1
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Kim D, Kim V, McCarty KD, Guengerich FP. Tight binding of cytochrome b 5 to cytochrome P450 17A1 is a critical feature of stimulation of C21 steroid lyase activity and androgen synthesis. J Biol Chem 2021; 296:100571. [PMID: 33753170 PMCID: PMC8080067 DOI: 10.1016/j.jbc.2021.100571] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/16/2021] [Accepted: 03/18/2021] [Indexed: 12/19/2022] Open
Abstract
It has been recognized for >50 years that cytochrome b5 (b5) stimulates some cytochrome P450 (P450)–catalyzed oxidations, but the basis of this function is still not understood well. The strongest stimulation of catalytic activity by b5 is in the P450 17A1 lyase reaction, an essential step in androgen synthesis from 21-carbon (C21) steroids, making this an excellent model system to interrogate b5 function. One of the issues in studying b5–P450 interactions has been the limited solution assay methods. We constructed a fluorescently labeled variant of human b5 that can be used in titrations. The labeled b5 bound to WT P450 17A1 with a Kd of 2.5 nM and rapid kinetics, on the order of 1 s−1. Only weak binding was observed with the clinical P450 17A1 variants E305G, R347H, and R358Q; these mutants are deficient in lyase activity, which has been hypothesized to be due to attenuated b5 binding. Kd values were not affected by the presence of P450 17A1 substrates. A peptide containing the P450 17A1 Arg-347/Arg-358 region attenuated Alexa 488-T70C-b5 fluorescence at higher concentrations. The addition of NADPH–P450 reductase (POR) to an Alexa 488-T70C-b5:P450 17A1 complex resulted in a concentration-dependent partial restoration of b5 fluorescence, indicative of a ternary P450:b5:POR complex, which was also supported by gel filtration experiments. Overall, these results are interpreted in the context of a dynamic and tight P450 17A1:b5 complex that also binds POR to form a catalytically competent ternary complex, and variants that disrupt this interaction have low catalytic activity.
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Affiliation(s)
- Donghak Kim
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA; Department of Biological Sciences, Konkuk University, Seoul, Republic of Korea
| | - Vitchan Kim
- Department of Biological Sciences, Konkuk University, Seoul, Republic of Korea
| | - Kevin D McCarty
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - F Peter Guengerich
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA.
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2
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Navapour L, Mogharrab N. In silico screening and analysis of nonsynonymous SNPs in human CYP1A2 to assess possible associations with pathogenicity and cancer susceptibility. Sci Rep 2021; 11:4977. [PMID: 33654112 PMCID: PMC7925555 DOI: 10.1038/s41598-021-83696-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 02/03/2021] [Indexed: 01/31/2023] Open
Abstract
Cytochrome P450 1A2 (CYP1A2) is one of the main hepatic CYPs involved in metabolism of carcinogens and clinically used drugs. Nonsynonymous single nucleotide polymorphisms (nsSNPs) of this enzyme could affect cancer susceptibility and drug efficiency. Hence, identification of human CYP1A2 pathogenic nsSNPs could be of great importance in personalized medicine and pharmacogenetics. Here, 176 nsSNPs of human CYP1A2 were evaluated using a variety of computational tools, of which 18 nsSNPs were found to be associated with pathogenicity. Further analysis suggested possible association of 9 nsSNPs (G73R, G73W, R108Q, R108W, E168K, E346K, R431W, F432S and R456H) with the risk of hepatocellular carcinoma. Molecular dynamics simulations revealed higher overall flexibility, decreased intramolecular hydrogen bonds and lower content of regular secondary structures for both cancer driver variants G73W and F432S when compared to the wild-type structure. In case of F432S, loss of the conserved hydrogen bond between Arg137 and heme propionate oxygen may affect heme stability and the observed significant rise in fluctuation of the CD loop could modify CYP1A2 interactions with its redox partners. Together, these findings propose CYP1A2 as a possible candidate for hepatocellular carcinoma and provide structural insights into how cancer driver nsSNPs could affect protein structure, heme stability and interaction network.
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Affiliation(s)
- Leila Navapour
- Biophysics and Computational Biology Laboratory (BCBL), Department of Biology, College of Sciences, Shiraz University, Shiraz, Iran
| | - Navid Mogharrab
- Biophysics and Computational Biology Laboratory (BCBL), Department of Biology, College of Sciences, Shiraz University, Shiraz, Iran.
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3
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Kumar A, Wilderman PR, Tu C, Shen S, Qu J, Estrada DF. Evidence of Allosteric Coupling between Substrate Binding and Adx Recognition in the Vitamin D Carbon-24 Hydroxylase CYP24A1. Biochemistry 2020; 59:1537-1548. [PMID: 32259445 PMCID: PMC7233526 DOI: 10.1021/acs.biochem.0c00107] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Metabolic inactivation of 1,25(OH)2D3 requires molecular recognition between the mitochondrial enzyme cytochrome P450 24A1 (CYP24A1) and its cognate redox partner adrenodoxin (Adx). Recent evidence supports a model of CYP24A1 function in which substrate binding and Adx recognition are structurally linked. However, the details of this allosteric connection are not clear. In this study, we utilize chemical cross-linking coupled to mass spectrometry, nuclear magnetic resonance (NMR) spectroscopy, and CYP24A1 functional assays to inform a working model of a CYP24A1-Adx complex. We report that differential cross-linking internal to CYP24A1 points toward an Adx-induced conformational change that perturbs the F and G helices, which are required for substrate binding. Moreover, the modeled complex suggests that a semiconserved nonpolar interaction at the interface may influence CYP24A1 regioselectivity. Taken together, these findings contribute to our understanding of Adx recognition in a critical vitamin D-inactivating enzyme and provide broader insight regarding the variability inherent in CYP-Adx interactions.
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Affiliation(s)
- Amit Kumar
- Department of Biochemistry, Jacobs School of Medicine, University at Buffalo, 955 Main Street, Buffalo NY 14203
| | - P. Ross Wilderman
- Department of Pharmaceutical Sciences, School of Pharmacy, 69 North Eagleville Road, University of Connecticut, Storrs, CT 06269
| | - Chengjian Tu
- Department of Pharmaceutical Sciences, School of Pharmacy, 318 Pharmacy Building, University at Buffalo, Buffalo NY 14214
| | - Shichen Shen
- Department of Pharmaceutical Sciences, School of Pharmacy, 318 Pharmacy Building, University at Buffalo, Buffalo NY 14214
| | - Jun Qu
- Department of Pharmaceutical Sciences, School of Pharmacy, 318 Pharmacy Building, University at Buffalo, Buffalo NY 14214
| | - D. Fernando Estrada
- Department of Biochemistry, Jacobs School of Medicine, University at Buffalo, 955 Main Street, Buffalo NY 14203
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4
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Abstract
![]()
Work on the electronic
structures of metal–oxo complexes
began in Copenhagen over 50 years ago. This work led to the prediction
that tetragonal multiply bonded transition metal–oxos would
not be stable beyond the iron–ruthenium–osmium oxo wall
in the periodic table and that triply bonded metal–oxos could
not be protonated, even in the strongest Brønsted acids. In this
theory, only double bonded metal–oxos could attract protons,
with basicities being a function of the electron donating ability
of ancillary ligands. Such correlations of electronic structure with
reactivity have gained importance in recent years, most notably owing
to the widespread recognition that high-valent iron–oxos are
intermediates in biological reactions critical to life on Earth. In this Account, we focus attention on the oxygenations of inert
organic substrates by cytochromes P450, as these reactions involve
multiply bonded iron–oxos. We emphasize that P450 iron–oxos
are strong oxidants, so strong that they would destroy nearby amino
acids if substrates are not oxygenated rapidly; it is our view that
these high-valent iron–oxos are such dangerous reactive oxygen
species that Nature surely found ways to disable them. Looking more
deeply into this matter, mainly by examining many thousands of structures
in the Protein Data Bank, we have found that P450s and other enzymes
that require oxygen for function have chains of tyrosines and tryptophans
that extend from active-site regions to protein surfaces. Tyrosines
are near the heme active sites in bacterial P450s, whereas tryptophan
is closest in most human enzymes. High-valent iron–oxo survival
times taken from hole hopping maps range from a few nanoseconds to
milliseconds, depending on the distance of the closest Trp or Tyr
residue to the heme. In our proposed mechanism, multistep hole tunneling
(hopping) through Tyr/Trp chains guides the damaging oxidizing hole
to the protein surface, where it can be quenched by soluble protein
or small molecule reductants. As the Earth’s oxygenic atmosphere
is believed to have developed about 2.5 billion years ago, the increase
in occurrence frequency of tyrosine and tryptophan since the last
universal evolutionary ancestor may be in part a consequence of enzyme
protective functions that developed to cope with the environmental
toxin, O2.
