAS), USTC, Hefei, Anhui, 230026, China
| | - HAIYAN LIU
- School of Life Science, University of Science and Technology of China (USTC), Laboratory of Structural Biology, Chinese Academy of Science (CAS), USTC, Hefei, Anhui, 230026, China
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16
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Han L, Liu J, Wang Z, Zhang K, Luo H, Xu B, Zou X, Zheng X, Ye B, Yu X. Shape-controlled synthesis of ZnSn(OH)6 crystallites and their HCHO-sensing properties. CrystEngComm 2012. [DOI: 10.1039/c2ce06583e] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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17
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Swiderek K, Paneth P. Importance of the lactate dehydrogenase quaternary structure in theoretical calculations. J Phys Chem B 2010; 114:3393-7. [PMID: 20155895 DOI: 10.1021/jp100026z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Using the example of lactate dehydrogenase, we show that enzyme quaternary structure has an important influence on the structure of the active site and that models that comprise all amino acids in the vicinity of an active site, but are missing this structural information, can lead to incorrect results. We also show that binding isotope effects are very sensitive to the geometric parameters, and thus one should be very cautious when interpreting results obtained with models that are too coarse. In terms of the type of hydrogen bonds, our results indicate that binding isotope effects are pronounced only when a hydrogen bond exhibits some covalent character.
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Affiliation(s)
- Katarzyna Swiderek
- Institute of Applied Radiation Chemistry, Technical University of Lodz, ulica Zeromskiego 116, 90-924 Lodz, Poland
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19
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Klusák V, Bařinka C, Plechanovová A, Mlčochová P, Konvalinka J, Rulíšek L, Lubkowski J. Reaction mechanism of glutamate carboxypeptidase II revealed by mutagenesis, X-ray crystallography, and computational methods. Biochemistry 2009; 48:4126-38. [PMID: 19301871 PMCID: PMC7289149 DOI: 10.1021/bi900220s] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Glutamate carboxypeptidase II (GCPII, EC 3.4.17.21) is a zinc-dependent exopeptidase and an important therapeutic target for neurodegeneration and prostate cancer. The hydrolysis of N-acetyl-l-aspartyl-l-glutamate (N-Ac-Asp-Glu), the natural dipeptidic substrate of the GCPII, is intimately involved in cellular signaling within the mammalian nervous system, but the exact mechanism of this reaction has not yet been determined. To investigate peptide hydrolysis by GCPII in detail, we constructed a mutant of human GCPII [GCPII(E424A)], in which Glu424, a putative proton shuttle residue, is substituted with alanine. Kinetic analysis of GCPII(E424A) using N-Ac-Asp-Glu as substrate revealed a complete loss of catalytic activity, suggesting the direct involvement of Glu424 in peptide hydrolysis. Additionally, we determined the crystal structure of GCPII(E424A) in complex with N-Ac-Asp-Glu at 1.70 A resolution. The presence of the intact substrate in the GCPII(E424A) binding cavity substantiates our kinetic data and allows a detailed analysis of GCPII/N-Ac-Asp-Glu interactions. The experimental data are complemented by the combined quantum mechanics/molecular mechanics calculations (QM/MM) which enabled us to characterize the transition states, including the associated reaction barriers, and provided detailed information concerning the GCPII reaction mechanism. The best estimate of the reaction barrier was calculated to be DeltaG(++) approximately 22(+/-5) kcal x mol(-1), which is in a good agreement with the experimentally observed reaction rate constant (k(cat) approximately 1 s(-1)). Combined together, our results provide a detailed and consistent picture of the reaction mechanism of this highly interesting enzyme at the atomic level.
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Affiliation(s)
- Vojtêch Klusák
- Institute of Organic Chemistry and Biochemistry, Gilead Sciences Research Center and IOCB, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Praha 6, Czech Republic
| | - Cyril Bařinka
- Macromolecular Crystallography Laboratory, National Cancer Institute at Frederick, 539 Boyles Street, Frederick, Maryland 21702
| | - Anna Plechanovová
- Institute of Organic Chemistry and Biochemistry, Gilead Sciences Research Center and IOCB, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Praha 6, Czech Republic
| | - Petra Mlčochová
- Institute of Organic Chemistry and Biochemistry, Gilead Sciences Research Center and IOCB, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Praha 6, Czech Republic,Department of Biochemistry, Faculty of Science, Charles University in Prague, Hlavova 2030, Praha 2, Czech Republic
| | - Jan Konvalinka
- Institute of Organic Chemistry and Biochemistry, Gilead Sciences Research Center and IOCB, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Praha 6, Czech Republic,Department of Biochemistry, Faculty of Science, Charles University in Prague, Hlavova 2030, Praha 2, Czech Republic
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry, Gilead Sciences Research Center and IOCB, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Praha 6, Czech Republic,Corresponding authors. L.R.: tel, +420-220-183-263; fax, + 420-220-183-578; . J.L.: tel, (301) 846-5494; fax, (301) 846-7517;
| | - Jacek Lubkowski
- Macromolecular Crystallography Laboratory, National Cancer Institute at Frederick, 539 Boyles Street, Frederick, Maryland 21702,Corresponding authors. L.R.: tel, +420-220-183-263; fax, + 420-220-183-578; . J.L.: tel, (301) 846-5494; fax, (301) 846-7517;
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20
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López-Canut V, Martí S, Bertrán J, Moliner V, Tuñón I. Theoretical Modeling of the Reaction Mechanism of Phosphate Monoester Hydrolysis in Alkaline Phosphatase. J Phys Chem B 2009; 113:7816-24. [DOI: 10.1021/jp901444g] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Violeta López-Canut
