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Warmack RA, Rees DC. Nitrogenase beyond the Resting State: A Structural Perspective. Molecules 2023; 28:7952. [PMID: 38138444 PMCID: PMC10745740 DOI: 10.3390/molecules28247952] [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: 11/06/2023] [Revised: 11/30/2023] [Accepted: 12/01/2023] [Indexed: 12/24/2023] Open
Abstract
Nitrogenases have the remarkable ability to catalyze the reduction of dinitrogen to ammonia under physiological conditions. How does this happen? The current view of the nitrogenase mechanism focuses on the role of hydrides, the binding of dinitrogen in a reductive elimination process coupled to loss of dihydrogen, and the binding of substrates to a binuclear site on the active site cofactor. This review focuses on recent experimental characterizations of turnover relevant forms of the enzyme determined by cryo-electron microscopy and other approaches, and comparison of these forms to the resting state enzyme and the broader family of iron sulfur clusters. Emerging themes include the following: (i) The obligatory coupling of protein and electron transfers does not occur in synthetic and small-molecule iron-sulfur clusters. The coupling of these processes in nitrogenase suggests that they may involve unique features of the cofactor, such as hydride formation on the trigonal prismatic arrangement of irons, protonation of belt sulfurs, and/or protonation of the interstitial carbon. (ii) Both the active site cofactor and protein are dynamic under turnover conditions; the changes are such that more highly reduced forms may differ in key ways from the resting-state structure. Homocitrate appears to play a key role in coupling cofactor and protein dynamics. (iii) Structural asymmetries are observed in nitrogenase under turnover-relevant conditions by cryo-electron microscopy, although the mechanistic relevance of these states (such as half-of-sites reactivity) remains to be established.
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Affiliation(s)
- Rebeccah A. Warmack
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | - Douglas C. Rees
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA
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2
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Sharma G, Merz KM. Formation of the Metal-Binding Core of the ZRT/IRT-like Protein (ZIP) Family Zinc Transporter. Biochemistry 2021; 60:2727-2738. [PMID: 34455776 DOI: 10.1021/acs.biochem.1c00415] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Zinc homeostasis in mammals is constantly and precisely maintained by sophisticated regulatory proteins. Among them, the Zrt/Irt-like protein (ZIP) regulates the influx of zinc into the cytoplasm. In this work, we have employed all-atom molecular dynamics simulations to investigate the Zn2+ transport mechanism in prokaryotic ZIP obtained from Bordetella bronchiseptica (BbZIP) in a membrane bilayer. Additionally, the structural and dynamical transformations of BbZIP during this process have been analyzed. This study allowed us to develop a hypothesis for the zinc influx mechanism and formation of the metal-binding site. We have created a model for the outward-facing form of BbZIP (experimentally only the inward-facing form has been characterized) that has allowed us, for the first time, to observe the Zn2+ ion entering the channel and binding to the negatively charged M2 site. It is thought that the M2 site is less favored than the M1 site, which then leads to metal ion egress; however, we have not observed the M1 site being occupied in our simulations. Furthermore, removing both Zn2+ ions from this complex resulted in the collapse of the metal-binding site, illustrating the "structural role" of metal ions in maintaining the binding site and holding the proteins together. Finally, due to the long Cd2+-residue bond distances observed in the X-ray structures, we have proposed the existence of an H3O+ ion at the M2 site that plays an important role in protein stability in the absence of the metal ion.