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Affiliation(s)
- Harry B. Gray
- Beckman Institute, California Institute of Technology, Pasadena, California 91125, United States
| | - Jay R. Winkler
- Beckman Institute, California Institute of Technology, Pasadena, California 91125, United States
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5
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Kung SH, Lund S, Murarka A, McPhee D, Paddon CJ. Approaches and Recent Developments for the Commercial Production of Semi-synthetic Artemisinin. FRONTIERS IN PLANT SCIENCE 2018; 9:87. [PMID: 29445390 PMCID: PMC5797932 DOI: 10.3389/fpls.2018.00087] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 01/15/2018] [Indexed: 05/20/2023]
Abstract
The antimalarial drug artemisinin is a natural product produced by the plant Artemisia annua. Extracts of A. annua have been used in Chinese herbal medicine for over two millennia. Following the re-discovery of A. annua extract as an effective antimalarial, and the isolation and structural elucidation of artemisinin as the active agent, it was recommended as the first-line treatment for uncomplicated malaria in combination with another effective antimalarial drug (Artemisinin Combination Therapy) by the World Health Organization (WHO) in 2002. Following the WHO recommendation, the availability and price of artemisinin fluctuated greatly, ranging from supply shortfalls in some years to oversupply in others. To alleviate these supply and price issues, a second source of artemisinin was sought, resulting in an effort to produce artemisinic acid, a late-stage chemical precursor of artemisinin, by yeast fermentation, followed by chemical conversion to artemisinin (i.e., semi-synthesis). Engineering to enable production of artemisinic acid in yeast relied on the discovery of A. annua genes encoding artemisinic acid biosynthetic enzymes, and synthetic biology to engineer yeast metabolism. The progress of this effort, which resulted in semi-synthetic artemisinin entering commercial production in 2013, is reviewed with an emphasis on recent publications and opportunities for further development. Aspects of both the biology of artemisinin production in A. annua, and yeast strain engineering are discussed, as are recent developments in the chemical conversion of artemisinic acid to artemisinin.
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6
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Hackett JC. Membrane-embedded substrate recognition by cytochrome P450 3A4. J Biol Chem 2018; 293:4037-4046. [PMID: 29382727 DOI: 10.1074/jbc.ra117.000961] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 01/26/2018] [Indexed: 12/15/2022] Open
Abstract
Cytochrome P450 3A4 (CYP3A4) is the dominant xenobiotic-metabolizing enzyme in the liver and intestine and is involved in the disposition of more than 50% of drugs. Because of its ability to bind multiple substrates, its reaction kinetics are complex, and its association with the microsomal membrane confounds our understanding of how this enzyme recognizes and recruits diverse substrates. Testosterone (TST) hydroxylation is the prototypical CYP3A4 reaction, displaying positive homotropic cooperativity with three binding sites. Here, exploiting the capability of accelerated molecular dynamics (aMD) to sample events in the millisecond regime, I performed >25-μs aMD simulations in the presence of three TST molecules. These simulations identified high-occupancy surface-binding sites as well as a pathway for TST ingress into the CYP3A4 active site originating in the membrane. Adaptive biasing force analysis of the latter pathway revealed a metastable intermediate that could constitute a third binding site at high TST concentrations. Prompted by the observation that interactions between TST and the G'-helix mobilize the ligand into the active site, a free-energy analysis of TST distribution in the membrane was conducted and revealed that the depth of the G'-helix is optimal for extracting TST. In summary, these simulations confirm separate, but adjacent substrate-binding sites within the enzyme and the existence of an auxiliary TST-binding site. The broader impact of these simulations is that they support a mechanism in which cytochromes P450 directly recruit membrane-solubilized substrates.
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Affiliation(s)
- John C Hackett
- From the Department of Physiology and Biophysics and the Massey Cancer Center, School of Medicine, Virginia Commonwealth University, Richmond, Virginia 23298-0035
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7
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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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8
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Liu Q, Remmelzwaal S, Heck AJR, Akhmanova A, Liu F. Facilitating identification of minimal protein binding domains by cross-linking mass spectrometry. Sci Rep 2017; 7:13453. [PMID: 29044157 PMCID: PMC5647383 DOI: 10.1038/s41598-017-13663-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 09/25/2017] [Indexed: 10/27/2022] Open
Abstract
Characterization of protein interaction domains is crucial for understanding protein functions. Here we combine cross-linking mass spectrometry (XL-MS) with deletion analysis to accurately locate minimal protein interaction domains. As a proof of concept, we investigated in detail the binding interfaces of two protein assemblies: the complex formed by MICAL3, ELKS and Rab8A, which is involved in exocytosis, and the complex of SLAIN2, CLASP2 and ch-TOG, which controls microtubule dynamics. We found that XL-MS provides valuable information to efficiently guide the design of protein fragments that are essential for protein interaction. However, we also observed a number of cross-links between polypeptide regions that were dispensable for complex formation, especially among intrinsically disordered sequences. Collectively, our results indicate that XL-MS, which renders distance restrains of linked residue pairs, accelerates the characterization of protein binding regions in combination with other biochemical approaches.
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Affiliation(s)
- Qingyang Liu
- Cell Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Sanne Remmelzwaal
- Cell Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CH, Utrecht, The Netherlands
| | - Anna Akhmanova
- Cell Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
| | - Fan Liu
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CH, Utrecht, The Netherlands.
- Leibniz Institute of Molecular Pharmacology (FMP), Robert-Rössle-Straße 10, 13125, Berlin, Germany.
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9
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Kandel SE, Han LW, Mao Q, Lampe JN. Digging Deeper into CYP3A Testosterone Metabolism: Kinetic, Regioselectivity, and Stereoselectivity Differences between CYP3A4/5 and CYP3A7. Drug Metab Dispos 2017; 45:1266-1275. [PMID: 28986474 DOI: 10.1124/dmd.117.078055] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 10/04/2017] [Indexed: 01/22/2023] Open
Abstract
The metabolism of testosterone to 6β-hydroxytestosterone (6β-OH-T) is a commonly used assay to evaluate human CYP3A enzyme activities. However, previous reports have indicated that CYP3A7 also produces 2α-hydroxytestosterone (2α-OH-T) and that a 2α-OH-T/6β-OH-T ratio may be a unique endogenous biomarker of the activity of the enzyme. Until now, the full metabolite and kinetic profile for testosterone hydroxylation by CYP3A7 has not been fully examined. To this end, we performed a complete kinetic analysis of the 6β-OH-T, 2α-OH-T, and 2β-hydroxytestosterone metabolites for recombinant Supersome CYP3A4, CYP3A5, and CYP3A7 enzymes and monitored metabolism in fetal and adult human liver microsomes for comparison. In general, a decrease in the velocity of the reaction was observed between CYP3A4 and the two other enzymes, with CYP3A7 showing the lowest metabolic capacity. Interestingly, we found that the 2α-OH-T/6β-OH-T ratio varied with substrate concentration when testosterone was incubated with CYP3A7, suggesting that this ratio would likely not function well as a biomarker for CYP3A7 activity. In silico docking studies revealed at least two different binding modes for testosterone between CYP3A4 and CYP3A7. In CYP3A4, the most energetically favorable docking mode places testosterone in a position with the methyl groups directed toward the heme iron, which is more favorable for oxidation at C6β, whereas for CYP3A7 the testosterone methyl groups are positioned away from the heme, which is more favorable for an oxidation event at C2α In conclusion, our data indicate an alternative binding mode for testosterone in CYP3A7 that favors the 2α-hydroxylation, suggesting significant structural differences in its active site compared with CYP3A4/5.
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Affiliation(s)
- Sylvie E Kandel
- Department of Pharmacology, Toxicology and Therapeutics, The University of Kansas Medical Center, Kansas City, Kansas (S.E.K., J.N.L.); Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, Washington (L.W.H., Q.M.); and The University of Kansas Liver Center, Kansas City, Kansas (J.N.L.)
| | - Lyrialle W Han
- Department of Pharmacology, Toxicology and Therapeutics, The University of Kansas Medical Center, Kansas City, Kansas (S.E.K., J.N.L.); Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, Washington (L.W.H., Q.M.); and The University of Kansas Liver Center, Kansas City, Kansas (J.N.L.)
| | - Qingcheng Mao
- Department of Pharmacology, Toxicology and Therapeutics, The University of Kansas Medical Center, Kansas City, Kansas (S.E.K., J.N.L.); Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, Washington (L.W.H., Q.M.); and The University of Kansas Liver Center, Kansas City, Kansas (J.N.L.)
| | - Jed N Lampe
- Department of Pharmacology, Toxicology and Therapeutics, The University of Kansas Medical Center, Kansas City, Kansas (S.E.K., J.N.L.); Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, Washington (L.W.H., Q.M.); and The University of Kansas Liver Center, Kansas City, Kansas (J.N.L.)