- Departament de Química Física, Universitat de València, València, Spain, Departament de Química Física i Analítica, Universitat Jaume I, Castelló, Spain, and Departament de Química, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Sergio Martí
- Departament de Química Física, Universitat de València, València, Spain, Departament de Química Física i Analítica, Universitat Jaume I, Castelló, Spain, and Departament de Química, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Juan Bertrán
- Departament de Química Física, Universitat de València, València, Spain, Departament de Química Física i Analítica, Universitat Jaume I, Castelló, Spain, and Departament de Química, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Vicente Moliner
- Departament de Química Física, Universitat de València, València, Spain, Departament de Química Física i Analítica, Universitat Jaume I, Castelló, Spain, and Departament de Química, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Iñaki Tuñón
- Departament de Química Física, Universitat de València, València, Spain, Departament de Química Física i Analítica, Universitat Jaume I, Castelló, Spain, and Departament de Química, Universitat Autònoma de Barcelona, Barcelona, Spain
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21
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Frison G, Ohanessian G. A comparative study of semiempirical, ab initio, and DFT methods in evaluating metal-ligand bond strength, proton affinity, and interactions between first and second shell ligands in Zn-biomimetic complexes. J Comput Chem 2008; 29:416-33. [PMID: 17631650 DOI: 10.1002/jcc.20800] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Although theoretical methods are now available which give very accurate results, often comparable to the experimental ones, modeling chemical or biological interesting systems often requires less demanding and less accurate theoretical methods, mainly due to computer limitations. Therefore, it is crucial to know the precision of such less reliable methods for relevant models and data. This has been done in this work for small zinc-active site models including O- (H(2)O and OH(-)) and N-donor (NH(3) and imidazole) ligands. Calculations using a number of quantum mechanical methods were carried out to determine their precision for geometries, coordination number relative stability, metal-ligand bond strengths, proton affinities, and interaction energies between first and second shell ligands. We have found that obtaining chemical accuracy can be as straightforward as HF geometry optimization with a double-zeta plus polarization basis followed by a B3LYP energy calculation with a triple-zeta quality basis set including diffuse and polarization functions. The use of levels as low as PM3 geometry optimization followed by a B3LYP single-point energy calculation with a double-zeta quality basis including polarization functions already yields useful trends in bond length, proton affinities or bond dissociation energies, provided that appropriate caution is taken with the optimized structures. The reliability of these levels of calculation has been successfully demonstrated for real biomimetic cases.
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Affiliation(s)
- Gilles Frison
- Laboratoire des Mécanismes Réactionnels, Département de Chimie, Ecole Polytechnique, CNRS, 91128 Palaiseau Cedex, France.
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22
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Estiu G, Suárez D, Merz KM. Quantum mechanical and molecular dynamics simulations of ureases and Zn beta-lactamases. J Comput Chem 2007; 27:1240-62. [PMID: 16773613 DOI: 10.1002/jcc.20411] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Herein we briefly review theoretical contributions that have increased our understanding of the structure and function of metallo-beta-lactamases and ureases. Both are bimetallic metalloenzymes, with the former containing two zinc ions and the latter containing two nickel ions. We describe the use of several different methodologies, including quantum chemical calculations, molecular dynamic simulations, as well as mixed QM/MM approaches and how they have impacted our understanding of the structure and function of metallo-beta-lactamases and ureases.
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Affiliation(s)
- Guillermina Estiu
- Department of Chemistry, Quantum Theory Project, University of Florida, 2328 New Physics Building, P.O. Box 118435, Gainesville, Florida 32611-8435, USA
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23
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Xu D, Guo H, Cui Q. Antibiotic Deactivation by a Dizinc β-Lactamase: Mechanistic Insights from QM/MM and DFT Studies. J Am Chem Soc 2007; 129:10814-22. [PMID: 17691780 DOI: 10.1021/ja072532m] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hybrid quantum mechanical/molecular mechanical (QM/MM) methods and density functional theory (DFT) were used to investigate the initial ring-opening step in the hydrolysis of moxalactam catalyzed by the dizinc L1 beta-lactamase from Stenotrophomonas maltophilia. Anchored at the enzyme active site via direct metal binding as suggested by a recent X-ray structure of an enzyme-product complex (Spencer, J.; et al. J. Am. Chem. Soc. 2005, 127, 14439), the substrate is well aligned with the nucleophilic hydroxide that bridges the two zinc ions. Both QM/MM and DFT results indicate that the addition of the hydroxide nucleophile to the carbonyl carbon in the substrate lactam ring leads to a metastable intermediate via a dominant nucleophilic addition barrier. The potential of mean force obtained by SCC-DFTB/MM simulations and corrected by DFT/MM calculations yields a reaction free energy barrier of 23.5 kcal/mol, in reasonable agreement with the experimental value of 18.5 kcal/mol derived from kcat of 0.15 s(-1). It is further shown that zinc-bound Asp120 plays an important role in aligning the nucleophile, but accepts the hydroxide proton only after the nucleophilic addition. The two zinc ions are found to participate intimately in the catalysis, consistent with the proposed mechanism. In particular, the Zn(1) ion is likely to serve as an "oxyanion hole" in stabilizing the carbonyl oxygen, while the Zn(2) ion acts as an electrophilic catalyst to stabilize the anionic nitrogen leaving group.
