1
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Sohraby F, Nunes-Alves A. Characterization of the Bottlenecks and Pathways for Inhibitor Dissociation from [NiFe] Hydrogenase. J Chem Inf Model 2024; 64:4193-4203. [PMID: 38728115 PMCID: PMC11134402 DOI: 10.1021/acs.jcim.4c00187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 04/24/2024] [Accepted: 04/30/2024] [Indexed: 05/12/2024]
Abstract
[NiFe] hydrogenases can act as efficient catalysts for hydrogen oxidation and biofuel production. However, some [NiFe] hydrogenases are inhibited by gas molecules present in the environment, such as O2 and CO. One strategy to engineer [NiFe] hydrogenases and achieve O2- and CO-tolerant enzymes is by introducing point mutations to block the access of inhibitors to the catalytic site. In this work, we characterized the unbinding pathways of CO in the complex with the wild-type and 10 different mutants of [NiFe] hydrogenase from Desulfovibrio fructosovorans using τ-random accelerated molecular dynamics (τRAMD) to enhance the sampling of unbinding events. The ranking provided by the relative residence times computed with τRAMD is in agreement with experiments. Extensive data analysis of the simulations revealed that from the two bottlenecks proposed in previous studies for the transit of gas molecules (residues 74 and 122 and residues 74 and 476), only one of them (residues 74 and 122) effectively modulates diffusion and residence times for CO. We also computed pathway probabilities for the unbinding of CO, O2, and H2 from the wild-type [NiFe] hydrogenase, and we observed that while the most probable pathways are the same, the secondary pathways are different. We propose that introducing mutations to block the most probable paths, in combination with mutations to open the main secondary path used by H2, can be a feasible strategy to achieve CO and O2 resistance in the [NiFe] hydrogenase from Desulfovibrio fructosovorans.
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Affiliation(s)
- Farzin Sohraby
- Institute of Chemistry, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Ariane Nunes-Alves
- Institute of Chemistry, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
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2
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Brocks C, Das CK, Duan J, Yadav S, Apfel UP, Ghosh S, Hofmann E, Winkler M, Engelbrecht V, Schäfer LV, Happe T. A Dynamic Water Channel Affects O 2 Stability in [FeFe]-Hydrogenases. CHEMSUSCHEM 2024; 17:e202301365. [PMID: 37830175 DOI: 10.1002/cssc.202301365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 10/05/2023] [Accepted: 10/11/2023] [Indexed: 10/14/2023]
Abstract
[FeFe]-hydrogenases are capable of reducing protons at a high rate. However, molecular oxygen (O2 ) induces the degradation of their catalytic cofactor, the H-cluster, which consists of a cubane [4Fe4S] subcluster (4FeH ) and a unique diiron moiety (2FeH ). Previous attempts to prevent O2 -induced damage have focused on enhancing the protein's sieving effect for O2 by blocking the hydrophobic gas channels that connect the protein surface and the 2FeH . In this study, we aimed to block an O2 diffusion pathway and shield 4FeH instead. Molecular dynamics (MD) simulations identified a novel water channel (WH ) surrounding the H-cluster. As this hydrophilic path may be accessible for O2 molecules we applied site-directed mutagenesis targeting amino acids along WH in proximity to 4FeH to block O2 diffusion. Protein film electrochemistry experiments demonstrate increased O2 stabilities for variants G302S and S357T, and MD simulations based on high-resolution crystal structures confirmed an enhanced local sieving effect for O2 in the environment of the 4FeH in both cases. The results strongly suggest that, in wild type proteins, O2 diffuses from the 4FeH to the 2FeH . These results reveal new strategies for improving the O2 stability of [FeFe]-hydrogenases by focusing on the O2 diffusion network near the active site.