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Affiliation(s)
- Gaurav Sharma
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Kenneth M Merz
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States.,Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, United States
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3
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Helliwell JR. Combining X-rays, neutrons and electrons, and NMR, for precision and accuracy in structure-function studies. Acta Crystallogr A Found Adv 2021; 77:173-185. [PMID: 33944796 PMCID: PMC8127390 DOI: 10.1107/s205327332100317x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 03/25/2021] [Indexed: 02/02/2023] Open
Abstract
The distinctive features of the physics-based probes used in understanding the structure of matter focusing on biological sciences, but not exclusively, are described in the modern context. This is set in a wider scope of holistic biology and the scepticism about `reductionism', what is called the `molecular level', and how to respond constructively. These topics will be set alongside the principles of accuracy and precision, and their boundaries. The combination of probes and their application together is the usual way of realizing accuracy. The distinction between precision and accuracy can be blurred by the predictive force of a precise structure, thereby lending confidence in its potential accuracy. These descriptions will be applied to the comparison of cryo and room-temperature protein crystal structures as well as the solid state of a crystal and the same molecules studied by small-angle X-ray scattering in solution and by electron microscopy on a sample grid. Examples will include: time-resolved X-ray Laue crystallography of an enzyme Michaelis complex formed directly in a crystal equivalent to in vivo; a new iodoplatin for radiation therapy predicted from studies of platin crystal structures; and the field of colouration of carotenoids, as an effective assay of function, i.e. their colouration, when unbound and bound to a protein. The complementarity of probes, as well as their combinatory use, is then at the foundation of real (biologically relevant), probe-artefacts-free, structure-function studies. The foundations of our methodologies are being transformed by colossal improvements in technologies of X-ray and neutron sources and their beamline instruments, as well as improved electron microscopes and NMR spectrometers. The success of protein structure prediction from gene sequence recently reported by CASP14 also opens new doors to change and extend the foundations of the structural sciences.
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Affiliation(s)
- John R. Helliwell
- Department of Chemistry, University of Manchester, Manchester, M13 9PL, United Kingdom
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Ikeda T, Saito K, Hasegawa R, Ishikita H. The Existence of an Isolated Hydronium Ion in the Interior of Proteins. Angew Chem Int Ed Engl 2017; 56:9151-9154. [PMID: 28613440 PMCID: PMC5575531 DOI: 10.1002/anie.201705512] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Indexed: 12/20/2022]
Abstract
Neutron diffraction analysis studies reported an isolated hydronium ion (H3O+) in the interior of d‐xylose isomerase (XI) and phycocyanobilin‐ferredoxin oxidoreductase (PcyA). H3O+ forms hydrogen bonds (H‐bonds) with two histidine side‐chains and a backbone carbonyl group in PcyA, whereas H3O+ forms H‐bonds with three acidic residues in XI. Using a quantum mechanical/molecular mechanical (QM/MM) approach, we analyzed stabilization of H3O+ by the protein environment. QM/MM calculations indicated that H3O+ was unstable in the PcyA crystal structure, releasing a proton to an H‐bond partner His88, producing H2O and protonated His88. On the other hand, H3O+ was stable in the XI crystal structure. H‐bond partners of isolated H3O+ would be practically limited to acidic residues such as aspartic and glutamic acids in the protein environment.
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Affiliation(s)
- Takuya Ikeda
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8654, Japan
| | - Keisuke Saito
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8654, Japan.,Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8904, Japan
| | - Ryo Hasegawa
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8654, Japan
| | - Hiroshi Ishikita
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8654, Japan.,Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8904, Japan
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Ikeda T, Saito K, Hasegawa R, Ishikita H. The Existence of an Isolated Hydronium Ion in the Interior of Proteins. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201705512] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Takuya Ikeda
- Department of Applied Chemistry The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8654 Japan