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Affiliation(s)
- Dingguo Xu
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, USA
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24
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Pal Chaudhuri U, Whiteaker LR, Mondal A, Klein EL, Powell DR, Houser RP. Substituted pyridylmethylamide ligands and their zinc complexes. Inorganica Chim Acta 2007. [DOI: 10.1016/j.ica.2007.05.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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25
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Wang C, Guo H. Inhibitor Binding by Metallo-β-lactamase IMP-1 from Pseudomonas aeruginosa: Quantum Mechanical/Molecular Mechanical Simulations. J Phys Chem B 2007; 111:9986-92. [PMID: 17663582 DOI: 10.1021/jp073864g] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The dynamics of the IMP-1 enzyme complexed with three prototypical inhibitors are investigated using a quantum mechanical/molecular mechanical (QM/MM) method based on the self-consistent-charge density-functional tight-binding model. The binding patterns of the inhibitors observed in X-ray diffraction experiments are well reproduced in 600 ps molecular dynamics simulations at room temperature. These inhibitors anchor themselves in the enzyme active site by direct coordination with the two zinc ions, displacing the hydroxide nucleophile that bridges the two zinc ions. In addition, they also interact with several active-site residues and those in two mobile loops. The excellent agreement with experimental structural data validates the QM/MM treatment used in our simulations.
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Affiliation(s)
- Canhui Wang
- Department of Chemistry, University of New Mexico, Albuquerque, New Mexico 87131, USA
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26
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27
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Meyer F. Clues to Dimetallohydrolase Mechanisms from Studies on Pyrazolate‐Based Bioinspired Dizinc Complexes – Experimental Evidence for a Functional Zn–O
2
H
3
–Zn Motif. Eur J Inorg Chem 2006. [DOI: 10.1002/ejic.200600590] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Franc Meyer
- Institut für Anorganische Chemie, Georg‐August‐Universität Göttingen Tammannstrasse 4, 37077 Göttingen, Germany, Fax: +49‐551‐393063
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28
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Desmarais W, Bienvenue DL, Bzymek KP, Petsko GA, Ringe D, Holz RC. The high-resolution structures of the neutral and the low pH crystals of aminopeptidase from Aeromonas proteolytica. J Biol Inorg Chem 2006; 11:398-408. [PMID: 16596389 DOI: 10.1007/s00775-006-0093-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2006] [Accepted: 02/10/2006] [Indexed: 10/24/2022]
Abstract
The aminopeptidase from Aeromonas proteolytica (AAP) contains two zinc ions in the active site and catalyzes the degradation of peptides. Herein we report the crystal structures of AAP at 0.95-A resolution at neutral pH and at 1.24-A resolution at low pH. The combination of these structures allowed the precise modeling of atomic positions, the identification of the metal bridging oxygen species, and insight into the physical properties of the metal ions. On the basis of these structures, a new putative catalytic mechanism is proposed for AAP that is likely relevant to all binuclear metalloproteases.
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Affiliation(s)
- William Desmarais
- Program in Biophysics and Structural Biology, Brandeis University, 415 South Street, Waltham, MA 02254-9110, USA
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29
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Abstract
The initial nucleophilic substitution step of biapenem hydrolysis catalyzed by a subclass B2 metallo-beta-lactamase (CphA from Aeromonas hydrophila) is investigated using hybrid quantum mechanical/molecular mechanical methods and density functional theory. We focused on a recently proposed catalytic mechanism that involves a non-metal-binding water nucleophile in the active site of the monozinc CphA. Both theoretical models identified a single transition state featuring nearly concomitant nucleophilic addition and elimination steps, and the activation free energy from the potential of mean force calculations was estimated to be approximately 14 kcal/mol. The theoretical results also identified the general base for activating the water nucleophile to be the metal-binding Asp-120 rather than His-118, as suggested earlier. The protonation of Asp-120 leads to cleavage of the O(delta2)-Zn coordination bond, whereas the negatively charged nitrogen leaving group resulting from the ring opening replaces Asp-120 as the fourth ligand of the sole zinc ion. The electrophilic catalysis by the metal ion provides sufficient stabilization for the leaving group to avoid a tetrahedral intermediate. The theoretical studies provided detailed insights into the catalytic strategy of this unique metallo-beta-lactamase.
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Affiliation(s)
- Dingguo Xu
- Department of Chemistry, University of New Mexico, Albuquerque, New Mexico 87131
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30
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Costello A, Periyannan G, Yang KW, Crowder MW, Tierney DL. Site-selective binding of Zn(II) to metallo-beta-lactamase L1 from Stenotrophomonas maltophilia. J Biol Inorg Chem 2006; 11:351-8. [PMID: 16489411 DOI: 10.1007/s00775-006-0083-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2005] [Accepted: 01/20/2006] [Indexed: 11/27/2022]
Abstract
Extended X-ray absorption fine structure studies of the metallo-beta-lactamase L1 from Stenotrophomonas maltophilia containing 1 and 2 equiv of Zn(II) and containing 2 equiv of Zn(II) plus hydrolyzed nitrocefin are presented. The data indicate that the first, catalytically dominant metal ion is bound by L1 at the consensus Zn1 site. The data further suggest that binding of the first metal helps preorganize the ligands for binding of the second metal ion. The di-Zn enzyme displays a well-defined metal-metal interaction at 3.42 A. Reaction with the beta-lactam antibiotic nitrocefin results in a product-bound species, in which the ring-opened lactam rotates in the active site to present the S1 sulfur atom of nitrocefin to one of the metal ions for coordination. The product bridges the two metal ions, with a concomitant lengthening of the Zn-Zn interaction to 3.62 A.
