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Sagiroglugil M, Yasar F. Catalytic Reaction Mechanism of Bacterial GH92 α-1,2-Mannosidase: A QM/MM Metadynamics Study. Chemphyschem 2023; 24:e202300628. [PMID: 37782219 DOI: 10.1002/cphc.202300628] [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: 09/01/2023] [Revised: 09/23/2023] [Accepted: 10/01/2023] [Indexed: 10/03/2023]
Abstract
The catalytic mechanism of aC a + 2 ${C{a}^{+2}}$ -dependent family 92 α ${{\rm \alpha }}$ -mannosidase, which is abundantly present in human gut flora and malfunctions leading to the lysosomal storage disease α-mannosidosis, has been investigated using quantum mechanics/molecular mechanics and metadynamics methods. Computational efforts show that the enzyme follows a conformational itinerary of and theC a + 2 ${C{a}^{+2}}$ ion serves a dual purpose, as it not only distorts the sugar ring but also plays a crucial role in orchestrating the arrangement of catalytic residues. This orchestration, in turn, contributes to the facilitation of O S 2 ${{{\rm \ }}^{{\rm O}}{{\rm S}}_{2}}$ conformers for the ensuing reaction. This mechanistic insight is well-aligned with the experimental predictions of the catalytic pathway, and the computed energies are of the same order of magnitude as the experimental estimations. Hence, our results extend the mechanistic understanding of glycosidases.
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Affiliation(s)
- Mert Sagiroglugil
- Department of Physics Engineering, Hacettepe University, Üniversiteler Mahallesi Beytepe Kampüsü, 06800, Ankara, Turkey
- Current Address: Departament de Química Inorgànica i Orgànica (Seccióde Química Orgànica), Institut de Química Teòrica i Computacional (IQTCUB) Universitat de Barcelona, Carrer de Martí i Franquès, 1, 08028, Barcelona, Spain
| | - Fatih Yasar
- Department of Physics Engineering, Hacettepe University, Üniversiteler Mahallesi Beytepe Kampüsü, 06800, Ankara, Turkey
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Paiva P, Medina FE, Viegas M, Ferreira P, Neves RPP, Sousa JPM, Ramos MJ, Fernandes PA. Animal Fatty Acid Synthase: A Chemical Nanofactory. Chem Rev 2021; 121:9502-9553. [PMID: 34156235 DOI: 10.1021/acs.chemrev.1c00147] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Fatty acids are crucial molecules for most living beings, very well spread and conserved across species. These molecules play a role in energy storage, cell membrane architecture, and cell signaling, the latter through their derivative metabolites. De novo synthesis of fatty acids is a complex chemical process that can be achieved either by a metabolic pathway built by a sequence of individual enzymes, such as in most bacteria, or by a single, large multi-enzyme, which incorporates all the chemical capabilities of the metabolic pathway, such as in animals and fungi, and in some bacteria. Here we focus on the multi-enzymes, specifically in the animal fatty acid synthase (FAS). We start by providing a historical overview of this vast field of research. We follow by describing the extraordinary architecture of animal FAS, a homodimeric multi-enzyme with seven different active sites per dimer, including a carrier protein that carries the intermediates from one active site to the next. We then delve into this multi-enzyme's detailed chemistry and critically discuss the current knowledge on the chemical mechanism of each of the steps necessary to synthesize a single fatty acid molecule with atomic detail. In line with this, we discuss the potential and achieved FAS applications in biotechnology, as biosynthetic machines, and compare them with their homologous polyketide synthases, which are also finding wide applications in the same field. Finally, we discuss some open questions on the architecture of FAS, such as their peculiar substrate-shuttling arm, and describe possible reasons for the emergence of large megasynthases during evolution, questions that have fascinated biochemists from long ago but are still far from answered and understood.
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Affiliation(s)
- Pedro Paiva
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Fabiola E Medina
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, Autopista Concepción-Talcahuano, 7100 Talcahuano, Chile
| | - Matilde Viegas
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Pedro Ferreira
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Rui P P Neves
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - João P M Sousa
- LAQV, 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
- LAQV, 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
- LAQV, 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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Parise A, Russo N, Marino T. The platination mechanism of RNase A by arsenoplatin: insight from the theoretical study. Inorg Chem Front 2021. [DOI: 10.1039/d0qi01165g] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A detailed metalation process of the bovine pancreatic ribonuclease (RNase A) by a novel multitarget anti-cancer agent arsenoplatin-1, ([Pt(μ-NHC(CH3)O)2ClAs(OH)2]), performed at DFT level and using different models size is provided.
