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Serafim LF, Jayasinghe-Arachchige VM, Wang L, Rathee P, Yang J, Moorkkannur N S, Prabhakar R. Distinct chemical factors in hydrolytic reactions catalyzed by metalloenzymes and metal complexes. Chem Commun (Camb) 2023. [PMID: 37366367 DOI: 10.1039/d3cc01380d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
The selective hydrolysis of the extremely stable phosphoester, peptide and ester bonds of molecules by bio-inspired metal-based catalysts (metallohydrolases) is required in a wide range of biological, biotechnological and industrial applications. Despite the impressive advances made in the field, the ultimate goal of designing efficient enzyme mimics for these reactions is still elusive. Its realization will require a deeper understanding of the diverse chemical factors that influence the activities of both natural and synthetic catalysts. They include catalyst-substrate complexation, non-covalent interactions and the electronic nature of the metal ion, ligand environment and nucleophile. Based on our computational studies, their roles are discussed for several mono- and binuclear metallohydrolases and their synthetic analogues. Hydrolysis by natural metallohydrolases is found to be promoted by a ligand environment with low basicity, a metal bound water and a heterobinuclear metal center (in binuclear enzymes). Additionally, peptide and phosphoester hydrolysis is dominated by two competing effects, i.e. nucleophilicity and Lewis acid activation, respectively. In synthetic analogues, hydrolysis is facilitated by the inclusion of a second metal center, hydrophobic effects, a biological metal (Zn, Cu and Co) and a terminal hydroxyl nucleophile. Due to the absence of the protein environment, hydrolysis by these small molecules is exclusively influenced by nucleophile activation. The results gleaned from these studies will enhance the understanding of fundamental principles of multiple hydrolytic reactions. They will also advance the development of computational methods as a predictive tool to design more efficient catalysts for hydrolysis, Diels-Alder reaction, Michael addition, epoxide opening and aldol condensation.
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Affiliation(s)
- Leonardo F Serafim
- Department of Chemistry, University of Miami, Coral Gables, FL 33146, USA.
| | | | - Lukun Wang
- Department of Chemistry, University of Miami, Coral Gables, FL 33146, USA.
| | - Parth Rathee
- Department of Chemistry, University of Miami, Coral Gables, FL 33146, USA.
| | - Jiawen Yang
- Department of Chemistry, University of Miami, Coral Gables, FL 33146, USA.
| | | | - Rajeev Prabhakar
- Department of Chemistry, University of Miami, Coral Gables, FL 33146, USA.
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2
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The Effects of the Metal Ion Substitution into the Active Site of Metalloenzymes: A Theoretical Insight on Some Selected Cases. Catalysts 2020. [DOI: 10.3390/catal10091038] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
A large number of enzymes need a metal ion to express their catalytic activity. Among the different roles that metal ions can play in the catalytic event, the most common are their ability to orient the substrate correctly for the reaction, to exchange electrons in redox reactions, to stabilize negative charges. In many reactions catalyzed by metal ions, they behave like the proton, essentially as Lewis acids but are often more effective than the proton because they can be present at high concentrations at neutral pH. In an attempt to adapt to drastic environmental conditions, enzymes can take advantage of the presence of many metal species in addition to those defined as native and still be active. In fact, today we know enzymes that contain essential bulk, trace, and ultra-trace elements. In this work, we report theoretical results obtained for three different enzymes each of which contains different metal ions, trying to highlight any differences in their working mechanism as a function of the replacement of the metal center at the active site.
