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Tripathi A, Dubey KD. The mechanistic insights into different aspects of promiscuity in metalloenzymes. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2024; 141:23-66. [PMID: 38960476 DOI: 10.1016/bs.apcsb.2023.12.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Abstract
Enzymes are nature's ultimate machinery to catalyze complex reactions. Though enzymes are evolved to catalyze specific reactions, they also show significant promiscuity in reactions and substrate selection. Metalloenzymes contain a metal ion or metal cofactor in their active site, which is crucial in their catalytic activity. Depending on the metal and its coordination environment, the metal ion or cofactor may function as a Lewis acid or base and a redox center and thus can catalyze a plethora of natural reactions. In fact, the versatility in the oxidation state of the metal ions provides metalloenzymes with a high level of catalytic adaptability and promiscuity. In this chapter, we discuss different aspects of promiscuity in metalloenzymes by using several recent experimental and theoretical works as case studies. We start our discussion by introducing the concept of promiscuity and then we delve into the mechanistic insight into promiscuity at the molecular level.
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Affiliation(s)
- Ankita Tripathi
- Department of Chemistry, School of Natural Science, Shiv Nadar Institution of Eminence, Greater Noida, Uttar Pradesh, India
| | - Kshatresh Dutta Dubey
- Department of Chemistry, School of Natural Science, Shiv Nadar Institution of Eminence, Greater Noida, Uttar Pradesh, India.
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Ciardullo G, Parise A, Prejanò M, Marino T. Viral RNA Replication Suppression of SARS-CoV-2: Atomistic Insights into Inhibition Mechanisms of RdRp Machinery by ddhCTP. J Chem Inf Model 2024; 64:1593-1604. [PMID: 38412057 DOI: 10.1021/acs.jcim.3c01919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
The nonstructural protein 12, known as RNA-dependent RNA polymerase (RdRp), is essential for both replication and repair of the viral genome. The RdRp of SARS-CoV-2 has been used as a promising candidate for drug development since the inception of the COVID-19 spread. In this work, we performed an in silico investigation on the insertion of the naturally modified pyrimidine nucleobase ddhCTP into the SARS-CoV-2 RdRp active site, in a comparative analysis with the natural one (CTP). The modification in ddhCTP involves the removal of the 3'-hydroxyl group that prevents the addition of subsequent nucleotides into the nascent strand, acting as an RNA chain terminator inhibitor. Quantum mechanical investigations helped to shed light on the mechanistic source of RdRp activity on the selected nucleobases, and comprehensive all-atom simulations provided insights about the structural rearrangements occurring in the active-site region when inorganic pyrophosphate (PPi) is formed. Subsequently, the intricate pathways for the release of PPi, the catalytic product of RdRp, were investigated using Umbrella Sampling simulations. The results are in line with the available experimental data and contribute to a more comprehensive point of view on such an important viral enzyme.