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Affiliation(s)
- Claudia Brocks
- Faculty of Biology and Biotechnology, Photobiotechnology, Ruhr University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany
| | - Chandan K Das
- Faculty of Chemistry and Biochemistry, Center for Theoretical Chemistry, Ruhr University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany
| | - Jifu Duan
- Faculty of Biology and Biotechnology, Photobiotechnology, Ruhr University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany
| | - Shanika Yadav
- Faculty of Chemistry and Biochemistry, Inorganic Chemistry, Ruhr University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany
| | - Ulf-Peter Apfel
- Faculty of Chemistry and Biochemistry, Inorganic Chemistry, Ruhr University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany
| | - Subhasri Ghosh
- Faculty of Biology and Biotechnology, Photobiotechnology, Ruhr University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany
| | - Eckhard Hofmann
- Faculty of Biology and Biotechnology, X-ray structure analysis of proteins, Ruhr University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany
| | - Martin Winkler
- Electrobiotechnology, TUM Campus Straubing, Schulgasse 22, Straubing, 94315, Germany
| | - Vera Engelbrecht
- Faculty of Biology and Biotechnology, Photobiotechnology, Ruhr University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany
| | - Lars V Schäfer
- Faculty of Chemistry and Biochemistry, Center for Theoretical Chemistry, Ruhr University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany
| | - Thomas Happe
- Faculty of Biology and Biotechnology, Photobiotechnology, Ruhr University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany
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3
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Zacarias S, Temporão A, Carpentier P, van der Linden P, Pereira IAC, Matias PM. Exploring the gas access routes in a [NiFeSe] hydrogenase using crystals pressurized with krypton and oxygen. J Biol Inorg Chem 2020; 25:863-874. [PMID: 32865640 DOI: 10.1007/s00775-020-01814-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 08/20/2020] [Indexed: 11/25/2022]
Abstract
Hydrogenases are metalloenzymes that catalyse both H2 evolution and uptake. They are gas-processing enzymes with deeply buried active sites, so the gases diffuse through channels that connect the active site to the protein surface. The [NiFeSe] hydrogenases are a special class of hydrogenases containing a selenocysteine as a nickel ligand; they are more catalytically active and less O2-sensitive than standard [NiFe] hydrogenases. Characterisation of the channel system of hydrogenases is important to understand how the inhibitor oxygen reaches the active site to cause oxidative damage. To this end, crystals of Desulfovibrio vulgaris Hildenborough [NiFeSe] hydrogenase were pressurized with krypton and oxygen, and a method for tracking labile O2 molecules was developed, for mapping a hydrophobic channel system similar to that of the [NiFe] enzymes as the major route for gas diffusion.
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Affiliation(s)
- Sónia Zacarias
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Adriana Temporão
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Philippe Carpentier
- European Synchrotron Radiation Facility, Grenoble, France
- Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Laboratoire Chimie et Biologie des Métaux (LCBM), Université Grenoble Alpes, CNRS, CEA, Grenoble, France
| | - Peter van der Linden
- Partnership for Soft Condensed Matter, European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, 38043, Grenoble, France
| | - Inês A C Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Pedro M Matias
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal.
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2780-901, Oeiras, Portugal.
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4
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Domene C, Jorgensen C, Schofield CJ. Mechanism of Molecular Oxygen Diffusion in a Hypoxia-Sensing Prolyl Hydroxylase Using Multiscale Simulation. J Am Chem Soc 2020; 142:2253-2263. [DOI: 10.1021/jacs.9b09236] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Carmen Domene
- Chemistry Research Laboratory, Mansfield Road, University of Oxford, Oxford OX1 3TA, United Kingdom
- Department of Chemistry, Britannia House, King’s College London, 7 Trinity Street, London SE1 1DB, United Kingdom
- Department of Chemistry, University of Bath, Claverton Down Bath BA2 7AY, United Kingdom
| | - Christian Jorgensen
- Department of Chemistry, Britannia House, King’s College London, 7 Trinity Street, London SE1 1DB, United Kingdom
| | - Christopher J. Schofield
- Chemistry Research Laboratory, Mansfield Road, University of Oxford, Oxford OX1 3TA, United Kingdom
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5
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Wang J, Peng C, Yu Y, Chen Z, Xu Z, Cai T, Shao Q, Shi J, Zhu W. Exploring Conformational Change of Adenylate Kinase by Replica Exchange Molecular Dynamic Simulation. Biophys J 2020; 118:1009-1018. [PMID: 31995738 DOI: 10.1016/j.bpj.2020.01.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 12/28/2019] [Accepted: 01/03/2020] [Indexed: 12/19/2022] Open
Abstract
Replica exchange molecular dynamics (REMD) simulation is a popular enhanced sampling method that is widely used for exploring the atomic mechanism of protein conformational change. However, the requirement of huge computational resources for REMD, especially with the explicit solvent model, largely limits its application. In this study, the availability and efficiency of a variant of velocity-scaling REMD (vsREMD) was assessed with adenylate kinase as an example. Although vsREMD achieved results consistent with those from conventional REMD and experimental studies, the number of replicas required for vsREMD (30) was much less than that for conventional REMD (80) to achieve a similar acceptance rate (∼0.2), demonstrating high efficiency of vsREMD to characterize the protein conformational change and associated free-energy profile. Thus, vsREMD is a highly efficient approach for studying the large-scale conformational change of protein systems.
