1
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Jiang T, Wan G, Zhang H, Gyawali YP, Underbakke ES, Feng C. Mapping the Intersubunit Interdomain FMN-Heme Interactions in Neuronal Nitric Oxide Synthase by Targeted Quantitative Cross-Linking Mass Spectrometry. Biochemistry 2024; 63:1395-1411. [PMID: 38747545 DOI: 10.1021/acs.biochem.4c00157] [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] [Indexed: 05/29/2024]
Abstract
Nitric oxide synthase (NOS) in mammals is a family of multidomain proteins in which interdomain electron transfer (IET) is controlled by domain-domain interactions. Calmodulin (CaM) binds to the canonical CaM-binding site in the linker region between the FMN and heme domains of NOS and allows tethered FMN domain motions, enabling an intersubunit FMN-heme IET in the output state for NO production. Our previous cross-linking mass spectrometric (XL MS) results demonstrated site-specific protein dynamics in the CaM-responsive regions of rat neuronal NOS (nNOS) reductase construct, a monomeric protein [Jiang et al., Biochemistry, 2023, 62, 2232-2237]. In this work, we have extended our combined approach of XL MS structural mapping and AlphaFold structural prediction to examine the homodimeric nNOS oxygenase/FMN (oxyFMN) construct, an established model of the NOS output state. We employed parallel reaction monitoring (PRM) based quantitative XL MS (qXL MS) to assess the CaM-induced changes in interdomain dynamics and interactions. Intersubunit cross-links were identified by mapping the cross-links onto top AlphaFold structural models, which was complemented by comparing their relative abundances in the cross-linked dimeric and monomeric bands. Furthermore, contrasting the CaM-free and CaM-bound nNOS samples shows that CaM enables the formation of the intersubunit FMN-heme docking complex and that CaM binding induces extensive, allosteric conformational changes across the NOS regions. Moreover, the observed cross-links sites specifically respond to changes in ionic strength. This indicates that interdomain salt bridges are responsible for stabilizing and orienting the output state for efficient FMN-heme IET. Taken together, our targeted qXL MS results have revealed that CaM and ionic strength modulate specific dynamic changes in the CaM/FMN/heme complexes, particularly in the context of intersubunit interdomain FMN-heme interactions.
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Affiliation(s)
- Ting Jiang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Guanghua Wan
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Haikun Zhang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Yadav Prasad Gyawali
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Eric S Underbakke
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011, United States
| | - Changjian Feng
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico, Albuquerque, New Mexico 87131, United States
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
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2
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Bizet M, Byrne D, Biaso F, Gerbaud G, Etienne E, Briola G, Guigliarelli B, Urban P, Dorlet P, Kalai T, Truan G, Martinho M. Structural insights into the semiquinone form of human Cytochrome P450 reductase by DEER distance measurements between a native flavin and a spin labelled non-canonical amino acid. Chemistry 2024; 30:e202304307. [PMID: 38277424 DOI: 10.1002/chem.202304307] [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: 12/22/2023] [Revised: 01/25/2024] [Accepted: 01/26/2024] [Indexed: 01/28/2024]
Abstract
The flavoprotein Cytochrome P450 reductase (CPR) is the unique electron pathway from NADPH to Cytochrome P450 (CYPs). The conformational dynamics of human CPR in solution, which involves transitions from a "locked/closed" to an "unlocked/open" state, is crucial for electron transfer. To date, however, the factors guiding these changes remain unknown. By Site-Directed Spin Labelling coupled to Electron Paramagnetic Resonance spectroscopy, we have incorporated a non-canonical amino acid onto the flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD) domains of soluble human CPR, and labelled it with a specific nitroxide spin probe. Taking advantage of the endogenous FMN cofactor, we successfully measured for the first time, the distance distribution by DEER between the semiquinone state FMNH• and the nitroxide. The DEER data revealed a salt concentration-dependent distance distribution, evidence of an "open" CPR conformation at high salt concentrations exceeding previous reports. We also conducted molecular dynamics simulations which unveiled a diverse ensemble of conformations for the "open" semiquinone state of the CPR at high salt concentration. This study unravels the conformational landscape of the one electron reduced state of CPR, which had never been studied before.
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Affiliation(s)
- Maxime Bizet
- Aix Marseille Univ, CNRS, Bioénergétique et Ingénierie des Protéines, IMM, 13402, Marseille, France
| | - Deborah Byrne
- Protein Expression Facility, Aix Marseille Univ, CNRS, IMM, 13402, Marseille, France
| | - Frédéric Biaso
- Aix Marseille Univ, CNRS, Bioénergétique et Ingénierie des Protéines, IMM, 13402, Marseille, France
| | - Guillaume Gerbaud
- Aix Marseille Univ, CNRS, Bioénergétique et Ingénierie des Protéines, IMM, 13402, Marseille, France
| | - Emilien Etienne
- Aix Marseille Univ, CNRS, Bioénergétique et Ingénierie des Protéines, IMM, 13402, Marseille, France
| | - Giuseppina Briola
- Aix Marseille Univ, CNRS, Bioénergétique et Ingénierie des Protéines, IMM, 13402, Marseille, France
| | - Bruno Guigliarelli
- Aix Marseille Univ, CNRS, Bioénergétique et Ingénierie des Protéines, IMM, 13402, Marseille, France
| | - Philippe Urban
- TBI, Université de Toulouse, CNRS, INRAE, INSA, 31077, Toulouse, France
| | - Pierre Dorlet
- Aix Marseille Univ, CNRS, Bioénergétique et Ingénierie des Protéines, IMM, 13402, Marseille, France
| | - Tamas Kalai
- Department of Organic and Medicinal Chemistry, Faculty of Pharmacy, University of Pécs, PO Box 99 Szigeti st. 12, H-7602 7624, Pécs, Hungary
| | - Gilles Truan
- TBI, Université de Toulouse, CNRS, INRAE, INSA, 31077, Toulouse, France
| | - Marlène Martinho
- Aix Marseille Univ, CNRS, Bioénergétique et Ingénierie des Protéines, IMM, 13402, Marseille, France
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3
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Tumbic GW, Li J, Jiang T, Hossan MY, Feng C, Thielges MC. Interdomain Interactions Modulate the Active Site Dynamics of Human Inducible Nitric Oxide Synthase. J Phys Chem B 2022; 126:6811-6819. [PMID: 36056879 PMCID: PMC10110350 DOI: 10.1021/acs.jpcb.2c04091] [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] [Indexed: 11/28/2022]
Abstract
Nitric oxide synthase (NOS) is a homodimeric flavohemoprotein responsible for catalyzing the oxidation of l-arginine (l-Arg) to citrulline and nitric oxide. Electrons are supplied for the reaction via interdomain electron transfer between an N-terminal heme-containing oxygenase domain and a FMN-containing (sub)domain of a C-terminal reductase domain. Extensive attention has focused on elucidating how conformational dynamics regulate electron transfer between the domains. Here we investigate the impact of the interdomain FMN-heme interaction on the heme active site dynamics of inducible NOS (iNOS). Steady state linear and time-resolved two-dimensional infrared (2D IR) spectroscopy was applied to probe a CO ligand at the heme within the oxygenase domain for full-length and truncated or mutated constructs of human iNOS. Whereas the linear IR spectra of the CO ligand were identical among the constructs, 2D IR spectroscopy revealed variation in the frequency dynamics. The wild-type constructs that can properly form the FMN/oxygenase docked state due to the presence of both the FMN and oxygenase domains showed slower dynamics than the oxygenase domain alone. Introduction of the mutation (E546N) predicted to perturb electrostatic interactions between the domains resulted in measured dynamics intermediate between those for the full-length and individual oxygenase domain, consistent with perturbation to the docked/undocked equilibrium. These results indicate that docking of the FMN domain to the oxygenase domain not only brings the FMN cofactor within electron transfer distance of the heme domain but also modulates the dynamics sensed by the CO ligand within the active site in a way expected to promote efficient electron transfer.