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Affiliation(s)
- Giada Ciardullo
- Dipartimento di Chimica E Tecnologie Chimiche, Laboratorio PROMOCS Cubo 14C, Università della Calabria, RENDE (CS) I-87036, Italy
| | - Angela Parise
- Consiglio Nazionale Delle Ricerche (CNR)-IOM C/O International School for Advanced Studies (SISSA/ISAS), Via Bonomea 265, Trieste 34136, Italy
| | - Mario Prejanò
- Dipartimento di Chimica E Tecnologie Chimiche, Laboratorio PROMOCS Cubo 14C, Università della Calabria, RENDE (CS) I-87036, Italy
| | - Tiziana Marino
- Dipartimento di Chimica E Tecnologie Chimiche, Laboratorio PROMOCS Cubo 14C, Università della Calabria, RENDE (CS) I-87036, Italy
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3
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QM and QM/MM study on inhibition mechanism of polyphenolic compounds as non-classical inhibitors of α-human carbonic anhydrase (II). Theor Chem Acc 2021. [DOI: 10.1007/s00214-021-02839-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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4
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Parise A, Romeo I, Russo N, Marino T. The Se-S Bond Formation in the Covalent Inhibition Mechanism of SARS-CoV-2 Main Protease by Ebselen-like Inhibitors: A Computational Study. Int J Mol Sci 2021; 22:9792. [PMID: 34575955 PMCID: PMC8467846 DOI: 10.3390/ijms22189792] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/03/2021] [Accepted: 09/07/2021] [Indexed: 12/20/2022] Open
Abstract
The inhibition mechanism of the main protease (Mpro) of SARS-CoV-2 by ebselen (EBS) and its analog with a hydroxyl group at position 2 of the benzisoselenazol-3(2H)-one ring (EBS-OH) was studied by using a density functional level of theory. Preliminary molecular dynamics simulations on the apo form of Mpro were performed taking into account both the hydrogen donor and acceptor natures of the Nδ and Nε of His41, a member of the catalytic dyad. The potential energy surfaces for the formation of the Se-S covalent bond mediated by EBS and EBS-OH on Mpro are discussed in detail. The EBS-OH shows a distinctive behavior with respect to EBS in the formation of the noncovalent complex. Due to the presence of canonical H-bonds and noncanonical ones involving less electronegative atoms, such as sulfur and selenium, the influence on the energy barriers and reaction energy of the Minnesota hybrid meta-GGA functionals M06, M06-2X and M08HX, and the more recent range-separated hybrid functional wB97X were also considered. The knowledge of the inhibition mechanism of Mpro by the small protease inhibitors EBS or EBS-OH can enlarge the possibilities for designing more potent and selective inhibitor-based drugs to be used in combination with other antiviral therapies.
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Affiliation(s)
- Angela Parise
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, Via Pietro Bucci, 87036 Arcavacata di Rende, CS, Italy; (A.P.); (I.R.); (N.R.)
- Institut de Chimie Physique UMR8000, Université Paris-Saclay, CNRS, 91405 Orsay, France
| | - Isabella Romeo
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, Via Pietro Bucci, 87036 Arcavacata di Rende, CS, Italy; (A.P.); (I.R.); (N.R.)
| | - Nino Russo
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, Via Pietro Bucci, 87036 Arcavacata di Rende, CS, Italy; (A.P.); (I.R.); (N.R.)
| | - Tiziana Marino
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, Via Pietro Bucci, 87036 Arcavacata di Rende, CS, Italy; (A.P.); (I.R.); (N.R.)
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5
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Fu Y, Fan F, Zhang Y, Wang B, Cao Z. Conformational Change of H64 and Substrate Transportation: Insight Into a Full Picture of Enzymatic Hydration of CO 2 by Carbonic Anhydrase. Front Chem 2021; 9:706959. [PMID: 34307302 PMCID: PMC8299336 DOI: 10.3389/fchem.2021.706959] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 06/28/2021] [Indexed: 11/13/2022] Open
Abstract
The enzymatic hydration of CO2 into HCO3 - by carbonic anhydrase (CA) is highly efficient and environment-friendly measure for CO2 sequestration. Here extensive MM MD and QM/MM MD simulations were used to explore the whole enzymatic process, and a full picture of the enzymatic hydration of CO2 by CA was achieved. Prior to CO2 hydration, the proton transfer from the water molecule (WT1) to H64 is the rate-limiting step with the free energy barrier of 10.4 kcal/mol, which leads to the ready state with the Zn-bound OH-. The nucleophilic attack of OH- on CO2 produces HCO3 - with the free energy barrier of 4.4 kcal/mol and the free energy release of about 8.0 kcal/mol. Q92 as the key residue manipulates both CO2 transportation to the active site and release of HCO3 -. The unprotonated H64 in CA prefers in an inward orientation, while the outward conformation is favorable energetically for its protonated counterpart. The conformational transition of H64 between inward and outward correlates with its protonation state, which is mediated by the proton transfer and the product release. The whole enzymatic cycle has the free energy span of 10.4 kcal/mol for the initial proton transfer step and the free energy change of -6.5 kcal/mol. The mechanistic details provide a comprehensive understanding of the entire reversible conversion of CO2 into bicarbonate and roles of key residues in chemical and nonchemical steps for the enzymatic hydration of CO2.