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Affiliation(s)
- Jinan Wang
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
| | - Cheng Peng
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China; University of Chinese Academy of Sciences, Beijing, China
| | - Yuqu Yu
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Zhaoqiang Chen
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Zhijian Xu
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China; University of Chinese Academy of Sciences, Beijing, China
| | - Tingting Cai
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Qiang Shao
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China; University of Chinese Academy of Sciences, Beijing, China
| | - Jiye Shi
- UCB Biopharma SPRL, Braine-l'Alleud, Belgium
| | - Weiliang Zhu
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China; Open Studio for Druggability Research of Marine Lead Compounds, Qingdao National Laboratory for Marine Science and Technology, Jimo, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China.
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6
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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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7
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Foskolou IP, Jorgensen C, Leszczynska KB, Olcina MM, Tarhonskaya H, Haisma B, D'Angiolella V, Myers WK, Domene C, Flashman E, Hammond EM. Ribonucleotide Reductase Requires Subunit Switching in Hypoxia to Maintain DNA Replication. Mol Cell 2017; 66:206-220.e9. [PMID: 28416140 PMCID: PMC5405111 DOI: 10.1016/j.molcel.2017.03.005] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 02/13/2017] [Accepted: 03/07/2017] [Indexed: 02/07/2023]
Abstract
Cells exposed to hypoxia experience replication stress but do not accumulate DNA damage, suggesting sustained DNA replication. Ribonucleotide reductase (RNR) is the only enzyme capable of de novo synthesis of deoxyribonucleotide triphosphates (dNTPs). However, oxygen is an essential cofactor for mammalian RNR (RRM1/RRM2 and RRM1/RRM2B), leading us to question the source of dNTPs in hypoxia. Here, we show that the RRM1/RRM2B enzyme is capable of retaining activity in hypoxia and therefore is favored over RRM1/RRM2 in order to preserve ongoing replication and avoid the accumulation of DNA damage. We found two distinct mechanisms by which RRM2B maintains hypoxic activity and identified responsible residues in RRM2B. The importance of RRM2B in the response to tumor hypoxia is further illustrated by correlation of its expression with a hypoxic signature in patient samples and its roles in tumor growth and radioresistance. Our data provide mechanistic insight into RNR biology, highlighting RRM2B as a hypoxic-specific, anti-cancer therapeutic target. RRM2B is induced in response to hypoxia in both cell models and patient datasets RRM2B retains activity in hypoxic conditions and is the favored RNR subunit in hypoxia Loss of RRM2B has detrimental consequences for cell fate, specifically in hypoxia RRM2B depletion enhanced hypoxic-specific apoptosis and increased radiosensitivity
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Affiliation(s)
- Iosifina P Foskolou
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Christian Jorgensen
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, UK
| | - Katarzyna B Leszczynska
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Monica M Olcina
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Hanna Tarhonskaya
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Bauke Haisma
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Vincenzo D'Angiolella
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - William K Myers
- Inorganic Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QR, UK
| | - Carmen Domene
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, UK; Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Emily Flashman
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Ester M Hammond
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK.
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8
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Structural Plasticity in Globins: Role of Protein Dynamics in Defining Ligand Migration Pathways. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2016; 105:59-80. [PMID: 27567484 DOI: 10.1016/bs.apcsb.2016.07.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Globins are a family of proteins characterized by the presence of the heme prosthetic group and involved in variety of biological functions in the cell. Due to their biological relevance and widespread distribution in all kingdoms of life, intense research efforts have been devoted to disclosing the relationships between structural features, protein dynamics, and function. Particular attention has been paid to the impact of differences in amino acid sequence on the topological features of docking sites and cavities and to the influence of conformational flexibility in facilitating the migration of small ligands through these cavities. Often, tunnels are carved in the interior of globins, and ligand exchange is regulated by gating residues. Understanding the subtle intricacies that relate the differences in sequence with the structural and dynamical features of globins with the ultimate aim of rationalizing the thermodynamics and kinetics of ligand binding continues to be a major challenge in the field. Due to the evolution of computational techniques, significant advances into our understanding of these questions have been made. In this review we focus our attention on the analysis of the ligand migration pathways as well as the function of the structural cavities and tunnels in a series of representative globins, emphasizing the synergy between experimental and theoretical approaches to gain a comprehensive knowledge into the molecular mechanisms of this diverse family of proteins.
