1
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Shams Ghamsary M, Ghiasi M, Naghavi SS. Insight into the activation mechanism of carbonic anhydrase(II) through 2-(2-aminoethyl)-pyridine: a promising pathway for enhanced enzymatic activity. Phys Chem Chem Phys 2024; 26:10382-10391. [PMID: 38502117 DOI: 10.1039/d3cp05687b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
Activation of human carbonic anhydrase II (hCA II) holds great promise for treating memory loss symptoms associated with Alzheimer's disease. Despite its importance, the activation mechanism of hCA II has been largely overlooked in favor of the well-studied inhibition mechanism. To address this unexplored realm, we use first-principles calculations to tease out the activation mechanism of hCA II using 2-(2-aminoethyl)-pyridine (2-2AEPy), a promising in vitro activator. We explored both stepwise and concerted mechanisms via both available nitrogen sites of 2-2AEPy: (i) aminoethyl group (Nα) and (ii) pyridine ring (Nβ). Our results show that a concerted mechanism via Nα holds the key to hCA II activation. The activation process of the concerted mechanism exhibits the characteristics of an exergonic reaction, wherein the transition state resembles the reactant with a notably low imaginary frequency of 452.4i cm-1 and barrier height of 5.2 kcal mol-1. Such meager transition barriers propel the activation of hCA II at in vivo temperatures. These findings initiate future research into hCA II activation mechanisms and the development of efficient activators, which may lead to promising therapeutic interventions for Alzheimer's disease.
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Affiliation(s)
- Masoumeh Shams Ghamsary
- Department of Physical and Computational Chemistry, Shahid Beheshti University, Tehran 1983969411, Iran.
| | - Mina Ghiasi
- Department of Physical Chemistry and Nano chemistry, Faculty of Chemistry, Alzahra University, 1993893973, Tehran, Iran.
| | - S Shahab Naghavi
- Department of Physical and Computational Chemistry, Shahid Beheshti University, Tehran 1983969411, Iran.
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2
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Li RN, Chen SL. Mechanistic Insights into the N-Hydroxylations Catalyzed by the Binuclear Iron Domain of SznF Enzyme: Key Piece in the Synthesis of Streptozotocin. Chemistry 2024; 30:e202303845. [PMID: 38212866 DOI: 10.1002/chem.202303845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 01/10/2024] [Accepted: 01/11/2024] [Indexed: 01/13/2024]
Abstract
SznF, a member of the emerging family of heme-oxygenase-like (HO-like) di-iron oxidases and oxygenases, employs two distinct domains to catalyze the conversion of Nω-methyl-L-arginine (L-NMA) into N-nitroso-containing product, which can subsequently be transformed into streptozotocin. Using unrestricted density functional theory (UDFT) with the hybrid functional B3LYP, we have mechanistically investigated the two sequential hydroxylations of L-NMA catalyzed by SznF's binuclear iron central domain. Mechanism B primarily involves the O-O bond dissociation, forming Fe(IV)=O, induced by the H+/e- introduction to the FeA side of μ-1,2-peroxo-Fe2(III/III), the substrate hydrogen abstraction by Fe(IV)=O, and the hydroxyl rebound to the substrate N radical. The stochastic addition of H+/e- to the FeB side (mechanism C) can transition to mechanism B, thereby preventing enzyme deactivation. Two other competing mechanisms, involving the direct O-O bond dissociation (mechanism A) and the addition of H2O as a co-substrate (mechanism D), have been ruled out.
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Affiliation(s)
- Rui-Ning Li
- 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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3
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Zhao W, Geng H, Dan Z, Zeng Y, Wang M, Xu W, Hu Z, Huang W. The Alpha Subunit of Mitochondrial Processing Peptidase Participated in Fertility Restoration in Honglian-CMS Rice. Int J Mol Sci 2023; 24:ijms24065442. [PMID: 36982518 PMCID: PMC10049570 DOI: 10.3390/ijms24065442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/09/2023] [Accepted: 03/09/2023] [Indexed: 03/18/2023] Open
Abstract
The cytoplasmic male sterility (CMS) and nuclear-controlled fertility restoration system is a favorable tool for the utilization of heterosis in plant hybrid breeding. Many restorer-of-fertility (Rf) genes have been characterized in various species over the decades, but more detailed work is needed to investigate the fertility restoration mechanism. Here, we identified an alpha subunit of mitochondrial processing peptidase (MPPA) that is involved in the fertility restoration process in Honglian-CMS rice. MPPA is a mitochondrial localized protein and interacted with the RF6 protein encoded by the Rf6. MPPA indirectly interacted with hexokinase 6, namely another partner of RF6, to form a protein complex with the same molecular weight as the mitochondrial F1F0-ATP synthase in processing the CMS transcript. Loss-of-function of MPPA resulted in a defect in pollen fertility, the mppa+/− heterozygotes showed semi-sterility phenotype and the accumulation of CMS-associated protein ORFH79, showing restrained processing of the CMS-associated atp6-OrfH79 in the mutant plant. Taken together, these results threw new light on the process of fertility restoration by investigating the RF6 fertility restoration complex. They also reveal the connections between signal peptide cleavage and the fertility restoration process in Honglian-CMS rice.