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Affiliation(s)
- Yuzhuang Fu
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| | - Fangfang Fan
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, China
| | - Yuwei Zhang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| | - Zexing Cao
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
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6
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QM study of carbon dioxide (CO2) and carbonyl sulfide (COS) degradation by cluster model of Carbonic anhydrase enzyme. COMPUT THEOR CHEM 2021. [DOI: 10.1016/j.comptc.2021.113188] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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7
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Spinello A, Borišek J, Pavlin M, Janoš P, Magistrato A. Computing Metal-Binding Proteins for Therapeutic Benefit. ChemMedChem 2021; 16:2034-2049. [PMID: 33740297 DOI: 10.1002/cmdc.202100109] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Indexed: 01/18/2023]
Abstract
Over one third of biomolecules rely on metal ions to exert their cellular functions. Metal ions can play a structural role by stabilizing the structure of biomolecules, a functional role by promoting a wide variety of biochemical reactions, and a regulatory role by acting as messengers upon binding to proteins regulating cellular metal-homeostasis. These diverse roles in biology ascribe critical implications to metal-binding proteins in the onset of many diseases. Hence, it is of utmost importance to exhaustively unlock the different mechanistic facets of metal-binding proteins and to harness this knowledge to rationally devise novel therapeutic strategies to prevent or cure pathological states associated with metal-dependent cellular dysfunctions. In this compendium, we illustrate how the use of a computational arsenal based on docking, classical, and quantum-classical molecular dynamics simulations can contribute to extricate the minutiae of the catalytic, transport, and inhibition mechanisms of metal-binding proteins at the atomic level. This knowledge represents a fertile ground and an essential prerequisite for selectively targeting metal-binding proteins with small-molecule inhibitors aiming to (i) abrogate deregulated metal-dependent (mis)functions or (ii) leverage metal-dyshomeostasis to selectively trigger harmful cells death.
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Affiliation(s)
- Angelo Spinello
- National Research Council of Italy (CNR)-, Institute of Materials (IOM) c/o International School for Advanced Studies (SISSA), via Bonomea 265, 34136, Trieste, Italy
| | - Jure Borišek
- National Institute of Chemistry Institution Hajdrihova ulica 19, 1000, Ljubljana, Slovenia
| | - Matic Pavlin
- Laboratory of Microsensor Structures and Electronics Faculty of Electrical Engineering, University of Ljubljana Tržaška cesta 25, 1000, Ljubljana, Slovenia
| | - Pavel Janoš
- National Research Council of Italy (CNR)-, Institute of Materials (IOM) c/o International School for Advanced Studies (SISSA), via Bonomea 265, 34136, Trieste, Italy
| | - Alessandra Magistrato
- National Research Council of Italy (CNR)-, Institute of Materials (IOM) c/o International School for Advanced Studies (SISSA), via Bonomea 265, 34136, Trieste, Italy
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8
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Castro AMD, Prasavath D, Bevilaqua JV, Portugal CA, Neves LA, Crespo JG. Role of water on deep eutectic solvents (DES) properties and gas transport performance in biocatalytic supported DES membranes. Sep Purif Technol 2021. [DOI: 10.1016/j.seppur.2020.117763] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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9
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Palermo G, Spinello A, Saha A, Magistrato A. Frontiers of metal-coordinating drug design. Expert Opin Drug Discov 2020; 16:497-511. [PMID: 33874825 DOI: 10.1080/17460441.2021.1851188] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Introduction: The occurrence of metal ions in biomolecules is required to exert vital cellular functions. Metal-containing biomolecules can be modulated by small-molecule inhibitors targeting their metal-moiety. As well, the discovery of cisplatin ushered the rational discovery of metal-containing-drugs. The use of both drug types exploiting metal-ligand interactions is well established to treat distinct pathologies. Therefore, characterizing and leveraging metal-coordinating drugs is a pivotal, yet challenging, part of medicinal chemistry.Area covered: Atomic-level simulations are increasingly employed to overcome the challenges met by traditional drug-discovery approaches and to complement wet-lab experiments in elucidating the mechanisms of drugs' action. Multiscale simulations, allow deciphering the mechanism of metal-binding inhibitors and metallo-containing-drugs, enabling a reliable description of metal-complexes in their biological environment. In this compendium, the authors review selected applications exploiting the metal-ligand interactions by focusing on understanding the mechanism and design of (i) inhibitors targeting iron and zinc-enzymes, and (ii) ruthenium and gold-based anticancer agents targeting the nucleosome and aquaporin protein, respectively.Expert opinion: The showcased applications exemplify the current role and the potential of atomic-level simulations and reveal how their synergic use with experiments can contribute to uncover fundamental mechanistic facets and exploit metal-ligand interactions in medicinal chemistry.
