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Campelo D, Esteves F, Brito Palma B, Costa Gomes B, Rueff J, Lautier T, Urban P, Truan G, Kranendonk M. Probing the Role of the Hinge Segment of Cytochrome P450 Oxidoreductase in the Interaction with Cytochrome P450. Int J Mol Sci 2018; 19:ijms19123914. [PMID: 30563285 PMCID: PMC6321550 DOI: 10.3390/ijms19123914] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 12/04/2018] [Accepted: 12/05/2018] [Indexed: 01/08/2023] Open
Abstract
NADPH-cytochrome P450 reductase (CPR) is the unique redox partner of microsomal cytochrome P450s (CYPs). CPR exists in a conformational equilibrium between open and closed conformations throughout its electron transfer (ET) function. Previously, we have shown that electrostatic and flexibility properties of the hinge segment of CPR are critical for ET. Three mutants of human CPR were studied (S243P, I245P and R246A) and combined with representative human drug-metabolizing CYPs (isoforms 1A2, 2A6 and 3A4). To probe the effect of these hinge mutations different experimental approaches were employed: CYP bioactivation capacity of pre-carcinogens, enzyme kinetic analysis, and effect of the ionic strength and cytochrome b5 (CYB5) on CYP activity. The hinge mutations influenced the bioactivation of pre-carcinogens, which seemed CYP isoform and substrate dependent. The deviations of Michaelis-Menten kinetic parameters uncovered tend to confirm this discrepancy, which was confirmed by CYP and hinge mutant specific salt/activity profiles. CPR/CYB5 competition experiments indicated a less important role of affinity in CPR/CYP interaction. Overall, our data suggest that the highly flexible hinge of CPR is responsible for the existence of a conformational aggregate of different open CPR conformers enabling ET-interaction with structural varied redox partners.
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Affiliation(s)
- Diana Campelo
- Center for Toxicogenomics and Human Health, Genetics, Oncology and Human Toxicology, NOVA Medical School, Faculdade de Ciências Médicas, Universidade Nova de Lisboa, 1150-082 Lisbon, Portugal.
| | - Francisco Esteves
- Center for Toxicogenomics and Human Health, Genetics, Oncology and Human Toxicology, NOVA Medical School, Faculdade de Ciências Médicas, Universidade Nova de Lisboa, 1150-082 Lisbon, Portugal.
| | - Bernardo Brito Palma
- Center for Toxicogenomics and Human Health, Genetics, Oncology and Human Toxicology, NOVA Medical School, Faculdade de Ciências Médicas, Universidade Nova de Lisboa, 1150-082 Lisbon, Portugal.
| | - Bruno Costa Gomes
- Center for Toxicogenomics and Human Health, Genetics, Oncology and Human Toxicology, NOVA Medical School, Faculdade de Ciências Médicas, Universidade Nova de Lisboa, 1150-082 Lisbon, Portugal.
| | - José Rueff
- Center for Toxicogenomics and Human Health, Genetics, Oncology and Human Toxicology, NOVA Medical School, Faculdade de Ciências Médicas, Universidade Nova de Lisboa, 1150-082 Lisbon, Portugal.
| | - Thomas Lautier
- LISBP, Université de Toulouse, CNRS, INRA, INSA, 31077 Toulouse CEDEX 04, France.
| | - Philippe Urban
- LISBP, Université de Toulouse, CNRS, INRA, INSA, 31077 Toulouse CEDEX 04, France.
| | - Gilles Truan
- LISBP, Université de Toulouse, CNRS, INRA, INSA, 31077 Toulouse CEDEX 04, France.
| | - Michel Kranendonk
- Center for Toxicogenomics and Human Health, Genetics, Oncology and Human Toxicology, NOVA Medical School, Faculdade de Ciências Médicas, Universidade Nova de Lisboa, 1150-082 Lisbon, Portugal.