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Affiliation(s)
- Alison Costello
- Department of Chemistry, University of New Mexico, 87131, Albuquerque, NM, USA
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31
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Bauer-Siebenlist B, Dechert S, Meyer F. Biomimetic Hydrolysis of Penicillin G Catalyzed by Dinuclear Zinc(II) Complexes: Structure-Activity Correlations in β-Lactamase Model Systems. Chemistry 2005; 11:5343-52. [PMID: 16003817 DOI: 10.1002/chem.200401272] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
A series of highly preorganized pyrazolate-based dinuclear zinc complexes has been studied as functional synthetic analogues of metallo-beta-lactamases, a class of bacterial enzymes that cause serious clinical problems because of their degradation of common beta-lactam antibiotics. We have investigated the hydrolytic cleavage of penicillin G mediated by the different dinuclear zinc complexes, and have deduced structure-activity correlations. While cooperative effects of the adjacent metal ions might be operative, these are found to either enhance or diminish beta-lactamase activity with respect to a single free zinc. Drastic differences in activity are ascribed to a lack of accessible binding sites after incorporation of the substrate within the bimetallic pocket of 2 and 4, whereas partial detachment of hemilabile ligand side arms in 1 and 3 opens up available coordination sites for nucleophile activation and/or for binding and polarisation of the beta-lactam amide oxygen atom. This interpretation has been corroborated by NMR spectroscopic and mass spectrometric evidence as well as by X-ray crystallography of several adducts formed between the pyrazolate-based dinuclear zinc scaffolds and the small substrate analogue oxazetidinylacetate (oaa), 5-7. In all adducts, the carboxylate group of oaa is the primary anchoring site and is nested in a bridging position within the bimetallic pocket. However, zinc binding of the beta-lactam amide oxygen atom has been confirmed crystallographically for the first time in 7, in which additional open-site coordination sites are available.
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Affiliation(s)
- Bernhard Bauer-Siebenlist
- Institut für Anorganische Chemie der Georg-August-Universität Göttingen, Tammannstrasse 4, 37077 Göttingen, Germany
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32
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Weston J. Mode of action of bi- and trinuclear zinc hydrolases and their synthetic analogues. Chem Rev 2005; 105:2151-74. [PMID: 15941211 DOI: 10.1021/cr020057z] [Citation(s) in RCA: 272] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jennie Weston
- Institut für Organische und Makromolekulare Chemie, Friedrich-Schiller-Universität, Jena, Germany.
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33
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Antony J, Piquemal JP, Gresh N. Complexes of thiomandelate and captopril mercaptocarboxylate inhibitors to metallo-β-lactamase by polarizable molecular mechanics. Validation on model binding sites by quantum chemistry. J Comput Chem 2005; 26:1131-47. [PMID: 15937993 DOI: 10.1002/jcc.20245] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Using the polarizable molecular mechanics method SIBFA, we have performed a search for the most stable binding modes of D- and L-thiomandelate to a 104-residue model of the metallo-beta-lactamase from B. fragilis, an enzyme involved in the acquired resistance of bacteria to antibiotics. Energy balances taking into account solvation effects computed with a continuum reaction field procedure indicated the D-isomer to be more stably bound than the L-one, conform to the experimental result. The most stably bound complex has the S(-) ligand bridging monodentately the two Zn(II) cations and one carboxylate O(-) H-bonded to the Asn193 side chain. We have validated the SIBFA energy results by performing additional SIBFA as well as quantum chemical (QC) calculations on small (88 atoms) model complexes extracted from the 104-residue complexes, which include the residues involved in inhibitor binding. Computations were done in parallel using uncorrelated (HF) as well as correlated (DFT, LMP2, MP2) computations, and the comparisons extended to corresponding captopril complexes (Antony et al., J Comput Chem 2002, 23, 1281). The magnitudes of the SIBFA intermolecular interaction energies were found to correctly reproduce their QC counterparts and their trends for a total of twenty complexes.