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Affiliation(s)
- Giulia Palermo
- Department of Bioengineering and Department of Chemistry, University of California Riverside, Riverside, United States
| | - Angelo Spinello
- National Research Council (CNR) of Italy, Institute of Material (IOM) @ International School for Advanced Studies (SISSA), Trieste, Italy
| | - Aakash Saha
- Department of Bioengineering, University of California Riverside, Riverside, United States
| | - Alessandra Magistrato
- National Research Council (CNR) of Italy, Institute of Material (IOM) @ International School for Advanced Studies (SISSA), Trieste, Italy
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10
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Prejanò M, Romeo I, Russo N, Marino T. On the Catalytic Activity of the Engineered Coiled-Coil Heptamer Mimicking the Hydrolase Enzymes: Insights from a Computational Study. Int J Mol Sci 2020; 21:E4551. [PMID: 32604744 PMCID: PMC7352413 DOI: 10.3390/ijms21124551] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 06/22/2020] [Accepted: 06/24/2020] [Indexed: 01/22/2023] Open
Abstract
Recently major advances were gained on the designed proteins aimed to generate biomolecular mimics of proteases. Although such enzyme-like catalysts must still suffer refinements for improving the catalytic activity, at the moment, they represent a good example of artificial enzymes to be tested in different fields. Herein, a de novo designed homo-heptameric peptide assembly (CC-Hept) where the esterase activity towards p-nitro-phenylacetate was obtained for introduction of the catalytic triad (Cys-His-Glu) into the hydrophobic matrix, is the object of the present combined molecular dynamics and quantum mechanics/molecular mechanics investigation. Constant pH Molecular Dynamics simulations on the apoform of CC-Hept suggested that the Cys residues are present in the protonated form. Molecular dynamics (MD) simulations of the enzyme-substrate complex evidenced the attitude of the enzyme-like system to retain water molecules, necessary in the hydrolytic reaction, in correspondence of the active site, represented by the Cys-His-Glu triad on each of the seven chains, without significant structural perturbations. A detailed reaction mechanism of esterase activity of CC-Hept-Cys-His-Glu was investigated on the basis of the quantum mechanics/molecular mechanics calculations employing a large quantum mechanical (QM) region of the active site. The proposed mechanism is consistent with available esterases kinetics and structural data. The roles of the active site residues were also evaluated. The deacylation phase emerged as the rate-determining step, in agreement with esterase activity of other natural proteases.
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Affiliation(s)
| | | | - Nino Russo
- Department of Chemistry and Chemical Technologies, University of Calabria, 87036 Arcavacata di Rende, Cosenza, Italy; (M.P.); (I.R.)
| | - Tiziana Marino
- Department of Chemistry and Chemical Technologies, University of Calabria, 87036 Arcavacata di Rende, Cosenza, Italy; (M.P.); (I.R.)
