1
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Richard AM, Estrada DF, Flynn L, Pochapsky SS, Scott EE, Pochapsky TC. Tracking protein-protein interactions by NMR: conformational selection in human steroidogenic cytochrome P450 CYP17A1 induced by cytochrome b5. Phys Chem Chem Phys 2024; 26:16980-16988. [PMID: 38842434 PMCID: PMC11186455 DOI: 10.1039/d4cp01268b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 05/26/2024] [Indexed: 06/07/2024]
Abstract
The human steroidogenic cytochrome P450 CYP17A1 catalyzes two types of reactions in the biosynthetic pathway leading from pregnenolone to testosterone and several other steroid hormones. The first is the hydroxylation of pregnenolone or progesterone to the corresponding 17α-hydroxy steroid, followed by a lyase reaction that converts these 17α-hydroxy intermediates to the androgens dehydroepiandrosterone and androstenedione, respectively. cytochrome b5 (cytb5) is known to act as both an effector and electron donor for the lyase oxidations, markedly stimulating the rate of the lyase reaction in its presence relative to the rate in its absence. Extensive sequential backbone 1H,15N and 13C nuclear magnetic resonance assignments have now been made for oxidized CYP17A1 bound to the prostate cancer drug and inhibitor abiraterone. This is the first eukaryotic P450 for which such assignments are now available. These assignments allow more complete interpretation of the structural perturbations observed upon cytb5 addition. Possible mechanism(s) for the effector activity of cytb5 are discussed in light of this new information.
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Affiliation(s)
- Alaina M Richard
- Chemical Biology Program, University of Michigan, Ann Arbor, MI 48109, USA
| | - D Fernando Estrada
- Department of Medicinal Chemistry, University of Kansas, 1251 Wescoe Hall Drive, Lawrence, Kansas 66045, USA
| | - Liam Flynn
- Department of Chemistry, Brandeis University, 415 South St., Waltham, MA 02454-9110, USA.
| | - Susan Sondej Pochapsky
- Department of Chemistry, Brandeis University, 415 South St., Waltham, MA 02454-9110, USA.
| | - Emily E Scott
- Chemical Biology Program, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Medicinal Chemistry, University of Kansas, 1251 Wescoe Hall Drive, Lawrence, Kansas 66045, USA
- Departments of Medicinal Chemistry, Pharmacology, and Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Thomas C Pochapsky
- Department of Chemistry, Brandeis University, 415 South St., Waltham, MA 02454-9110, USA.
- Department of Biochemistry and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, 415 South St., Waltham, MA 02454-9110, USA
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2
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Doğru EK, Sakallı T, Liu G, Sayers Z, Surmeli NB. Small angle X-ray scattering analysis of thermophilic cytochrome P450 CYP119 and the effects of the N-terminal histidine tag. Int J Biol Macromol 2024; 265:131026. [PMID: 38522710 DOI: 10.1016/j.ijbiomac.2024.131026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 03/26/2024]
Abstract
Combining size exclusion chromatography-small angle X-ray scattering (SEC-SAXS) and molecular dynamics (MD) analysis is a promising approach to investigate protein behavior in solution, particularly for understanding conformational changes due to substrate binding in cytochrome P450s (CYPs). This study investigates conformational changes in CYP119, a thermophilic CYP from Sulfolobus acidocaldarius that exhibits structural flexibility similar to mammalian CYPs. Although the crystal structure of ligand-free (open state) and ligand-bound (closed state) forms of CYP119 is known, the overall structure of the enzyme in solution has not been explored until now. It was found that theoretical scattering profiles from the crystal structures of CYP119 did not align with the SAXS data, but conformers from MD simulations, particularly starting from the open state (46 % of all frames), agreed well. Interestingly, a small percentage of closed-state conformers also fit the data (9 %), suggesting ligand-free CYP119 samples ligand-bound conformations. Ab initio SAXS models for N-His tagged CYP119 revealed a tail-like unfolded structure impacting protein flexibility, which was confirmed by in silico modeling. SEC-SAXS analysis of N-His CYP119 indicated pentameric structures in addition to monomers in solution, affecting the stability and activity of the enzyme. This study adds insights into the conformational dynamics of CYP119 in solution.