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10
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Bhatt MR, Khatri Y, Rodgers RJ, Martin LL. Role of cytochrome b5 in the modulation of the enzymatic activities of cytochrome P450 17α-hydroxylase/17,20-lyase (P450 17A1). J Steroid Biochem Mol Biol 2017; 170:2-18. [PMID: 26976652 DOI: 10.1016/j.jsbmb.2016.02.033] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 02/25/2016] [Accepted: 02/27/2016] [Indexed: 12/13/2022]
Abstract
Cytochrome b5 (cyt b5) is a small hemoprotein that plays a significant role in the modulation of activities of an important steroidogenic enzyme, cytochrome P450 17α-hydroxylase/17,20-lyase (P450 17A1, CYP17A1). Located in the zona fasciculata and zona reticularis of the adrenal cortex and in the gonads, P450 17A1 catalyzes two different reactions in the steroidogenic pathway; the 17α-hydroxylation and 17,20-lyase, in the endoplasmic reticulum of these respective tissues. The activities of P450 17A1 are regulated by cyt b5 that enhances the 17,20-lyase reaction by promoting the coupling of P450 17A1 and cytochrome P450 reductase (CPR), allosterically. Cyt b5 can also act as an electron donor to enhance the 16-ene-synthase activity of human P450 17A1. In this review, we discuss the many roles of cyt b5 and focus on the modulation of CYP17A1 activities by cyt b5 and the mechanisms involved.
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Affiliation(s)
- Megh Raj Bhatt
- Everest Biotech Pvt. Ltd., Khumaltar, Lalitpur, P.O. Box 21608, Kathmandu 44600, Nepal
| | - Yogan Khatri
- Institute of Biochemistry, Saarland University, 66123 Saarbrücken, Germany
| | - Raymond J Rodgers
- School of Medicine, Robinson Research Institute, University of Adelaide, Adelaide SA 5005, Australia
| | - Lisandra L Martin
- School of Chemistry, Monash University, Clayton, 3800, Victoria, Australia.
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11
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Yablokov E, Florinskaya A, Medvedev A, Sergeev G, Strushkevich N, Luschik A, Shkel T, Haidukevich I, Gilep A, Usanov S, Ivanov A. Thermodynamics of interactions between mammalian cytochromes P450 and b5. Arch Biochem Biophys 2017; 619:10-15. [DOI: 10.1016/j.abb.2017.02.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 02/20/2017] [Accepted: 02/21/2017] [Indexed: 10/20/2022]
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12
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Gao J, Tian X, Zhou J, Cui MZ, Zhang HF, Gao N, Wen Q, Qiao HL. From Genotype to Phenotype: Cytochrome P450 2D6-Mediated Drug Clearance in Humans. Mol Pharm 2017; 14:649-657. [DOI: 10.1021/acs.molpharmaceut.6b00920] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Jie Gao
- Institute
of Clinical Pharmacology, Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Xin Tian
- Institute
of Clinical Pharmacology, Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Jun Zhou
- Institute
of Clinical Pharmacology, Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Ming-Zhu Cui
- Institute
of Clinical Pharmacology, Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Hai-Feng Zhang
- Institute
of Clinical Pharmacology, Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Na Gao
- Institute
of Clinical Pharmacology, Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Qiang Wen
- Institute
of Clinical Pharmacology, Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Hai-Ling Qiao
- Institute
of Clinical Pharmacology, Zhengzhou University, Zhengzhou, Henan 450052, China
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13
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Ershov P, Yablokov E, Mezentsev Y, Kalushskiy L, Florinskaya A, Veselovsky A, Gnedenko O, Gilep A, Usanov S, Medvedev A, Ivanov A. The effect of isatin on protein-protein interactions between cytochrome b5 and cytochromes P450. ACTA ACUST UNITED AC 2017; 63:170-175. [DOI: 10.18097/pbmc20176302170] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Cytochromes P450 (CYP) are involved in numerous biochemical processes including metabolism of xenobiotics, biosynthesis of cholesterol, steroid hormones etc. Since some CYP catalyze indol oxidation to isatin, we have hypothesized that isatin can regulate protein-protein interactions (PPI) between components of the CYP system thus representing a (negative?) feedback mechanism. The aim of this study was to investigate a possible effect of isatin on interaction of human CYP with cytochrome b5 (CYB5A). Using the optical biosensor test system employing surface plasmon resonance (SPR) we have investigated interaction of immobilized CYB5A with various CYP in the absence and in the presence of isatin. The SPR-based experiments have shown that a high concentration of isatin (270 mM) increases Kd values for complexes CYB5A/CYP3А5 and CYB5A/CYP3A4 (twofold and threefold, respectively), but has no influence on complex formation between CYB5A and other CYP (including indol-metabolizing CYP2C19 and CYP2E1). Isatin injection to the optical biosensor chip with the preformed molecular complex CYB5A/CYP3A4 caused a 30%-increase in its dissociation rate. Molecular docking manipulations have shown that isatin can influence interaction of CYP3А5 or CYP3A4 with CYB5A acting at the contact region of CYB5A/CYP.
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Affiliation(s)
- P.V. Ershov
- Institute of Biomedical Chemistry, Moscow, Russia
| | | | | | | | | | | | | | - A.A. Gilep
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk, Belarus
| | - S.A. Usanov
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk, Belarus
| | | | - A.S. Ivanov
- Institute of Biomedical Chemistry, Moscow, Russia
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14
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Kim SM, Wang Y, Nabavi N, Liu Y, Correia MA. Hepatic cytochromes P450: structural degrons and barcodes, posttranslational modifications and cellular adapters in the ERAD-endgame. Drug Metab Rev 2016; 48:405-33. [PMID: 27320797 DOI: 10.1080/03602532.2016.1195403] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The endoplasmic reticulum (ER)-anchored hepatic cytochromes P450 (P450s) are enzymes that metabolize endo- and xenobiotics i.e. drugs, carcinogens, toxins, natural and chemical products. These agents modulate liver P450 content through increased synthesis or reduction via inactivation and/or proteolytic degradation, resulting in clinically significant drug-drug interactions. P450 proteolytic degradation occurs via ER-associated degradation (ERAD) involving either of two distinct routes: Ubiquitin (Ub)-dependent 26S proteasomal degradation (ERAD/UPD) or autophagic lysosomal degradation (ERAD/ALD). CYP3A4, the major human liver/intestinal P450, and the fast-turnover CYP2E1 species are degraded via ERAD/UPD entailing multisite protein phosphorylation and subsequent ubiquitination by gp78 and CHIP E3 Ub-ligases. We are gaining insight into the nature of the structural determinants involved in CYP3A4 and CYP2E1 molecular recognition in ERAD/UPD [i.e. K48-linked polyUb chains and linear and/or "conformational" phosphodegrons consisting either of consecutive sequences on surface loops and/or disordered regions, or structurally-assembled surface clusters of negatively charged acidic (Asp/Glu) and phosphorylated (Ser/Thr) residues, within or vicinal to which, Lys-residues are targeted for ubiquitination]. Structural inspection of select human liver P450s reveals that such linear or conformational phosphodegrons may indeed be a common P450-ERAD/UPD feature. By contrast, although many P450s such as the slow-turnover CYP2E1 species and rat liver CYP2B1 and CYP2C11 are degraded via ERAD/ALD, little is known about the mechanism of their ALD-targeting. On the basis of our current knowledge of ALD-substrate targeting, we propose a tripartite conjunction of K63-linked Ub-chains, P450 structural "LIR" motifs and selective cellular "cargo receptors" as plausible P450-ALD determinants.
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Affiliation(s)
- Sung-Mi Kim
- a Department of Cellular & Molecular Pharmacology , University of California San Francisco , San Francisco , CA , USA
| | - YongQiang Wang
- a Department of Cellular & Molecular Pharmacology , University of California San Francisco , San Francisco , CA , USA
| | - Noushin Nabavi
- a Department of Cellular & Molecular Pharmacology , University of California San Francisco , San Francisco , CA , USA
| | - Yi Liu
- a Department of Cellular & Molecular Pharmacology , University of California San Francisco , San Francisco , CA , USA
| | - Maria Almira Correia
- a Department of Cellular & Molecular Pharmacology , University of California San Francisco , San Francisco , CA , USA ;,b Department of Pharmaceutical Chemistry , University of California San Francisco , San Francisco , CA , USA ;,c Department of Bioengineering and Therapeutic Sciences , University of California San Francisco , San Francisco , CA , USA ;,d The Liver Center, University of California San Francisco , San Francisco , CA , USA
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15
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Scott EE, Wolf CR, Otyepka M, Humphreys SC, Reed JR, Henderson CJ, McLaughlin LA, Paloncýová M, Navrátilová V, Berka K, Anzenbacher P, Dahal UP, Barnaba C, Brozik JA, Jones JP, Estrada DF, Laurence JS, Park JW, Backes WL. The Role of Protein-Protein and Protein-Membrane Interactions on P450 Function. Drug Metab Dispos 2016; 44:576-90. [PMID: 26851242 PMCID: PMC4810767 DOI: 10.1124/dmd.115.068569] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 02/03/2016] [Indexed: 11/22/2022] Open
Abstract
This symposium summary, sponsored by the ASPET, was held at Experimental Biology 2015 on March 29, 2015, in Boston, Massachusetts. The symposium focused on: 1) the interactions of cytochrome P450s (P450s) with their redox partners; and 2) the role of the lipid membrane in their orientation and stabilization. Two presentations discussed the interactions of P450s with NADPH-P450 reductase (CPR) and cytochrome b5. First, solution nuclear magnetic resonance was used to compare the protein interactions that facilitated either the hydroxylase or lyase activities of CYP17A1. The lyase interaction was stimulated by the presence of b5 and 17α-hydroxypregnenolone, whereas the hydroxylase reaction was predominant in the absence of b5. The role of b5 was also shown in vivo by selective hepatic knockout of b5 from mice expressing CYP3A4 and CYP2D6; the lack of b5 caused a decrease in the clearance of several substrates. The role of the membrane on P450 orientation was examined using computational methods, showing that the proximal region of the P450 molecule faced the aqueous phase. The distal region, containing the substrate-access channel, was associated with the membrane. The interaction of NADPH-P450 reductase (CPR) with the membrane was also described, showing the ability of CPR to "helicopter" above the membrane. Finally, the endoplasmic reticulum (ER) was shown to be heterogeneous, having ordered membrane regions containing cholesterol and more disordered regions. Interestingly, two closely related P450s, CYP1A1 and CYP1A2, resided in different regions of the ER. The structural characteristics of their localization were examined. These studies emphasize the importance of P450 protein organization to their function.
