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Rozza AM, Menyhárd DK, Oláh J. Gas Sensing by Bacterial H-NOX Proteins: An MD Study. Molecules 2020; 25:molecules25122882. [PMID: 32585836 PMCID: PMC7356049 DOI: 10.3390/molecules25122882] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 06/17/2020] [Accepted: 06/17/2020] [Indexed: 01/08/2023] Open
Abstract
Gas sensing is crucial for both prokaryotes and eukaryotes and is primarily performed by heme-based sensors, including H-NOX domains. These systems may provide a new, alternative mode for transporting gaseous molecules in higher organisms, but for the development of such systems, a detailed understanding of the ligand-binding properties is required. Here, we focused on ligand migration within the protein matrix: we performed molecular dynamics simulations on three bacterial (Ka, Ns and Cs) H-NOX proteins and studied the kinetics of CO, NO and O2 diffusion. We compared the response of the protein structure to the presence of ligands, diffusion rate constants, tunnel systems and storage pockets. We found that the rate constant for diffusion decreases in the O2 > NO > CO order in all proteins, and in the Ns > Ks > Cs order if single-gas is considered. Competition between gases seems to seriously influence the residential time of ligands spent in the distal pocket. The channel system is profoundly determined by the overall fold, but the sidechain pattern has a significant role in blocking certain channels by hydrophobic interactions between bulky groups, cation-π interactions or hydrogen bonding triads. The majority of storage pockets are determined by local sidechain composition, although certain functional cavities, such as the distal and proximal pockets are found in all systems. A major guideline for the design of gas transport systems is the need to chemically bind the gas molecule to the protein, possibly joining several proteins with several heme groups together.
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Affiliation(s)
- Ahmed M. Rozza
- Department of Inorganic and Analytical Chemistry, Budapest University of Technology, Budapest Szent Gellért tér 4, H-1111 Budapest, Hungary;
- Department of Biotechnology, Faculty of Agriculture, Al-Azhar University, Cairo 11651, Egypt
| | - Dóra K. Menyhárd
- Laboratory of Structural Chemistry and Biology & MTA-ELTE Protein Modelling Research Group, Institute of Chemistry, Eötvös Loránd University, Pázmány Péter sétány 1/A, 1117 Budapest, Hungary
- Correspondence: (D.K.M.); (J.O.)
| | - Julianna Oláh
- Department of Inorganic and Analytical Chemistry, Budapest University of Technology, Budapest Szent Gellért tér 4, H-1111 Budapest, Hungary;
- Correspondence: (D.K.M.); (J.O.)
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Lu Y, Koo J. O 2 sensitivity and H 2 production activity of hydrogenases-A review. Biotechnol Bioeng 2019; 116:3124-3135. [PMID: 31403182 DOI: 10.1002/bit.27136] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Revised: 07/23/2019] [Accepted: 08/05/2019] [Indexed: 01/24/2023]
Abstract
Hydrogenases are metalloproteins capable of catalyzing the interconversion between molecular hydrogen and protons and electrons. The iron-sulfur clusters within the enzyme enable rapid relay of electrons which are either consumed or generated at the active site. Their unparalleled catalytic efficiency has attracted attention, especially for potential use in H2 production and/or fuel cell technologies. However, there are limitations to using hydrogenases, especially due to their high O2 sensitivity. The subclass, called [FeFe] hydrogenases, are particularly more vulnerable to O2 but proficient in H2 production. In this review, we provide an overview of mechanistic and protein engineering studies focused on understanding and enhancing O2 tolerance of the enzyme. The emphasis is on ongoing studies that attempt to overcome O2 sensitivity of the enzyme while it catalyzes H2 production in an aerobic environment. We also discuss pioneering attempts to utilize the enzyme in biological H2 production and other industrial processes, as well as our own perspective on future applications.
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Affiliation(s)
- Yuan Lu
- Department of Chemical Engineering, Tsinghua University, Beijing, China
| | - Jamin Koo
- Department of Chemical Engineering, Hongik University, Seoul, Republic of Korea
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del Barrio M, Sensi M, Orain C, Baffert C, Dementin S, Fourmond V, Léger C. Electrochemical Investigations of Hydrogenases and Other Enzymes That Produce and Use Solar Fuels. Acc Chem Res 2018. [PMID: 29517230 DOI: 10.1021/acs.accounts.7b00622] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Many enzymes that produce or transform small molecules such as O2, H2, and CO2 embed inorganic cofactors based on transition metals. Their active site, where the chemical reaction occurs, is buried in and protected by the protein matrix, and connected to the solvent in several ways: chains of redox cofactors mediate long-range electron transfer; static or dynamic tunnels guide the substrate, product and inhibitors; amino acids and water molecules transfer protons. The catalytic mechanism of these enzymes is therefore delocalized over the protein and involves many different steps, some of which determine the response of the enzyme under conditions of stress (extreme redox conditions, presence of inhibitors, light), the catalytic rates in the two directions of the reaction and their ratio (the "catalytic bias"). Understanding all the steps in the catalytic cycle, including those that occur on sites of the protein that are remote from the active site, requires a combination of biochemical, structural, spectroscopic, theoretical, and kinetic methods. Here we argue that kinetics should be used to the fullest extent, by extracting quantitative information from the comparison of data and kinetic models and by exploring the combination of experimental kinetics and theoretical chemistry. In studies of these catalytic mechanisms, direct electrochemistry, the technique which we use and contribute to develop, has become unescapable. It simply consists in monitoring the changes in activity of an enzyme that is wired to an electrode by recording an electric current. We have described kinetic models that can be used to make sense of these data and to learn about various aspects of the mechanism that are difficult to probe using more conventional methods: long-range electron transfer, diffusion along gas channels, redox-driven (in)activations, active site chemistry and photoreactivity under conditions of turnover. In this Account, we highlight a few results that illustrate our approach. We describe how electrochemistry can be used to monitor substrate and inhibitor diffusion along the gas channels of hydrogenases and we discuss how the kinetics of intramolecular diffusion relates to global properties such as resistance to oxygen and catalytic bias. The kinetics and/or thermodynamics of intramolecular electron transfer may also affect the catalytic bias, the catalytic potentials on either side of the equilibrium potential, and the overpotentials for catalysis (defined as the difference between the catalytic potentials and the open circuit potential). This is understood by modeling the shape of the steady-state catalytic response of the enzyme. Other determinants of the catalytic rate, such as domain motions, have been probed by examining the transient catalytic response recorded at fast scan rates. Last, we show that combining electrochemical investigations and MD, DFT, and TD-DFT calculations is an original way of probing the reactivity of the H-cluster of hydrogenase, in particular its reactions with CO, O2, and light. This approach contrasts with the usual strategy which aims at stabilizing species that are presumed to be catalytic intermediates, and determining their structure using spectroscopic or structural methods.