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3
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Theoretical Study of VX Hydrolysis Mechanism Catalyzed by Phosphotriesterase Mutant H254R. ChemistrySelect 2020. [DOI: 10.1002/slct.202002112] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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4
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Sharma G, Jayasinghe-Arachchige VM, Hu Q, Schenk G, Prabhakar R. Effect of Chemically Distinct Substrates on the Mechanism and Reactivity of a Highly Promiscuous Metallohydrolase. ACS Catal 2020. [DOI: 10.1021/acscatal.9b04847] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Gaurav Sharma
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | | | - Qiaoyu Hu
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | - Gerhard Schenk
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Rajeev Prabhakar
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
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Yan J, Chen S. How To Produce Methane Precursor in the Upper Ocean by An Untypical Non‐Heme Fe‐Dependent Methylphosphonate Synthase? Chemphyschem 2020; 21:385-396. [DOI: 10.1002/cphc.202000025] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Indexed: 12/19/2022]
Affiliation(s)
- Ji‐Fan Yan
- Key Laboratory of Cluster Science of Ministry of Education School of Chemistry and Chemical Engineering Beijing Institute of Technology Beijing 100081 China
| | - Shi‐Lu Chen
- Key Laboratory of Cluster Science of Ministry of Education School of Chemistry and Chemical Engineering Beijing Institute of Technology Beijing 100081 China
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6
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Guanidine- and purine-functionalized ligands of FeIIIZnII complexes: effects on the hydrolysis of DNA. J Biol Inorg Chem 2019; 24:675-691. [DOI: 10.1007/s00775-019-01680-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 06/21/2019] [Indexed: 01/01/2023]
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7
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Marino T, Prejanò M, Russo N. How Metal Coordination in the Ca-, Ce-, and Eu-Containing Methanol Dehydrogenase Enzymes Can Influence the Catalysis: A Theoretical Point of View. TRANSITION METALS IN COORDINATION ENVIRONMENTS 2019. [DOI: 10.1007/978-3-030-11714-6_16] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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8
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Prejanò M, Marino T, Russo N. QM Cluster or QM/MM in Computational Enzymology: The Test Case of LigW-Decarboxylase. Front Chem 2018; 6:249. [PMID: 30003076 PMCID: PMC6031855 DOI: 10.3389/fchem.2018.00249] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 06/08/2018] [Indexed: 11/13/2022] Open
Abstract
The catalytic mechanism of the decarboxylation of 5-carboxyvanillate by LigW producing vanillic acid has been studied by using QM cluster and hybrid QM/MM methodologies. In the QM cluster model, the environment of a small QM model is treated with a bulky potential while two QM/MM models studies include partial and full protein with and without explicitly treated water solvent. The studied reaction involves two sequential steps: the protonation of the carbon of the 5-carboxy-vanillate substrate and the decarboxylation of the intermediate from which results deprotonated vanillic acid as product. The structures and energetics obtained by using three structural models and two density functionals are quite consistent to each other. This indicates that the small QM cluster model of the presently considered enzymatic reaction is appropriate enough and the reaction is mainly influenced by the active site.
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Affiliation(s)
- Mario Prejanò
- Dipartimento Di Chimica e Tecnologie Chimiche, Università della Calabria, Rende, Italy
| | - Tiziana Marino
- Dipartimento Di Chimica e Tecnologie Chimiche, Università della Calabria, Rende, Italy
| | - Nino Russo
- Dipartimento Di Chimica e Tecnologie Chimiche, Università della Calabria, Rende, Italy
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9
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Prejanò M, Marino T, Russo N. How Can Methanol Dehydrogenase from Methylacidiphilum fumariolicum
Work with the Alien CeIII
Ion in the Active Center? A Theoretical Study. Chemistry 2017; 23:8652-8657. [DOI: 10.1002/chem.201700381] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Indexed: 01/27/2023]
Affiliation(s)
- Mario Prejanò
- Dipartimento di Chimica e Tecnologie Chimiche; Università della Calabria; 87036 Arcavacata di Rende (CS) Italy
| | - Tiziana Marino
- Dipartimento di Chimica e Tecnologie Chimiche; Università della Calabria; 87036 Arcavacata di Rende (CS) Italy
| | - Nino Russo
- Dipartimento di Chimica e Tecnologie Chimiche; Università della Calabria; 87036 Arcavacata di Rende (CS) Italy
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10
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Brás NF, Ferreira P, Calixto AR, Jaspars M, Houssen W, Naismith JH, Fernandes PA, Ramos MJ. The Catalytic Mechanism of the Marine-Derived Macrocyclase PatGmac. Chemistry 2016; 22:13089-97. [PMID: 27389424 DOI: 10.1002/chem.201601670] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2016] [Indexed: 11/11/2022]
Abstract
Cyclic peptides are a class of compounds with high therapeutic potential, possessing bioactivities including antitumor and antiviral (including anti-HIV). Despite their desirability, efficient design and production of these compounds has not been achieved to date. The catalytic mechanism of patellamide macrocyclization by the PatG macrocyclase domain has been computationally investigated by using quantum mechanics/molecular mechanics methodology, specifically ONIOM(M06/6-311++G(2d,2p):ff94//B3LYP/6-31G(d):ff94). The mechanism proposed herein begins with a proton transfer from Ser783 to His 618 and from the latter to Asp548. Nucleophilic attack of Ser783 on the substrate leads to the formation of an acyl-enzyme covalent complex. The leaving group Ala-Tyr-Asp-Gly (AYDG) of the substrate is protonated by the substrate's N terminus, leading to the breakage of the P1-P1' bond. Finally, the substrate's N terminus attacks the P1 residue, decomposing the acyl-enzyme complex forming the macrocycle. The formation and decomposition of the acyl-enzyme complex have the highest activation free energies (21.1 kcal mol(-1) and 19.8 kcal mol(-1) respectively), typical of serine proteases. Understanding the mechanism behind the macrocyclization of patellamides will be important to the application of the enzymes in the pharmaceutical and biotechnological industries.