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Affiliation(s)
- Jens Antony
- Freie Universität Berlin, FB Mathematik und Informatik, Institut für Mathematik II, AG Biocomputing, Arnimallee 2-6, D-14195 Berlin, Germany
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34
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35
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Alcaide B, Sáez E. Diastereoselective Route to Novel Fused or Bridged Tricyclic β-Lactams through Intramolecular Nitrone-Alkene Cycloaddition of 2-Azetidinone-Tethered Alkenylaldehydes - Synthetic Applications to Carbacephams and Cyclic β-Amino Acid Derivatives. European J Org Chem 2005. [DOI: 10.1002/ejoc.200400792] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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36
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Yao L, Sklenak S, Yan H, Cukier RI. A Molecular Dynamics Exploration of the Catalytic Mechanism of Yeast Cytosine Deaminase. J Phys Chem B 2005; 109:7500-10. [PMID: 16851861 DOI: 10.1021/jp044828+] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Yeast cytosine deaminase (yCD), a zinc metalloenzyme of significant biomedical interest, is investigated by a series of molecular dynamics simulations in its free form and complexed with its reactant (cytosine), product (uracil), several reaction intermediates, and an intermediate analogue. Quantum chemical calculations, used to construct a model for the catalytic Zn ion with its ligands (two cysteines, a histidine, and one water) show, by comparison with crystal structure data, that the cysteines are deprotonated and the histidine is monoprotonated. The simulations suggest that Glu64 plays a critical role in the catalysis by yCD. The rotation of the Glu64 side-chain carboxyl group that can be protonated or deprotonated permits it to act as a proton shuttle between the Zn-bound water and cytosine and subsequent reaction intermediates. Free energy methods are used to obtain the barriers for these rotations, and they are sufficiently small to permit rotation on a nanosecond time scale. In the course of the reaction, cytosine reorients to a geometry to favor nucleophilic attack by a Zn-bound hydroxide. A stable position for a reaction product, ammonia, was located in the active site, and the free energy of exchange with a water molecule was evaluated. The simulations also reveal small motions of the C-terminus and the loop that contains Phe114 that may be important for reactant binding and product release.
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Affiliation(s)
- Lishan Yao
- Department of Chemistry, MSU Center for Biological Modeling, Michigan State University, East Lansing, Michigan 48824, USA
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37
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Yamaguchi Y, Kuroki T, Yasuzawa H, Higashi T, Jin W, Kawanami A, Yamagata Y, Arakawa Y, Goto M, Kurosaki H. Probing the role of Asp-120(81) of metallo-beta-lactamase (IMP-1) by site-directed mutagenesis, kinetic studies, and X-ray crystallography. J Biol Chem 2005; 280:20824-32. [PMID: 15788415 DOI: 10.1074/jbc.m414314200] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Metallo-beta-lactamase IMP-1 is a di-Zn(II) metalloenzyme that efficiently hydrolyzes beta-lactam antibiotics. Wild-type (WT) IMP-1 has a conserved Asp-120(81) in the active site, which plays an important role in catalysis. To probe the catalytic role of Asp-120(81) in IMP-1, the IMP-1 mutants, D120(81)A and D120(81)E, were prepared by site-directed mutagenesis, and various kinetics studies were conducted. The IMP-1 mutants exhibited 10(2)-10(4)-fold drops in k(cat) values compared with WT despite the fact that they contained two Zn(II) ions in the active site. To evaluate the acid-base characteristics of Asp-120(81), the pH dependence for hydrolysis was examined by stopped-flow studies. No observable pK(a) values between pH 5 and 9 were found for WT and D120(81)A. The rapid mixing of equimolar amounts of nitrocefin and all enzymes failed to result in the detection of an anion intermediate of nitrocefin at 650 nm. These results suggest that Asp-120(81) of IMP-1 is not a factor in decreasing the pK(a) for the water bridging two Zn(II) ions and is not a proton donor to the anionic intermediate. In the case of D120(81)E, the nitrocefin hydrolysis product, which shows a maximum absorption at 460 nm, was bound to D120(81)E in the protonated form. The three-dimensional structures of D120(81)A and D120(81)E were also determined at 2.0 and 3.0 A resolutions, respectively. In the case of D120(81)E, the Zn-Zn distance was increased by 0.3 A compared with WT, due to the change in the coordination mode of Glu-120(81)OE1 and the positional shift in the conserved His-263(197) at the active site.
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Affiliation(s)
- Yoshihiro Yamaguchi
- Department of Structure-Function Physical Chemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-Honmachi, Kumamoto 862-0973, Japan.
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38
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Free radical synthesis of benzofused tricyclic β-lactams by intramolecular cyclization of 2-azetidinone-tethered haloarenes. Tetrahedron 2005. [DOI: 10.1016/j.tet.2005.01.082] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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39
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Alcaide B, de Murga RM, Pardo C, Rodríguez-Ranera C. Access to enantiopure polycyclic β-lactams by Diels–Alder reaction of novel inner-outer-ring 2-(silyloxy)dienes with a carbacepham skeleton. Tetrahedron Lett 2004. [DOI: 10.1016/j.tetlet.2004.08.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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40
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Garrity JD, Pauff JM, Crowder MW. Probing the dynamics of a mobile loop above the active site of L1, a metallo-beta-lactamase from Stenotrophomonas maltophilia, via site-directed mutagenesis and stopped-flow fluorescence spectroscopy. J Biol Chem 2004; 279:39663-70. [PMID: 15271998 DOI: 10.1074/jbc.m406826200] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A structural feature shared by the metallo-beta-lactamases is a flexible loop of amino acids that extends over their active sites and that has been proposed to move during the catalytic cycle of the enzymes, clamping down on substrate. To probe the movement of this loop (residues 152-164), a site-directed mutant of metallo-beta-lactamase L1 was engineered that contained a Trp residue on the loop to serve as a fluorescent probe. It was necessary first, however, to evaluate the contribution of each native Trp residue to the fluorescence changes observed during the catalytic cycle of wild-type L1. Five site-directed mutants of L1 (W39F, W53F, W204F, W206F, and W269F) were prepared and characterized using metal analyses, CD spectroscopy, steady-state kinetics, stopped-flow fluorescence, and fluorescence titrations. All mutants retained the wild-type tertiary structure and bound Zn(II) at levels comparable with wild type and exhibited only slight (<10-fold) decreases in k(cat) values as compared with wild-type L1 for all substrates tested. Fluorescence studies revealed a single mutant, W39F, to be void of the fluorescence changes observed with wild-type L1 during substrate binding and catalysis. Using W39F as a template, a Trp residue was added to the flexile loop over the active site of L1, to generate the double mutant, W39F/D160W. This double mutant retained all the structural and kinetic characteristics of wild-type L1. Stopped-flow fluorescence and rapid-scanning UV-visible studies revealed the motion of the loop (k(obs) = 27 +/- 2 s(-1)) to be similar to the formation rate of a reaction intermediate (k(obs) = 25 +/- 2 s(-1)).