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11
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Mirzaei MS, Taherpour AA, Mirzaei S. Proton shuttle efficiency of bicarbonate: A theoretical study on tautomerization and CO2 hydration. Tetrahedron 2019. [DOI: 10.1016/j.tet.2019.130693] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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12
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Prejanò M, Medina FE, Fernandes PA, Russo N, Ramos MJ, Marino T. The Catalytic Mechanism of Human Transketolase. Chemphyschem 2019; 20:2881-2886. [PMID: 31489766 DOI: 10.1002/cphc.201900650] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 08/29/2019] [Indexed: 01/10/2023]
Abstract
We have computationally determined the catalytic mechanism of human transketolase (hTK) using a cluster model approach and density functional theory calculations. We were able to determine all the relevant structures, bringing solid evidences to the proposed experimental mechanism, and to add important detail to the structure of the transition states and the energy profile associated with catalysis. Furthermore, we have established the existence of a crucial intermediate of the catalytic cycle, in agreement with experiments. The calculated data brought new insights to hTK's catalytic mechanism, providing free-energy values for the chemical reaction, as well as adding atomistic detail to the experimental mechanism.
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Affiliation(s)
- Mario Prejanò
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, Via Ponte Pietro Bucci, 87036, Arcavacata di Rende (CS), Italy
| | - Fabiola Estefany Medina
- UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
| | - Pedro Alexandrino Fernandes
- UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
| | - Nino Russo
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, Via Ponte Pietro Bucci, 87036, Arcavacata di Rende (CS), Italy
| | - Maria Joao Ramos
- UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
| | - Tiziana Marino
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, Via Ponte Pietro Bucci, 87036, Arcavacata di Rende (CS), Italy
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13
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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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14
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Song R, Wu X, Xue B, Yang Y, Huang W, Zeng G, Wang J, Li W, Cao Y, Wang W, Lu J, Dong H. Principles Governing Catalytic Activity of Self-Assembled Short Peptides. J Am Chem Soc 2018; 141:223-231. [PMID: 30562022 DOI: 10.1021/jacs.8b08893] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Molecular self-assembly provides a chemical strategy for the synthesis of nanostructures by using the principles of nature, and peptides serve as the promising building blocks to construct adaptable molecular architectures. Recently, a series of heptapeptides with alternative hydrophobic and hydrophilic residues were reported to form amyloid-like structures, which are capable of catalyzing acyl ester hydrolysis with remarkable efficiency. However, information remains elusive about the atomic structures of the fibrils. What is the origin of the sequence-dependent catalytic activity? How is the ester hydrolysis catalyzed by the fibrils? In this work, the atomic structures of the aggregates were determined by using molecular modeling and further validated by solid-state NMR experiments, where the fibril with high activity adopts twisted parallel configuration within each layer, and the one with low activity is in flat antiparallel configuration. The polymorphism originates from the interactions between different regions of the building block peptides, where the delicate balance between rigidity and flexibility plays an important role. We further show that the p-nitrophenylacetate ( pNPA) hydrolysis reactions catalyzed by two different fibrils follow a similar mechanism, and the difference in microenvironment at the active site between the natural enzyme and the present self-assembled fibrils should account for the discrepancy in catalytic activities. The present work provides understanding of the structure and function of self-assembled fibrils formed with short peptides at an atomic level and thus sheds new insight on designing aggregates with better functions.