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9
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Rasmussen M, Abdellaoui S, Minteer SD. Enzymatic biofuel cells: 30 years of critical advancements. Biosens Bioelectron 2016; 76:91-102. [DOI: 10.1016/j.bios.2015.06.029] [Citation(s) in RCA: 373] [Impact Index Per Article: 46.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2015] [Revised: 06/05/2015] [Accepted: 06/15/2015] [Indexed: 12/14/2022]
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10
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Computation of Rate Constants for Diffusion of Small Ligands to and from Buried Protein Active Sites. Methods Enzymol 2016; 578:299-326. [DOI: 10.1016/bs.mie.2016.05.039] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
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11
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De Sancho D, Kubas A, Wang PH, Blumberger J, Best RB. Identification of Mutational Hot Spots for Substrate Diffusion: Application to Myoglobin. J Chem Theory Comput 2015; 11:1919-27. [PMID: 26574395 PMCID: PMC6132223 DOI: 10.1021/ct5011455] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The pathways by which small molecules (substrates or inhibitors) access active sites are a key aspect of the function of enzymes and other proteins. A key problem in designing or altering such proteins is to identify sites for mutation that will have the desired effect on the substrate transport properties. While specific access channels have been invoked in the past, molecular simulations suggest that multiple routes are possible, complicating the analysis. This complexity, however, can be captured by a Markov State Model (MSM) of the ligand diffusion process. We have developed a sensitivity analysis of the resulting rate matrix, which identifies the locations where mutations should have the largest effect on the diffusive on rate. We apply this method to myoglobin, which is the best characterized example both from experiment and simulation. We validate the approach by translating the sensitivity parameter obtained from this method into the CO binding rates in myoglobin upon mutation, resulting in a semi-quantitative correlation with experiments. The model is further validated against an explicit simulation for one of the experimental mutants.
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Affiliation(s)
- David De Sancho
- Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, United Kingdom
- CIC nanoGUNE , Tolosa Hiribidea 76, 20018 Donostia-San Sebastian, Spain
- IKERBASQUE, Basque Foundation for Science , Maria Diaz de Haro 3, 48013 Bilbao, Spain
| | - Adam Kubas
- Department of Physics and Astronomy, University College London , Gower Street, London WC1E 6BT, United Kingdom
| | - Po-Hung Wang
- Department of Physics and Astronomy, University College London , Gower Street, London WC1E 6BT, United Kingdom
- Theoretical Molecular Science Laboratory , 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Jochen Blumberger
- Department of Physics and Astronomy, University College London , Gower Street, London WC1E 6BT, United Kingdom
| | - Robert B Best
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892-0520, United States
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12
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Oteri F, Baaden M, Lojou E, Sacquin-Mora S. Multiscale Simulations Give Insight into the Hydrogen In and Out Pathways of [NiFe]-Hydrogenases from Aquifex aeolicus and Desulfovibrio fructosovorans. J Phys Chem B 2014; 118:13800-11. [DOI: 10.1021/jp5089965] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Francesco Oteri
- Laboratoire
de Biochimie Théorique, CNRS UPR9080, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Marc Baaden
- Laboratoire
de Biochimie Théorique, CNRS UPR9080, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Elisabeth Lojou
- Bioénergétique
et Ingénierie des Protéines, Institut de Microbiologie
de la Méditerranée, CNRS, Aix Marseille University, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex, France
| | - Sophie Sacquin-Mora
- Laboratoire
de Biochimie Théorique, CNRS UPR9080, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
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13
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Finkelmann AR, Stiebritz MT, Reiher M. Activation Barriers of Oxygen Transformation at the Active Site of [FeFe] Hydrogenases. Inorg Chem 2014; 53:11890-902. [DOI: 10.1021/ic501049z] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Arndt R. Finkelmann
- Laboratorium
für Physikalische
Chemie, ETH Zürich, Valdimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Martin T. Stiebritz
- Laboratorium
für Physikalische
Chemie, ETH Zürich, Valdimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Markus Reiher
- Laboratorium
für Physikalische
Chemie, ETH Zürich, Valdimir-Prelog-Weg 2, 8093 Zürich, Switzerland
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14
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Kubas A, De Sancho D, Best RB, Blumberger J. Aerobic damage to [FeFe]-hydrogenases: activation barriers for the chemical attachment of O2. Angew Chem Int Ed Engl 2014; 53:4081-4. [PMID: 24615978 PMCID: PMC4143129 DOI: 10.1002/anie.201400534] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Indexed: 11/11/2022]