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Affiliation(s)
- James D Garrity
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, USA
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41
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Rittenhouse RC, Apostoluk WK, Miller JH, Straatsma TP. Characterization of the active site of DNA polymerase beta by molecular dynamics and quantum chemical calculation. Proteins 2004; 53:667-82. [PMID: 14579358 DOI: 10.1002/prot.10451] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
It is well established that the fully formed polymerase active site of the DNA repair enzyme, polymerase beta (pol beta), including two bound Mg2+ cations and the nucleoside triphosphate (dNTP) substrate, exists at only one point in the catalytic cycle just prior to the chemical nucleotidyl transfer step. The structure of the active conformation has been the subject of much interest as it relates to the mechanism of the chemical step and also to the question of fidelity assurance. Although crystal structures of ternary pol beta-(primer-template) DNA-dNTP complexes have provided the main structural features of the active site, they are necessarily incomplete due to intentional alterations (e.g., removal of the 3'OH groups from primer and substrate) needed to obtain a structure from midcycle. Working from the crystal structure closest to the fully formed active site [Protein Data Bank (PDB) code: 1bpy], two molecular dynamics (MD) simulations of the solvated ternary complex were performed: one with the missing 3'OHs restored, via modeling, to the primer and substrate, and the other without restoration of the 3'OHs. The results of the simulations, together with ab initio optimizations on simplified active-site models, indicate that the missing primer 3'OH in the crystal structure is responsible for a significant perturbation in the coordination sphere of the catalytic cation and allow us to suggest several corrections and additions to the active-site structure as observed by crystallography. In addition, the calculations help to resolve questions raised regarding the protonation states of coordinating ligands.
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Affiliation(s)
- Robert C Rittenhouse
- Computational Biosciences Group, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
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42
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Brothers EN, Suarez D, Deerfield DW, Merz KM. PM3-compatible zinc parameters optimized for metalloenzyme active sites. J Comput Chem 2004; 25:1677-92. [PMID: 15362125 DOI: 10.1002/jcc.20086] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Recent studies have shown that semiempirical methods (e.g., PM3 and AM1) for zinc-containing compounds are unreliable for modeling structures containing zinc ions with ligand environments similar to those observed in zinc metalloenzymes. To correct these deficiencies a reparameterization of zinc at the PM3 level was undertaken. In this effort we included frequency corrected B3LYP/6-311G* zinc metalloenzyme ligand environments along with previously utilized experimental data. Average errors for the heats of formation have been reduced from 46.9 kcal/mol (PM3) to 14.2 kcal/mol for this new parameter set, termed ZnB for "Zinc, Biological." In addition, the new parameter sets predict geometries for the Bacillus fragilis active site model and other zinc metalloenzyme mimics that are qualitatively in agreement with high-level ab initio results, something existing parameter sets failed to do.
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Affiliation(s)
- Edward N Brothers
- Department of Chemistry, 152 Davey Laboratory, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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43
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Dal Peraro M, Vila AJ, Carloni P. Substrate binding to mononuclear metallo-β-lactamase from Bacillus cereus. Proteins 2003; 54:412-23. [PMID: 14747990 DOI: 10.1002/prot.10554] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Structure and dynamics of substrate binding (cefotaxime) to the catalytic pocket of the mononuclear zinc-beta-lactamase from Bacillus cereus are investigated by molecular dynamics simulations. The calculations, which are based on the hydrogen-bond pattern recently proposed by Dal Peraro et al. (J Biol Inorg Chem 2002; 7:704-712), are carried out for both the free and the complexed enzyme. In the resting state, active site pattern and temperature B-factors are in agreement with crystallographic data. In the complexed form, cefotaxime is accommodated into a stable orientation in the catalytic pocket within the nanosecond timescale, interacting with the enzyme zinc-bound hydroxide and the surrounding loops. The beta-lactam ring remains stable and very close to the hydroxide nucleophile agent, giving a stable representation of the productive enzyme-substrate complex.
