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Singh S, Gyawali YP, Jiang T, Bukowski GS, Zheng H, Zhang H, Owopetu R, Thielges MC, Feng C. Probing calmodulin-NO synthase interactions via site-specific infrared spectroscopy: an introductory investigation. J Biol Inorg Chem 2024; 29:243-250. [PMID: 38580821 PMCID: PMC11181464 DOI: 10.1007/s00775-024-02046-0] [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: 11/03/2023] [Accepted: 01/15/2024] [Indexed: 04/07/2024]
Abstract
Calmodulin (CaM) binds to a linker between the oxygenase and reductase domains of nitric oxide synthase (NOS) to regulate the functional conformational dynamics. Specific residues on the interdomain interface guide the domain-domain docking to facilitate the electron transfer in NOS. Notably, the docking interface between CaM and the heme-containing oxygenase domain of NOS is isoform specific, which is only beginning to be investigated. Toward advancing understanding of the distinct CaM-NOS docking interactions by infrared spectroscopy, we introduced a cyano-group as frequency-resolved vibrational probe into CaM individually and when associated with full-length and a bi-domain oxygenase/FMN construct of the inducible NOS isoform (iNOS). Site-specific, selective labeling with p-cyano-L-phenylalanine (CNF) by amber suppression of CaM bound to the iNOS has been accomplished by protein coexpression due to the instability of recombinant iNOS protein alone. We introduced CNF at residue 108, which is at the putative CaM-heme (NOS) docking interface. CNF was also introduced at residue 29, which is distant from the docking interface. FT IR data show that the 108 site is sensitive to CaM-NOS complex formation, while insensitivity to its association with the iNOS protein or peptide was observed for the 29 site. Moreover, narrowing of the IR bands at residue 108 suggests the C≡N probe experiences a more limited distribution of environments, indicating side chain restriction apparent for the complex with iNOS. This initial work sets the stage for residue-specific characterizations of structural dynamics of the docked states of NOS proteins.
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Affiliation(s)
- Swapnil Singh
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA
| | - Yadav Prasad Gyawali
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Ting Jiang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Gregory S Bukowski
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA
| | - Huayu Zheng
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Haikun Zhang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Rebecca Owopetu
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico, Albuquerque, NM, 87131, USA
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Megan C Thielges
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA.
| | - Changjian Feng
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico, Albuquerque, NM, 87131, USA.
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM, 87131, USA.
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2
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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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3
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Zheng H, Li J, Feng C. An isoform-specific pivot modulates the electron transfer between the flavin mononucleotide and heme centers in inducible nitric oxide synthase. J Biol Inorg Chem 2020; 25:1097-1105. [PMID: 33057871 PMCID: PMC7669679 DOI: 10.1007/s00775-020-01824-w] [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: 06/14/2020] [Accepted: 09/24/2020] [Indexed: 11/25/2022]
Abstract
Intraprotein interdomain electron transfer (IET) between the flavin mononucleotide (FMN) and heme centers is an obligatory step in nitric oxide synthase (NOS) enzymes. An isoform-specific pivotal region near Leu406 in the heme domain of human inducible NOS (iNOS) was proposed to mediate the FMN-heme domain-domain alignment (J Inorg Biochem 153:186-196, 2015). The FMN-heme IET rate is a measure of the interdomain FMN/heme complex formation. In this work, the FMN-heme IET kinetics in the wild type (wt) human iNOS oxygenase/FMN (oxyFMN) construct were directly measured by laser flash photolysis with added synthetic peptide related to the pivotal region, in comparison with the wt construct alone. The IET rates were decreased by the iNOS HKL peptide in a dose-saturable fashion, and the inhibitory effect was abolished by a single L406 → E mutation in the peptide. A similar trend in change of the NO synthesis activity of wt iNOS holoenzyme by the peptides was observed. These data, along with the kinetics and modeling results for the L406T and L406F mutant oxyFMN proteins, indicated that the Leu406 residue modulates the FMN-heme IET through hydrophobic interactions. Moreover, the IET rates were analyzed for the wt iNOS oxyFMN protein in the presence of nNOS or eNOS-derived peptide related to the equivalent pivotal heme domain site. These results together indicate that the isoform-specific pivotal region at the heme domain specifically interacts with the conserved FMN domain surface, to facilitate proper interdomain docking for the FMN-heme IET in NOS.