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2
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Impact of A90P, F106L and H64V mutations on neuroglobin stability and ligand binding kinetics. J Biol Inorg Chem 2018; 24:39-52. [DOI: 10.1007/s00775-018-1625-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 10/08/2018] [Indexed: 12/22/2022]
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3
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Samhan-Arias AK, Almeida RM, Ramos S, Cordas CM, Moura I, Gutierrez-Merino C, Moura JJG. Topography of human cytochrome b 5/cytochrome b 5 reductase interacting domain and redox alterations upon complex formation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2017; 1859:78-87. [PMID: 28958890 DOI: 10.1016/j.bbabio.2017.10.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 10/23/2017] [Accepted: 10/27/2017] [Indexed: 10/18/2022]
Abstract
Cytochrome b5 is the main electron acceptor of cytochrome b5 reductase. The interacting domain between both human proteins has been unidentified up to date and very little is known about its redox properties modulation upon complex formation. In this article, we characterized the protein/protein interacting interface by solution NMR and molecular docking. In addition, upon complex formation, we measured an increase of cytochrome b5 reductase flavin autofluorescence that was dependent upon the presence of cytochrome b5. Data analysis of these results allowed us to calculate a dissociation constant value between proteins of 0.5±0.1μM and a 1:1 stoichiometry for the complex formation. In addition, a 30mV negative shift of cytochrome b5 reductase redox potential in presence of cytochrome b5 was also measured. These experiments suggest that the FAD group of cytochrome b5 reductase increase its solvent exposition upon complex formation promoting an efficient electron transfer between the proteins.
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Affiliation(s)
- Alejandro K Samhan-Arias
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, NOVA, 2829-516 Caparica, Portugal.
| | - Rui M Almeida
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, NOVA, 2829-516 Caparica, Portugal
| | - Susana Ramos
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, NOVA, 2829-516 Caparica, Portugal
| | - Cristina M Cordas
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, NOVA, 2829-516 Caparica, Portugal
| | - Isabel Moura
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, NOVA, 2829-516 Caparica, Portugal
| | - Carlos Gutierrez-Merino
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, Institute of Molecular Pathology Biomarkers, University of Extremadura, 06006 Badajoz, Spain
| | - José J G Moura
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, NOVA, 2829-516 Caparica, Portugal.
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4
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Bart AG, Scott EE. Structural and functional effects of cytochrome b5 interactions with human cytochrome P450 enzymes. J Biol Chem 2017; 292:20818-20833. [PMID: 29079577 DOI: 10.1074/jbc.ra117.000220] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Revised: 10/22/2017] [Indexed: 02/04/2023] Open
Abstract
The small heme-containing protein cytochrome b5 can facilitate, inhibit, or have no effect on cytochrome P450 catalysis, often in a P450-dependent and substrate-dependent manner that is not well understood. Herein, solution NMR was used to identify b5 residues interacting with different human drug-metabolizing P450 enzymes. NMR results revealed that P450 enzymes bound to either b5 α4-5 (CYP2A6 and CYP2E1) or this region and α2-3 (CYP2D6 and CYP3A4) and suggested variation in the affinity for b5 Mutations of key b5 residues suggest not only that different b5 surfaces are responsible for binding different P450 enzymes, but that these different complexes are relevant to the observed effects on P450 catalysis.
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Affiliation(s)
| | - Emily E Scott
- From the Biophysics Program and .,the Departments of Medicinal Chemistry and Pharmacology, University of Michigan, Ann Arbor, Michigan 48109
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5
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Estrada DF, Laurence JS, Scott EE. Cytochrome P450 17A1 Interactions with the FMN Domain of Its Reductase as Characterized by NMR. J Biol Chem 2015; 291:3990-4003. [PMID: 26719338 DOI: 10.1074/jbc.m115.677294] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Indexed: 11/06/2022] Open
Abstract
To accomplish key physiological processes ranging from drug metabolism to steroidogenesis, human microsomal cytochrome P450 enzymes require the sequential input of two electrons delivered by the FMN domain of NADPH-cytochrome P450 reductase. Although some human microsomal P450 enzymes can instead accept the second electron from cytochrome b5, for human steroidogenic CYP17A1, the cytochrome P450 reductase FMN domain delivers both electrons, and b5 is an allosteric modulator. The structural basis of these key but poorly understood protein interactions was probed by solution NMR using the catalytically competent soluble domains of each protein. Formation of the CYP17A1·FMN domain complex induced differential line broadening of the NMR signal for each protein. Alterations in the exchange dynamics generally occurred for residues near the surface of the flavin mononucleotide, including 87-90 (loop 1), and for key CYP17A1 active site residues. These interactions were modulated by the identity of the substrate in the buried CYP17A1 active site and by b5. The FMN domain outcompetes b5 for binding to CYP17A1 in the three-component system. These results and comparison with previous NMR studies of the CYP17A1·b5 complex suggest a model of CYP17A1 enzyme regulation.