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Affiliation(s)
- Weibo Zhao
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (W.Z.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Han Geng
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (W.Z.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Zhiwu Dan
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (W.Z.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yafei Zeng
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (W.Z.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Mingyue Wang
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (W.Z.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Wuwu Xu
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (W.Z.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Zhongli Hu
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (W.Z.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Wenchao Huang
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (W.Z.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
- Correspondence:
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4
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Li RN, Chen SL. Mechanism for the Halogenation and Azidation of Lysine Catalyzed by Non-heme Iron BesD Enzyme. Chem Asian J 2022; 17:e202200438. [PMID: 35763338 DOI: 10.1002/asia.202200438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 06/23/2022] [Indexed: 11/09/2022]
Abstract
Selective halogenation is important in synthetic chemistry. BesD, a new member of the non-heme Fe(II)/α-ketoglutarate (αKG)-dependent halogenase family, can activate the sp3 C-H bond and halogenate lysine, in particular without a carrier protein. Using the density functional calculations, a chlorination mechanism in BesD has been proposed, mainly including the formation of Cl-Fe(IV)=O through the αKG decarboxylation, the isomerization of Cl-Fe(IV)=O, the substrate hydrogen abstraction by Fe(IV)=O, and the rebound of chloro to the substrate carbon radical. The hydrogen abstraction is rate-limiting. The isomerization of Cl-Fe(IV)=O is essential for the hydrogen abstraction and the chiral selectivity. The BesD-catalyzed bromination and azidation of lysine adopt the same mechanism as the chlorination. The hardly-changed overall barriers indicate that the introduced ligands (X) do not affect the reaction rate significantly, implying that the X-introduced reactions catalyzed by BesD may be extended to other X anions.
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Affiliation(s)
- Rui-Ning Li
- Beijing Institute of Technology, School of Chemistry and Chemical Engineering, 100081, Beijing, CHINA
| | - Shi-Lu Chen
- Beijing Institute of Technology, School of Chemistry and Chemical Engineering, 5th, ZhongGuanCun South Street, 100081, Beijing, CHINA
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5
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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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6
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Ghiasi M, Shahabi P, Supuran CT. Quantum mechanical study on the activation mechanism of human carbonic anhydrase VII cluster model with bis-histamine schiff bases and bis-spinaceamine derivatives. Bioorg Med Chem 2021; 44:116276. [PMID: 34225168 DOI: 10.1016/j.bmc.2021.116276] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 06/10/2021] [Accepted: 06/10/2021] [Indexed: 02/05/2023]
Abstract
The activation mechanism of human carbonic anhydrase (hCA) isoform VII, hCA VII, with histamine, histamine bis-Schiff bases and bis-spinaceamine derivatives has been investigated using quantum mechanical calculations. The DFT-D3 method has been employed to calculate in detail the electronic structure and electronic energy of different compounds and complexes throughout the reaction pathway. The model system of hCA VII included the core catalytic center, the Zn2+ ion, its three histidine ligands and a hydroxide ion or water molecule coordinated to it. Furthermore, Thr199, Glu106 and the deep water molecule were considered in the model. Five activators of this enzyme, including histamine as standard, in complex with the cluster model of hCA VII were investigated. Thermodynamic functions for the overall reaction and for the complexation between activators and hCA VII were evaluated. Our results demonstrate that the protonatable moiety of these activators participates in proton transfer reactions from the zinc-bound water molecule to the reaction medium, promoting the formation of the catalytically active zinc hydroxide species of the enzyme. The QM analysis revealed that the electrostatic interactions between activators and hCA VII are the driving force of the enzyme-activator complex formation.