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Affiliation(s)
- Goran W Tumbic
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Jinghui Li
- Department of Pharmaceutical Sciences, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Ting Jiang
- Department of Pharmaceutical Sciences, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Md Yeathad Hossan
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Changjian Feng
- Department of Pharmaceutical Sciences, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Megan C Thielges
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
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4
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Stewart AM, Shanmugam M, Kutta RJ, Scrutton NS, Lovett JE, Hay S. Combined Pulsed Electron Double Resonance EPR and Molecular Dynamics Investigations of Calmodulin Suggest Effects of Crowding Agents on Protein Structures. Biochemistry 2022; 61:1735-1742. [PMID: 35979922 PMCID: PMC9454100 DOI: 10.1021/acs.biochem.2c00099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Calmodulin (CaM) is a highly dynamic Ca2+-binding
protein
that exhibits large conformational changes upon binding Ca2+ and target proteins. Although it is accepted that CaM exists in
an equilibrium of conformational states in the absence of target protein,
the physiological relevance of an elongated helical linker region
in the Ca2+-replete form has been highly debated. In this
study, we use PELDOR (pulsed electron–electron double resonance)
EPR measurements of a doubly spin-labeled CaM variant to assess the
conformational states of CaM in the apo-, Ca2+-bound, and
Ca2+ plus target peptide-bound states. Our findings are
consistent with a three-state conformational model of CaM, showing
a semi-open apo-state, a highly extended Ca2+-replete state,
and a compact target protein-bound state. Molecular dynamics simulations
suggest that the presence of glycerol, and potentially other molecular
crowding agents, has a profound effect on the relative stability of
the different conformational states. Differing experimental conditions
may explain the discrepancies in the literature regarding the observed
conformational state(s) of CaM, and our PELDOR measurements show good
evidence for an extended conformation of Ca2+-replete CaM
similar to the one observed in early X-ray crystal structures.
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Affiliation(s)
- Andrew M Stewart
- The Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames 50011, Iowa, United States.,Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Muralidharan Shanmugam
- Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Roger J Kutta
- Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.,Institute of Physical and Theoretical Chemistry, University of Regensburg, Regensburg 93040, Germany
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Janet E Lovett
- SUPA School of Physics and Astronomy and BSRC, The University of St Andrews, St Andrews KY16 9SS, U.K
| | - Sam Hay
- Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
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5
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Hedison T, Iorgu AI, Calabrese D, Heyes DJ, Shanmugam M, Scrutton NS. Solution-State Inter-Copper Distribution of Redox Partner-Linked Copper Nitrite Reductases: A Pulsed Electron-Electron Double Resonance Spectroscopy Study. J Phys Chem Lett 2022; 13:6927-6934. [PMID: 35867774 PMCID: PMC9358711 DOI: 10.1021/acs.jpclett.2c01584] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 07/19/2022] [Indexed: 06/15/2023]
Abstract
Copper nitrite reductases (CuNiRs) catalyze the reduction of nitrite to form nitric oxide. In recent years, new classes of redox partner linked CuNiRs have been isolated and characterized by crystallographic techniques. Solution-state biophysical studies have shed light on the complex catalytic mechanisms of these enzymes and implied that protein dynamics may play a role in CuNiR catalysis. To investigate the structural, dynamical, and functional relationship of these CuNiRs, we have used protein reverse engineering and pulsed electron-electron double resonance (PELDOR) spectroscopy to determine their solution-state inter-copper distributions. Data show the multidimensional conformational landscape of this family of enzymes and the role of tethering in catalysis. The importance of combining high-resolution crystallographic techniques and low-resolution solution-state approaches in determining the structures and mechanisms of metalloenzymes is emphasized by our approach.