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Affiliation(s)
- Huayu Zheng
- College of Pharmacy, University of New Mexico, Albuquerque, NM, 87131, USA
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Jinghui Li
- College of Pharmacy, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Changjian Feng
- College of Pharmacy, University of New Mexico, Albuquerque, NM, 87131, USA.
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM, 87131, USA.
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4
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Bignon E, Rizza S, Filomeni G, Papaleo E. Use of Computational Biochemistry for Elucidating Molecular Mechanisms of Nitric Oxide Synthase. Comput Struct Biotechnol J 2019; 17:415-429. [PMID: 30996821 PMCID: PMC6451115 DOI: 10.1016/j.csbj.2019.03.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 03/17/2019] [Accepted: 03/21/2019] [Indexed: 12/25/2022] Open
Abstract
Nitric oxide (NO) is an essential signaling molecule in the regulation of multiple cellular processes. It is endogenously synthesized by NO synthase (NOS) as the product of L-arginine oxidation to L-citrulline, requiring NADPH, molecular oxygen, and a pterin cofactor. Two NOS isoforms are constitutively present in cells, nNOS and eNOS, and a third is inducible (iNOS). Despite their biological relevance, the details of their complex structural features and reactivity mechanisms are still unclear. In this review, we summarized the contribution of computational biochemistry to research on NOS molecular mechanisms. We described in detail its use in studying aspects of structure, dynamics and reactivity. We also focus on the numerous outstanding questions in the field that could benefit from more extensive computational investigations.
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Affiliation(s)
- Emmanuelle Bignon
- Computational Biology Laboratory, Danish Cancer Society Research Center, Strandboulevarden 49, 2100 Copenhagen, Denmark
| | - Salvatore Rizza
- Redox Signaling and Oxidative Stress Group, Cell Stress and Survival Unit, Danish Cancer Society Research Center, Strandboulevarden 49, 2100 Copenhagen, Denmark
| | - Giuseppe Filomeni
- Redox Signaling and Oxidative Stress Group, Cell Stress and Survival Unit, Danish Cancer Society Research Center, Strandboulevarden 49, 2100 Copenhagen, Denmark.,Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Elena Papaleo
- Computational Biology Laboratory, Danish Cancer Society Research Center, Strandboulevarden 49, 2100 Copenhagen, Denmark.,Translational Disease Systems Biology, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research University of Copenhagen, Copenhagen, Denmark
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5
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Stuehr DJ, Haque MM. Nitric oxide synthase enzymology in the 20 years after the Nobel Prize. Br J Pharmacol 2019; 176:177-188. [PMID: 30402946 PMCID: PMC6295403 DOI: 10.1111/bph.14533] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 10/25/2018] [Accepted: 10/31/2018] [Indexed: 12/31/2022] Open
Abstract
This review briefly summarizes what was known about NOS enzymology at the time of the Nobel Prize award in 1998 and then discusses from the author's perspective some of the advances in NOS enzymology over the subsequent 20 years, focused on five aspects: the maturation process of NOS enzymes and its regulation; the mechanism of NO synthesis; the redox roles played by the 6R-tetrahydrobiopterin cofactor; the role of protein conformational behaviour in enabling NOS electron transfer and its regulation by NOS structural elements and calmodulin, and the catalytic cycling pathways of NOS enzymes and their influence on NOS activity. LINKED ARTICLES: This article is part of a themed section on Nitric Oxide 20 Years from the 1998 Nobel Prize. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v176.2/issuetoc.
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Affiliation(s)
- Dennis J Stuehr
- Department of Inflammation and Immunity, Lerner Research InstituteThe Cleveland ClinicClevelandOHUSA
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6
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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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7
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Li J, Zheng H, Wang W, Miao Y, Sheng Y, Feng C. Role of an isoform-specific residue at the calmodulin-heme (NO synthase) interface in the FMN - heme electron transfer. FEBS Lett 2018; 592:2425-2431. [PMID: 29904908 DOI: 10.1002/1873-3468.13158] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 05/31/2018] [Accepted: 06/05/2018] [Indexed: 12/18/2022]
Abstract
The interface between calmodulin (CaM) and the NO synthase (NOS) heme domain is the least characterized interprotein interface that the NOS isoforms must traverse through during catalysis. Our previous molecular dynamics simulations predicted a salt bridge between K497 in human inducible NOS (iNOS) heme domain and D118(CaM). Herein, the FMN - heme interdomain electron transfer (IET) rate was found to be notably decreased by charge-reversal mutation, while the IET in the iNOS K497D mutant is significantly restored by the CaM D118K mutation. The results of wild-type protein with added synthetic peptides further demonstrate the critical nature of K497 relative to the rest of the peptide sequence in modulating the IET. These data provide definitive evidence supporting the regulatory role of the isoform-specific K497 residue.
