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The changing face of SDS denaturation: Complexes of Thermomyces lanuginosus lipase with SDS at pH 4.0, 6.0 and 8.0. J Colloid Interface Sci 2022; 614:214-232. [DOI: 10.1016/j.jcis.2021.12.188] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/16/2021] [Accepted: 12/29/2021] [Indexed: 12/15/2022]
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Das A, Weigle AT, Arnold WR, Kim JS, Carnevale LN, Huff HC. CYP2J2 Molecular Recognition: A New Axis for Therapeutic Design. Pharmacol Ther 2020; 215:107601. [PMID: 32534953 PMCID: PMC7773148 DOI: 10.1016/j.pharmthera.2020.107601] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 05/28/2020] [Indexed: 12/11/2022]
Abstract
Cytochrome P450 (CYP) epoxygenases are a special subset of heme-containing CYP enzymes capable of performing the epoxidation of polyunsaturated fatty acids (PUFA) and the metabolism of xenobiotics. This dual functionality positions epoxygenases along a metabolic crossroad. Therefore, structure-function studies are critical for understanding their role in bioactive oxy-lipid synthesis, drug-PUFA interactions, and for designing therapeutics that directly target the epoxygenases. To better exploit CYP epoxygenases as therapeutic targets, there is a need for improved understanding of epoxygenase structure-function. Of the characterized epoxygenases, human CYP2J2 stands out as a potential target because of its role in cardiovascular physiology. In this review, the early research on the discovery and activity of epoxygenases is contextualized to more recent advances in CYP epoxygenase enzymology with respect to PUFA and drug metabolism. Additionally, this review employs CYP2J2 epoxygenase as a model system to highlight both the seminal works and recent advances in epoxygenase enzymology. Herein we cover CYP2J2's interactions with PUFAs and xenobiotics, its tissue-specific physiological roles in diseased states, and its structural features that enable epoxygenase function. Additionally, the enumeration of research on CYP2J2 identifies the future needs for the molecular characterization of CYP2J2 to enable a new axis of therapeutic design.
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Affiliation(s)
- Aditi Das
- Department of Comparative Biosciences, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA; Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA; Division of Nutritional Sciences, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA; Center for Biophysics and Computational Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA; Department of Bioengineering, Neuroscience Program, Beckman Institute for Advanced Science and Technology, Cancer Center at Illinois, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA.
| | - Austin T Weigle
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - William R Arnold
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Justin S Kim
- Division of Nutritional Sciences, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Lauren N Carnevale
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Hannah C Huff
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
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Mass Spectrometry- and Computational Structural Biology-Based Investigation of Proteins and Peptides. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1140:265-287. [PMID: 31347053 DOI: 10.1007/978-3-030-15950-4_15] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Recent developments of mass spectrometry (MS) allow us to identify, estimate, and characterize proteins and protein complexes. At the same time, structural biology helps to determine the protein structure and its structure-function relationship. Together, they aid to understand the protein structure, property, function, protein-complex assembly, protein-protein interaction, and dynamics. The present chapter is organized with illustrative results to demonstrate how experimental mass spectrometry can be combined with computational structural biology for detailed studies of protein's structures. We have used tumor differentiation factor protein/peptide as ligand and Hsp70/Hsp90 as receptor protein as examples to study ligand-protein interaction. To investigate possible protein conformation, we will describe two proteins-lysozyme and myoglobin. As an application of MS-based assignment of disulfide bridges, the case of the spider venom polypeptide Phα1β will also be discussed.
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Šrejber M, Navrátilová V, Paloncýová M, Bazgier V, Berka K, Anzenbacher P, Otyepka M. Membrane-attached mammalian cytochromes P450: An overview of the membrane's effects on structure, drug binding, and interactions with redox partners. J Inorg Biochem 2018; 183:117-136. [DOI: 10.1016/j.jinorgbio.2018.03.002] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 02/16/2018] [Accepted: 03/01/2018] [Indexed: 01/08/2023]
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Mak PJ, Denisov IG. Spectroscopic studies of the cytochrome P450 reaction mechanisms. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2018; 1866:178-204. [PMID: 28668640 PMCID: PMC5709052 DOI: 10.1016/j.bbapap.2017.06.021] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 06/22/2017] [Indexed: 10/19/2022]
Abstract
The cytochrome P450 monooxygenases (P450s) are thiolate heme proteins that can, often under physiological conditions, catalyze many distinct oxidative transformations on a wide variety of molecules, including relatively simple alkanes or fatty acids, as well as more complex compounds such as steroids and exogenous pollutants. They perform such impressive chemistry utilizing a sophisticated catalytic cycle that involves a series of consecutive chemical transformations of heme prosthetic group. Each of these steps provides a unique spectral signature that reflects changes in oxidation or spin states, deformation of the porphyrin ring or alteration of dioxygen moieties. For a long time, the focus of cytochrome P450 research was to understand the underlying reaction mechanism of each enzymatic step, with the biggest challenge being identification and characterization of the powerful oxidizing intermediates. Spectroscopic methods, such as electronic absorption (UV-Vis), electron paramagnetic resonance (EPR), nuclear magnetic resonance (NMR), electron nuclear double resonance (ENDOR), Mössbauer, X-ray absorption (XAS), and resonance Raman (rR), have been useful tools in providing multifaceted and detailed mechanistic insights into the biophysics and biochemistry of these fascinating enzymes. The combination of spectroscopic techniques with novel approaches, such as cryoreduction and Nanodisc technology, allowed for generation, trapping and characterizing long sought transient intermediates, a task that has been difficult to achieve using other methods. Results obtained from the UV-Vis, rR and EPR spectroscopies are the main focus of this review, while the remaining spectroscopic techniques are briefly summarized. This article is part of a Special Issue entitled: Cytochrome P450 biodiversity and biotechnology, edited by Erika Plettner, Gianfranco Gilardi, Luet Wong, Vlada Urlacher, Jared Goldstone.