Abstract
[FeFe]-hydrogenases are the best natural hydrogen-producing enzymes but their biotechnological exploitation is hampered by their extreme oxygen sensitivity. The free energy profile for the chemical attachment of O2 to the enzyme active site was investigated by using a range-separated density functional re-parametrized to reproduce high-level ab initio data. An activation free-energy barrier of 13 kcal mol(-1) was obtained for chemical bond formation between the di-iron active site and O2, a value in good agreement with experimental inactivation rates. The oxygen binding can be viewed as an inner-sphere electron-transfer process that is strongly influenced by Coulombic interactions with the proximal cubane cluster and the protein environment. The implications of these results for future mutation studies with the aim of increasing the oxygen tolerance of this enzyme are discussed.
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Affiliation(s)
- Adam Kubas
- Department of Physics and Astronomy, University College LondonGower Street, London WC1E 6BT (UK)
| | - David De Sancho
- Department of Chemistry, Cambridge UniversityLensfield Road, Cambridge CB2 1EW (UK)
| | - Robert B Best
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthBethesda, MD 20892-0520 (USA)
| | - Jochen Blumberger
- Department of Physics and Astronomy, University College LondonGower Street, London WC1E 6BT (UK)
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15
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Smith D, Danyal K, Raugei S, Seefeldt LC. Substrate channel in nitrogenase revealed by a molecular dynamics approach. Biochemistry 2014; 53:2278-85. [PMID: 24654842 DOI: 10.1021/bi401313j] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Mo-dependent nitrogenase catalyzes the biological reduction of N2 to two NH3 molecules at FeMo-cofactor buried deep inside the MoFe protein. Access of substrates, such as N2, to the active site is likely restricted by the surrounding protein, requiring substrate channels that lead from the surface to the active site. Earlier studies on crystallographic structures of the MoFe protein have suggested three putative substrate channels. Here, we have utilized submicrosecond atomistic molecular dynamics simulations to allow the nitrogenase MoFe protein to explore its conformational space in an aqueous solution at physiological ionic strength, revealing a putative substrate channel. The viability of this observed channel was tested by examining the free energy of passage of N2 from the surface through the channel to FeMo-cofactor, resulting in the discovery of a very low energy barrier. These studies point to a viable substrate channel in nitrogenase that appears during thermal motions of the protein in an aqueous environment and that approaches a face of FeMo-cofactor earlier implicated in substrate binding.
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Affiliation(s)
- Dayle Smith
- Pacific Northwestern National Laboratory , Richland, Washington 99352, United States
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16
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Kubas A, De Sancho D, Best RB, Blumberger J. Aerobic Damage to [FeFe]-Hydrogenases: Activation Barriers for the Chemical Attachment of O2. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201400534] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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17
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Topin J, Diharce J, Fiorucci S, Antonczak S, Golebiowski J. O2 Migration Rates in [NiFe] Hydrogenases. A Joint Approach Combining Free-Energy Calculations and Kinetic Modeling. J Phys Chem B 2014; 118:676-81. [DOI: 10.1021/jp4093964] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Jérémie Topin
- Institut de Chimie de Nice, UMR 7272, Université de Nice-Sophia Antipolis, CNRS, Parc Valrose, 06108 Nice Cedex 2, France
| | - Julien Diharce
- Institut de Chimie de Nice, UMR 7272, Université de Nice-Sophia Antipolis, CNRS, Parc Valrose, 06108 Nice Cedex 2, France
| | - Sébastien Fiorucci
- Institut de Chimie de Nice, UMR 7272, Université de Nice-Sophia Antipolis, CNRS, Parc Valrose, 06108 Nice Cedex 2, France
| | - Serge Antonczak
- Institut de Chimie de Nice, UMR 7272, Université de Nice-Sophia Antipolis, CNRS, Parc Valrose, 06108 Nice Cedex 2, France
| | - Jérôme Golebiowski
- Institut de Chimie de Nice, UMR 7272, Université de Nice-Sophia Antipolis, CNRS, Parc Valrose, 06108 Nice Cedex 2, France
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18