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Affiliation(s)
- Jinghui Li
- College of Pharmacy, University of New Mexico, Albuquerque, NM, USA
| | - Huayu Zheng
- College of Pharmacy, University of New Mexico, Albuquerque, NM, USA.,Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM, USA
| | - Wei Wang
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM, USA
| | - Yubin Miao
- Department of Radiology, School of Medicine, University of Colorado Denver, Aurora, CO, USA
| | - Yinghong Sheng
- Department of Chemistry & Physics, College of Arts & Sciences, Florida Gulf Coast University, Fort Myers, FL, USA
| | - Changjian Feng
- College of Pharmacy, University of New Mexico, Albuquerque, NM, USA.,Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM, USA
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8
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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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9
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Astashkin AV, Li J, Zheng H, Miao Y, Feng C. A docked state conformational dynamics model to explain the ionic strength dependence of FMN - heme electron transfer in nitric oxide synthase. J Inorg Biochem 2018; 184:146-155. [PMID: 29751215 DOI: 10.1016/j.jinorgbio.2018.03.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 03/09/2018] [Accepted: 03/22/2018] [Indexed: 10/17/2022]
Abstract
The FMN-heme interdomain electron transfer (IET) in nitric oxide synthase (NOS) is a key stage of the electron transport chain, which supplies the catalytic heme site(s) with the NADPH-derived electrons. While there is a recognition that this IET depends on both the electron tunneling and the conformational dynamics, the detailed mechanism remains unclear. In this work, the IET kinetics were measured by laser flash photolysis for a bidomain oxygenase/FMN (oxyFMN) construct of human inducible NOS (iNOS) over the ionic strength range from 0.1 to 0.5 M. The forward (heme → FMN, kETf) and backward (FMN → heme, kETb) intrinsic IET rate constants were determined from the analysis of the observed IET rates using the additional information regarding the conformational dynamics obtained from the FMN fluorescence lifetime measurements and theoretical estimates. Both kETf and kETb exhibit a bell-shaped dependence on the ionic strength, I, with the maximum rates corresponding to I ~ 0.2 M. This dependence was explained using a new model, which considers the effect of formation of pairs between the protein surface charged residues and solution ions on the docked state dynamics. The trial simulations of the intrinsic IET rate dependences using this model show that the data can be reproduced using reasonable energetic, structural, and chemical parameters. The suggested model can explain both the monophasic and biphasic ionic strength dependences and can be used to rationalize the interprotein/interdomain electron transfer rates for other types of protein systems where the docked state is sufficiently long-lived.
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Affiliation(s)
- Andrei V Astashkin
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
| | - 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; Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM 87131, USA
| | - Yubin Miao
- Department of Radiology, School of Medicine, University of Colorado Denver, Aurora, CO 80045, USA
| | - Changjian Feng
- College of Pharmacy, University of New Mexico, Albuquerque, NM 87131, USA; Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM 87131, USA.