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Affiliation(s)
- Natércia F Brás
- UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
| | - Pedro Ferreira
- UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
| | - Ana R Calixto
- UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
| | - Marcel Jaspars
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Old Aberdeen, AB24 3UE, Scotland, UK
| | - Wael Houssen
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, AB25 2ZD, Scotland, UK.,Pharmacognosy Department, Faculty of Pharmacy, Mansoura University, Mansoura, 35516, Egypt
| | - James H Naismith
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, Scotland, UK
| | - Pedro A Fernandes
- UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
| | - Maria J Ramos
- UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal.
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11
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Esteves LF, Rey NA, Dos Santos HF, Costa LAS. Theoretical Proposal for the Whole Phosphate Diester Hydrolysis Mechanism Promoted by a Catalytic Promiscuous Dinuclear Copper(II) Complex. Inorg Chem 2016; 55:2806-18. [DOI: 10.1021/acs.inorgchem.5b02604] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lucas F. Esteves
- NEQC (Núcleo de Estudos em Quı́mica
Computacional), Departamento de Quı́mica, Instituto de
Ciências Exatas (ICE), Universidade Federal de Juiz de Fora, Campus Universitário
Martelos, 36036-900 Juiz de Fora, Minas Gerais, Brazil
| | - Nicolás A. Rey
- Laboratório
de Síntese Orgânica e Quı́mica de Coordenação
Aplicada a Sistemas Biológicos (LABSO-BIO), Departamento de
Quı́mica, Centro Técnico Científico (CTC), PUC-Rio, 22453-900 Rio de Janeiro, Rio
de Janeiro, Brazil
| | - Hélio F. Dos Santos
- NEQC (Núcleo de Estudos em Quı́mica
Computacional), Departamento de Quı́mica, Instituto de
Ciências Exatas (ICE), Universidade Federal de Juiz de Fora, Campus Universitário
Martelos, 36036-900 Juiz de Fora, Minas Gerais, Brazil
| | - Luiz Antônio S. Costa
- NEQC (Núcleo de Estudos em Quı́mica
Computacional), Departamento de Quı́mica, Instituto de
Ciências Exatas (ICE), Universidade Federal de Juiz de Fora, Campus Universitário
Martelos, 36036-900 Juiz de Fora, Minas Gerais, Brazil
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12
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Liao RZ, Siegbahn PEM. Phosphate Hydrolysis by the Fe2–Ca3-Dependent Alkaline Phosphatase PhoX: Mechanistic Insights from DFT calculations. Inorg Chem 2015; 54:11941-7. [DOI: 10.1021/acs.inorgchem.5b02268] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Rong-Zhen Liao
- Key Laboratory of Material Chemistry for
Energy Conversion and Storage, Ministry of Education, School of Chemistry
and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Per E. M. Siegbahn
- Department
of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-10691 Stockholm, Sweden
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13
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Alberto ME, Pinto G, Russo N, Toscano M. Triesterase and Promiscuous Diesterase Activities of a Di-CoII-Containing Organophosphate Degrading Enzyme Reaction Mechanisms. Chemistry 2015; 21:3736-45. [DOI: 10.1002/chem.201405593] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Indexed: 01/08/2023]
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14
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Araújo AR, Ribeiro AJM, Fernandes PA, Ramos MJ. Catalytic Mechanism of Retroviral Integrase for the Strand Transfer Reaction Explored by QM/MM Calculations. J Chem Theory Comput 2014; 10:5458-66. [DOI: 10.1021/ct500570g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Ana R. Araújo
- REQUIMTE,
Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - António J. M. Ribeiro
- REQUIMTE,
Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Pedro A. Fernandes
- REQUIMTE,
Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Maria J. Ramos
- REQUIMTE,
Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
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15
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Piazzetta P, Marino T, Russo N. Insight into the promiscuous activity of human carbonic anhydrase against the cyanic acid substrate from a combined QM and QM/MM investigation. Phys Chem Chem Phys 2014; 16:16671-6. [DOI: 10.1039/c4cp02363c] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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16