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Affiliation(s)
- Tobias
M. Hedison
- Manchester
Institute of Biotechnology and Department of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
- EPSRC/BBSRC
funded Future Biomanufacturing Research Hub, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Andreea I. Iorgu
- Manchester
Institute of Biotechnology and Department of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Donato Calabrese
- Manchester
Institute of Biotechnology and Department of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Derren J. Heyes
- Manchester
Institute of Biotechnology and Department of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Muralidharan Shanmugam
- Manchester
Institute of Biotechnology and Department of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Nigel S. Scrutton
- Manchester
Institute of Biotechnology and Department of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
- EPSRC/BBSRC
funded Future Biomanufacturing Research Hub, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
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6
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He Y, Haque MM, Stuehr DJ, Lu HP. Conformational States and Fluctuations in Endothelial Nitric Oxide Synthase under Calmodulin Regulation. Biophys J 2021; 120:5196-5206. [PMID: 34748763 DOI: 10.1016/j.bpj.2021.11.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 09/30/2021] [Accepted: 11/02/2021] [Indexed: 11/30/2022] Open
Abstract
Mechanisms that regulate nitric oxide synthase enzymes (NOS) are of interest in biology and medicine. Although NOS catalysis relies on domain motions and is activated by calmodulin (CaM) binding, the relationships are unclear. We used single-molecule fluorescence resonance energy transfer (FRET) spectroscopy to elucidate the conformational states distribution and associated conformational fluctuation dynamics of the two NOS electron transfer domains in a FRET dye-labeled endothelial NOS reductase domain (eNOSr) and to understand how CaM affects the dynamics to regulate catalysis by shaping the spatial and temporal conformational behaviors of eNOSr. In addition, we developed and applied a new imaging approach capable of recording 3D FRET efficiency vs time images to characterize the impact on dynamic conformal states of the eNOSr enzyme by the binding of CaM, which identifies clearly that CaM binding generates an extra new open state of eNOSr, resolving more detailed NOS conformational states and their fluctuation dynamics. We identified a new output state that has an extra-open FAD-FMN conformation that is only populated in the CaM-bound eNOSr. This may reveal the critical role of CaM in triggering NOS activity as it gives conformational flexibility for eNOSr to assume the electron transfer output FMN-Heme state. Our results provide a dynamic link to recently reported EM static structure analyses and demonstrate a capable approach in probing and simultaneously analyzing all of the conformational states, their fluctuations, and the fluctuation dynamics for understanding the mechanism of NOS electron transfer, involving electron transfer amongst FAD, FMN, and Heme domains, during NO synthesis.
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Affiliation(s)
- Yufan He
- Center for Photochemical Sciences, Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403
| | - Mohammad Mahfuzul Haque
- Department of Inflammation and Immunology, Lerner Research Institute, The Cleveland Clinic, 9500 Euclid Avenue, Cleveland Clinic, Cleveland, Ohio, 44195
| | - Dennis J Stuehr
- Department of Inflammation and Immunology, Lerner Research Institute, The Cleveland Clinic, 9500 Euclid Avenue, Cleveland Clinic, Cleveland, Ohio, 44195.
| | - H Peter Lu
- Center for Photochemical Sciences, Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403.
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7
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Monoclonal antibody stability can be usefully monitored using the excitation-energy-dependent fluorescence edge-shift. Biochem J 2021; 477:3599-3612. [PMID: 32869839 PMCID: PMC7527260 DOI: 10.1042/bcj20200580] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 08/27/2020] [Accepted: 09/01/2020] [Indexed: 11/17/2022]
Abstract
Among the major challenges in the development of biopharmaceuticals are structural heterogeneity and aggregation. The development of a successful therapeutic monoclonal antibody (mAb) requires both a highly active and also stable molecule. Whilst a range of experimental (biophysical) approaches exist to track changes in stability of proteins, routine prediction of stability remains challenging. The fluorescence red edge excitation shift (REES) phenomenon is sensitive to a range of changes in protein structure. Based on recent work, we have found that quantifying the REES effect is extremely sensitive to changes in protein conformational state and dynamics. Given the extreme sensitivity, potentially this tool could provide a ‘fingerprint’ of the structure and stability of a protein. Such a tool would be useful in the discovery and development of biopharamceuticals and so we have explored our hypothesis with a panel of therapeutic mAbs. We demonstrate that the quantified REES data show remarkable sensitivity, being able to discern between structurally identical antibodies and showing sensitivity to unfolding and aggregation. The approach works across a broad concentration range (µg–mg/ml) and is highly consistent. We show that the approach can be applied alongside traditional characterisation testing within the context of a forced degradation study (FDS). Most importantly, we demonstrate the approach is able to predict the stability of mAbs both in the short (hours), medium (days) and long-term (months). The quantified REES data will find immediate use in the biopharmaceutical industry in quality assurance, formulation and development. The approach benefits from low technical complexity, is rapid and uses instrumentation which exists in most biochemistry laboratories without modification.
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8
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Breslmayr E, Laurent CVFP, Scheiblbrandner S, Jerkovic A, Heyes DJ, Oostenbrink C, Ludwig R, Hedison TM, Scrutton NS, Kracher D. Protein Conformational Change Is Essential for Reductive Activation of Lytic Polysaccharide Monooxygenase by Cellobiose Dehydrogenase. ACS Catal 2020; 10:4842-4853. [PMID: 32382450 PMCID: PMC7199207 DOI: 10.1021/acscatal.0c00754] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 03/30/2020] [Indexed: 12/30/2022]
Abstract
Large-scale protein domain dynamics and electron transfer are often associated. However, as protein motions span a broad range of time and length scales, it is often challenging to identify and thus link functionally relevant dynamic changes to electron transfer in proteins. It is hypothesized that large-scale domain motions direct electrons through a FAD and a heme b cofactor of the fungal cellobiose dehydrogenase (CDH) enzymes to the type-II copper center (T2Cu) of the polysaccharide-degrading lytic polysaccharide monooxygenases (LPMOs). However, as of yet, domain motions in CDH have not been linked formally to enzyme-catalyzed electron transfer reactions. The detailed structural features of CDH, which govern the functional conformational landscapes of the enzyme, have only been partially resolved. Here, we use a combination of pressure, viscosity, ionic strength, and temperature perturbation stopped-flow studies to probe the conformational landscape associated with the electron transfer reactions of CDH. Through the use of molecular dynamics simulations, potentiometry, and stopped-flow spectroscopy, we investigated how a conserved Tyr99 residue plays a key role in shaping the conformational landscapes for both the interdomain electron transfer reactions of CDH (from FAD to heme) and the delivery of electrons from the reduced heme cofactor to the LPMO T2Cu. Our studies show how motions gate the electron transfer within CDH and from CDH to LPMO and illustrate the conformational landscape for interdomain and interprotein electron transfer in this extracellular fungal electron transfer chain.