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Affiliation(s)
- Matteo Dal Peraro
- International School for Advanced Studies, SISSA and INFM-DEMOCRITOS, Trieste, Italy
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44
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Garrity JD, Carenbauer AL, Herron LR, Crowder MW. Metal binding Asp-120 in metallo-beta-lactamase L1 from Stenotrophomonas maltophilia plays a crucial role in catalysis. J Biol Chem 2003; 279:920-7. [PMID: 14573595 DOI: 10.1074/jbc.m309852200] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Metallo-beta-lactamase L1 from Stenotrophomonas maltophilia is a dinuclear Zn(II) enzyme that contains a metal-binding aspartic acid in a position to potentially play an important role in catalysis. The presence of this metal-binding aspartic acid appears to be common to most dinuclear, metal-containing, hydrolytic enzymes; particularly those with a beta-lactamase fold. In an effort to probe the catalytic and metal-binding role of Asp-120 in L1, three site-directed mutants (D120C, D120N, and D120S) were prepared and characterized using metal analyses, circular dichroism spectroscopy, and presteady-state and steady-state kinetics. The D120C, D120N, and D120S mutants were shown to bind 1.6 +/- 0.2, 1.8 +/- 0.2, and 1.1 +/- 0.2 mol of Zn(II) per monomer, respectively. The mutants exhibited 10- to 1000-fold drops in kcat values as compared with wild-type L1, and a general trend of activity, wild-type > D120N > D120C and D120S, was observed for all substrates tested. Solvent isotope and pH dependence studies indicate one or more protons in flight, with pKa values outside the range of pH 5-10 (except D120N), during a rate-limiting step for all the enzymes. These data demonstrate that Asp-120 is crucial for L1 to bind its full complement of Zn(II) and subsequently for proper substrate binding to the enzyme. This work also confirms that Asp-120 plays a significant role in catalysis, presumably via hydrogen bonding with water, assisting in formation of the bridging hydroxide/water, and a rate-limiting proton transfer in the hydrolysis reaction.
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Affiliation(s)
- James D Garrity
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, USA
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45
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Dal Peraro M, Vila AJ, Carloni P. Protonation state of Asp120 in the binuclear active site of the metallo-beta-lactamase from Bacteroides fragilis. Inorg Chem 2003; 42:4245-7. [PMID: 12844290 DOI: 10.1021/ic026059j] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The determination of the protonation state of enzyme active sites may be crucial for the investigation of their mechanism of action. In the bizinc beta-lactamase family of enzymes, no consensus has been reached on the protonation state of a fully conserved amino acid present in the active site, Asp120. To address this issue, we carry out here density functional theory (DFT) calculations on large models (based on Bacteroides fragilis X-ray structure) which include the metal coordination polyhedron and groups interacting with it. Our calculations suggest that Asp120 is ionized. The relevance of this finding for site-directed mutagenesis experiments on the 120 position and on the mechanism of action is discussed.
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Affiliation(s)
- Matteo Dal Peraro
- International School for Advanced Studies, SISSA and INFM-DEmocritos MOdeling Center for Research in aTOmistic Simulation, via Beirut 2-4, 34014 Trieste, Italy
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46
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Goto M, Yasuzawa H, Higashi T, Yamaguchi Y, Kawanami A, Mifune S, Mori H, Nakayama H, Harada K, Arakawa Y. Dependence of hydrolysis of beta-lactams with a zinc(II)-beta-lactamase produced from Serratia marcescens (IMP-1) on pH and concentration of zinc(II) ion: dissociation of Zn(II) from IMP-1 in acidic medium. Biol Pharm Bull 2003; 26:589-94. [PMID: 12736495 DOI: 10.1248/bpb.26.589] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The pH dependence for the hydrolysis of beta-lactam antibiotics by a metallo-beta-lactamase (IMP-1) produced from Serratia marcescens was investigated varying the concentration of Zn(II). The activity of IMP-1 for imipenem was decreased at pH less than pH 5.3 without external addition of Zn(II) ions but was recovered with addition of Zn(II). Varying the concentration of external Zn(II), the molar activity of the enzyme, k(obs), that was defined by the velocity of hydrolysis of imipenem/concentration of IMP-1 was expressed by k(obs)=v(init)/[E](T)=k(max)[Zn]/(K(d)+[Zn]) in which K(d) stands for the dissociation constant between Zn(II) and IMP-1. The dissociation constants, K(d), vary with pH; K(d)=840 x 10(-6) M at pH 4.3 and K(d)=0.19 x 10(-6) M at pH 6.0. The plot of -log K(d) against pH showed a straight line having a slope of 4.0 below pH 5.0, showing the existence of four functional groups which may be protonated upon dissociation of Zn(II) ion(s). The k(cat), K(m), and k(cat)/K(m) of hydrolysis of imipenem and cephalothin in the presence of sufficient concentration of Zn(NO(3))(2) for saturation of IMP-1 with Zn(II) showed similar dependency to each other on pH between pH 6.0 and 9.0.
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Affiliation(s)
- Masafumi Goto
- Laboratory of Pharmaceutical Physical Chemistry, Faculty of Pharmaceutical Sciences, Kumamoto University, Honmachi, Japan.
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Joshi SN, Phalgune U, Bhawal B, Deshmukh A. Diastereospecific synthesis of novel [3.6.6.4.7]-fused pentacyclic β-lactams by 6-exo-trig, 7-endo-dig tandem radical cyclization. Tetrahedron Lett 2003. [DOI: 10.1016/s0040-4039(03)00117-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Suárez D, Díaz N, Merz KM. Molecular dynamics simulations of the dinuclear zinc-beta-lactamase from Bacteroides fragilis complexed with imipenem. J Comput Chem 2002; 23:1587-600. [PMID: 12395427 DOI: 10.1002/jcc.10157] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Herein, we present results from MD simulations of the Michaelis complex formed between the dizinc beta-lactamase from B. fragilis and imipenem. We considered two catalytically important configurations, which differ in the presence or absence of a hydroxide bridge connecting the two zinc ions in the active site. The structural and dynamical effects induced by substrate binding, the specific roles of the conserved residues and the zinc-bound water molecules, the near attack conformers of the Michaelis complex, and so forth, are discussed in detail. The relative stability of the two configurations was estimated from QM linear scaling calculations on the enzyme-substrate complex combined with Poisson-Boltzmann electrostatic calculations and normal mode calculations. Importantly, we find that the two configurations have similar energies, indicating that these two structures could readily be interchanged, thereby facilitating catalysis. The configuration with the hydroxide bound to the two zinc ions is predicted to be the resting form of the enzyme, while the configuration without the bridge is the reactive form that was found to place the hydroxide in position to attack the carbonyl of the beta-lactam ring. Thus, we propose that the enzyme initiates catalysis by converting from the hydroxide bridge form into the configuration that lacks the hydroxide bridge. This interconversion increases the nucleophilicity of the hydroxide ion and exposes it to the beta-lactam carbonyl, which ultimately facilitates nucleophilic attack. The implications of the observed modes of binding, the possible influence of mutating the Lys184 and Asn193 residues on substrate binding, and the reaction mechanism are also discussed in detail.