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Affiliation(s)
- Melisa del Barrio
- Aix Marseille Univ., CNRS, BIP, Laboratoire
de Bioénergétique et Ingénierie des Protéines,
UMR7281, Marseille France
| | - Matteo Sensi
- Aix Marseille Univ., CNRS, BIP, Laboratoire
de Bioénergétique et Ingénierie des Protéines,
UMR7281, Marseille France
| | - Christophe Orain
- Aix Marseille Univ., CNRS, BIP, Laboratoire
de Bioénergétique et Ingénierie des Protéines,
UMR7281, Marseille France
| | - Carole Baffert
- Aix Marseille Univ., CNRS, BIP, Laboratoire
de Bioénergétique et Ingénierie des Protéines,
UMR7281, Marseille France
| | - Sébastien Dementin
- Aix Marseille Univ., CNRS, BIP, Laboratoire
de Bioénergétique et Ingénierie des Protéines,
UMR7281, Marseille France
| | - Vincent Fourmond
- Aix Marseille Univ., CNRS, BIP, Laboratoire
de Bioénergétique et Ingénierie des Protéines,
UMR7281, Marseille France
| | - Christophe Léger
- Aix Marseille Univ., CNRS, BIP, Laboratoire
de Bioénergétique et Ingénierie des Protéines,
UMR7281, Marseille France
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4
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Lábas A, Menyhárd DK, Harvey JN, Oláh J. First Principles Calculation of the Reaction Rates for Ligand Binding to Myoglobin: The Cases of NO and CO. Chemistry 2018; 24:5350-5358. [PMID: 29285802 DOI: 10.1002/chem.201704867] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Indexed: 12/12/2022]
Abstract
Ligand binding by proteins is among the most fundamental processes in nature. Among these processes the binding of small gas molecules, such as O2 , CO and NO to heme proteins has traditionally received vivid interest, which was further boosted by their recently recognized significant role in gas sensing in the body. At the heart of the binding of these ligands to the heme group is the spinforbidden reaction between high-spin iron(II) and the ligand yielding a low-spin adduct. We use computational means to address the complete mechanism of CO and NO binding by myoglobin. Considering that it involves several steps occurring on different time scales, molecular dynamics simulations were performed to address the diffusion of the ligand through the enzyme, and DFT calculations in combination with statistical rate calculation to investigate the spin-forbidden reaction. The calculations yielded rate constants in qualitative agreement with experiments and revealed that the bottleneck of NO and CO binding is different; for NO, diffusion was found to be rate-limiting, whereas for CO, the spin-forbidden step is the slowest.
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Affiliation(s)
- Anikó Lábas
- Department of Inorganic Chemistry, Budapest University of Technology and Economics, H-1111, Budapest, Szent Gellért tér 4., Hungary
| | - Dóra K Menyhárd
- MTA-ELTE Protein Modelling Research Group, H-1117, Budapest, Pázmány Péter st. 1/A, Hungary
| | - Jeremy N Harvey
- Department of Chemistry, KU Leuven, B-3001, Leuven Celestijnenlaan 200F- box 2404, Belgium
| | - Julianna Oláh
- Department of Inorganic Chemistry, Budapest University of Technology and Economics, H-1111, Budapest, Szent Gellért tér 4., Hungary
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Quantum chemical approaches to [NiFe] hydrogenase. Essays Biochem 2017; 61:293-303. [PMID: 28487405 DOI: 10.1042/ebc20160079] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 02/22/2017] [Accepted: 03/01/2017] [Indexed: 11/17/2022]
Abstract
The mechanism by which [NiFe] hydrogenase catalyses the oxidation of molecular hydrogen is a significant yet challenging topic in bioinorganic chemistry. With far-reaching applications in renewable energy and carbon mitigation, significant effort has been invested in the study of these complexes. In particular, computational approaches offer a unique perspective on how this enzyme functions at an electronic and atomistic level. In this article, we discuss state-of-the art quantum chemical methods and how they have helped deepen our comprehension of [NiFe] hydrogenase. We outline the key strategies that can be used to compute the (i) geometry, (ii) electronic structure, (iii) thermodynamics and (iv) kinetic properties associated with the enzymatic activity of [NiFe] hydrogenase and other bioinorganic complexes.
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