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Affiliation(s)
- Ruiheng Song
- Kuang Yaming Honors School , Nanjing University , Nanjing 210023 , China
| | - Xialian Wu
- School of Life Science and Technology , ShanghaiTech University , Shanghai 201210 , China.,University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Bin Xue
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics , Nanjing University , Nanjing 210093 , China
| | - Yuqin Yang
- Kuang Yaming Honors School , Nanjing University , Nanjing 210023 , China
| | - Wenmao Huang
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics , Nanjing University , Nanjing 210093 , China
| | - Guixiang Zeng
- Kuang Yaming Honors School , Nanjing University , Nanjing 210023 , China.,Institute for Brain Sciences , Nanjing University , Nanjing 210023 , China
| | - Jian Wang
- School of Life Science and Technology , ShanghaiTech University , Shanghai 201210 , China
| | - Wenfei Li
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics , Nanjing University , Nanjing 210093 , China.,Institute for Brain Sciences , Nanjing University , Nanjing 210023 , China
| | - Yi Cao
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics , Nanjing University , Nanjing 210093 , China.,Institute for Brain Sciences , Nanjing University , Nanjing 210023 , China
| | - Wei Wang
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics , Nanjing University , Nanjing 210093 , China.,Institute for Brain Sciences , Nanjing University , Nanjing 210023 , China
| | - Junxia Lu
- School of Life Science and Technology , ShanghaiTech University , Shanghai 201210 , China
| | - Hao Dong
- Kuang Yaming Honors School , Nanjing University , Nanjing 210023 , China.,Institute for Brain Sciences , Nanjing University , Nanjing 210023 , China
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Chen G, Kong X, Lu D, Wu J, Liu Z. Kinetics of CO 2 diffusion in human carbonic anhydrase: a study using molecular dynamics simulations and the Markov-state model. Phys Chem Chem Phys 2018; 19:11690-11697. [PMID: 28435964 DOI: 10.1039/c7cp00887b] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Molecular dynamics (MD) simulations, in combination with the Markov-state model (MSM), were applied to probe CO2 diffusion from an aqueous solution into the active site of human carbonic anhydrase II (hCA-II), an enzyme useful for enhanced CO2 capture and utilization. The diffusion process in the hydrophobic pocket of hCA-II was illustrated in terms of a two-dimensional free-energy landscape. We found that CO2 diffusion in hCA-II is a rate-limiting step in the CO2 diffusion-binding-reaction process. The equilibrium distribution of CO2 shows its preferential accumulation within a hydrophobic domain in the protein core region. An analysis of the committors and reactive fluxes indicates that the main pathway for CO2 diffusion into the active site of hCA-II is through a binding pocket where residue Gln136 contributes to the maximal flux. The simulation results offer a new perspective on the CO2 hydration kinetics and useful insights toward the development of novel biochemical processes for more efficient CO2 sequestration and utilization.
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Affiliation(s)
- Gong Chen
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, China.
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16
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Piazzetta P, Marino T, Russo N, Salahub DR. The role of metal substitution in the promiscuity of natural and artificial carbonic anhydrases. Coord Chem Rev 2017. [DOI: 10.1016/j.ccr.2016.12.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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17
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Piazzetta P, Marino T, Russo N. Mechanistic Explanation of the Weak Carbonic Anhydrase's Esterase Activity. Molecules 2017; 22:E1009. [PMID: 28629166 PMCID: PMC6152773 DOI: 10.3390/molecules22061009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 06/08/2017] [Accepted: 06/13/2017] [Indexed: 11/16/2022] Open
Abstract
In order to elucidate the elementary mechanism of the promiscuous esterase activity of human carbonic anhydrase (h-CA), we present an accurate theoretical investigation on the hydrolysis of fully-acetylated d-glucose functionalized as sulfamate. This h-CA's inhibitor is of potential relevance in cancer therapy. The study has been performed within the framework of three-layer ONIOM (QM-high:QM'-medium:MM-low) hybrid approach. The computations revealed that the hydrolysis process is not energetically favored, in agreement with the observed weak carbonic anhydrase's esterase activity.
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Affiliation(s)
- Paolo Piazzetta
- Dipartimento di Chimica e Tecnologie Chimiche (CTC), Università della Calabria, 87036 Arcavacata di Rende (CS), Italy.
| | - Tiziana Marino
- Dipartimento di Chimica e Tecnologie Chimiche (CTC), Università della Calabria, 87036 Arcavacata di Rende (CS), Italy.
| | - Nino Russo
- Dipartimento di Chimica e Tecnologie Chimiche (CTC), Università della Calabria, 87036 Arcavacata di Rende (CS), Italy.