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Affiliation(s)
- Dimas Suárez
- Departamento de Química Física y Analítica, Universidad de Oviedo, Julián Clavería 8, 33006 Oviedo, Asturias, Spain
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Antony J, Gresh N, Olsen L, Hemmingsen L, Schofield CJ, Bauer R. Binding of D- and L-captopril inhibitors to metallo-beta-lactamase studied by polarizable molecular mechanics and quantum mechanics. J Comput Chem 2002; 23:1281-96. [PMID: 12210153 DOI: 10.1002/jcc.10111] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The bacterial Zn2+ metallo-beta-lactamase from B. fragilis is a zinc-enzyme with two potential metal ion binding sites. It cleaves the lactam ring of antibiotics, thus contributing to the acquired resistance of bacteria against antibiotics. The present study bears on the binuclear form of the enzyme. We compare several possible binding modes of captopril, a mercaptocarboxamide inhibitor of several zinc-metalloenzymes. Two diastereoisomers of captopril were considered, with either a D- or an L-proline residue. We have used the polarizable molecular mechanics procedure SIBFA (Sum of Interactions Between Fragments ab initio computed). Two beta-lactamase models were considered, encompassing 104 and 188 residues, respectively. The energy balances included the inter and intramolecular interaction energies as well as the contribution from solvation computed using a continuum reaction field procedure. The thiolate ion of the inhibitor is binding to both metal ions, expelling the bridging solvent molecule from the uncomplexed enzyme. Different competing binding modes of captopril were considered, either where the inhibitor binds in a monodentate mode to the zinc cations only with its thiolate ion, or in bidentate modes involving additional zinc binding by its carboxylate or ketone carbonyl groups. The additional coordination by the inhibitor's carboxylate or carbonyl group always occurs at the zinc ion, which is bound by a histidine, a cysteine, and an aspartate side chain. For both diastereomers, the energy balances favor monodentate binding of captopril via S-. The preference over bidentate binding is small. The interaction energies were recomputed in model sites restricted to captopril, the Zn2+ cations, and their coordinating end side chains from beta-lactamase (98 atoms). The interaction energies and their ranking among competing arrangements were consistent with those computed by ab initio HF and DFT procedures.
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Affiliation(s)
- Jens Antony
- Department of Mathematics and Physics, The Royal Veterinary and Agricultural University, DK-1871 Frederiksberg C, Denmark
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Castillo R, Silla E, Tuñón I. Role of protein flexibility in enzymatic catalysis: quantum mechanical-molecular mechanical study of the deacylation reaction in class A beta-lactamases. J Am Chem Soc 2002; 124:1809-16. [PMID: 11853460 DOI: 10.1021/ja017156z] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We present a theoretical study of a mechanism for the hydrolysis of the acyl-enzyme complex formed by a class A beta-lactamase (TEM1) and an antibiotic (penicillanate), as a part of the process of antibiotic's inactivation by this type of enzymes. In the presented mechanism the carboxylate group of a particular residue (Glu166) activates a water molecule, accepting one of its protons, and afterward transfers this proton directly to the acylated serine residue (Ser70). In our study we employed a quantum mechanics (AM1)-molecular mechanics partition scheme (QM/MM) where all the atoms of the system were allowed to relax. For this purpose we used the GRACE procedure in which part of the system is used to define the Hessian matrix while the rest is relaxed at each step of the stationary structures search. By use of this computational scheme, the hydrolysis of the acyl-enzyme is described as a three-step process: The first step corresponds to the proton transfer from the hydrolytic water molecule to the carboxylate group of Glu166 and the subsequent formation of a tetrahedral adduct as a consequence of the attack of this activated water molecule to the carbonyl carbon atom of the beta-lactam. In the second step, the acyl-enzyme bond is broken, obtaining a negatively charged Ser70. In the last step this residue is protonated by means of a direct proton transfer from Glu166. The large mobility of Glu166, a residue that is placed in a Ohms-loop, is essential to facilitate this mechanism. The geometry of the acyl-enzyme complex shows a large distance between Glu166 and Ser70 and thus, if protein coordinates were kept frozen during the reaction path, it would be difficult to get a direct proton transfer between these two residues. This computational study shows how a flexible treatment suggests the feasibility of a mechanism that could have been discounted on the basis of crystallographic positions.
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Affiliation(s)
- Raquel Castillo
- Departament de Ciències Experimentals, Universitat Jaume I, 12080 Castelló, Spain
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