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Ribeiro JV, Cerqueira NMFSA, Fernandes PA, Ramos MJ. chem-path-tracker: An Automated Tool to Analyze Chemical Motifs in Molecular Structures. Chem Biol Drug Des 2014; 84:44-53. [DOI: 10.1111/cbdd.12349] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Revised: 04/16/2014] [Accepted: 04/20/2014] [Indexed: 01/25/2023]
Affiliation(s)
- João V. Ribeiro
- REQUIMTE; Departamento de Química e Bioquímica; Faculdade de Ciências; Universidade do Porto; Rua do Campo Alegre s/n Porto 4169-007 Portugal
| | - N. M. F. S. A. Cerqueira
- REQUIMTE; Departamento de Química e Bioquímica; Faculdade de Ciências; Universidade do Porto; Rua do Campo Alegre s/n Porto 4169-007 Portugal
| | - Pedro A. Fernandes
- REQUIMTE; Departamento de Química e Bioquímica; Faculdade de Ciências; Universidade do Porto; Rua do Campo Alegre s/n Porto 4169-007 Portugal
| | - Maria J. Ramos
- REQUIMTE; Departamento de Química e Bioquímica; Faculdade de Ciências; Universidade do Porto; Rua do Campo Alegre s/n Porto 4169-007 Portugal
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17
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Analyses of cobalt-ligand and potassium-ligand bond lengths in metalloproteins: trends and patterns. J Mol Model 2014; 20:2271. [PMID: 24850495 DOI: 10.1007/s00894-014-2271-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 04/23/2014] [Indexed: 10/25/2022]
Abstract
Cobalt and potassium are biologically important metal elements that are present in a large array of proteins. Cobalt is mostly found in vivo associated with a corrin ring, which represents the core of the vitamin B12 molecule. Potassium is the most abundant metal in the cytosol, and it plays a crucial role in maintaining membrane potential as well as correct protein function. Here, we report a thorough analysis of the geometric properties of cobalt and potassium coordination spheres that was performed with high resolution on a representative set of structures from the Protein Data Bank and complemented by quantum mechanical calculations realized at the DFT level of theory (B3LYP/ SDD) on mononuclear model systems. The results allowed us to draw interesting conclusions on the structural characteristics of both Co and K centers, and to evaluate the importance of effects such as their association energies and intrinsic thermodynamic stabilities. Overall, the results obtained provide useful data for enhancing the atomic models normally applied in theoretical and computational studies of Co or K proteins performed at the quantum mechanical level, and for developing molecular mechanical parameters for treating Co or K coordination spheres in molecular mechanics or molecular dynamics studies.
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Ribeiro AJM, Alberto ME, Ramos MJ, Fernandes PA, Russo N. The Catalytic Mechanism of Protein Phosphatase 5 Established by DFT Calculations. Chemistry 2013; 19:14081-9. [DOI: 10.1002/chem.201301565] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Indexed: 11/07/2022]
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Marino T, Russo N, Toscano M. What occurs by replacing Mn2+ with Co2+ in human arginase I: first-principles computational analysis. Inorg Chem 2012; 52:655-9. [PMID: 23273171 DOI: 10.1021/ic301703t] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The reaction mechanism of the dinuclear cobalt enzyme arginase is investigated using density functional theory. As an arginase-containing binuclear Mn(2)(2+) cluster, it catalyzes the hydrolysis of L-arginine in L-ornithine and urea. The bridging hydroxide is capable of performing nucleophilic attack on the iminium carbon ion from its bridging position, resulting in the formation of a tetrahedral intermediate, as was already obtained in a previous theoretical study on the manganese enzyme. Our theoretical investigation allows us to obtain an accurate potential energy profile and confirms that the coordination mode of the substrate to the dimetallic center is quite similar to that present in the manganese enzyme. In agreement with the experimental observations, our results show that both Mn- and Co-containing enzymes catalyze the same reaction with quite comparable energy barriers.
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Affiliation(s)
- Tiziana Marino
- Dipartimento di Chimica and Centro di Calcolo ad Alte Prestazioni per Elaborazioni Parallele e Distribuite, Universitá della Calabria, I-87030 Arcavacata di Rende (CS), Italy.