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Affiliation(s)
- Erik Breslmayr
- Manchester Institute of Biotechnology, The University of Manchester, M1 7DN Manchester, United Kingdom
- Biocatalysis and Biosensing Laboratory, Department of Food Science and Technology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
- Department of Material Sciences and Process Engineering, Institute of Molecular Modeling and Simulation, Muthgasse 18, 1190 Vienna, Austria
| | - Christophe V. F. P. Laurent
- Biocatalysis and Biosensing Laboratory, Department of Food Science and Technology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
- Department of Material Sciences and Process Engineering, Institute of Molecular Modeling and Simulation, Muthgasse 18, 1190 Vienna, Austria
| | - Stefan Scheiblbrandner
- Biocatalysis and Biosensing Laboratory, Department of Food Science and Technology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Anita Jerkovic
- Biocatalysis and Biosensing Laboratory, Department of Food Science and Technology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Derren J. Heyes
- Manchester Institute of Biotechnology, The University of Manchester, M1 7DN Manchester, United Kingdom
| | - Chris Oostenbrink
- Department of Material Sciences and Process Engineering, Institute of Molecular Modeling and Simulation, Muthgasse 18, 1190 Vienna, Austria
| | - Roland Ludwig
- Biocatalysis and Biosensing Laboratory, Department of Food Science and Technology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Tobias M. Hedison
- Manchester Institute of Biotechnology, The University of Manchester, M1 7DN Manchester, United Kingdom
- EPSRC/BBSRC funded Future Biomanufacturing Research Hub, The Manchester Institute of Biotechnology, The University of Manchester, M1 7DN Manchester, United Kingdom
| | - Nigel S. Scrutton
- Manchester Institute of Biotechnology, The University of Manchester, M1 7DN Manchester, United Kingdom
- EPSRC/BBSRC funded Future Biomanufacturing Research Hub, The Manchester Institute of Biotechnology, The University of Manchester, M1 7DN Manchester, United Kingdom
| | - Daniel Kracher
- Manchester Institute of Biotechnology, The University of Manchester, M1 7DN Manchester, United Kingdom
- Biocatalysis and Biosensing Laboratory, Department of Food Science and Technology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
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9
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Hedison TM, Scrutton NS. Tripping the light fantastic in membrane redox biology: linking dynamic structures to function in ER electron transfer chains. FEBS J 2019; 286:2004-2017. [PMID: 30657259 PMCID: PMC6563164 DOI: 10.1111/febs.14757] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Revised: 12/16/2018] [Accepted: 01/15/2019] [Indexed: 12/19/2022]
Abstract
How the dynamics of proteins assist catalysis is a contemporary issue in enzymology. In particular, this holds true for membrane‐bound enzymes, where multiple structural, spectroscopic and biochemical approaches are needed to build up a comprehensive picture of how dynamics influence enzyme reaction cycles. Of note are the recent studies of cytochrome P450 reductases (CPR)–P450 (CYP) endoplasmic reticulum redox chains, showing the relationship between dynamics and electron flow through flavin and haem redox centres and the impact this has on monooxygenation chemistry. These studies have led to deeper understanding of mechanisms of electron flow, including the timing and control of electron delivery to protein‐bound cofactors needed to facilitate CYP‐catalysed reactions. Individual and multiple component systems have been used to capture biochemical behaviour and these have led to the emergence of more integrated models of catalysis. Crucially, the effects of membrane environment and composition on reaction cycle chemistry have also been probed, including effects on coenzyme binding/release, thermodynamic control of electron transfer, conformational coupling between partner proteins and vectorial versus ‘off pathway’ electron flow. Here, we review these studies and discuss evidence for the emergence of dynamic structural models of electron flow along human microsomal CPR–P450 redox chains.
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Affiliation(s)
- Tobias M Hedison
- Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, UK
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, UK
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10
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Hedison TM, Heyes DJ, Shanmugam M, Iorgu AI, Scrutton NS. Solvent-slaved protein motions accompany proton coupled electron transfer reactions catalysed by copper nitrite reductase. Chem Commun (Camb) 2019; 55:5863-5866. [DOI: 10.1039/c9cc01026b] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A novel approach to study PCET reactions illustrates the importance of solvent-slaved protein motions in copper nitrite reductase catalysis.
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Affiliation(s)
- Tobias M. Hedison
- The Manchester Institute of Biotechnology
- University of Manchester
- Manchester
- UK
| | - Derren J. Heyes
- The Manchester Institute of Biotechnology
- University of Manchester
- Manchester
- UK
| | | | - Andreea I. Iorgu
- The Manchester Institute of Biotechnology
- University of Manchester
- Manchester
- UK
| | - Nigel S. Scrutton
- The Manchester Institute of Biotechnology
- University of Manchester
- Manchester
- UK
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11
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Molecular mechanism of metabolic NAD(P)H-dependent electron-transfer systems: The role of redox cofactors. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1860:233-258. [PMID: 30419202 DOI: 10.1016/j.bbabio.2018.11.014] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 10/30/2018] [Accepted: 11/07/2018] [Indexed: 12/14/2022]
Abstract
NAD(P)H-dependent electron-transfer (ET) systems require three functional components: a flavin-containing NAD(P)H-dehydrogenase, one-electron carrier and metal-containing redox center. In principle, these ET systems consist of one-, two- and three-components, and the electron flux from pyridine nucleotide cofactors, NADPH or NADH to final electron acceptor follows a linear pathway: NAD(P)H → flavin → one-electron carrier → metal containing redox center. In each step ET is primarily controlled by one- and two-electron midpoint reduction potentials of protein-bound redox cofactors in which the redox-linked conformational changes during the catalytic cycle are required for the domain-domain interactions. These interactions play an effective ET reactions in the multi-component ET systems. The microsomal and mitochondrial cytochrome P450 (cyt P450) ET systems, nitric oxide synthase (NOS) isozymes, cytochrome b5 (cyt b5) ET systems and methionine synthase (MS) ET system include a combination of multi-domain, and their organizations display similarities as well as differences in their components. However, these ET systems are sharing of a similar mechanism. More recent structural information obtained by X-ray and cryo-electron microscopy (cryo-EM) analysis provides more detail for the mechanisms associated with multi-domain ET systems. Therefore, this review summarizes the roles of redox cofactors in the metabolic ET systems on the basis of one-electron redox potentials. In final Section, evolutionary aspects of NAD(P)H-dependent multi-domain ET systems will be discussed.