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Wang PH, Bruschi M, De Gioia L, Blumberger J. Uncovering a dynamically formed substrate access tunnel in carbon monoxide dehydrogenase/acetyl-CoA synthase. J Am Chem Soc 2013; 135:9493-502. [PMID: 23713976 DOI: 10.1021/ja403110s] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The transport of small ligands to active sites of proteins is the basis of vital processes in biology such as enzymatic catalysis and cell signaling, but also of more destructive ones including enzyme inhibition and oxidative damage. Here, we show how a diffusion-reaction model solved by means of molecular dynamics and density functional theory calculations provides novel insight into the transport of small ligands in proteins. In particular, we unravel the existence of an elusive, dynamically formed gas channel, which CO2 takes to diffuse from the solvent to the active site (C-cluster) of the bifunctional multisubunit enzyme complex carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ACS). Two cavities forming this channel are temporarily created by protein fluctuations and are not apparent in the X-ray structures. The ligand transport is controlled by two residues at the end of this tunnel, His113 and His116, and occurs on the same time scale on which chemical binding to the active site takes place (0.1-1 ms), resulting in an overall binding rate on the second time scale. We find that upon reduction of CO2 to CO, the newly formed Fe-hydroxy ligand greatly strengthens the hydrogen-bond network, preventing CO from exiting the protein through the same way that CO2 takes to enter the protein. This is the basis for directional transport of CO from the production site (C-cluster of CODH subunit) to the utilization site (A-cluster of ACS subunit). In view of these results, a general picture emerges of how large proteins guide small ligands toward their active sites.
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Affiliation(s)
- Po-hung Wang
- Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
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19
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Abbruzzetti S, Spyrakis F, Bidon-Chanal A, Luque FJ, Viappiani C. Ligand migration through hemeprotein cavities: insights from laser flash photolysis and molecular dynamics simulations. Phys Chem Chem Phys 2013; 15:10686-701. [PMID: 23733145 DOI: 10.1039/c3cp51149a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The presence of cavities and tunnels in the interior of proteins, in conjunction with the structural plasticity arising from the coupling to the thermal fluctuations of the protein scaffold, has profound consequences on the pathways followed by ligands moving through the protein matrix. In this perspective we discuss how quantitative analysis of experimental rebinding kinetics from laser flash photolysis, trapping of unstable conformational states by embedding proteins within the nanopores of silica gels, and molecular simulations can synergistically converge to gain insight into the migration mechanism of ligands. We show how the evaluation of the free energy landscape for ligand diffusion based on the outcome of computational techniques can assist the definition of sound reaction schemes, leading to a comprehensive understanding of the broad range of chemical events and time scales that encompass the transport of small ligands in hemeproteins.
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Affiliation(s)
- Stefania Abbruzzetti
- Dipartimento di Fisica e Scienze della Terra, Università degli Studi di Parma, viale delle Scienze 7A, 43124, Parma, Italy
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20
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Winkler M, Esselborn J, Happe T. Molecular basis of [FeFe]-hydrogenase function: an insight into the complex interplay between protein and catalytic cofactor. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:974-85. [PMID: 23507618 DOI: 10.1016/j.bbabio.2013.03.004] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Revised: 02/21/2013] [Accepted: 03/08/2013] [Indexed: 12/20/2022]
Abstract
The precise electrochemical features of metal cofactors that convey the functions of redox enzymes are essentially determined by the specific interaction pattern between cofactor and enclosing protein environment. However, while biophysical techniques allow a detailed understanding of the features characterizing the cofactor itself, knowledge about the contribution of the protein part is much harder to obtain. [FeFe]-hydrogenases are an interesting class of enzymes that catalyze both, H2 oxidation and the reduction of protons to molecular hydrogen with significant efficiency. The active site of these proteins consists of an unusual prosthetic group (H-cluster) with six iron and six sulfur atoms. While H-cluster architecture and catalytic states during the different steps of H2 turnover have been thoroughly investigated during the last 20 years, possible functional contributions from the polypeptide framework were only assumed according to the level of conservancy and X-ray structure analyses. Due to the recent development of simpler and more efficient expression systems the role of single amino acids can now be experimentally investigated. This article summarizes, compares and categorizes the results of recent investigations based on site directed and random mutagenesis according to their informative value about structure function relationships in [FeFe]-hydrogenases. This article is part of a Special Issue entitled: Metals in Bioenergetics and Biomimetics Systems.