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Affiliation(s)
- D Fernando Estrada
- From the Department of Medicinal Chemistry, University of Kansas, Lawrence, Kansas 66045 and
| | - Jennifer S Laurence
- the Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas 66047
| | - Emily E Scott
- From the Department of Medicinal Chemistry, University of Kansas, Lawrence, Kansas 66045 and
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6
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Jeřábek P, Florián J, Stiborová M, Martínek V. Flexible docking-based molecular dynamics/steered molecular dynamics calculations of protein-protein contacts in a complex of cytochrome P450 1A2 with cytochrome b5. Biochemistry 2014; 53:6695-705. [PMID: 25313797 DOI: 10.1021/bi500814t] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Formation of transient complexes of cytochrome P450 (P450) with another protein of the endoplasmic reticulum membrane, cytochrome b5 (cyt b5), dictates the catalytic activities of several P450s. Therefore, we examined formation and binding modes of the complex of human P450 1A2 with cyt b5. Docking of soluble domains of these proteins was performed using an information-driven flexible docking approach implemented in HADDOCK. Stabilities of the five unique binding modes of the P450 1A2-cyt b5 complex yielded by HADDOCK were evaluated using explicit 10 ns molecular dynamics (MD) simulations in aqueous solution. Further, steered MD was used to compare the stability of the individual P450 1A2-cyt b5 binding modes. The best binding mode was characterized by a T-shaped mutual orientation of the porphyrin rings and a 10.7 Å distance between the two redox centers, thus satisfying the condition for a fast electron transfer. Mutagenesis studies and chemical cross-linking, which, in the absence of crystal structures, were previously used to deduce specific P450-cyt b5 interactions, indicated that the negatively charged convex surface of cyt b5 binds to the positively charged concave surface of P450. Our simulations further elaborate structural details of this interface, including nine ion pairs between R95, R100, R138, R362, K442, K455, and K465 side chains of P450 1A2 and E42, E43, E49, D65, D71, and heme propionates of cyt b5. The universal heme-centric system of internal coordinates was proposed to facilitate consistent classification of the orientation of the two porphyrins in any protein complex.
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Affiliation(s)
- Petr Jeřábek
- Department of Biochemistry, Faculty of Science, Charles University in Prague , Albertov 2030, 128 43 Prague 2, Czech Republic
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7
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Vivekanandan S, Ahuja S, Im SC, Waskell L, Ramamoorthy A. ¹H, ¹³C and ¹⁵N resonance assignments for the full-length mammalian cytochrome b₅ in a membrane environment. BIOMOLECULAR NMR ASSIGNMENTS 2014; 8:409-13. [PMID: 24105099 PMCID: PMC3981966 DOI: 10.1007/s12104-013-9528-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Accepted: 09/28/2013] [Indexed: 05/12/2023]
Abstract
Microsomal cytochrome b5 plays a key role in the oxidation of a variety of exogenous and endogenous compounds, including drugs, fatty acids, cholesterol and steroid hormones. To better understand its functional properties in a membrane mimic environment, we carried out high-resolution solution NMR studies. Here we report resonance assignments for full-length rabbit cytochrome b5 embedded in dodecylphosphocholine micelles.
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Affiliation(s)
| | - Shivani Ahuja
- Department of Chemistry and Biophysics, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Sang-Choul Im
- Department of Anesthesiology, University of Michigan, and VA Medical Center, Ann Arbor, MI 48105, USA
| | - Lucy Waskell
- Department of Anesthesiology, University of Michigan, and VA Medical Center, Ann Arbor, MI 48105, USA
| | - Ayyalusamy Ramamoorthy
- Department of Chemistry and Biophysics, University of Michigan, Ann Arbor, MI 48109-1055, USA
- To whom the correspondence should be addressed: Ayyalusamy Ramamoorthy, Department of Chemistry and Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, USA, Tel.: (734) 647-6572; Fax: (734) 764-3323;
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8
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Yamamoto K, Caporini MA, Im S, Waskell L, Ramamoorthy A. Shortening spin-lattice relaxation using a copper-chelated lipid at low-temperatures - A magic angle spinning solid-state NMR study on a membrane-bound protein. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2013; 237:175-181. [PMID: 24246881 PMCID: PMC3868731 DOI: 10.1016/j.jmr.2013.10.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 10/19/2013] [Accepted: 10/24/2013] [Indexed: 05/21/2023]
Abstract
Inherent low sensitivity of NMR spectroscopy has been a major disadvantage, especially to study biomolecules like membrane proteins. Recent studies have successfully demonstrated the advantages of performing solid-state NMR experiments at very low and ultralow temperatures to enhance the sensitivity. However, the long spin-lattice relaxation time, T1, at very low temperatures is a major limitation. To overcome this difficulty, we demonstrate the use of a copper-chelated lipid for magic angle spinning solid-state NMR measurements on cytochrome-b5 reconstituted in multilamellar vesicles. Our results on multilamellar vesicles containing as small as 0.5mol% of a copper-chelated lipid can significantly shorten T1 of protons, which can be used to considerably reduce the data collection time or to enhance the signal-to-noise ratio. We also monitored the effect of slow cooling on the resolution and sensitivity of (13)C and (15)N signals from the protein and (13)C signals from lipids.