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Affiliation(s)
- Mina Ghiasi
- Department of Chemistry, Faculty of Physics and Chemistry, Alzahra University, Tehran, Iran.
| | - Parisa Shahabi
- Department of Chemistry, Faculty of Physics and Chemistry, Alzahra University, Tehran, Iran
| | - Claudiu T Supuran
- Dipartimento Neurofarba, Sezione di, Scienze Farmaceutiche e Nutraceutiche, Universita degli Studi di Firenze, Sesto Fiorentino, Italy
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7
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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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8
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Prejanò M, Vidossich P, Russo N, De Vivo M, Marino T. Insights into the Catalytic Mechanism of Domains CD1 and CD2 in Histone Deacetylase 6 from Quantum Calculations. ACS Catal 2021. [DOI: 10.1021/acscatal.0c04729] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Mario Prejanò
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, Via Ponte Pietro Bucci, 87036 Arcavacata di Rende, Cosenza, Italy
| | - Pietro Vidossich
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Nino Russo
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, Via Ponte Pietro Bucci, 87036 Arcavacata di Rende, Cosenza, Italy
| | - Marco De Vivo
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Tiziana Marino
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, Via Ponte Pietro Bucci, 87036 Arcavacata di Rende, Cosenza, Italy
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9
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Prejanò M, Russo N, Marino T. How Lanthanide Ions Affect the Addition–Elimination Step of Methanol Dehydrogenases. Chemistry 2020; 26:11334-11339. [DOI: 10.1002/chem.202001855] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 05/04/2020] [Indexed: 01/15/2023]
Affiliation(s)
- Mario Prejanò
- Dipartimento di Chimica e Tecnologie ChimicheUniversità della Calabria 87036 Arcavacata di Rende (CS Italy
| | - Nino Russo
- Dipartimento di Chimica e Tecnologie ChimicheUniversità della Calabria 87036 Arcavacata di Rende (CS Italy
| | - Tiziana Marino
- Dipartimento di Chimica e Tecnologie ChimicheUniversità della Calabria 87036 Arcavacata di Rende (CS Italy
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10
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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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11
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Prejanò M, Marino T, Rizzuto C, Madrid Madrid JC, Russo N, Toscano M. Reaction Mechanism of Low-Spin Iron(III)- and Cobalt(III)-Containing Nitrile Hydratases: A Quantum Mechanics Investigation. Inorg Chem 2017; 56:13390-13400. [DOI: 10.1021/acs.inorgchem.7b02121] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mario Prejanò
- Department of Chemistry
and
Chemical Technologies, Università della Calabria, Via P. Bucci, I-87036 Arcavacata di Rende, Italy
| | - Tiziana Marino
- Department of Chemistry
and
Chemical Technologies, Università della Calabria, Via P. Bucci, I-87036 Arcavacata di Rende, Italy
| | - Carmen Rizzuto
- Department of Chemistry
and
Chemical Technologies, Università della Calabria, Via P. Bucci, I-87036 Arcavacata di Rende, Italy
| | - Josè Carlos Madrid Madrid
- Department of Chemistry
and
Chemical Technologies, Università della Calabria, Via P. Bucci, I-87036 Arcavacata di Rende, Italy
| | - Nino Russo
- Department of Chemistry
and
Chemical Technologies, Università della Calabria, Via P. Bucci, I-87036 Arcavacata di Rende, Italy
| | - Marirosa Toscano
- Department of Chemistry
and
Chemical Technologies, Università della Calabria, Via P. Bucci, I-87036 Arcavacata di Rende, Italy
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12
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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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13
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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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14
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Moreira C, Ramos MJ, Fernandes PA. Reaction Mechanism ofMycobacterium TuberculosisGlutamine Synthetase Using Quantum Mechanics/Molecular Mechanics Calculations. Chemistry 2016; 22:9218-25. [DOI: 10.1002/chem.201600305] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Indexed: 12/28/2022]
Affiliation(s)
- Cátia Moreira
- UCIBIO, REQUIMTE; Departamento de Química e Bioquímica; Faculdade de Ciências; Universidade do Porto; 4169-007 Porto Portugal
| | - Maria J. Ramos
- UCIBIO, REQUIMTE; Departamento de Química e Bioquímica; Faculdade de Ciências; Universidade do Porto; 4169-007 Porto Portugal