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Affiliation(s)
- Emily E Scott
- Departments of Medicinal Chemistry and Pharmaceutical Chemistry, The University of Kansas, Lawrence, Kansas (D.F.E, J.S.L., E.E.S.); Division of Cancer Research, School of Medicine, University of Dundee, Ninewells Hospital, Dundee, United Kingdom (C.R.W., C.J.H., L.A.M.); Regional Center of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science (M.O., M.P., V.N., K.B.) and Department of Pharmacology, Faculty of Medicine and Dentistry (P.A.), Palacký University, Olomouc, Czech Republic; Department of Chemistry, Washington State University, Pullman, Washington (S.C.H., U.P.D., C.B., J.A.B., J.P.J.); and Department of Pharmacology and Experimental Therapeutics, and the Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, Louisiana (J.R.R., J.W.P., W.L.B.)
| | - C Roland Wolf
- Departments of Medicinal Chemistry and Pharmaceutical Chemistry, The University of Kansas, Lawrence, Kansas (D.F.E, J.S.L., E.E.S.); Division of Cancer Research, School of Medicine, University of Dundee, Ninewells Hospital, Dundee, United Kingdom (C.R.W., C.J.H., L.A.M.); Regional Center of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science (M.O., M.P., V.N., K.B.) and Department of Pharmacology, Faculty of Medicine and Dentistry (P.A.), Palacký University, Olomouc, Czech Republic; Department of Chemistry, Washington State University, Pullman, Washington (S.C.H., U.P.D., C.B., J.A.B., J.P.J.); and Department of Pharmacology and Experimental Therapeutics, and the Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, Louisiana (J.R.R., J.W.P., W.L.B.)
| | - Michal Otyepka
- Departments of Medicinal Chemistry and Pharmaceutical Chemistry, The University of Kansas, Lawrence, Kansas (D.F.E, J.S.L., E.E.S.); Division of Cancer Research, School of Medicine, University of Dundee, Ninewells Hospital, Dundee, United Kingdom (C.R.W., C.J.H., L.A.M.); Regional Center of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science (M.O., M.P., V.N., K.B.) and Department of Pharmacology, Faculty of Medicine and Dentistry (P.A.), Palacký University, Olomouc, Czech Republic; Department of Chemistry, Washington State University, Pullman, Washington (S.C.H., U.P.D., C.B., J.A.B., J.P.J.); and Department of Pharmacology and Experimental Therapeutics, and the Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, Louisiana (J.R.R., J.W.P., W.L.B.)
| | - Sara C Humphreys
- Departments of Medicinal Chemistry and Pharmaceutical Chemistry, The University of Kansas, Lawrence, Kansas (D.F.E, J.S.L., E.E.S.); Division of Cancer Research, School of Medicine, University of Dundee, Ninewells Hospital, Dundee, United Kingdom (C.R.W., C.J.H., L.A.M.); Regional Center of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science (M.O., M.P., V.N., K.B.) and Department of Pharmacology, Faculty of Medicine and Dentistry (P.A.), Palacký University, Olomouc, Czech Republic; Department of Chemistry, Washington State University, Pullman, Washington (S.C.H., U.P.D., C.B., J.A.B., J.P.J.); and Department of Pharmacology and Experimental Therapeutics, and the Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, Louisiana (J.R.R., J.W.P., W.L.B.)
| | - James R Reed
- Departments of Medicinal Chemistry and Pharmaceutical Chemistry, The University of Kansas, Lawrence, Kansas (D.F.E, J.S.L., E.E.S.); Division of Cancer Research, School of Medicine, University of Dundee, Ninewells Hospital, Dundee, United Kingdom (C.R.W., C.J.H., L.A.M.); Regional Center of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science (M.O., M.P., V.N., K.B.) and Department of Pharmacology, Faculty of Medicine and Dentistry (P.A.), Palacký University, Olomouc, Czech Republic; Department of Chemistry, Washington State University, Pullman, Washington (S.C.H., U.P.D., C.B., J.A.B., J.P.J.); and Department of Pharmacology and Experimental Therapeutics, and the Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, Louisiana (J.R.R., J.W.P., W.L.B.)
| | - Colin J Henderson
- Departments of Medicinal Chemistry and Pharmaceutical Chemistry, The University of Kansas, Lawrence, Kansas (D.F.E, J.S.L., E.E.S.); Division of Cancer Research, School of Medicine, University of Dundee, Ninewells Hospital, Dundee, United Kingdom (C.R.W., C.J.H., L.A.M.); Regional Center of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science (M.O., M.P., V.N., K.B.) and Department of Pharmacology, Faculty of Medicine and Dentistry (P.A.), Palacký University, Olomouc, Czech Republic; Department of Chemistry, Washington State University, Pullman, Washington (S.C.H., U.P.D., C.B., J.A.B., J.P.J.); and Department of Pharmacology and Experimental Therapeutics, and the Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, Louisiana (J.R.R., J.W.P., W.L.B.)
| | - Lesley A McLaughlin
- Departments of Medicinal Chemistry and Pharmaceutical Chemistry, The University of Kansas, Lawrence, Kansas (D.F.E, J.S.L., E.E.S.); Division of Cancer Research, School of Medicine, University of Dundee, Ninewells Hospital, Dundee, United Kingdom (C.R.W., C.J.H., L.A.M.); Regional Center of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science (M.O., M.P., V.N., K.B.) and Department of Pharmacology, Faculty of Medicine and Dentistry (P.A.), Palacký University, Olomouc, Czech Republic; Department of Chemistry, Washington State University, Pullman, Washington (S.C.H., U.P.D., C.B., J.A.B., J.P.J.); and Department of Pharmacology and Experimental Therapeutics, and the Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, Louisiana (J.R.R., J.W.P., W.L.B.)
| | - Markéta Paloncýová
- Departments of Medicinal Chemistry and Pharmaceutical Chemistry, The University of Kansas, Lawrence, Kansas (D.F.E, J.S.L., E.E.S.); Division of Cancer Research, School of Medicine, University of Dundee, Ninewells Hospital, Dundee, United Kingdom (C.R.W., C.J.H., L.A.M.); Regional Center of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science (M.O., M.P., V.N., K.B.) and Department of Pharmacology, Faculty of Medicine and Dentistry (P.A.), Palacký University, Olomouc, Czech Republic; Department of Chemistry, Washington State University, Pullman, Washington (S.C.H., U.P.D., C.B., J.A.B., J.P.J.); and Department of Pharmacology and Experimental Therapeutics, and the Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, Louisiana (J.R.R., J.W.P., W.L.B.)
| | - Veronika Navrátilová
- Departments of Medicinal Chemistry and Pharmaceutical Chemistry, The University of Kansas, Lawrence, Kansas (D.F.E, J.S.L., E.E.S.); Division of Cancer Research, School of Medicine, University of Dundee, Ninewells Hospital, Dundee, United Kingdom (C.R.W., C.J.H., L.A.M.); Regional Center of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science (M.O., M.P., V.N., K.B.) and Department of Pharmacology, Faculty of Medicine and Dentistry (P.A.), Palacký University, Olomouc, Czech Republic; Department of Chemistry, Washington State University, Pullman, Washington (S.C.H., U.P.D., C.B., J.A.B., J.P.J.); and Department of Pharmacology and Experimental Therapeutics, and the Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, Louisiana (J.R.R., J.W.P., W.L.B.)
| | - Karel Berka
- Departments of Medicinal Chemistry and Pharmaceutical Chemistry, The University of Kansas, Lawrence, Kansas (D.F.E, J.S.L., E.E.S.); Division of Cancer Research, School of Medicine, University of Dundee, Ninewells Hospital, Dundee, United Kingdom (C.R.W., C.J.H., L.A.M.); Regional Center of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science (M.O., M.P., V.N., K.B.) and Department of Pharmacology, Faculty of Medicine and Dentistry (P.A.), Palacký University, Olomouc, Czech Republic; Department of Chemistry, Washington State University, Pullman, Washington (S.C.H., U.P.D., C.B., J.A.B., J.P.J.); and Department of Pharmacology and Experimental Therapeutics, and the Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, Louisiana (J.R.R., J.W.P., W.L.B.)