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Affiliation(s)
- Kazutoshi Yamamoto
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, United States
| | - Marc A Caporini
- Bruker BioSpin Corporation, 15 Fortune Drive, Billerica, MA 01821, United States
| | - Sangchoul Im
- Department of Anesthesiology, University of Michigan, VA Medical Center, Ann Arbor, MI, United States
| | - Lucy Waskell
- Department of Anesthesiology, University of Michigan, VA Medical Center, Ann Arbor, MI, United States
| | - Ayyalusamy Ramamoorthy
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, United States.
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9
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Johnson EF, Connick JP, Reed JR, Backes WL, Desai MC, Xu L, Estrada DF, Laurence JS, Scott EE. Correlating structure and function of drug-metabolizing enzymes: progress and ongoing challenges. Drug Metab Dispos 2013; 42:9-22. [PMID: 24130370 DOI: 10.1124/dmd.113.054627] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
This report summarizes a symposium sponsored by the American Society for Pharmacology and Experimental Therapeutics at Experimental Biology held April 20-24 in Boston, MA. Presentations discussed the status of cytochrome P450 (P450) knowledge, emphasizing advances and challenges in relating structure with function and in applying this information to drug design. First, at least one structure of most major human drug-metabolizing P450 enzymes is known. However, the flexibility of these active sites can limit the predictive value of one structure for other ligands. A second limitation is our coarse-grain understanding of P450 interactions with membranes, other P450 enzymes, NADPH-cytochrome P450 reductase, and cytochrome b5. Recent work has examined differential P450 interactions with reductase in mixed P450 systems and P450:P450 complexes in reconstituted systems and cells, suggesting another level of functional control. In addition, protein nuclear magnetic resonance is a new approach to probe these protein/protein interactions, identifying interacting b5 and P450 surfaces, showing that b5 and reductase binding are mutually exclusive, and demonstrating ligand modulation of CYP17A1/b5 interactions. One desired outcome is the application of such information to control drug metabolism and/or design selective P450 inhibitors. A final presentation highlighted development of a CYP3A4 inhibitor that slows clearance of human immunodeficiency virus drugs otherwise rapidly metabolized by CYP3A4. Although understanding P450 structure/function relationships is an ongoing challenge, translational advances will benefit from continued integration of existing and new biophysical approaches.
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Affiliation(s)
- Eric F Johnson
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California (E.F.J.); Department of Pharmacology and Experimental Therapeutics and the Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, Louisiana (J.P.C., J.R.R., W.L.B.); Department of Medicinal Chemistry, Gilead Sciences, Inc., Foster City, California (M.C.D., L.X.); Department of Pharmaceutical Chemistry (J.S.L.) and Department of Medicinal Chemistry (D.F.E., E.E.S.), University of Kansas, Lawrence, Kansas
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10
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Ahuja S, Jahr N, Im SC, Vivekanandan S, Popovych N, Le Clair SV, Huang R, Soong R, Xu J, Yamamoto K, Nanga RP, Bridges A, Waskell L, Ramamoorthy A. A model of the membrane-bound cytochrome b5-cytochrome P450 complex from NMR and mutagenesis data. J Biol Chem 2013; 288:22080-95. [PMID: 23709268 DOI: 10.1074/jbc.m112.448225] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Microsomal cytochrome b5 (cytb5) is a membrane-bound protein that modulates the catalytic activity of its redox partner, cytochrome P4502B4 (cytP450). Here, we report the first structure of full-length rabbit ferric microsomal cytb5 (16 kDa), incorporated in two different membrane mimetics (detergent micelles and lipid bicelles). Differential line broadening of the cytb5 NMR resonances and site-directed mutagenesis data were used to characterize the cytb5 interaction epitope recognized by ferric microsomal cytP450 (56 kDa). Subsequently, a data-driven docking algorithm, HADDOCK (high ambiguity driven biomolecular docking), was used to generate the structure of the complex between cytP4502B4 and cytb5 using experimentally derived restraints from NMR, mutagenesis, and the double mutant cycle data obtained on the full-length proteins. Our docking and experimental results point to the formation of a dynamic electron transfer complex between the acidic convex surface of cytb5 and the concave basic proximal surface of cytP4502B4. The majority of the binding energy for the complex is provided by interactions between residues on the C-helix and β-bulge of cytP450 and residues at the end of helix α4 of cytb5. The structure of the complex allows us to propose an interprotein electron transfer pathway involving the highly conserved Arg-125 on cytP450 serving as a salt bridge between the heme propionates of cytP450 and cytb5. We have also shown that the addition of a substrate to cytP450 likely strengthens the cytb5-cytP450 interaction. This study paves the way to obtaining valuable structural, functional, and dynamic information on membrane-bound complexes.