| | - Pedro Alexandrino Fernandes
- UCIBIO, REQUIMTE; Departamento de Química e Bioquímica; Faculdade de Ciências; Universidade do Porto; 4169-007 Porto Portugal
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15
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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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16
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Sheng X, Liu Y, Zhang R. A theoretical study of the catalytic mechanism of oxalyl-CoA decarboxylase, an enzyme for treating urolithiasis. RSC Adv 2014. [DOI: 10.1039/c4ra03611e] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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17
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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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18
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Manta B, Raushel FM, Himo F. Reaction Mechanism of Zinc-Dependent Cytosine Deaminase from Escherichia coli: A Quantum-Chemical Study. J Phys Chem B 2014; 118:5644-52. [DOI: 10.1021/jp501228s] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Bianca Manta
- Department
of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106
91 Stockholm, Sweden
| | - Frank M. Raushel
- Department of Chemistry, Texas A&M University, P.O. Box 30012, College Station, Texas 77842-3012, United States
| | - Fahmi Himo
- Department
of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106
91 Stockholm, Sweden
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19
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Piazzetta P, Marino T, Russo N. Promiscuous Ability of Human Carbonic Anhydrase: QM and QM/MM Investigation of Carbon Dioxide and Carbodiimide Hydration. Inorg Chem 2014; 53:3488-93. [DOI: 10.1021/ic402932y] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Paolo Piazzetta
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, 87036 Rende CS, Italy
| | - Tiziana Marino
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, 87036 Rende CS, Italy
| | - Nino Russo
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, 87036 Rende CS, Italy
- Departamento de Quimica,
Division de Ciencias Basicas e Ingenieria, Universidad, Autonoma Metropolitana-Iztapalapa, Av. San Rafael Atlixco No. 186, Col. Vicentina, CP 09340 Mexico D.F., Mexico
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20
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Blomberg MRA, Borowski T, Himo F, Liao RZ, Siegbahn PEM. Quantum chemical studies of mechanisms for metalloenzymes. Chem Rev 2014; 114:3601-58. [PMID: 24410477 DOI: 10.1021/cr400388t] [Citation(s) in RCA: 436] [Impact Index Per Article: 43.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Margareta R A Blomberg
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University , SE-106 91 Stockholm, Sweden
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21
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Bertini L, Bruschi M, Cosentino U, Greco C, Moro G, Zampella G, De Gioia L. Quantum mechanical methods for the investigation of metalloproteins and related bioinorganic compounds. Methods Mol Biol 2014; 1122:207-68. [PMID: 24639262 DOI: 10.1007/978-1-62703-794-5_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
It is well known that transition metal ions are often bound to proteins, conveying very specific functional properties. In fact, metalloproteins play crucial biological roles in the transport and activation of small molecules such as H2, O2, and N2, as well as in several other biochemical processes. However, even if the presence of transition metals in the active site of proteins allows a very rich biochemistry, the experimental disclosure of structure-activity relationships in metalloproteins is generally difficult exactly because of the presence of transition metals, which are intrinsically characterized by a very versatile and often elusive chemistry. For this reason, computational methods are becoming very popular tools in the characterization of metalloproteins. In particular, since computing power is becoming less and less expensive, due to the continuous technological development of CPUs, the computational tools suited to investigate metalloproteins are becoming more accessible and therefore more commonly used also in molecular biology and biochemistry laboratories. Here, we present the main procedures and computational methods based on quantum mechanics, which are commonly used to study the structural, electronic, and reactivity properties of metalloproteins and related bioinspired compounds, with a specific focus on the practical and technical aspects that must be generally tackled to properly study such biomolecular systems.