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20
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Marino T, Russo N, Toscano M. Catalytic Mechanism of the Arylsulfatase Promiscuous Enzyme fromPseudomonas Aeruginosa. Chemistry 2012; 19:2185-92. [DOI: 10.1002/chem.201201943] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Revised: 11/06/2012] [Indexed: 11/11/2022]
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21
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Comba P, Gahan LR, Mereacre V, Hanson GR, Powell AK, Schenk G, Zajaczkowski-Fischer M. Spectroscopic Characterization of the Active FeIIIFeIII and FeIIIFeII Forms of a Purple Acid Phosphatase Model System. Inorg Chem 2012; 51:12195-209. [DOI: 10.1021/ic301347t] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Peter Comba
- Universität Heidelberg, Anorganisch-Chemisches Institut, INF 270,
D-69120 Heidelberg, Germany
| | - Lawrence R. Gahan
- School of Chemistry and Molecular
Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Valeriu Mereacre
- Institut für Anorganische
Chemie, Karlsruher Institut für Technologie, Enesserstrasse 15, D-76131 Karlsruhe, Germany
| | - Graeme R. Hanson
- Centre for Advanced Imaging, The University of Queensland, Brisbane, Queensland
4072, Australia
| | - Annie K. Powell
- Institut für Anorganische
Chemie, Karlsruher Institut für Technologie, Enesserstrasse 15, D-76131 Karlsruhe, Germany
| | - Gerhard Schenk
- School of Chemistry and Molecular
Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
- Department
of Chemistry, National University of Ireland, Maynooth, Co. Kildare,
Ireland
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22
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Ribeiro AJM, Ramos MJ, Fernandes PA. The Catalytic Mechanism of HIV-1 Integrase for DNA 3′-End Processing Established by QM/MM Calculations. J Am Chem Soc 2012; 134:13436-47. [DOI: 10.1021/ja304601k] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- António J. M. Ribeiro
- REQUIMTE, Departamento de Química e Bioquímica,
Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Maria J. Ramos
- REQUIMTE, Departamento de Química e Bioquímica,
Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Pedro A. Fernandes
- REQUIMTE, Departamento de Química e Bioquímica,
Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
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23
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Comba P, Gahan LR, Hanson GR, Mereacre V, Noble CJ, Powell AK, Prisecaru I, Schenk G, Zajaczkowski-Fischer M. Monoesterase activity of a purple acid phosphatase mimic with a cyclam platform. Chemistry 2012; 18:1700-10. [PMID: 22234833 DOI: 10.1002/chem.201100229] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2011] [Revised: 09/26/2011] [Indexed: 12/22/2022]
Abstract
The synthesis and characterization of a novel dinucleating ligand L (L=4,11-dimethyl-1,8-bis{2-[N-(di-2-pyridylmethyl)amino]ethyl}cyclam) and its μ-oxo-bridged diferric complex [(H(2)L){Fe(III)(2)(O)}(Cl)(4)](2+) are reported. This diiron(III) complex is the first example of a truly functional purple acid phosphatase (PAP) mimic as it accelerates the hydrolysis of the activated phosphomonoester 2,4-dinitrophenyl phosphate (DNPP). The spectroscopic and kinetic data indicate that only substrates that are monodentately bound to one of the two ferric ions can be attacked by a suitable nucleophile. This is, most probably, a terminal iron(III)-bound hydroxide. DFT calculations support this assumption and also highlight the importance of secondary interactions, exerted by the protonated cyclam platform, for the positioning and activation of the iron(III)-bound substrate. Similar effects are postulated in the native enzyme but addressed in PAP mimics for the first time.
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Affiliation(s)
- Peter Comba
- Anorganisch-Chemisches Institut, Universität Heidelberg, INF 270, 69120 Heidelberg, Germany.