| | - Pavel Anzenbacher
- Departments of Medicinal Chemistry and Pharmaceutical Chemistry, The University of Kansas, Lawrence, Kansas (D.F.E, J.S.L., E.E.S.); Division of Cancer Research, School of Medicine, University of Dundee, Ninewells Hospital, Dundee, United Kingdom (C.R.W., C.J.H., L.A.M.); Regional Center of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science (M.O., M.P., V.N., K.B.) and Department of Pharmacology, Faculty of Medicine and Dentistry (P.A.), Palacký University, Olomouc, Czech Republic; Department of Chemistry, Washington State University, Pullman, Washington (S.C.H., U.P.D., C.B., J.A.B., J.P.J.); and Department of Pharmacology and Experimental Therapeutics, and the Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, Louisiana (J.R.R., J.W.P., W.L.B.)
| | - Upendra P Dahal
- Departments of Medicinal Chemistry and Pharmaceutical Chemistry, The University of Kansas, Lawrence, Kansas (D.F.E, J.S.L., E.E.S.); Division of Cancer Research, School of Medicine, University of Dundee, Ninewells Hospital, Dundee, United Kingdom (C.R.W., C.J.H., L.A.M.); Regional Center of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science (M.O., M.P., V.N., K.B.) and Department of Pharmacology, Faculty of Medicine and Dentistry (P.A.), Palacký University, Olomouc, Czech Republic; Department of Chemistry, Washington State University, Pullman, Washington (S.C.H., U.P.D., C.B., J.A.B., J.P.J.); and Department of Pharmacology and Experimental Therapeutics, and the Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, Louisiana (J.R.R., J.W.P., W.L.B.)
| | - Carlo Barnaba
- Departments of Medicinal Chemistry and Pharmaceutical Chemistry, The University of Kansas, Lawrence, Kansas (D.F.E, J.S.L., E.E.S.); Division of Cancer Research, School of Medicine, University of Dundee, Ninewells Hospital, Dundee, United Kingdom (C.R.W., C.J.H., L.A.M.); Regional Center of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science (M.O., M.P., V.N., K.B.) and Department of Pharmacology, Faculty of Medicine and Dentistry (P.A.), Palacký University, Olomouc, Czech Republic; Department of Chemistry, Washington State University, Pullman, Washington (S.C.H., U.P.D., C.B., J.A.B., J.P.J.); and Department of Pharmacology and Experimental Therapeutics, and the Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, Louisiana (J.R.R., J.W.P., W.L.B.)
| | - James A Brozik
- Departments of Medicinal Chemistry and Pharmaceutical Chemistry, The University of Kansas, Lawrence, Kansas (D.F.E, J.S.L., E.E.S.); Division of Cancer Research, School of Medicine, University of Dundee, Ninewells Hospital, Dundee, United Kingdom (C.R.W., C.J.H., L.A.M.); Regional Center of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science (M.O., M.P., V.N., K.B.) and Department of Pharmacology, Faculty of Medicine and Dentistry (P.A.), Palacký University, Olomouc, Czech Republic; Department of Chemistry, Washington State University, Pullman, Washington (S.C.H., U.P.D., C.B., J.A.B., J.P.J.); and Department of Pharmacology and Experimental Therapeutics, and the Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, Louisiana (J.R.R., J.W.P., W.L.B.)
| | - Jeffrey P Jones
- Departments of Medicinal Chemistry and Pharmaceutical Chemistry, The University of Kansas, Lawrence, Kansas (D.F.E, J.S.L., E.E.S.); Division of Cancer Research, School of Medicine, University of Dundee, Ninewells Hospital, Dundee, United Kingdom (C.R.W., C.J.H., L.A.M.); Regional Center of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science (M.O., M.P., V.N., K.B.) and Department of Pharmacology, Faculty of Medicine and Dentistry (P.A.), Palacký University, Olomouc, Czech Republic; Department of Chemistry, Washington State University, Pullman, Washington (S.C.H., U.P.D., C.B., J.A.B., J.P.J.); and Department of Pharmacology and Experimental Therapeutics, and the Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, Louisiana (J.R.R., J.W.P., W.L.B.)
| | - D Fernando Estrada
- Departments of Medicinal Chemistry and Pharmaceutical Chemistry, The University of Kansas, Lawrence, Kansas (D.F.E, J.S.L., E.E.S.); Division of Cancer Research, School of Medicine, University of Dundee, Ninewells Hospital, Dundee, United Kingdom (C.R.W., C.J.H., L.A.M.); Regional Center of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science (M.O., M.P., V.N., K.B.) and Department of Pharmacology, Faculty of Medicine and Dentistry (P.A.), Palacký University, Olomouc, Czech Republic; Department of Chemistry, Washington State University, Pullman, Washington (S.C.H., U.P.D., C.B., J.A.B., J.P.J.); and Department of Pharmacology and Experimental Therapeutics, and the Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, Louisiana (J.R.R., J.W.P., W.L.B.)
| | - Jennifer S Laurence
- Departments of Medicinal Chemistry and Pharmaceutical Chemistry, The University of Kansas, Lawrence, Kansas (D.F.E, J.S.L., E.E.S.); Division of Cancer Research, School of Medicine, University of Dundee, Ninewells Hospital, Dundee, United Kingdom (C.R.W., C.J.H., L.A.M.); Regional Center of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science (M.O., M.P., V.N., K.B.) and Department of Pharmacology, Faculty of Medicine and Dentistry (P.A.), Palacký University, Olomouc, Czech Republic; Department of Chemistry, Washington State University, Pullman, Washington (S.C.H., U.P.D., C.B., J.A.B., J.P.J.); and Department of Pharmacology and Experimental Therapeutics, and the Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, Louisiana (J.R.R., J.W.P., W.L.B.)
| | - Ji Won Park
- Departments of Medicinal Chemistry and Pharmaceutical Chemistry, The University of Kansas, Lawrence, Kansas (D.F.E, J.S.L., E.E.S.); Division of Cancer Research, School of Medicine, University of Dundee, Ninewells Hospital, Dundee, United Kingdom (C.R.W., C.J.H., L.A.M.); Regional Center of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science (M.O., M.P., V.N., K.B.) and Department of Pharmacology, Faculty of Medicine and Dentistry (P.A.), Palacký University, Olomouc, Czech Republic; Department of Chemistry, Washington State University, Pullman, Washington (S.C.H., U.P.D., C.B., J.A.B., J.P.J.); and Department of Pharmacology and Experimental Therapeutics, and the Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, Louisiana (J.R.R., J.W.P., W.L.B.)
| | - Wayne L Backes
- Departments of Medicinal Chemistry and Pharmaceutical Chemistry, The University of Kansas, Lawrence, Kansas (D.F.E, J.S.L., E.E.S.); Division of Cancer Research, School of Medicine, University of Dundee, Ninewells Hospital, Dundee, United Kingdom (C.R.W., C.J.H., L.A.M.); Regional Center of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science (M.O., M.P., V.N., K.B.) and Department of Pharmacology, Faculty of Medicine and Dentistry (P.A.), Palacký University, Olomouc, Czech Republic; Department of Chemistry, Washington State University, Pullman, Washington (S.C.H., U.P.D., C.B., J.A.B., J.P.J.); and Department of Pharmacology and Experimental Therapeutics, and the Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, Louisiana (J.R.R., J.W.P., W.L.B.)
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16
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Jeřábek P, Florián J, Martínek V. Membrane-Anchored Cytochrome P450 1A2–Cytochrome b5 Complex Features an X-Shaped Contact between Antiparallel Transmembrane Helices. Chem Res Toxicol 2016; 29:626-36. [DOI: 10.1021/acs.chemrestox.5b00349] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Petr Jeřábek
- Department
of Biochemistry, Faculty of Science, Charles University in Prague, Albertov 2030, 128 43 Prague 2, Czech Republic
| | - Jan Florián
- Department
of Chemistry and Biochemistry, Loyola University Chicago, 1032 West Sheridan
Road, Chicago, Illinois 60660, United States
| | - Václav Martínek
- Department
of Biochemistry, Faculty of Science, Charles University in Prague, Albertov 2030, 128 43 Prague 2, Czech Republic
- Department of Teaching and Didactics of Chemistry, Faculty of Science, Charles University in Prague, Albertov 3, 128 43 Prague 2, Czech Republic
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17
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Treuheit NA, Redhair M, Kwon H, McClary WD, Guttman M, Sumida JP, Atkins WM. Membrane Interactions, Ligand-Dependent Dynamics, and Stability of Cytochrome P4503A4 in Lipid Nanodiscs. Biochemistry 2016; 55:1058-69. [PMID: 26814638 DOI: 10.1021/acs.biochem.5b01313] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Membrane-bound cytochrome P4503A4 (CYP3A4) is the major source of enzymatic drug metabolism. Although several structural models of CYP3A4 in various ligand complexes are available, none includes a lipid bilayer. Details of the effects of the membrane on protein dynamics and solvation, and access channels for ligands, remain uncertain. H/D exchange mass spectrometry (H/DXMS) with ligand free CYP3A4 containing a deletion of residues 3-12, compared to that of the full length wild type, in lipid nanodiscs afforded 91% sequence coverage. Deuterium exchange was fast in the F- and G-helices, HI loop, and C-terminal loop. In contrast, there is very low exchange in the F'- and G'-helices. The results are consistent with the overall membrane orientation of CYP3A4 suggested by published MD simulations and spectroscopic results, and the solvent accessibility of the F/G loop suggests that it is not deeply membrane-embedded. Addition of ketoconazole results in only modest, but global, changes in solvent accessibility. Interestingly, with ketoconazole bound some peptides become less solvent accessible or dynamic, including the F- and G-helices, but several peptides demonstrate modestly increased accessibility. Differential scanning calorimetry (DSC) of CYP3A4-nanodiscs suggests membrane-induced stabilization compared to that of aggregated CYP3A4 in buffer, and this stabilization is enhanced upon addition of the ligand ketoconazole. This ligand-induced stabilization is accompanied by a very large increase in ΔH for CYP3A4 denaturation in nanodiscs, possibly due to increased CYP3A4-membrane interactions. Together, the results suggest a distinct orientation of CYP3A4 on the lipid membrane, and they highlight likely solvent access channels, which are consistent with several MD simulations.