| | - Keisuke Saito
- Department of Applied Chemistry The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8654 Japan
- Research Center for Advanced Science and Technology The University of Tokyo 4-6-1 Komaba, Meguro-ku Tokyo 153-8904 Japan
| | - Ryo Hasegawa
- Department of Applied Chemistry The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8654 Japan
| | - Hiroshi Ishikita
- Department of Applied Chemistry The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8654 Japan
- Research Center for Advanced Science and Technology The University of Tokyo 4-6-1 Komaba, Meguro-ku Tokyo 153-8904 Japan
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6
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Yee AW, Moulin M, Breteau N, Haertlein M, Mitchell EP, Cooper JB, Boeri Erba E, Forsyth VT. Impact of Deuteration on the Assembly Kinetics of Transthyretin Monitored by Native Mass Spectrometry and Implications for Amyloidoses. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201602747] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ai Woon Yee
- Life Sciences group, ILL 71 avenue des Martyrs 38042 Grenoble France
- Faculty of Natural SciencesKeele University Staffordshire ST5 5BG UK
| | - Martine Moulin
- Life Sciences group, ILL 71 avenue des Martyrs 38042 Grenoble France
- Faculty of Natural SciencesKeele University Staffordshire ST5 5BG UK
| | - Nina Breteau
- Life Sciences group, ILL 71 avenue des Martyrs 38042 Grenoble France
| | - Michael Haertlein
- Life Sciences group, ILL 71 avenue des Martyrs 38042 Grenoble France
| | - Edward P. Mitchell
- Faculty of Natural SciencesKeele University Staffordshire ST5 5BG UK
- ESRF 71 avenue des Martyrs 38042 Grenoble France
| | - Jonathan B. Cooper
- Laboratory of Protein Crystallography, Drug Discovery GroupWolfson Institute for Biomedical Research, UCL London WC1E 6BT UK
| | - Elisabetta Boeri Erba
- Univ. Grenoble Alpes, IBS 38044 Grenoble France
- CNRS, IBS 38044 Grenoble France
- CEA, IBS 38044 Grenoble France
| | - V. Trevor Forsyth
- Life Sciences group, ILL 71 avenue des Martyrs 38042 Grenoble France
- Faculty of Natural SciencesKeele University Staffordshire ST5 5BG UK
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7
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Yee AW, Moulin M, Breteau N, Haertlein M, Mitchell EP, Cooper JB, Boeri Erba E, Forsyth VT. Impact of Deuteration on the Assembly Kinetics of Transthyretin Monitored by Native Mass Spectrometry and Implications for Amyloidoses. Angew Chem Int Ed Engl 2016; 55:9292-6. [PMID: 27311939 PMCID: PMC5094506 DOI: 10.1002/anie.201602747] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Indexed: 01/13/2023]
Abstract
It is well established that the formation of transthyretin (TTR) amyloid fibrils is linked to the destabilization and dissociation of its tetrameric structure into insoluble aggregates. Isotope labeling is used for the study of TTR by NMR, neutron diffraction, and mass spectrometry (MS). Here MS, thioflavin T fluorescence, and crystallographic data demonstrate that while the X-ray structures of unlabeled and deuterium-labeled TTR are essentially identical, subunit exchange kinetics and amyloid formation are accelerated for the deuterated protein. However, a slower subunit exchange is noted in deuterated solvent, reflecting the poorer solubility of non-polar protein side chains in such an environment. These observations are important for the interpretation of kinetic studies involving deuteration. The destabilizing effects of TTR deuteration are rather similar in character to those observed for aggressive mutations of TTR such as L55P (associated with familial amyloid polyneuropathy).
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Affiliation(s)
- Ai Woon Yee
- Life Sciences group, ILL, 71 avenue des Martyrs, 38042, Grenoble, France
- Faculty of Natural Sciences, Keele University, Staffordshire, ST5 5BG, UK
| | - Martine Moulin
- Life Sciences group, ILL, 71 avenue des Martyrs, 38042, Grenoble, France
- Faculty of Natural Sciences, Keele University, Staffordshire, ST5 5BG, UK
| | - Nina Breteau
- Life Sciences group, ILL, 71 avenue des Martyrs, 38042, Grenoble, France
| | - Michael Haertlein
- Life Sciences group, ILL, 71 avenue des Martyrs, 38042, Grenoble, France
| | - Edward P Mitchell
- Faculty of Natural Sciences, Keele University, Staffordshire, ST5 5BG, UK
- ESRF, 71 avenue des Martyrs, 38042, Grenoble, France
| | - Jonathan B Cooper
- Laboratory of Protein Crystallography, Drug Discovery Group, Wolfson Institute for Biomedical Research, UCL, London, WC1E 6BT, UK
| | - Elisabetta Boeri Erba
- Univ. Grenoble Alpes, IBS, 38044, Grenoble, France.
- CNRS, IBS, 38044, Grenoble, France.
- CEA, IBS, 38044, Grenoble, France.
| | - V Trevor Forsyth
- Life Sciences group, ILL, 71 avenue des Martyrs, 38042, Grenoble, France.
- Faculty of Natural Sciences, Keele University, Staffordshire, ST5 5BG, UK.