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24
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Alberto ME, Marino T, Russo N, Sicilia E, Toscano M. The performance of density functional based methods in the description of selected biological systems and processes. Phys Chem Chem Phys 2012; 14:14943-53. [DOI: 10.1039/c2cp41836c] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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25
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Sousa SF, Fernandes PA, Ramos MJ. Computational enzymatic catalysis – clarifying enzymatic mechanisms with the help of computers. Phys Chem Chem Phys 2012; 14:12431-41. [DOI: 10.1039/c2cp41180f] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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26
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Passos Ó, Fernandes PA, Ramos MJ. QM/MM Study of the Catalytic Mechanism of GalNAc Removal from GM2 Ganglioside Catalyzed by Human β-HexosaminidaseA. J Phys Chem B 2011; 115:14751-9. [DOI: 10.1021/jp205826n] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Óscar Passos
- Requimte, Faculty of Sciences, Porto University, Rua do Campo Alegre S/N, 4169-007 Porto, Portugal
| | | | - Maria João Ramos
- Requimte, Faculty of Sciences, Porto University, Rua do Campo Alegre S/N, 4169-007 Porto, Portugal
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27
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Amata O, Marino T, Russo N, Toscano M. A Proposal for Mitochondrial Processing Peptidase Catalytic Mechanism. J Am Chem Soc 2011; 133:17824-31. [DOI: 10.1021/ja207065v] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Orazio Amata
- Dipartimento di Chimica and Centro di Calcolo ad Alte Prestazioni per Elaborazioni Parallele e Distribuite-Centro d'Eccellenza MURST, Universita' della Calabria, I-87030 Arcavacata di Rende (CS), Italy
| | - Tiziana Marino
- Dipartimento di Chimica and Centro di Calcolo ad Alte Prestazioni per Elaborazioni Parallele e Distribuite-Centro d'Eccellenza MURST, Universita' della Calabria, I-87030 Arcavacata di Rende (CS), Italy
| | - Nino Russo
- Dipartimento di Chimica and Centro di Calcolo ad Alte Prestazioni per Elaborazioni Parallele e Distribuite-Centro d'Eccellenza MURST, Universita' della Calabria, I-87030 Arcavacata di Rende (CS), Italy
| | - Marirosa Toscano
- Dipartimento di Chimica and Centro di Calcolo ad Alte Prestazioni per Elaborazioni Parallele e Distribuite-Centro d'Eccellenza MURST, Universita' della Calabria, I-87030 Arcavacata di Rende (CS), Italy
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28
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Oliveira EF, Cerqueira NMFSA, Fernandes PA, Ramos MJ. Mechanism of Formation of the Internal Aldimine in Pyridoxal 5′-Phosphate-Dependent Enzymes. J Am Chem Soc 2011; 133:15496-505. [DOI: 10.1021/ja204229m] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Eduardo F. Oliveira
- REQUIMTE, Faculdade de Ciências, Universidade do Porto, Rua Campo Alegre 687, 4169-007 Porto, Portugal
| | | | - Pedro A. Fernandes
- REQUIMTE, Faculdade de Ciências, Universidade do Porto, Rua Campo Alegre 687, 4169-007 Porto, Portugal
| | - Maria J. Ramos
- REQUIMTE, Faculdade de Ciências, Universidade do Porto, Rua Campo Alegre 687, 4169-007 Porto, Portugal
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29
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Copper(II) and zinc(II) chemistry of a new hexadentate cyclam-based bis-di-2-pyridylmethanamine ligand. J INCL PHENOM MACRO 2011. [DOI: 10.1007/s10847-011-9967-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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30
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Alberto ME, Leopoldini M, Russo N. Can Human Prolidase Enzyme Use Different Metals for Full Catalytic Activity? Inorg Chem 2011; 50:3394-403. [DOI: 10.1021/ic1022517] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Marta E. Alberto
- Dipartimento di Chimica and Centro di Calcolo ad Alte Prestazioni per Elaborazioni Parallele e Distribuite-Centro d'Eccellenza MIUR, Universita' della Calabria, I-87030 Arcavacata di Rende (CS), Italy
| | - Monica Leopoldini
- Dipartimento di Chimica and Centro di Calcolo ad Alte Prestazioni per Elaborazioni Parallele e Distribuite-Centro d'Eccellenza MIUR, Universita' della Calabria, I-87030 Arcavacata di Rende (CS), Italy
| | - Nino Russo
- Dipartimento di Chimica and Centro di Calcolo ad Alte Prestazioni per Elaborazioni Parallele e Distribuite-Centro d'Eccellenza MIUR, Universita' della Calabria, I-87030 Arcavacata di Rende (CS), Italy
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31
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Amata O, Marino T, Russo N, Toscano M. Catalytic activity of a ζ-class zinc and cadmium containing carbonic anhydrase. Compared work mechanisms. Phys Chem Chem Phys 2011; 13:3468-77. [DOI: 10.1039/c0cp01053g] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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