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12
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Arnett DC, Bailey SK, Johnson CK. Exploring the conformations of nitric oxide synthase with fluorescence. Front Biosci (Landmark Ed) 2018; 23:2133-2145. [PMID: 29772550 DOI: 10.2741/4694] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Multi-domain oxidoreductases are a family of enzymes that catalyze oxidation-reduction reactions through a series of electron transfers. Efficient electron transfer requires a sequence of protein conformations that position electron donor and acceptor domains in close proximity to each other so that electron transfer can occur efficiently. An example is mammalian nitric oxide synthase (NOS), which consists of an N-terminal oxygenase domain containing heme and a C-terminal reductase domain containing NADPH/FAD and FMN subdomains. We describe the use of time-resolved and single-molecule fluorescence to detect and characterize the conformations and conformational dynamics of the neuronal and endothelial isoforms of NOS. Fluorescence signals are provided by a fluorescent dye attached to the Ca2+-signaling protein calmodulin (CaM), which regulates NOS activity. Time-resolved fluorescence decays reveal the presence of at least four underlying conformational states that are differentiated by the extent of fluorescence quenching. Single-molecule fluorescence displays transitions between conformational states on the time scales of milliseconds to seconds. This review describes the type of information available by analysis of time-resolved and single-molecule fluorescence experiments.
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Affiliation(s)
- David C Arnett
- Department of Chemistry, Northwestern College, 101 7th Street SW, Orange City, IA 51041
| | - Sheila K Bailey
- Department of Chemistry, University of Kansas, 1251 Wescoe Drive, Lawrence, KS 66045
| | - Carey K Johnson
- Department of Chemistry, University of Kansas, 1251 Wescoe Drive, Lawrence, KS 66045,
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13
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Li J, Zheng H, Feng C. Deciphering mechanism of conformationally controlled electron transfer in nitric oxide synthases. FRONT BIOSCI-LANDMRK 2018; 23:1803-1821. [PMID: 29772530 PMCID: PMC11167721 DOI: 10.2741/4674] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Electron transfer is a fundamental process in life that is very often coupled to catalysis within redox enzymes through a stringent control of protein conformational movements. Mammalian nitric oxide synthase (NOS) proteins are redox flavo-hemoproteins consisting of multiple modular domains. The NOS enzyme is exquisitely regulated in vivo by its partner, the Ca2+ sensing protein calmodulin (CaM), to control production of nitric oxide (NO). The importance of functional domain motion in NOS regulation has been increasingly recognized. The significant size and flexibility of NOS is a tremendous challenge to the mechanistic studies. Herein recent applications of modern biophysical techniques to NOS problems have been critically analyzed. It is important to note that any current biophysical technique alone can only probe partial aspects of the conformational dynamics due to limitations in the technique itself and/or the sample preparations. It is necessary to combine the latest methods to comprehensively quantitate the key conformational aspects (conformational states and distribution, conformational change rates, and domain interacting interfaces) governing the electron transfer. This is to answer long-standing central questions about the NOS isoforms by defining how specific CaM-NOS interactions and regulatory elements underpin the distinct conformational behavior of the NOS isoform, which in turn determine unique electron transfer and NO synthesis properties. This review is not intended as comprehensive, but as a discussion of prospects that promise impact on important questions in the NOS enzymology field.
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Affiliation(s)
- Jinghui Li
- College of Pharmacy, University of New Mexico, Albuquerque, NM 87131, USA
| | - Huayu Zheng
- College of Pharmacy, University of New Mexico, Albuquerque, NM 87131, USA
| | - Changjian Feng
- University of New Mexico, MSC 09 5360, Albuquerque, NM 87131,
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14
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Hedison TM, Hay S, Scrutton NS. A perspective on conformational control of electron transfer in nitric oxide synthases. Nitric Oxide 2017; 63:61-67. [PMID: 27619338 PMCID: PMC5295631 DOI: 10.1016/j.niox.2016.09.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 09/05/2016] [Accepted: 09/06/2016] [Indexed: 01/20/2023]
Abstract
This perspective reviews single molecule and ensemble fluorescence spectroscopy studies of the three tissue specific nitric oxide synthase (NOS) isoenzymes and the related diflavin oxidoreductase cytochrome P450 reductase. The focus is on the role of protein dynamics and the protein conformational landscape and we discuss how recent fluorescence-based studies have helped in illustrating how the nature of the NOS conformational landscape relates to enzyme turnover and catalysis.
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Affiliation(s)
- Tobias M Hedison
- Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom
| | - Sam Hay
- Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom.
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15
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Piazza M, Taiakina V, Dieckmann T, Guillemette JG. Structural Consequences of Calmodulin EF Hand Mutations. Biochemistry 2017; 56:944-956. [PMID: 28121131 DOI: 10.1021/acs.biochem.6b01296] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Calmodulin (CaM) is a cytosolic Ca2+-binding protein that serves as a control element for many enzymes. It consists of two globular domains, each containing two EF hand pairs capable of binding Ca2+, joined by a flexible central linker region. CaM is able to bind and activate its target proteins in the Ca2+-replete and Ca2+-deplete forms. To study the Ca2+-dependent/independent properties of binding and activation of target proteins by CaM, CaM constructs with Ca2+-binding disrupting mutations of Asp to Ala at position one of each EF hand have been used. These CaM mutant proteins are deficient in binding Ca2+ in either the N-lobe EF hands (CaM12), C-lobe EF hands (CaM34), or all four EF hands (CaM1234). To investigate potential structural changes these mutations may cause, we performed detailed NMR studies of CaM12, CaM34, and CaM1234 including determining the solution structure of CaM1234. We then investigated if these CaM mutants affected the interaction of CaM with a target protein known to interact with apoCaM by determining the solution structure of CaM34 bound to the iNOS CaM binding domain peptide. The structures provide direct structural evidence of changes that are present in these Ca2+-deficient CaM mutants and show these mutations increase the hydrophobic exposed surface and decrease the electronegative surface potential throughout each lobe of CaM. These Ca2+-deficient CaM mutants may not be a true representation of apoCaM and may not allow for native-like interactions of apoCaM with its target proteins.