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Affiliation(s)
- A. Parise
- Dipartimento di Chimica e Tecnologie Chimiche
- Università della Calabria
- 87036 Arcavacata di Rende
- Italy
- Université Paris-Saclay
| | - N. Russo
- Dipartimento di Chimica e Tecnologie Chimiche
- Università della Calabria
- 87036 Arcavacata di Rende
- Italy
| | - T. Marino
- Dipartimento di Chimica e Tecnologie Chimiche
- Università della Calabria
- 87036 Arcavacata di Rende
- Italy
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Piech O, Cox RJ. Reengineering the programming of a functional domain of an iterative highly reducing polyketide synthase. RSC Adv 2020; 10:18469-18476. [PMID: 35517211 PMCID: PMC9053739 DOI: 10.1039/d0ra04026f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 05/05/2020] [Indexed: 12/17/2022] Open
Abstract
A structural model of the enoyl reductase (ER) catalytic domain of the fungal highly-reducing polyketide synthase squalestatin tetraketide synthase (SQTKS) was developed. Simulated docking of substrates and inhibitors allowed the definition of active site residues involved in catalysis and substrate selectivity. These were investigated in silico with the aim of extending the substrate scope. Residues were identified which limit the substrate selectivity of the SQTKS ER, and these were mutated and the engineered ER domain assayed in vitro. Significant changes to the programming of the mutant SQTKS ER domains were observed allowing the processing of longer and more methylated substrates.
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Affiliation(s)
- Oliver Piech
- Institute for Organic Chemistry, Leibniz University of Hannover Schneiderberg 1B 30167 Hannover Germany .,BMWZ, Leibniz University of Hannover Schneiderberg 38 30167 Hannover Germany
| | - Russell J Cox
- Institute for Organic Chemistry, Leibniz University of Hannover Schneiderberg 1B 30167 Hannover Germany .,BMWZ, Leibniz University of Hannover Schneiderberg 38 30167 Hannover Germany
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Magalhães RP, Fernandes HS, Sousa SF. Modelling Enzymatic Mechanisms with QM/MM Approaches: Current Status and Future Challenges. Isr J Chem 2020. [DOI: 10.1002/ijch.202000014] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Rita P. Magalhães
- UCIBIO@REQUIMTE, BioSIMDepartamento de Biomedicina, Faculdade de Medicina da Universidade do Porto Alameda Professor Hernâni Monteiro 4200-319 Porto Portugal
| | - Henriques S. Fernandes
- UCIBIO@REQUIMTE, BioSIMDepartamento de Biomedicina, Faculdade de Medicina da Universidade do Porto Alameda Professor Hernâni Monteiro 4200-319 Porto Portugal
| | - Sérgio F. Sousa
- UCIBIO@REQUIMTE, BioSIMDepartamento de Biomedicina, Faculdade de Medicina da Universidade do Porto Alameda Professor Hernâni Monteiro 4200-319 Porto Portugal
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Prejanò M, Medina FE, Ramos MJ, Russo N, Fernandes PA, Marino T. How the Destabilization of a Reaction Intermediate Affects Enzymatic Efficiency: The Case of Human Transketolase. ACS Catal 2020; 10:2872-2881. [PMID: 33828899 PMCID: PMC8016368 DOI: 10.1021/acscatal.9b04690] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 02/04/2020] [Indexed: 12/16/2022]
Abstract
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Atomic
resolution X-ray crystallography has shown that an intermediate
(the X5P-ThDP adduct) of the catalytic cycle of transketolase (TK)
displays a significant, putatively highly energetic, out-of-plane
distortion in a sp2 carbon
adjacent to a lytic bond, suggested to lower the barrier of the subsequent
step, and thus was postulated to embody a clear-cut demonstration
of the intermediate destabilization effect. The lytic
bond of the subsequent rate-limiting step was very elongated in the
X-ray structure (1.61 Å), which was proposed to be a consequence
of the out-of-plane distortion. Here we use high-level QM and QM/MM
calculations to study the intermediate destabilization effect. We show that the intrinsic energy penalty for the observed
distortion is small (0.2 kcal·mol–1) and that
the establishment of a favorable hydrogen bond within X5P-ThDP, instead
of enzyme steric strain, was found to be the main cause for the distortion.
As the net energetic effect of the distortion is small, the establishment
of the internal hydrogen bond (−0.6 kcal·mol–1) offsets the associated penalty. This makes the distorted structure
more stable than the nondistorted one. Even though the energy contributions
determined here are close to the accuracy of the computational methods
in estimating penalties for geometric distortions, our data show that
the intermediate destabilization effect provides
a small contribution to the observed reaction rate and does not represent
a catalytic effect that justifies the many orders of magnitude which
enzymes accelerate reaction rates. The results help to understand
the intrinsic enzymatic machinery behind enzyme’s amazing proficiency.
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Affiliation(s)
- Mario Prejanò
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, 87036 Arcavacata di Rende (CS), Italy
| | - Fabiola E. Medina
- UCIBIO, REQUIMTE, Departamento de Quı́mica e Bioquı́mica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Maria J. Ramos
- UCIBIO, REQUIMTE, Departamento de Quı́mica e Bioquı́mica, 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, 87036 Arcavacata di Rende (CS), Italy
| | - Pedro A. Fernandes
- UCIBIO, REQUIMTE, Departamento de Quı́mica e Bioquı́mica, 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, 87036 Arcavacata di Rende (CS), Italy
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