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Affiliation(s)
- Nicholas A Treuheit
- Department of Medicinal Chemistry, University of Washington , Box 357610, Seattle, Washington 98195-7610, United States
| | - Michelle Redhair
- Department of Medicinal Chemistry, University of Washington , Box 357610, Seattle, Washington 98195-7610, United States
| | - Hyewon Kwon
- Department of Medicinal Chemistry, University of Washington , Box 357610, Seattle, Washington 98195-7610, United States
| | - Wynton D McClary
- Department of Medicinal Chemistry, University of Washington , Box 357610, Seattle, Washington 98195-7610, United States
| | - Miklos Guttman
- Department of Medicinal Chemistry, University of Washington , Box 357610, Seattle, Washington 98195-7610, United States
| | - John P Sumida
- Department of Medicinal Chemistry, University of Washington , Box 357610, Seattle, Washington 98195-7610, United States
| | - William M Atkins
- Department of Medicinal Chemistry, University of Washington , Box 357610, Seattle, Washington 98195-7610, United States
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18
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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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19
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Gricman Ł, Vogel C, Pleiss J. Identification of universal selectivity-determining positions in cytochrome P450 monooxygenases by systematic sequence-based literature mining. Proteins 2015; 83:1593-603. [DOI: 10.1002/prot.24840] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 05/22/2015] [Accepted: 05/26/2015] [Indexed: 12/21/2022]
Affiliation(s)
- Łukasz Gricman
- Institute of Technical Biochemistry, University of Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Constantin Vogel
- Institute of Technical Biochemistry, University of Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Jürgen Pleiss
- Institute of Technical Biochemistry, University of Stuttgart; Allmandring 31 70569 Stuttgart Germany
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20
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Zhang H, Gao N, Liu T, Fang Y, Qi B, Wen Q, Zhou J, Jia L, Qiao H. Effect of Cytochrome b5 Content on the Activity of Polymorphic CYP1A2, 2B6, and 2E1 in Human Liver Microsomes. PLoS One 2015; 10:e0128547. [PMID: 26046844 PMCID: PMC4457846 DOI: 10.1371/journal.pone.0128547] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 04/28/2015] [Indexed: 11/18/2022] Open
Abstract
Human cytochrome b5 (Cyt b5) plays important roles in cytochrome P450 (CYP)-mediated drug metabolism. However, the expression level of Cyt b5 in normal human liver remains largely unknown. The effect of Cyt b5 on overall CYP activity in human liver microsomes (HLM) has rarely been reported and the relationship between Cyt b5 and the activity of polymorphic CYP has not been systematically investigated. In this study, we found that the median value of Cyt b5 protein was 270.01 pmol/mg from 123 HLM samples, and 12- and 19-fold individual variation was observed in Cyt b5 mRNA and protein levels, respectively. Gender and smoking clearly influenced Cyt b5 content. In addition, we found that Cyt b5 protein levels significantly correlated with the overall activity of CYP1A2, 2B6, and 2E1 in HLM. However, when the CYP activities were sorted by single nucleotide polymorphisms (SNP), the effect of Cyt b5 protein on the kinetic parameters varied greatly. There were significant correlations between Cyt b5 content and Vmax and CLint of CYP1A2 wild-types (3860GG, 2159GG, and 5347CC) as well as homozygous mutants (163AA and 3113GG). In contrast to Vmax and CLint, the Km of CYP2B6 516GG and 785AA genotypes was inversely associated with Cyt b5 content. Correlations between Cyt b5 content and Vmax and CLint of CYP2E1 -1293GG, -1293GC, 7632TT, 7632TA, -333TT, and -352AA genotypes were also observed. In conclusion, Cyt b5 expression levels varied considerably in the Chinese cohort from this study. Cyt b5 had significant impact on the overall activity of CYP1A2, 2B6, and 2E1 in HLM and the effects of Cyt b5 protein on polymorphic CYP1A2, 2B6, and 2E1 activity were SNP-dependent. These findings suggest that Cyt b5 plays an important role in CYP-mediated activities in HLM and may possibly be a contributing factor for the individual variation observed in CYP enzyme activities.
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Affiliation(s)
- Haifeng Zhang
- Institute of Clinical Pharmacology, Zhengzhou University, Zhengzhou, China
| | - Na Gao
- Institute of Clinical Pharmacology, Zhengzhou University, Zhengzhou, China
| | - Tingting Liu
- Institute of Clinical Pharmacology, Zhengzhou University, Zhengzhou, China
| | - Yan Fang
- Institute of Clinical Pharmacology, Zhengzhou University, Zhengzhou, China
| | - Bing Qi
- Institute of Clinical Pharmacology, Zhengzhou University, Zhengzhou, China
| | - Qiang Wen
- Institute of Clinical Pharmacology, Zhengzhou University, Zhengzhou, China
| | - Jun Zhou
- Institute of Clinical Pharmacology, Zhengzhou University, Zhengzhou, China
| | - Linjing Jia
- Institute of Clinical Pharmacology, Zhengzhou University, Zhengzhou, China
| | - Hailing Qiao
- Institute of Clinical Pharmacology, Zhengzhou University, Zhengzhou, China
- * E-mail:
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21
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Tran BQ, Goodlett DR, Goo YA. Advances in protein complex analysis by chemical cross-linking coupled with mass spectrometry (CXMS) and bioinformatics. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1864:123-9. [PMID: 26025770 DOI: 10.1016/j.bbapap.2015.05.015] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 05/07/2015] [Accepted: 05/18/2015] [Indexed: 01/12/2023]
Abstract
For the analysis of protein-protein interactions and protein conformations, cross-linking coupled with mass spectrometry (CXMS) has become an essential tool in recent years. A variety of cross-linking reagents are used to covalently link interacting amino acids to identify protein-binding partners. The spatial proximity of cross-linked amino acid residues is used to elucidate structural models of protein complexes. The main challenges for mapping protein-protein interaction are low stoichiometry and low frequency of cross-linked peptides relative to unmodified linear peptides as well as accurate and efficient matches to corresponding peptide sequences with low false discovery rates for identifying the site of cross-link. We evaluate the current state of chemical cross-linking and mass spectrometry applications with the special emphasis on the recent development of informatics data processing and analysis tools that help complexity of interpreting CXMS data. This article is part of a Special Issue entitled:Physiological Enzymology and Protein Functions.
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Affiliation(s)
- Bao Quoc Tran
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD, USA.
| | - David R Goodlett
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD, USA.
| | - Young Ah Goo
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD, USA.
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22
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Hlavica P. Mechanistic basis of electron transfer to cytochromes p450 by natural redox partners and artificial donor constructs. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 851:247-97. [PMID: 26002739 DOI: 10.1007/978-3-319-16009-2_10] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Cytochromes P450 (P450s) are hemoproteins catalyzing oxidative biotransformation of a vast array of natural and xenobiotic compounds. Reducing equivalents required for dioxygen cleavage and substrate hydroxylation originate from different redox partners including diflavin reductases, flavodoxins, ferredoxins and phthalate dioxygenase reductase (PDR)-type proteins. Accordingly, circumstantial analysis of structural and physicochemical features governing donor-acceptor recognition and electron transfer poses an intriguing challenge. Thus, conformational flexibility reflected by togging between closed and open states of solvent exposed patches on the redox components was shown to be instrumental to steered electron transmission. Here, the membrane-interactive tails of the P450 enzymes and donor proteins were recognized to be crucial to proper orientation toward each other of surface sites on the redox modules steering functional coupling. Also, mobile electron shuttling may come into play. While charge-pairing mechanisms are of primary importance in attraction and complexation of the redox partners, hydrophobic and van der Waals cohesion forces play a minor role in docking events. Due to catalytic plasticity of P450 enzymes, there is considerable promise in biotechnological applications. Here, deeper insight into the mechanistic basis of the redox machinery will permit optimization of redox processes via directed evolution and DNA shuffling. Thus, creation of hybrid systems by fusion of the modified heme domain of P450s with proteinaceous electron carriers helps obviate the tedious reconstitution procedure and induces novel activities. Also, P450-based amperometric biosensors may open new vistas in pharmaceutical and clinical implementation and environmental monitoring.