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10
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Haque MM, Tejero J, Bayachou M, Kenney CT, Stuehr DJ. A cross-domain charge interaction governs the activity of NO synthase. J Biol Chem 2018; 293:4545-4554. [PMID: 29414777 DOI: 10.1074/jbc.ra117.000635] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Revised: 01/17/2018] [Indexed: 11/06/2022] Open
Abstract
NO synthase (NOS) enzymes perform interdomain electron transfer reactions during catalysis that may rely on complementary charge interactions at domain-domain interfaces. Guided by our previous results and a computer-generated domain-docking model, we assessed the importance of cross-domain charge interactions in the FMN-to-heme electron transfer in neuronal NOS (nNOS). We reversed the charge of three residues (Glu-762, Glu-816, and Glu-819) that form an electronegative triad on the FMN domain and then individually reversed the charges of three electropositive residues (Lys-423, Lys-620, and Lys-660) on the oxygenase domain (NOSoxy), to potentially restore a cross-domain charge interaction with the triad, but in reversed polarity. Charge reversal of the triad completely eliminated heme reduction and NO synthesis in nNOS. These functions were partly restored by the charge reversal at oxygenase residue Lys-423, but not at Lys-620 or Lys-660. Full recovery of heme reduction was probably muted by an accompanying change in FMN midpoint potential that made electron transfer to the heme thermodynamically unfavorable. Our results provide direct evidence that cross-domain charge pairing is required for the FMN-to-heme electron transfer in nNOS. The unique ability of charge reversal at position 423 to rescue function indicates that it participates in an essential cross-domain charge interaction with the FMN domain triad. This supports our domain-docking model and suggests that it may depict a productive electron transfer complex formed during nNOS catalysis.
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Affiliation(s)
- Mohammad Mahfuzul Haque
- From the Departments of Pathobiology, Lerner Research Institute, The Cleveland Clinic, Cleveland, Ohio 44195
| | - Jesús Tejero
- the Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, and
| | - Mekki Bayachou
- the Department of Chemistry, Cleveland State University, Cleveland, Ohio 44115
| | - Claire T Kenney
- From the Departments of Pathobiology, Lerner Research Institute, The Cleveland Clinic, Cleveland, Ohio 44195
| | - Dennis J Stuehr
- From the Departments of Pathobiology, Lerner Research Institute, The Cleveland Clinic, Cleveland, Ohio 44195,
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11
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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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12
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Poulos TL, Li H. Nitric oxide synthase and structure-based inhibitor design. Nitric Oxide 2016; 63:68-77. [PMID: 27890696 DOI: 10.1016/j.niox.2016.11.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 11/09/2016] [Accepted: 11/21/2016] [Indexed: 11/24/2022]
Abstract
Once it was discovered that the enzyme nitric oxide synthase (NOS) is responsible for the biosynthesis of NO, NOS became a drug target. Particularly important is the over production of NO by neuronal NOS (nNOS) in various neurodegenerative disorders. After the various NOS isoforms were identified, inhibitor development proceeded rapidly. It soon became evident, however, that isoform selectivity presents a major challenge. All 3 human NOS isoforms, nNOS, eNOS (endothelial NOS), and iNOS (inducible NOS) have nearly identical active site structures thus making selective inhibitor design especially difficult. Of particular importance is the avoidance of inhibiting eNOS owing to its vital role in the cardiovascular system. This review summarizes some of the history of NOS inhibitor development and more recent advances in developing isoform selective inhibitors using primarily structure-based approaches.
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Affiliation(s)
- Thomas L Poulos
- Departments of Molecular Biology & Biochemistry, Pharmaceutical Sciences, and Chemistry, University of California, Irvine, Irvine, CA 92697-3900, USA.
| | - Huiying Li
- Departments of Molecular Biology & Biochemistry, Pharmaceutical Sciences, and Chemistry, University of California, Irvine, Irvine, CA 92697-3900, USA
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13
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Chen L, Zheng H, Li W, Li W, Miao Y, Feng C. Role of a Conserved Tyrosine Residue in the FMN-Heme Interdomain Electron Transfer in Inducible Nitric Oxide Synthase. J Phys Chem A 2016; 120:7610-7616. [PMID: 27633182 DOI: 10.1021/acs.jpca.6b08207] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The interdomain electron transfer (IET) between the flavin mononucleotide (FMN) and heme domains is essential in the biosynthesis of nitric oxide (NO) by the NO synthase (NOS) enzymes. A conserved tyrosine residue in the FMN domain (Y631 in human inducible NOS) was proposed to be a key part of the electron transfer pathway in the FMN/heme docked complex model. In the present study, the FMN-heme IET kinetics in the Y631F mutant and wild type of a bidomain oxygenase/FMN construct of human inducible NOS were determined by laser flash photolysis. The rate constant of the Y631F mutant is significantly decreased by ∼75% (compared to the wild type), showing that the tyrosine residue indeed facilitates the FMN-heme IET through the protein medium. The IET rate constant of the wild type protein decreases from 345 to 242 s-1 on going from H2O to 95% D2O, giving a solvent kinetic isotope effect of 1.4. In contrast, no deuterium isotope effect was observed for the Tyr-to-Phe mutant. Moreover, an appreciable change in the wild type iNOS IET rate constant value was observed upon changing pH. These results indicate that the FMN-heme IET is proton coupled, in which the conserved tyrosine residue may play an important role.