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Affiliation(s)
- Luca Bertini
- Department of Environmental Science, University of Milano-Bicocca, Milan, Italy
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23
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Wang K, Hou Q, Liu Y. Insight into the mechanism of aminomutase reaction: A case study of phenylalanine aminomutase by computational approach. J Mol Graph Model 2013; 46:65-73. [DOI: 10.1016/j.jmgm.2013.09.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Revised: 08/28/2013] [Accepted: 09/25/2013] [Indexed: 11/24/2022]
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24
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Kučera T, Otyepka M, Matušková A, Samad A, Kutejová E, Janata J. A computational study of the glycine-rich loop of mitochondrial processing peptidase. PLoS One 2013; 8:e74518. [PMID: 24058582 PMCID: PMC3772902 DOI: 10.1371/journal.pone.0074518] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Accepted: 08/02/2013] [Indexed: 11/21/2022] Open
Abstract
An all atomic, non-restrained molecular dynamics (MD) simulation in explicit water was used to study in detail the structural features of the highly conserved glycine-rich loop (GRL) of the α-subunit of the yeast mitochondrial processing peptidase (MPP) and its importance for the tertiary and quaternary conformation of MPP. Wild-type and GRL-deleted MPP structures were studied using non-restrained MD simulations, both in the presence and the absence of a substrate in the peptidase active site. Targeted MD simulations were employed to study the mechanism of substrate translocation from the GRL to the active site. We demonstrate that the natural conformational flexibility of the GRL is crucial for the substrate translocation process from outside the enzyme towards the MPP active site. We show that the α-helical conformation of the substrate is important not only during its initial interaction with MPP (i.e. substrate recognition), but also later, at least during the first third of the substrate translocation trajectory. Further, we show that the substrate remains in contact with the GRL during the whole first half of the translocation trajectory and that hydrophobic interactions play a major role. Finally, we conclude that the GRL acts as a precisely balanced structural element, holding the MPP subunits in a partially closed conformation regardless the presence or absence of a substrate in the active site.
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Affiliation(s)
- Tomáš Kučera
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
- Department of Biochemistry, Faculty of Science, Charles University, Prague, Czech Republic
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Anna Matušková
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Abdul Samad
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Eva Kutejová
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
- Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Jiří Janata
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
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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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26
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Lind MES, Himo F. Quantum chemistry as a tool in asymmetric biocatalysis: limonene epoxide hydrolase test case. Angew Chem Int Ed Engl 2013; 52:4563-7. [PMID: 23512539 PMCID: PMC3734700 DOI: 10.1002/anie.201300594] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Indexed: 12/24/2022]
Affiliation(s)
- Maria E S Lind
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, 10691 Stockholm, Sweden
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Lind MES, Himo F. Quantum Chemistry as a Tool in Asymmetric Biocatalysis: Limonene Epoxide Hydrolase Test Case. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201300594] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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28
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Syrén PO, Le Joubioux F, Ben Henda Y, Maugard T, Hult K, Graber M. Proton Shuttle Mechanism in the Transition State of Lipase-Catalyzed N-Acylation of Amino Alcohols. ChemCatChem 2013. [DOI: 10.1002/cctc.201200751] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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29
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Martínez-Salgado JL, León-Ramírez CG, Pacheco AB, Ruiz-Herrera J, de la Rosa APB. Analysis of the regulation of the Ustilago maydis proteome by dimorphism, pH or MAPK and GCN5 genes. J Proteomics 2013; 79:251-62. [PMID: 23305952 DOI: 10.1016/j.jprot.2012.12.022] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Revised: 10/23/2012] [Accepted: 12/30/2012] [Indexed: 11/18/2022]
Abstract
Ustilago maydis is a dimorphic corn pathogenic basidiomycota whose haploid cells grow in yeast form at pH7, while at pH3 they grow in the mycelial form. Two-dimensional gel electrophoresis (2-DE) coupled with LC-ESI/MS-MS was used to analyze the differential accumulation of proteins in yeast against mycelial morphologies. 2-DE maps were obtained in the pH range of 5-8 and 404 total protein spots were separated. From these, 43 were differentially accumulated when comparing strains FB2wt, constitutive yeast CL211, and constitutive mycelial GP25 growing at pH7 against pH3. Differentially accumulated proteins in response to pH are related with defense against reactive oxygen species or toxic compounds. Up-accumulation of CipC and down-accumulation of Hmp1 were specifically related with mycelial growth. Changes in proteins that were affected by mutation in the gene encoding the adaptor of a MAPK pathway (CL211 strain) were UM521* and transcription factors Btf3, Sol1 and Sti1. Mutation of GCN5 (GP25 strain) affected the accumulation of Rps19-ribosomal protein, Mge1-heath shock protein, and Lpd1-dihydrolipoamide dehydrogenase. Our results complement the information about the genes and proteins related with the dimorphic transition in U. maydis and changes in proteins affected by mutations in a MAPK pathway and GCN5 gene.
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Affiliation(s)
- José L Martínez-Salgado
- IPICyT, Instituto Potosino de Investigación Científica y Tecnológica. Camino a La Presa San José No. 2055, Lomas 4ª Sección, 78216, San Luis Potosí, SLP, Mexico
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30
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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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31
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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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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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