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Gerlits O, Wymore T, Das A, Shen CH, Parks JM, Smith JC, Weiss KL, Keen DA, Blakeley MP, Louis JM, Langan P, Weber IT, Kovalevsky A. Long-Range Electrostatics-Induced Two-Proton Transfer Captured by Neutron Crystallography in an Enzyme Catalytic Site. Angew Chem Int Ed Engl 2016; 55:4924-7. [PMID: 26958828 DOI: 10.1002/anie.201509989] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 01/27/2016] [Indexed: 11/11/2022]
Abstract
Neutron crystallography was used to directly locate two protons before and after a pH-induced two-proton transfer between catalytic aspartic acid residues and the hydroxy group of the bound clinical drug darunavir, located in the catalytic site of enzyme HIV-1 protease. The two-proton transfer is triggered by electrostatic effects arising from protonation state changes of surface residues far from the active site. The mechanism and pH effect are supported by quantum mechanics/molecular mechanics (QM/MM) calculations. The low-pH proton configuration in the catalytic site is deemed critical for the catalytic action of this enzyme and may apply more generally to other aspartic proteases. Neutrons therefore represent a superb probe to obtain structural details for proton transfer reactions in biological systems at a truly atomic level.
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Affiliation(s)
- Oksana Gerlits
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Troy Wymore
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Amit Das
- Solid State Physics Division, BARC, Trombay, Mumbai, 400085, India
| | - Chen-Hsiang Shen
- Departments of Chemistry and Biology, Georgia State University, Atlanta, GA, 30302, USA
| | - Jerry M Parks
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Jeremy C Smith
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Kevin L Weiss
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - David A Keen
- ISIS Facility, Rutherford Appleton Laboratory, Harwell Oxford, Didcot, OX11 0QX, UK
| | - Matthew P Blakeley
- Large-Scale Structures Group, Institut Laue Langevin, 71 avenue des Martyrs - CS 20156, 38042, Grenoble Cedex 9, France
| | - John M Louis
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD, 20892-0520, USA
| | - Paul Langan
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Irene T Weber
- Departments of Chemistry and Biology, Georgia State University, Atlanta, GA, 30302, USA
| | - Andrey Kovalevsky
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
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9
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Gerlits O, Wymore T, Das A, Shen CH, Parks JM, Smith JC, Weiss KL, Keen DA, Blakeley MP, Louis JM, Langan P, Weber IT, Kovalevsky A. Long-Range Electrostatics-Induced Two-Proton Transfer Captured by Neutron Crystallography in an Enzyme Catalytic Site. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201509989] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Oksana Gerlits
- Biology and Soft Matter Division; Oak Ridge National Laboratory; Oak Ridge TN 37831 USA
| | - Troy Wymore
- UT/ORNL Center for Molecular Biophysics; Biosciences Division; Oak Ridge National Laboratory; Oak Ridge TN 37831 USA
| | - Amit Das
- Solid State Physics Division; BARC; Trombay Mumbai 400085 India
| | - Chen-Hsiang Shen
- Departments of Chemistry and Biology; Georgia State University; Atlanta GA 30302 USA
| | - Jerry M. Parks
- UT/ORNL Center for Molecular Biophysics; Biosciences Division; Oak Ridge National Laboratory; Oak Ridge TN 37831 USA
| | - Jeremy C. Smith
- UT/ORNL Center for Molecular Biophysics; Biosciences Division; Oak Ridge National Laboratory; Oak Ridge TN 37831 USA
| | - Kevin L. Weiss
- Biology and Soft Matter Division; Oak Ridge National Laboratory; Oak Ridge TN 37831 USA
| | - David A. Keen
- ISIS Facility; Rutherford Appleton Laboratory; Harwell Oxford Didcot OX11 0QX UK
| | - Matthew P. Blakeley
- Large-Scale Structures Group; Institut Laue Langevin; 71 avenue des Martyrs - CS 20156 38042 Grenoble Cedex 9 France
| | - John M. Louis
- Laboratory of Chemical Physics; National Institute of Diabetes and Digestive and Kidney Diseases; National Institutes of Health, DHHS; Bethesda MD 20892-0520 USA
| | - Paul Langan
- Biology and Soft Matter Division; Oak Ridge National Laboratory; Oak Ridge TN 37831 USA
| | - Irene T. Weber
- Departments of Chemistry and Biology; Georgia State University; Atlanta GA 30302 USA
| | - Andrey Kovalevsky
- Biology and Soft Matter Division; Oak Ridge National Laboratory; Oak Ridge TN 37831 USA
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