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Affiliation(s)
- Li Chen
- College of Pharmacy, University of New Mexico , Albuquerque, New Mexico 87131, United States
| | - Huayu Zheng
- 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
| | - Wenbing Li
- College of Pharmacy, University of New Mexico , Albuquerque, New Mexico 87131, United States
| | - Wei Li
- College of Pharmacy, University of New Mexico , Albuquerque, New Mexico 87131, United States
| | - Yubin Miao
- Radiology, University of Colorado Denver , Denver, Colorado 80045, United States
| | - Changjian Feng
- 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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Haque MM, Ray SS, Stuehr DJ. Phosphorylation Controls Endothelial Nitric-oxide Synthase by Regulating Its Conformational Dynamics. J Biol Chem 2016; 291:23047-23057. [PMID: 27613870 DOI: 10.1074/jbc.m116.737361] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Indexed: 11/06/2022] Open
Abstract
The activity of endothelial NO synthase (eNOS) is triggered by calmodulin (CaM) binding and is often further regulated by phosphorylation at several positions in the enzyme. Phosphorylation at Ser1179 occurs in response to diverse physiologic stimuli and increases the NO synthesis and cytochrome c reductase activities of eNOS, thereby enhancing its participation in biological signal cascades. Despite its importance, the mechanism by which Ser1179 phosphorylation increases eNOS activity is not understood. To address this, we used stopped-flow spectroscopy and computer modeling approaches to determine how the phosphomimetic mutation (S1179D) may impact electron flux through eNOS and the conformational behaviors of its reductase domain, both in the absence and presence of bound CaM. We found that S1179D substitution in CaM-free eNOS had multiple effects; it increased the rate of flavin reduction, altered the conformational equilibrium of the reductase domain, and increased the rate of its conformational transitions. We found these changes were equivalent in degree to those caused by CaM binding to wild-type eNOS, and the S1179D substitution together with CaM binding caused even greater changes in these parameters. The modeling indicated that the changes caused by the S1179D substitution, despite being restricted to the reductase domain, are sufficient to explain the stimulation of both the cytochrome c reductase and NO synthase activities of eNOS. This helps clarify how Ser1179 phosphorylation regulates eNOS and provides a foundation to compare its regulation by other phosphorylation events.
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Affiliation(s)
- Mohammad Mahfuzul Haque
- From the Department of Pathobiology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195
| | - Sougata Sinha Ray
- From the Department of Pathobiology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195
| | - Dennis J Stuehr
- From the Department of Pathobiology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195
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Astashkin AV, Feng C. Solving Kinetic Equations for the Laser Flash Photolysis Experiment on Nitric Oxide Synthases: Effect of Conformational Dynamics on the Interdomain Electron Transfer. J Phys Chem A 2015; 119:11066-75. [PMID: 26477677 DOI: 10.1021/acs.jpca.5b08414] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The production of nitric oxide by the nitric oxide synthase (NOS) enzyme depends on the interdomain electron transfer (IET) between the flavin mononucleotide (FMN) and heme domains. Although the rate of this IET has been measured by laser flash photolysis (LFP) for various NOS proteins, no rigorous analysis of the relevant kinetic equations was performed so far. In this work, we provide an analytical solution of the kinetic equations underlying the LFP approach. The derived expressions reveal that the bulk IET rate is significantly affected by the conformational dynamics that determines the formation and dissociation rates of the docking complex between the FMN and heme domains. We show that in order to informatively study the electron transfer across the NOS enzyme, LFP should be used in combination with other spectroscopic methods that could directly probe the docking equilibrium and the conformational change rate constants. The implications of the obtained analytical expressions for the interpretation of the LFP results from various native and modified NOS proteins are discussed. The mathematical formulas derived in this work should also be applicable for interpreting the IET kinetics in other modular redox enzymes.
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Affiliation(s)
- Andrei V Astashkin
- Department of Chemistry and Biochemistry, University of Arizona , Tucson, Arizona 85721, United States
| | - Changjian Feng
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico , Albuquerque, New Mexico 87131, United States
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