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Affiliation(s)
- Michael Piazza
- Department of Chemistry, University of Waterloo , Waterloo, Ontario N2L 3G1, Canada
| | - Valentina Taiakina
- Department of Chemistry, University of Waterloo , Waterloo, Ontario N2L 3G1, Canada
| | - Thorsten Dieckmann
- Department of Chemistry, University of Waterloo , Waterloo, Ontario N2L 3G1, Canada
| | - J Guy Guillemette
- Department of Chemistry, University of Waterloo , Waterloo, Ontario N2L 3G1, Canada
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16
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Piazza M, Dieckmann T, Guillemette JG. Structural Studies of a Complex Between Endothelial Nitric Oxide Synthase and Calmodulin at Physiological Calcium Concentration. Biochemistry 2016; 55:5962-5971. [DOI: 10.1021/acs.biochem.6b00821] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Michael Piazza
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Thorsten Dieckmann
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - J. Guy Guillemette
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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17
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Hedison TM, Leferink NGH, Hay S, Scrutton NS. Correlating Calmodulin Landscapes with Chemical Catalysis in Neuronal Nitric Oxide Synthase using Time-Resolved FRET and a 5-Deazaflavin Thermodynamic Trap. ACS Catal 2016; 6:5170-5180. [PMID: 27563493 PMCID: PMC4993522 DOI: 10.1021/acscatal.6b01280] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Revised: 06/23/2016] [Indexed: 11/28/2022]
Abstract
![]()
A major challenge in enzymology is
the need to correlate the dynamic
properties of enzymes with, and understand the impact on, their catalytic
cycles. This is especially the case with large, multicenter enzymes
such as the nitric oxide synthases (NOSs), where the importance of
dynamics has been inferred from a variety of structural, single-molecule,
and ensemble spectroscopic approaches but where motions have not been
correlated experimentally with mechanistic steps in the reaction cycle.
Here we take such an approach. Using time-resolved spectroscopy employing
absorbance and Förster resonance energy transfer (FRET) and
exploiting the properties of a flavin analogue (5-deazaflavin mononucleotide
(5-dFMN)) and isotopically labeled nicotinamide coenzymes, we correlate
the timing of CaM structural changes when bound to neuronal nitric
oxide synthase (nNOS) with the nNOS catalytic cycle. We show that
remodeling of CaM occurs early in the electron transfer sequence (FAD
reduction), not at later points in the reaction cycle (e.g., FMN reduction).
Conformational changes are tightly correlated with FAD reduction kinetics
and reflect a transient “opening” and then “closure”
of the bound CaM molecule. We infer that displacement of the C-terminal
tail on binding NADPH and subsequent FAD reduction are the likely
triggers of conformational change. By combining the use of cofactor/coenzyme
analogues and time-resolved FRET/absorbance spectrophotometry, we
show how the reaction cycles of complex enzymes can be simplified,
enabling a detailed study of the relationship between protein dynamics
and reaction cycle chemistry—an approach that can also be used
with other complex multicenter enzymes.
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Affiliation(s)
- Tobias M. Hedison
- Manchester Synthetic Biology
Research Centre for Fine and Speciality Chemicals (SYNBIOCHEM), Manchester
Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - Nicole G. H. Leferink
- Manchester Synthetic Biology
Research Centre for Fine and Speciality Chemicals (SYNBIOCHEM), Manchester
Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - Sam Hay
- Manchester Synthetic Biology
Research Centre for Fine and Speciality Chemicals (SYNBIOCHEM), Manchester
Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - Nigel S. Scrutton
- Manchester Synthetic Biology
Research Centre for Fine and Speciality Chemicals (SYNBIOCHEM), Manchester
Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, United Kingdom
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18
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Catici DAM, Amos HE, Yang Y, van den Elsen JMH, Pudney CR. The red edge excitation shift phenomenon can be used to unmask protein structural ensembles: implications for NEMO-ubiquitin interactions. FEBS J 2016; 283:2272-84. [PMID: 27028374 DOI: 10.1111/febs.13724] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 03/29/2016] [Indexed: 02/02/2023]
Abstract
To understand complex molecular interactions, it is necessary to account for molecular flexibility and the available equilibrium of conformational states. Only a small number of experimental approaches can access such information. Potentially steady-state red edge excitation shift (REES) spectroscopy can act as a qualitative metric of changes to the protein free energy landscape (FEL) and the equilibrium of conformational states. First, we validate this hypothesis using a single Trp-containing protein, NF-κB essential modulator (NEMO). We provide detailed evidence from chemical denaturation studies, macromolecular crowding studies, and the first report of the pressure dependence of the REES effect. Combination of these data demonstrate that the REES effect can report on the 'ruggedness' of the FEL and we present a phenomenological model, based on realistic physical interpretations, for fitting steady-state REES data to allow quantification of this aspect of the REES effect. We test the conceptual framework we have developed by correlating findings from NEMO ligand-binding studies with the REES data in a range of NEMO-ligand binary complexes. Our findings shed light on the nature of the interaction between NEMO and poly-ubiquitin, suggesting that NEMO is differentially regulated by poly-ubiquitin chain length and that this regulation occurs via a modulation of the available equilibrium of conformational states, rather than gross structural change. This study therefore demonstrates the potential of REES as a powerful tool for tackling contemporary issues in structural biology and biophysics and elucidates novel information on the structure-function relationship of NEMO and key interaction partners.
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Affiliation(s)
- Dragana A M Catici
- Department of Biology and Biochemistry, Faculty of Science, University of Bath, UK
| | - Hope E Amos
- Department of Biology and Biochemistry, Faculty of Science, University of Bath, UK
| | - Yi Yang
- Department of Biology and Biochemistry, Faculty of Science, University of Bath, UK
| | | | - Christopher R Pudney
- Department of Biology and Biochemistry, Faculty of Science, University of Bath, UK
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19
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He Y, Haque MM, Stuehr DJ, Lu HP. Single-molecule spectroscopy reveals how calmodulin activates NO synthase by controlling its conformational fluctuation dynamics. Proc Natl Acad Sci U S A 2015; 112:11835-40. [PMID: 26311846 PMCID: PMC4586839 DOI: 10.1073/pnas.1508829112] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mechanisms that regulate the nitric oxide synthase enzymes (NOS) are of interest in biology and medicine. Although NOS catalysis relies on domain motions, and is activated by calmodulin binding, the relationships are unclear. We used single-molecule fluorescence resonance energy transfer (FRET) spectroscopy to elucidate the conformational states distribution and associated conformational fluctuation dynamics of the two electron transfer domains in a FRET dye-labeled neuronal NOS reductase domain, and to understand how calmodulin affects the dynamics to regulate catalysis. We found that calmodulin alters NOS conformational behaviors in several ways: It changes the distance distribution between the NOS domains, shortens the lifetimes of the individual conformational states, and instills conformational discipline by greatly narrowing the distributions of the conformational states and fluctuation rates. This information was specifically obtainable only by single-molecule spectroscopic measurements, and reveals how calmodulin promotes catalysis by shaping the physical and temporal conformational behaviors of NOS.