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Affiliation(s)
- Piotr J Mak
- Department of Chemistry, Saint Louis University, St. Louis, MO, United States.
| | - Ilia G Denisov
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL, United States.
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Abstract
Objective: The aim of this study was to summarize the interactions between hepatitis C virus (HCV) infection and iron overload, and to understand the mechanisms of iron overload in chronic hepatitis C (CHC) and the role iron plays in HCV life cycle. Data Sources: This review was based on data in articles published in the PubMed databases up to January 28, 2017, with the keywords “hepatitis C virus”, “iron overload”, “iron metabolism”, “hepcidin”, “translation”, and “replication”. Study Selection: Articles related to iron metabolism, iron overload in patients with CHC, or the effects of iron on HCV life cycle were selected for the review. Results: Iron overload is common in patients with CHC. The mechanisms involve decreased hepcidin levels caused by HCV through signal transducer and activator of transcription 3, mitogen-activated protein kinase, or bone morphogenetic protein/SMAD signaling pathways, and the altered expression of other iron-metabolism-related genes. Some studies found that iron increases HCV replication, while other studies found the opposite result. Most of the studies suggest the positive role of iron on HCV translation, the mechanisms of which involve increased expression levels of factors associated with HCV internal ribosome entry site-dependent translation, such as eukaryotic initiation factor 3 and La protein. Conclusion: The growing literature demonstrates that CHC leads to iron overload, and iron affects the HCV life cycle in turn. Further research should be conducted to clarify the mechanism involved in the complicated interaction between iron and HCV.
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Affiliation(s)
- Dong-Mei Zou
- Department of Hematology, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
| | - Wan-Ling Sun
- Department of Hematology, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
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McClelland LJ, Steele HBB, Whitby FG, Mou TC, Holley D, Alexander Ross JB, Sprang SR, Bowler BE. Cytochrome c Can Form a Well-Defined Binding Pocket for Hydrocarbons. J Am Chem Soc 2016; 138:16770-16778. [PMID: 27990813 PMCID: PMC5564421 DOI: 10.1021/jacs.6b10745] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Cytochrome c can acquire peroxidase activity when it binds to cardiolipin in mitochondrial membranes. The resulting oxygenation of cardiolipin by cytochrome c provides an early signal for the onset of apoptosis. The structure of this enzyme-substrate complex is a matter of considerable debate. We present three structures at 1.7-2.0 Å resolution of a domain-swapped dimer of yeast iso-1-cytochrome c with the detergents, CYMAL-5, CYMAL-6, and ω-undecylenyl-β-d-maltopyranoside, bound in a channel that places the hydrocarbon moieties of these detergents next to the heme. The heme is poised for peroxidase activity with water bound in place of Met80, which serves as the axial heme ligand when cytochrome c functions as an electron carrier. The hydroxyl group of Tyr67 sits 3.6-4.0 Å from the nearest carbon of the detergents, positioned to act as a relay in radical abstraction during peroxidase activity. Docking studies with linoleic acid, the most common fatty acid component of cardiolipin, show that C11 of linoleic acid can sit adjacent to Tyr67 and the heme, consistent with the oxygenation pattern observed in lipidomics studies. The well-defined hydrocarbon binding pocket provides atomic resolution evidence for the extended lipid anchorage model for cytochrome c/cardiolipin binding. Dimer dissociation/association kinetics for yeast versus equine cytochrome c indicate that formation of mammalian cytochrome c dimers in vivo would require catalysis. However, the dimer structure shows that only a modest deformation of monomeric cytochrome c would suffice to form the hydrocarbon binding site occupied by these detergents.
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Affiliation(s)
- Levi J. McClelland
- Department of Chemistry & Biochemistry, University of Montana, Missoula, Montana, 59812, United States
- Division of Biological Sciences, University of Montana, Missoula, Montana, 59812, United States
- Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, Montana, 59812, United States
| | - Harmen B. B. Steele
- Department of Chemistry & Biochemistry, University of Montana, Missoula, Montana, 59812, United States
- Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, Montana, 59812, United States
| | - Frank G. Whitby
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah, 84112, United States
| | - Tung-Chung Mou
- Division of Biological Sciences, University of Montana, Missoula, Montana, 59812, United States
- Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, Montana, 59812, United States
| | - David Holley
- Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, Montana, 59812, United States
| | - J. B. Alexander Ross
- Department of Chemistry & Biochemistry, University of Montana, Missoula, Montana, 59812, United States
- Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, Montana, 59812, United States
| | - Stephen R. Sprang
- Division of Biological Sciences, University of Montana, Missoula, Montana, 59812, United States
- Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, Montana, 59812, United States
| | - Bruce E. Bowler
- Department of Chemistry & Biochemistry, University of Montana, Missoula, Montana, 59812, United States
- Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, Montana, 59812, United States
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