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Affiliation(s)
- Martin Winkler
- Ruhr-Universität Bochum, Fakultät für Biologie und Biotechnologie, Lehrstuhl für Biochemie der Pflanzen, AG Photobiotechnologie, Bochum, Germany
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21
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Structural features of [NiFeSe] and [NiFe] hydrogenases determining their different properties: a computational approach. J Biol Inorg Chem 2012; 17:543-55. [PMID: 22286956 DOI: 10.1007/s00775-012-0875-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2011] [Accepted: 01/12/2012] [Indexed: 10/14/2022]
Abstract
Hydrogenases are metalloenzymes that catalyze the reversible reaction H(2)<->2H(+) + 2e(-), being potentially useful in H(2) production or oxidation. [NiFeSe] hydrogenases are a particularly interesting subgroup of the [NiFe] class that exhibit tolerance to O(2) inhibition and produce more H(2) than standard [NiFe] hydrogenases. However, the molecular determinants responsible for these properties remain unknown. Hydrophobic pathways for H(2) diffusion have been identified in [NiFe] hydrogenases, as have proton transfer pathways, but they have never been studied in [NiFeSe] hydrogenases. Our aim was, for the first time, to characterize the H(2) and proton pathways in a [NiFeSe] hydrogenase and compare them with those in a standard [NiFe] hydrogenase. We performed molecular dynamics simulations of H(2) diffusion in the [NiFeSe] hydrogenase from Desulfomicrobium baculatum and extended previous simulations of the [NiFe] hydrogenase from Desulfovibrio gigas (Teixeira et al. in Biophys J 91:2035-2045, 2006). The comparison showed that H(2) density near the active site is much higher in [NiFeSe] hydrogenase, which appears to have an alternative route for the access of H(2) to the active site. We have also determined a possible proton transfer pathway in the [NiFeSe] hydrogenase from D. baculatum using continuum electrostatics and Monte Carlo simulation and compared it with the proton pathway we found in the [NiFe] hydrogenase from D. gigas (Teixeira et al. in Proteins 70:1010-1022, 2008). The residues constituting both proton transfer pathways are considerably different, although in the same region of the protein. These results support the hypothesis that some of the special properties of [NiFeSe] hydrogenases could be related to differences in the H(2) and proton pathways.
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22
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Mechanistic insight into the blocking of CO diffusion in [NiFe]-hydrogenase mutants through multiscale simulation. Proc Natl Acad Sci U S A 2012; 109:6399-404. [PMID: 22493222 DOI: 10.1073/pnas.1121176109] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
[NiFe]-hydrogenases are fascinating biological catalysts with potential application in biofuel cells. However, a severe problem in practical application is the strong sensitivity of hydrogenase to gaseous inhibitor molecules such as CO and O(2). Recently, a number of successful protein engineering studies have been reported that aimed at lowering the access of diatomic inhibitors to the active site pocket, but the molecular mechanism conferring increased resistance remained unclear. Here we use a multiscale simulation approach combining molecular dynamics with a master equation formalism to explain the steady drop in CO diffusion rate observed for the mutants V74M L122A, V74M L122M, and V74M of Desulfovibrio fructosovorans [NiFe]-hydrogenase. We find that diffusion in these variants is controlled by two gates, one between residues 74 and 476 and the other between residues 74 and 122. The existence of two control points in different locations explains why the reduction in the experimental diffusion rate does not simply correlate with the width of the main gas channel. We also find that in the more effective mutation (V74M) CO molecules are still able to reach the active site through transitions that are gated by the microsecond dihedral motions of the side chain of R476 and the thermal fluctuations of the width of the gas channel defined by M74 and L122. Reflecting on the molecular information gained from simulation, we discuss future mutation experiments that could further lower the diffusion rates of small ligands inhibiting [NiFe]-hydrogenase.