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Affiliation(s)
- Peter Hlavica
- Walther-Straub-Institut für Pharmakologie und Toxikologie der LMU, Goethestrasse 33, 80336, München, Germany,
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23
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Wang Y, Kim SM, Trnka MJ, Liu Y, Burlingame AL, Correia MA. Human liver cytochrome P450 3A4 ubiquitination: molecular recognition by UBC7-gp78 autocrine motility factor receptor and UbcH5a-CHIP-Hsc70-Hsp40 E2-E3 ubiquitin ligase complexes. J Biol Chem 2014; 290:3308-32. [PMID: 25451919 DOI: 10.1074/jbc.m114.611525] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
CYP3A4 is an abundant and catalytically dominant human liver endoplasmic reticulum-anchored cytochrome P450 enzyme engaged in the biotransformation of endo- and xenobiotics, including >50% of clinically relevant drugs. Alterations of CYP3A4 protein turnover can influence clinically relevant drug metabolism and bioavailability and drug-drug interactions. This CYP3A4 turnover involves endoplasmic reticulum-associated degradation via the ubiquitin (Ub)-dependent 26 S proteasomal system that relies on two highly complementary E2 Ub-conjugating-E3 Ub-ligase (UBC7-gp78 and UbcH5a-C terminus of Hsc70-interacting protein (CHIP)-Hsc70-Hsp40) complexes, as well as protein kinases (PK) A and C. We have documented that CYP3A4 Ser/Thr phosphorylation (Ser(P)/Thr(P)) by PKA and/or PKC accelerates/enhances its Lys ubiquitination by either of these E2-E3 systems. Intriguingly, CYP3A4 Ser(P)/Thr(P) and ubiquitinated Lys residues reside within the cytosol-accessible surface loop and/or conformationally assembled acidic Asp/Glu clusters, leading us to propose that such post-translational Ser/Thr protein phosphorylation primes CYP3A4 for ubiquitination. Herein, this possibility was examined through various complementary approaches, including site-directed mutagenesis, chemical cross-linking, peptide mapping, and LC-MS/MS analyses. Our findings reveal that such CYP3A4 Asp/Glu/Ser(P)/Thr(P) surface clusters are indeed important for its intermolecular electrostatic interactions with each of these E2-E3 subcomponents. By imparting additional negative charge to these Asp/Glu clusters, such Ser/Thr phosphorylation would generate P450 phosphodegrons for molecular recognition by the E2-E3 complexes, thereby controlling the timing of CYP3A4 ubiquitination and endoplasmic reticulum-associated degradation. Although the importance of phosphodegrons in the CHIP targeting of its substrates is known, to our knowledge this is the first example of phosphodegron involvement in gp78-substrate recruitment, an important step in CYP3A4 proteasomal degradation.
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Affiliation(s)
- YongQiang Wang
- From the Departments of Cellular and Molecular Pharmacology
| | - Sung-Mi Kim
- From the Departments of Cellular and Molecular Pharmacology
| | | | - Yi Liu
- From the Departments of Cellular and Molecular Pharmacology
| | | | - Maria Almira Correia
- From the Departments of Cellular and Molecular Pharmacology, Pharmaceutical Chemistry, and Bioengineering and Therapeutic Sciences, The Liver Center, University of California at San Francisco, San Francisco, California 94158-2517
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24
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Peng HM, Liu J, Forsberg SE, Tran HT, Anderson SM, Auchus RJ. Catalytically relevant electrostatic interactions of cytochrome P450c17 (CYP17A1) and cytochrome b5. J Biol Chem 2014; 289:33838-49. [PMID: 25315771 DOI: 10.1074/jbc.m114.608919] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Two acidic residues, Glu-48 and Glu-49, of cytochrome b5 (b5) are essential for stimulating the 17,20-lyase activity of cytochrome P450c17 (CYP17A1). Substitution of Ala, Gly, Cys, or Gln for these two glutamic acid residues abrogated all capacity to stimulate 17,20-lyase activity. Mutations E49D and E48D/E49D retained 23 and 38% of wild-type activity, respectively. Using the zero-length cross-linker ethyl-3-(3-dimethylaminopropyl)carbodiimide, we obtained cross-linked heterodimers of b5 and CYP17A1, wild-type, or mutations R347K and R358K. In sharp contrast, the b5 double mutation E48G/E49G did not form cross-linked complexes with wild-type CYP17A1. Mass spectrometric analysis of the CYP17A1-b5 complexes identified two cross-linked peptide pairs as follows: CYP17A1-WT: (84)EVLIKK(89)-b5: (53)EQAGGDATENFEDVGHSTDAR(73) and CYP17A1-R347K: (341)TPTISDKNR(349)-b5: (40)FLEEHPGGEEVLR(52). Using these two sites of interaction and Glu-48/Glu-49 in b5 as constraints, protein docking calculations based on the crystal structures of the two proteins yielded a structural model of the CYP17A1-b5 complex. The appositional surfaces include Lys-88, Arg-347, and Arg-358/Arg-449 of CYP17A1, which interact with Glu-61, Glu-42, and Glu-48/Glu-49 of b5, respectively. Our data reveal the structural basis of the electrostatic interactions between these two proteins, which is critical for 17,20-lyase activity and androgen biosynthesis.
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Affiliation(s)
- Hwei-Ming Peng
- From the Division of Metabolism, Endocrinology, and Diabetes, Department of Internal Medicine
| | - Jiayan Liu
- From the Division of Metabolism, Endocrinology, and Diabetes, Department of Internal Medicine
| | - Sarah E Forsberg
- From the Division of Metabolism, Endocrinology, and Diabetes, Department of Internal Medicine
| | | | - Sean M Anderson
- From the Division of Metabolism, Endocrinology, and Diabetes, Department of Internal Medicine
| | - Richard J Auchus
- From the Division of Metabolism, Endocrinology, and Diabetes, Department of Internal Medicine, the Department of Pharmacology, University of Michigan, Ann Arbor, Michigan 48109
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25
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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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26
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Cheng G, Liu C, Wang X, Ma H, Pan Y, Huang L, Hao H, Dai M, Yuan Z. Structure-function analysis of porcine cytochrome P450 3A29 in the hydroxylation of T-2 toxin as revealed by docking and mutagenesis studies. PLoS One 2014; 9:e106769. [PMID: 25184434 PMCID: PMC4153680 DOI: 10.1371/journal.pone.0106769] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 08/08/2014] [Indexed: 11/18/2022] Open
Abstract
T-2 toxin, one of the type A trichothecenes, presents a potential hazard to human and animal health. Our previous work demonstrated that porcine cytochrome P450 3A29 (CYP3A29) played an important role in the hydroxylation of T-2 toxin. To identify amino acids involved in this metabolic process, T-2 toxin was docked into a homology model of CYP3A29 based on a crystal structure of CYP3A4 using AutoDock 4.0. Nine residues of CYP3A29, Arg105, Arg106, Phe108, Ser119, Lys212, Phe213, Phe215, Arg372 and Glu374, which were found within 5 Å around T-2 toxin were subjected to site-directed mutagenesis. In the oxidation of nifedipine, the CLint value of R106A was increased by nearly two-folds compared with the wild-type CYP3A29, while the substrate affinities and CLint values of S119A and K212A were significantly reduced. In the hydroxylation of T-2 toxin, the generation of 3′-OH-T-2 by R105A, S119A and K212A was significantly less than that by the wild-type, whereas R106A slightly increased the generation of 3′-OH-T-2. These results were further confirmed by isothermal titration calorimetry analysis, suggesting that these four residues are important in the hydroxylation of T-2 toxin and Arg105 may be a specific recognition site for the toxin. Our study suggests a possible structure-function relationship of CYP3A29 in the hydroxylation of T-2 toxin, providing with new insights into the mechanism of CYP3A enzymes in the biotransformation of T-2 toxin.