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18
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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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19
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Piazzetta P, Marino T, Russo N, Salahub DR. Explicit Water Molecules Play a Key Role in the Mechanism of Rhodium-Substituted Human Carbonic Anhydrase. ChemCatChem 2017. [DOI: 10.1002/cctc.201601433] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Paolo Piazzetta
- Dipartimento di Chimica e Tecnologie Chimiche (CTC); Universitá della Calabria; 87036 Arcavacata di Rende CS Italy
| | - Tiziana Marino
- Dipartimento di Chimica e Tecnologie Chimiche (CTC); Universitá della Calabria; 87036 Arcavacata di Rende CS Italy
| | - Nino Russo
- Dipartimento di Chimica e Tecnologie Chimiche (CTC); Universitá della Calabria; 87036 Arcavacata di Rende CS Italy
| | - Dennis R. Salahub
- Department of Chemistry; Institute for Quantum Science and Technology; Centre for Molecular Simulation, BI 556; University of Calgary; 2500 University Drive NW Calgary Alberta T2N 1N4 Canada
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20
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Piazzetta P, Marino T, Russo N. The working mechanism of the β-carbonic anhydrase degrading carbonyl sulphide (COSase): a theoretical study. Phys Chem Chem Phys 2016; 17:14843-8. [PMID: 25980540 DOI: 10.1039/c4cp05975a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In order to give insights into the working mechanism of the novel characterized enzyme carbonyl sulphide hydrolase (COSase), which efficiently converts COS into H2S and CO2, we have performed a detailed theoretical investigation using the framework of density functional theory (using B3LYP and M06 exchange-correlation functionals) by the cluster model approach. In the final part of the reaction the metal ion is unable to form a pentacoordinated species. The B3LYP-D3 and M06 potential energy surfaces have a very similar shape. The elucidation of the catalytic reduction of COS is important in view of its role in environmental chemistry.
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Affiliation(s)
- P Piazzetta
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, Cubo 14C, Via P. Bucci, 87036 Arcavacata di Rende (CS), Italy.
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21
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Theoretical investigation on the restoring step of the carbonic anhydrase catalytic cycle for natural and promiscuous substrates. Arch Biochem Biophys 2015; 582:101-6. [DOI: 10.1016/j.abb.2015.03.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Revised: 03/06/2015] [Accepted: 03/25/2015] [Indexed: 11/19/2022]
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22
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Piazzetta P, Marino T, Russo N, Salahub DR. Direct Hydrogenation of Carbon Dioxide by an Artificial Reductase Obtained by Substituting Rhodium for Zinc in the Carbonic Anhydrase Catalytic Center. A Mechanistic Study. ACS Catal 2015. [DOI: 10.1021/acscatal.5b00185] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- P. Piazzetta
- Dipartimento
di Chimica e Tecnologie Chimiche, Università della Calabria, 87036Rende, Italy
| | - T. Marino
- Dipartimento
di Chimica e Tecnologie Chimiche, Università della Calabria, 87036Rende, Italy
| | - N. Russo
- Dipartimento
di Chimica e Tecnologie Chimiche, Università della Calabria, 87036Rende, Italy
| | - D. R. Salahub
- Department
of Chemistry, IQST − Institute for Quantum Science and Technology,
CMS − Centre for Molecular Simulation, BI 556, University of Calgary, 2500 University Drive NW, Calgary, Alberta Canada T2N 1N4
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23
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Muñoz Robles V, Ortega-Carrasco E, Alonso-Cotchico L, Rodriguez-Guerra J, Lledós A, Maréchal JD. Toward the Computational Design of Artificial Metalloenzymes: From Protein–Ligand Docking to Multiscale Approaches. ACS Catal 2015. [DOI: 10.1021/acscatal.5b00010] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Victor Muñoz Robles
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola
del Vallès, Barcelona, Spain
| | - Elisabeth Ortega-Carrasco
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola
del Vallès, Barcelona, Spain
| | - Lur Alonso-Cotchico
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola
del Vallès, Barcelona, Spain
| | - Jaime Rodriguez-Guerra
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola
del Vallès, Barcelona, Spain
| | - Agustí Lledós
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola
del Vallès, Barcelona, Spain
| | - Jean-Didier Maréchal
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola
del Vallès, Barcelona, Spain
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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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