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Affiliation(s)
- Shivani Ahuja
- Department of Chemistry and Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, USA
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11
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Estrada DF, Laurence JS, Scott EE. Substrate-modulated cytochrome P450 17A1 and cytochrome b5 interactions revealed by NMR. J Biol Chem 2013; 288:17008-17018. [PMID: 23620596 DOI: 10.1074/jbc.m113.468926] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The membrane heme protein cytochrome b5 (b5) can enhance, inhibit, or have no effect on cytochrome P450 (P450) catalysis, depending on the specific P450, substrate, and reaction conditions, but the structural basis remains unclear. Here the interactions between the soluble domain of microsomal b5 and the catalytic domain of the bifunctional steroidogenic cytochrome P450 17A1 (CYP17A1) were investigated. CYP17A1 performs both steroid hydroxylation, which is unaffected by b5, and an androgen-forming lyase reaction that is facilitated 10-fold by b5. NMR chemical shift mapping of b5 titrations with CYP17A1 indicates that the interaction occurs in an intermediate exchange regime and identifies charged surface residues involved in the protein/protein interface. The role of these residues is confirmed by disruption of the complex upon mutagenesis of either the anionic b5 residues (Glu-48 or Glu-49) or the corresponding cationic CYP17A1 residues (Arg-347, Arg-358, or Arg-449). Cytochrome b5 binding to CYP17A1 is also mutually exclusive with binding of NADPH-cytochrome P450 reductase. To probe the differential effects of b5 on the two CYP17A1-mediated reactions and, thus, communication between the superficial b5 binding site and the buried CYP17A1 active site, CYP17A1/b5 complex formation was characterized with either hydroxylase or lyase substrates bound to CYP17A1. Significantly, the CYP17A1/b5 interaction is stronger when the hydroxylase substrate pregnenolone is present in the CYP17A1 active site than when the lyase substrate 17α-hydroxypregnenolone is in the active site. These findings form the basis for a clearer understanding of this important interaction by directly measuring the reversible binding of the two proteins, providing evidence of communication between the CYP17A1 active site and the superficial proximal b5 binding site.
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Affiliation(s)
| | | | - Emily E Scott
- Departments of Medicinal Chemistry, Lawrence, Kansas 66045.
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Parthasarathy S, Altuve A, Terzyan S, Zhang X, Kuczera K, Rivera M, Benson DR. Accommodating a nonconservative internal mutation by water-mediated hydrogen bonding between β-sheet strands: a comparison of human and rat type B (mitochondrial) cytochrome b5. Biochemistry 2011; 50:5544-54. [PMID: 21574570 DOI: 10.1021/bi2004729] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Mammalian type B (mitochondrial) b(5) cytochromes exhibit greater amino acid sequence diversity than their type A (microsomal) counterparts, as exemplified by the type B proteins from human (hCYB5B) and rat (rCYB5B). The comparison of X-ray crystal structures of hCYB5B and rCYB5B reported herein reveals a striking difference in packing involving the five-strand β-sheet, which can be attributed to fully buried residue 21 in strand β4. The greater bulk of Leu21 in hCYB5B in comparison to that of Thr21 in rCYB5B results in a substantial displacement of the first two residues in β5, and consequent loss of two of the three hydrogen bonds between β5 and β4. Hydrogen bonding between the residues is instead mediated by two well-ordered, fully buried water molecules. In a 10 ns molecular dynamics simulation, one of the buried water molecules in the hCYB5B structure exchanged readily with solvent via intermediates having three water molecules sandwiched between β4 and β5. When the buried water molecules were removed prior to a second 10 ns simulation, β4 and β5 formed persistent hydrogen bonds identical to those in rCYB5B, but the Leu21 side chain was forced to adopt a rarely observed conformation. Despite the apparently greater ease of access of water to the interior of hCYB5B than of rCYB5B suggested by these observations, the two proteins exhibit virtually identical stability, dynamic, and redox properties. The results provide new insight into the factors stabilizing the cytochrome b(5) fold.
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