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Affiliation(s)
- Guyue Cheng
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, China
| | - Changcun Liu
- National Reference Laboratory of Veterinary Drug Residues (HZAU), MOA Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, China
| | - Xu Wang
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, China
| | - Hongmin Ma
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education) at the School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Yuanhu Pan
- National Reference Laboratory of Veterinary Drug Residues (HZAU), MOA Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, China
| | - Lingli Huang
- National Reference Laboratory of Veterinary Drug Residues (HZAU), MOA Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, China
| | - Haihong Hao
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, China
| | - Menghong Dai
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, China
| | - Zonghui Yuan
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, China
- National Reference Laboratory of Veterinary Drug Residues (HZAU), MOA Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, China
- * E-mail:
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27
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Sterckx YGJ, Volkov AN. Cofactor-Dependent Structural and Binding Properties of Yeast Cytochrome c Peroxidase. Biochemistry 2014; 53:4526-36. [DOI: 10.1021/bi500603w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yann G. J. Sterckx
- Research
Unit for Cellular and Molecular Immunology (CMIM), Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
- Structural
Biology Research Center, VIB, Pleinlaan 2, 1050 Brussels, Belgium
| | - Alexander N. Volkov
- Structural
Biology Research Center, VIB, Pleinlaan 2, 1050 Brussels, Belgium
- Jean
Jeener NMR Centre, Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
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28
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Chemical cross-linking/mass spectrometry targeting acidic residues in proteins and protein complexes. Proc Natl Acad Sci U S A 2014; 111:9455-60. [PMID: 24938783 DOI: 10.1073/pnas.1320298111] [Citation(s) in RCA: 185] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The study of proteins and protein complexes using chemical cross-linking followed by the MS identification of the cross-linked peptides has found increasingly widespread use in recent years. Thus far, such analyses have used almost exclusively homobifunctional, amine-reactive cross-linking reagents. Here we report the development and application of an orthogonal cross-linking chemistry specific for carboxyl groups. Chemical cross-linking of acidic residues is achieved using homobifunctional dihydrazides as cross-linking reagents and a coupling chemistry at neutral pH that is compatible with the structural integrity of most protein complexes. In addition to cross-links formed through insertion of the dihydrazides with different spacer lengths, zero-length cross-link products are also obtained, thereby providing additional structural information. We demonstrate the application of the reaction and the MS identification of the resulting cross-linked peptides for the chaperonin TRiC/CCT and the 26S proteasome. The results indicate that the targeting of acidic residues for cross-linking provides distance restraints that are complementary and orthogonal to those obtained from lysine cross-linking, thereby expanding the yield of structural information that can be obtained from cross-linking studies and used in hybrid modeling approaches.
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29
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Correia MA, Wang Y, Kim SM, Guan S. Hepatic cytochrome P450 ubiquitination: conformational phosphodegrons for E2/E3 recognition? IUBMB Life 2014; 66:78-88. [PMID: 24488826 DOI: 10.1002/iub.1247] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Accepted: 01/19/2014] [Indexed: 01/25/2023]
Abstract
Hepatic endoplasmic reticulum (ER) integral cytochromes P450 (P450s) are monooxygenases engaged in the biotransformation and elimination of endo- as well as xenobiotics. Of the human liver P450s, CYP3A4 is the major and most dominant catalyst responsible for the biotransformation of over 50% of clinically prescribed drugs. CYP2E1 metabolizes smaller molecular weight compounds (EtOH), carcinogens, environmental toxins, and endobiotics, and is justly implicated in various toxigenic/pathogenic mechanisms of human disease. Both P450s are notorious for their potential to generate pathogenic reactive oxygen species (ROS) during futile oxidative cycling and/or oxidative uncoupling. Such ROS not only oxidatively damage the P450 catalytic cage, but on their escape into the cytosol, also the P450 outer surface and any surrounding cell organelles. Given their ER-monotopic topology coupled with this high potential to acquire oxidative lesions in their cytosolic (C) domain, not surprisingly these P450 proteins exhibit shorter lifespans and are excellent prototype substrates of ER-associated degradation ("ERAD-C") pathway. Indeed, we have shown that both CYP3A4 and CYP2E1 incur ERAD-C, during which they are first phosphorylated by protein kinases A and C, which greatly enhance/accelerate their ubiquitination by UBC7/gp78 and UbcH5a/CHIP/Hsp70/Hsp40 E2/E3 ubiquitin ligase complexes. Such P450 phosphorylation occurs on Ser/Thr residues within linear sequences as well as spatially clustered acidic (Asp/Glu) residues. We propose that such S/T phosphorylation within these clusters creates negatively charged patches or conformational phosphodegrons for interaction with positively charged E2/E3 domains. Such P450 S/T phosphorylation we posit serves as a molecular switch to turn on its ubiquitination and ERAD-C.
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Affiliation(s)
- Maria Almira Correia
- Department of Cellular & Molecular Pharmacology, University of California, San Francisco, CA; Department of Pharmaceutical Chemistry, University of California, San Francisco, CA; Department of Bioengineering & Therapeutic Sciences, University of California, San Francisco, CA; The Liver Center, University of California, San Francisco, CA
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30
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Sriswasdi S, Harper SL, Tang HY, Speicher DW. Enhanced identification of zero-length chemical cross-links using label-free quantitation and high-resolution fragment ion spectra. J Proteome Res 2014; 13:898-914. [PMID: 24369724 DOI: 10.1021/pr400953w] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Chemical cross-linking coupled to mass spectrometry provides structural information that is useful for probing protein conformations and providing experimental support for molecular models. "Zero-length" cross-links have greater value for these applications than longer cross-links because they provide more stringent distance constraints. However, this method is less commonly utilized because it cannot take advantage of isotopic labels, MS-labile bonds, or enrichment tags to facilitate identification. In this study, we combined label-free precursor ion quantitation and targeted tandem mass spectrometry with a new software tool, Zero-length Cross-link Miner (ZXMiner), to form a multitiered analysis strategy. A major, critical objective was to simultaneously achieve very high accuracy with essentially no false-positive cross-link identifications while maintaining a good depth of analysis. Our strategy was optimized on several proteins with known crystal structures. Comparison of ZXMiner to several existing cross-link analysis software showed that other algorithms detected less true positive cross-links and were far less accurate. Although prior use of zero-length cross-linking was typically restricted to small proteins, ZXMiner and the associated strategy enable facile analysis of very large protein complexes. This was demonstrated by identification of zero-length cross-links using purified 526 kDa spectrin heterodimers and intact red cell membranes and membrane skeletons.
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Affiliation(s)
- Sira Sriswasdi
- Center for Systems and Computational Biology and Molecular and Cellular Oncogenesis Program, The Wistar Institute , 3601 Spruce Street, Philadelphia, Pennsylvania 19104, United States
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31
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Peng HM, Auchus RJ. Two surfaces of cytochrome b5 with major and minor contributions to CYP3A4-catalyzed steroid and nifedipine oxygenation chemistries. Arch Biochem Biophys 2013; 541:53-60. [PMID: 24256945 DOI: 10.1016/j.abb.2013.11.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Revised: 10/22/2013] [Accepted: 11/04/2013] [Indexed: 10/26/2022]
Abstract
Conserved human cytochrome b5 (b5) residues D58 and D65 are critical for interactions with CYP2E1 and CYP2C19, whereas E48 and E49 are essential for stimulating the 17,20-lyase activity of CYP17A1. Here, we show that b5 mutations E48G, E49G, D58G, and D65G have reduced capacity to stimulate CYP3A4-catalyzed progesterone and testosterone 6β-hydroxylation or nifedipine oxidation. The b5 double mutation D58G/D65G fails to stimulate these reactions, similar to CYP2E1 and CYP2C19, whereas mutation E48G/E49G retains 23-42% of wild-type stimulation. Neither mutation impairs the activity stimulation of wild-type b5, nor does mutation D58G/D65G impair the partial stimulation of mutations E48G or E48G/E49G. For assays reconstituted with a single phospholipid, phosphatidyl serine afforded the highest testosterone 6β-hydroxylase activity with wild-type b5 but the poorest activity with b5 mutation E48G/E49G, and the activity stimulation of mutation E48G/E49G was lost at [NaCl]>50mM. Cross-linking of CYP3A4 and b5 decreased in the order wild-type>E48G/E49G>D58G/D65G and varied with phospholipid. We conclude that two b5 acidic surfaces, primarily the domain including residues D58-D65, participate in the stimulation of CYP3A4 activities. Our data suggest that a minor population of CYP3A4 molecules remains sensitive to b5 mutation E48G/E49G, consistent with phospholipid-dependent conformational heterogeneity of CYP3A4.
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Affiliation(s)
- Hwei-Ming Peng
- Division of Metabolism, Endocrinology, and Diabetes, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, United States
| | - Richard J Auchus
- Division of Metabolism, Endocrinology, and Diabetes, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, United States.
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32
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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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33
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Lin YW, Wang J. Structure and function of heme proteins in non-native states: a mini-review. J Inorg Biochem 2013; 129:162-71. [PMID: 23916118 DOI: 10.1016/j.jinorgbio.2013.07.023] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 07/11/2013] [Accepted: 07/13/2013] [Indexed: 12/12/2022]
Abstract
Heme proteins perform various biological functions ranging from electron transfer, oxygen binding and transport, catalysis, to signaling. Although adopting proper native states is very important for these functions, progresses in representative heme proteins, including cytochrome c (cyt c), cytochrome b5 (cyt b5), myoglobin (Mb), neuroglobin (Ngb), cytochrome P450 (CYP) and heme-based sensor proteins such as CO sensor CooA, showed that various native functions, or new functions evolved, are also closely associated with non-native states. The structure and function relationship of heme proteins in non-native states is thus as important as that in native states for elucidating the precise roles of heme proteins in biological systems.
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Affiliation(s)
- Ying-Wu Lin
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China.
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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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