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24
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Topin J, Rousset M, Antonczak S, Golebiowski J. Kinetics and thermodynamics of gas diffusion in a NiFe hydrogenase. Proteins 2011; 80:677-82. [PMID: 22189859 DOI: 10.1002/prot.23248] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2011] [Revised: 11/08/2011] [Accepted: 11/09/2011] [Indexed: 11/12/2022]
Abstract
We have investigated O₂ and H₂ transport across a NiFe hydrogenase at the atomic scale by means of computational methods. The Wild Type protein has been compared with the V74Q mutant. Two distinct methodologies have been applied to study the gas access to the active site. Temperature locally enhanced sampling simulations have emphasized the importance of protein dynamics on gas diffusion. The O₂ diffusion free energy profiles, obtained by umbrella sampling, are in agreement with the known kinetic data and show that in the V74Q mutant, the inhibition process is lowered from both a kinetic and a thermodynamic point of view.
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Affiliation(s)
- Jérémie Topin
- LCMBA-UMR CNRS 6001, Institut de Chimie de Nice, Université de Nice-Sophia Antipolis, Faculté des Sciences, 06108 Nice Cedex 2, France
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25
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Abstract
The H(2)-evolving potential of [FeFe] hydrogenases is severely limited by the oxygen sensitivity of this class of enzymes. Recent experimental studies on hydrogenase from C. reinhardtii point to O(2)-induced structural changes in the [Fe(4)S(4)] subsite of the H cluster. Here, we investigate the mechanistic basis of this observation by means of density functional theory. Unexpectedly, we find that the isolated H cluster shows a pathological catalytic activity for the formation of reactive oxygen species such as O(2)(-) and HO(2)(-). After protonation of O(2)(-), an OOH radical may coordinate to the Fe atoms of the cubane, whereas H(2)O(2) specifically reacts with the S atoms of the cubane-coordinating cysteine residues. Both pathways are accompanied by significant structural distortions that compromise cluster integrity and thus catalytic activity. These results explain the experimental observation that O(2)-induced inhibition is accompanied by distortions of the [Fe(4)S(4)] moiety and account for the irreversibility of this process.
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Affiliation(s)
- Marta K. Bruska
- Laboratorium für Physikalische Chemie, ETH Zurich, Wolfgang-Pauli-Strasse 10 8093 Zürich, Switzerland
| | - Martin T. Stiebritz
- Laboratorium für Physikalische Chemie, ETH Zurich, Wolfgang-Pauli-Strasse 10 8093 Zürich, Switzerland
| | - Markus Reiher
- Laboratorium für Physikalische Chemie, ETH Zurich, Wolfgang-Pauli-Strasse 10 8093 Zürich, Switzerland
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26
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Forti F, Boechi L, Bikiel D, Martí MA, Nardini M, Bolognesi M, Viappiani C, Estrin D, Luque FJ. Ligand Migration in Methanosarcina acetivorans Protoglobin: Effects of Ligand Binding and Dimeric Assembly. J Phys Chem B 2011; 115:13771-80. [DOI: 10.1021/jp208562b] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Flavio Forti
- Departament de Fisicoquímica and Institut de Biomedicina, Facultat de Farmàcia, Universitat de Barcelona, Avinguda Diagonal 643, E-08028, Barcelona, Spain
| | - Leonardo Boechi
- Departamento de Química Inorgánica, Analítica, y Química Física, INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina
| | - Damian Bikiel
- Departamento de Química Inorgánica, Analítica, y Química Física, INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina
| | - Marcelo A. Martí
- Departamento de Química Inorgánica, Analítica, y Química Física, INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina
| | - Marco Nardini
- Dipartimento di Scienze Biomolecolari e Biotecnologie and CIMAINA, Università degli Studi di Milano, I-20131 Milano, Italy
| | - Martino Bolognesi
- Dipartimento di Scienze Biomolecolari e Biotecnologie and CIMAINA, Università degli Studi di Milano, I-20131 Milano, Italy
| | - Cristiano Viappiani
- Dipartimento di Fisica, Università degli Studi di Parma, Parma, Italy
- NEST, Istituto Nanoscienze-CNR, Italy
| | - Darío Estrin
- Departamento de Química Inorgánica, Analítica, y Química Física, INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina
| | - F. Javier Luque
- Departament de Fisicoquímica and Institut de Biomedicina, Facultat de Farmàcia, Universitat de Barcelona, Avinguda Diagonal 643, E-08028, Barcelona, Spain
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