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Affiliation(s)
- Yufan He
- Center for Photochemical Sciences, Department of Chemistry, Bowling Green State University, Bowling Green, OH 43403
| | - Mohammad Mahfuzul Haque
- Department of Pathobiology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195
| | - Dennis J Stuehr
- Department of Pathobiology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195
| | - H Peter Lu
- Center for Photochemical Sciences, Department of Chemistry, Bowling Green State University, Bowling Green, OH 43403;
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20
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Hedison TM, Hay S, Scrutton NS. Real-time analysis of conformational control in electron transfer reactions of human cytochrome P450 reductase with cytochrome c. FEBS J 2015; 282:4357-75. [PMID: 26307151 PMCID: PMC4973710 DOI: 10.1111/febs.13501] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 07/21/2015] [Accepted: 08/21/2015] [Indexed: 11/27/2022]
Abstract
Protein domain dynamics and electron transfer chemistry are often associated, but real‐time analysis of domain motion in enzyme‐catalysed reactions and the elucidation of mechanistic schemes that relate these motions to the reaction chemistry are major challenges for biological catalysis research. Previously we suggested that reduction of human cytochrome P450 reductase with the reducing coenzyme NADPH is accompanied by major structural re‐orientation of the FMN‐ and FAD‐binding domains through an inferred dynamic cycle of ‘open’ and ‘closed’ conformations of the enzyme (PLoS Biol, 2011, e1001222). However, these studies were restricted to stopped‐flow/FRET analysis of the reductive half‐reaction, and were compromised by fluorescence quenching of the acceptor by the flavin cofactors. Here we have improved the design of the FRET system, by using dye pairs with near‐IR fluorescence, and extended studies on human cytochrome P450 reductase to the oxidative half‐reaction using a double‐mixing stopped‐flow assay, thereby analysing in real‐time conformational dynamics throughout the complete catalytic cycle. We correlate redox changes accompanying the reaction chemistry with protein dynamic changes observed by FRET, and show that redox chemistry drives a major re‐orientation of the protein domains in both the reductive and oxidative half‐reactions. Our studies using the tractable (soluble) surrogate electron acceptor cytochrome c provide a framework for analysing mechanisms of electron transfer in the endoplasmic reticulum between cytochrome P450 reductase and cognate P450 enzymes. More generally, our work emphasizes the importance of protein dynamics in intra‐ and inter‐protein electron transfer, and establishes methodology for real‐time analysis of structural changes throughout the catalytic cycle of complex redox proteins.
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Affiliation(s)
- Tobias M Hedison
- Manchester Institute of Biotechnology and Faculty of Life Sciences, University of Manchester, UK
| | - Sam Hay
- Manchester Institute of Biotechnology and Faculty of Life Sciences, University of Manchester, UK
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology and Faculty of Life Sciences, University of Manchester, UK
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21
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Sheng Y, Zhong L, Guo D, Lau G, Feng C. Insight into structural rearrangements and interdomain interactions related to electron transfer between flavin mononucleotide and heme in nitric oxide synthase: A molecular dynamics study. J Inorg Biochem 2015; 153:186-196. [PMID: 26277414 DOI: 10.1016/j.jinorgbio.2015.08.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2015] [Revised: 06/29/2015] [Accepted: 08/05/2015] [Indexed: 10/23/2022]
Abstract
Calmodulin (CaM) binding to nitric oxide synthase (NOS) enables a conformational change, in which the FMN domain shuttles between the FAD and heme domains to deliver electrons to the active site heme center. A clear understanding of this large conformational change is critical, since this step is the rate-limiting in NOS catalysis. Herein molecular dynamics simulations were conducted on a model of an oxygenase/FMN (oxyFMN) construct of human inducible NOS (iNOS). This is to investigate the structural rearrangements and the domain interactions related to the FMN-heme interdomain electron transfer (IET). We carried out simulations on the iNOS oxyFMN·CaM complex models in [Fe(III)][FMNH(-)] and [Fe(II)][FMNH] oxidation states, the pre- and post-IET states. The comparison of the dynamics and conformations of the iNOS construct at the two oxidation states has allowed us to identify key factors related to facilitating the FMN-heme IET process. The computational results demonstrated, for the first time, that the conformational change is redox-dependent. Predictions of the key interacting sites in optimal interdomain FMN/heme docking are well supported by experimental data in the literature. An intra-subunit pivot region is predicted to modulate the FMN domain motion and correlate with existence of a bottleneck in the conformational sampling that leads to the electron transfer-competent state. Interactions of the residues identified in this work are proposed to ensure that the FMN domain moves with appropriate degrees of freedom and docks to proper positions at the heme domain, resulting in efficient IET and nitric oxide production.
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Affiliation(s)
- Yinghong Sheng
- Department of Chemistry & Physics, College of Arts & Sciences, Florida Gulf Coast University, 10501 FGCU Blvd. S., Fort Myers, FL 33965, USA.
| | - Linghao Zhong
- Pennsylvania State University at Mont Alto, 1 Campus Drive, Mont Alto, PA 17237, USA
| | - Dahai Guo
- Department of Bioengineering and Software Engineering, U.A. Whitaker College of Engineering, Florida Gulf Coast University, 10501 FGCU Blvd. S., Fort Myers, FL 33965, USA
| | - Gavin Lau
- Department of Chemistry & Physics, College of Arts & Sciences, Florida Gulf Coast University, 10501 FGCU Blvd. S., Fort Myers, FL 33965, USA
| | - Changjian Feng
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico, Albuquerque, NM 87131, USA.
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22
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Arnett DC, Persechini A, Tran QK, Black DJ, Johnson CK. Fluorescence quenching studies of structure and dynamics in calmodulin-eNOS complexes. FEBS Lett 2015; 589:1173-8. [PMID: 25871521 DOI: 10.1016/j.febslet.2015.03.035] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Revised: 03/17/2015] [Accepted: 03/31/2015] [Indexed: 10/23/2022]
Abstract
Activation of endothelial nitric oxide synthase (eNOS) by calmodulin (CaM) facilitates formation of a sequence of conformational states that is not well understood. Fluorescence decays of fluorescently labeled CaM bound to eNOS reveal four distinct conformational states and single-molecule fluorescence trajectories show multiple fluorescence states with transitions between states occurring on time scales of milliseconds to seconds. A model is proposed relating fluorescence quenching states to enzyme conformations. Specifically, we propose that the most highly quenched state corresponds to CaM docked to an oxygenase domain of the enzyme. In single-molecule trajectories, this state occurs with time lags consistent with the oxygenase activity of the enzyme.
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Affiliation(s)
- David C Arnett
- Department of Chemistry, University of Kansas, Lawrence, KS 66045, USA; Department of Chemistry, Northwestern College, Orange City, IA 51041, USA
| | - Anthony Persechini
- Division of Molecular Biology and Biochemistry and Division of Cell Biology and Biophysics, University of Missouri at Kansas City, Kansas City, MO 64410, USA
| | - Quang-Kim Tran
- Division of Molecular Biology and Biochemistry and Division of Cell Biology and Biophysics, University of Missouri at Kansas City, Kansas City, MO 64410, USA
| | - D J Black
- Division of Molecular Biology and Biochemistry and Division of Cell Biology and Biophysics, University of Missouri at Kansas City, Kansas City, MO 64410, USA
| | - Carey K Johnson
- Department of Chemistry, University of Kansas, Lawrence, KS 66045, USA.
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23
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Leferink NGH, Hay S, Rigby SEJ, Scrutton NS. Towards the free energy landscape for catalysis in mammalian nitric oxide synthases. FEBS J 2014; 282:3016-29. [PMID: 25491181 DOI: 10.1111/febs.13171] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2014] [Revised: 12/05/2014] [Accepted: 12/05/2014] [Indexed: 01/30/2023]
Abstract
The general requirement for conformational sampling in biological electron transfer reactions catalysed by multi-domain redox systems has been emphasized in recent years. Crucially, we lack insight into the extent of the conformational space explored and the nature of the energy landscapes associated with these reactions. The nitric oxide synthases (NOS) produce the signalling molecule NO through a series of complex electron transfer reactions. There is accumulating evidence that protein domain dynamics and calmodulin binding are implicated in regulating electron flow from NADPH, through the FAD and FMN cofactors, to the haem oxygenase domain, where NO is generated. Simple models based on static crystal structures of the isolated reductase domain have suggested a role for large-scale motions of the FMN-binding domain in shuttling electrons from the reductase domain to the oxygenase domain. However, detailed insight into the higher-order domain architecture and dynamic structural transitions in NOS enzymes during enzyme turnover is lacking. In this review, we discuss the recent advances made towards mapping the catalytic free energy landscapes of NOS enzymes through integration of both structural techniques (e.g. cryo-electron microscopy) and biophysical techniques (e.g. pulsed-electron paramagnetic resonance). The general picture that emerges from these experiments is that NOS enzymes exist in an equilibrium of conformations, comprising a 'rugged' or 'frustrated' energy landscape, with a key regulatory role for calmodulin in driving vectorial electron transfer by altering the conformational equilibrium. A detailed understanding of these landscapes may provide new opportunities for discovery of isoform-specific inhibitors that bind at the dynamic interfaces of these multi-dimensional energy landscapes.
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Affiliation(s)
- Nicole G H Leferink
- Manchester Institute of Biotechnology and Faculty of Life Sciences, The University of Manchester, UK
| | - Sam Hay
- Manchester Institute of Biotechnology and Faculty of Life Sciences, The University of Manchester, UK
| | - Stephen E J Rigby
- Manchester Institute of Biotechnology and Faculty of Life Sciences, The University of Manchester, UK
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology and Faculty of Life Sciences, The University of Manchester, UK
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24
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Astashkin AV, Chen L, Zhou X, Li H, Poulos TL, Liu KJ, Guillemette JG, Feng C. Pulsed electron paramagnetic resonance study of domain docking in neuronal nitric oxide synthase: the calmodulin and output state perspective. J Phys Chem A 2014; 118:6864-72. [PMID: 25046446 PMCID: PMC4148148 DOI: 10.1021/jp503547w] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The binding of calmodulin (CaM) to neuronal nitric oxide synthase (nNOS) enables formation of the output state of nNOS for nitric oxide production. Essential to NOS function is the geometry and dynamics of CaM docking to the NOS oxygenase domain, but little is known about these details. In the present work, the domain docking in a CaM-bound oxygenase/FMN (oxyFMN) construct of nNOS was investigated using the relaxation-induced dipolar modulation enhancement (RIDME) technique, which is a pulsed electron paramagnetic resonance technique sensitive to the magnetic dipole interaction between the electron spins. A cysteine was introduced at position 110 of CaM, after which a nitroxide spin label was attached at the position. The RIDME study of the magnetic dipole interaction between the spin label and the ferric heme centers in the oxygenase domain of nNOS revealed that, with increasing [Ca(2+)], the concentration of nNOS·CaM complexes increases and reaches a maximum at [Ca(2+)]/[CaM] ≥ 4. The RIDME kinetics of CaM-bound nNOS represented monotonous decays without well-defined oscillations. The analysis of these kinetics based on the structural models for the open and docked states has shown that only about 15 ± 3% of the CaM-bound nNOS is in the docked state at any given time, while the remaining 85 ± 3% of the protein is in the open conformations characterized by a wide distribution of distances between the bound CaM and the oxygenase domain. The results of this investigation are consistent with a model that the Ca(2+)-CaM interaction causes CaM docking with the oxygenase domain. The low population of the docked state indicates that the CaM-controlled docking between the FMN and heme domains is highly dynamic.
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Affiliation(s)
- Andrei V Astashkin
- Department of Chemistry and Biochemistry, University of Arizona , Tucson, Arizona 85721, United States
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