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Affiliation(s)
- Ekin Kestevur Doğru
- İzmir Institute of Technology, Faculty of Engineering, Department of Bioengineering, 35430 Urla, Izmir, Türkiye
| | - Tuğçe Sakallı
- İzmir Institute of Technology, Faculty of Engineering, Department of Bioengineering, 35430 Urla, Izmir, Türkiye
| | - Goksin Liu
- Sabancı University, Faculty of Engineering and Natural Sciences, Orhanli, Tuzla 34956, Istanbul, Türkiye
| | - Zehra Sayers
- Sabancı University, Faculty of Engineering and Natural Sciences, Orhanli, Tuzla 34956, Istanbul, Türkiye
| | - Nur Basak Surmeli
- İzmir Institute of Technology, Faculty of Engineering, Department of Bioengineering, 35430 Urla, Izmir, Türkiye.
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3
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Jiang P, Jin H, Zhang G, Zhang W, Liu W, Zhu Y, Zhang C, Zhang L. A Mechanistic Understanding of the Distinct Regio- and Chemoselectivity of Multifunctional P450s by Structural Comparison of IkaD and CftA Complexed with Common Substrates. Angew Chem Int Ed Engl 2023; 62:e202310728. [PMID: 37917570 DOI: 10.1002/anie.202310728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 10/28/2023] [Accepted: 11/02/2023] [Indexed: 11/04/2023]
Abstract
Regio- and chemoselective C-H activation at multi-positions of a single molecule is fascinating but chemically challenging. The homologous cytochrome P450 enzymes IkaD and CftA catalyze multiple C-H oxidations on the same polycyclic tetramate macrolactam (PoTeM) ikarugamycin, with distinct regio- and chemoselectivity. Herein we provide mechanistic understanding of their functional differences by solving crystal structures of IkaD and CftA in complex with ikarugamycin and unnatural substrates. Distinct conformations of the F/G region in IkaD and CftA are found to differentiate the orientation of PoTeM substrates, by causing different binding patterns with polar moieties to determine site selection, oxidation order, and chemoselectivity. Fine-tuning the polar subpocket altered the regioselectivity of IkaD, indicating that substrate re-orientation by mutating residues distal to the oxidation site could serve as an important method in future engineering of P450 enzymes.
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Affiliation(s)
- Peng Jiang
- Key Laboratory of Tropical Marine Bioresources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Science, Guangzhou, 510301, China
- University of Chinese Academy of Science, 19 Yuquan Road, Beijing, 100049, China
| | - Hongbo Jin
- Key Laboratory of Tropical Marine Bioresources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Science, Guangzhou, 510301, China
| | - Guangtao Zhang
- Key Laboratory of Tropical Marine Bioresources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Science, Guangzhou, 510301, China
| | - Wenjun Zhang
- Key Laboratory of Tropical Marine Bioresources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Science, Guangzhou, 510301, China
- University of Chinese Academy of Science, 19 Yuquan Road, Beijing, 100049, China
- Sanya Institute of Oceanology Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya, 572000, China
| | - Wei Liu
- Key Laboratory of Tropical Marine Bioresources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Science, Guangzhou, 510301, China
| | - Yiguang Zhu
- Key Laboratory of Tropical Marine Bioresources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Science, Guangzhou, 510301, China
- University of Chinese Academy of Science, 19 Yuquan Road, Beijing, 100049, China
- Sanya Institute of Oceanology Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya, 572000, China
| | - Changsheng Zhang
- Key Laboratory of Tropical Marine Bioresources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Science, Guangzhou, 510301, China
- University of Chinese Academy of Science, 19 Yuquan Road, Beijing, 100049, China
- Sanya Institute of Oceanology Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya, 572000, China
| | - Liping Zhang
- Key Laboratory of Tropical Marine Bioresources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Science, Guangzhou, 510301, China
- University of Chinese Academy of Science, 19 Yuquan Road, Beijing, 100049, China
- Sanya Institute of Oceanology Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya, 572000, China
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4
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Kumar A, Estrada DF. Structural basis of bidirectional allostery across the heme in a cytochrome P450 enzyme. J Biol Chem 2023; 299:104977. [PMID: 37390989 PMCID: PMC10416055 DOI: 10.1016/j.jbc.2023.104977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 06/02/2023] [Accepted: 06/22/2023] [Indexed: 07/02/2023] Open
Abstract
Cytochromes P450 (CYPs) are heme-containing enzymes that are present in all kingdoms of life and share a structurally homologous, globular protein fold. CYPs utilize structures distal to the heme to recognize and coordinate substrates, while the necessary interactions with redox partner proteins are mediated at the opposite, proximal surface. In the current study, we investigated the functional allostery across the heme for the bacterial enzyme CYP121A1, which utilizes a non-polar distal-to-distal dimer interface for specific binding of its dicyclotyrosine substrate. Fluorine-detected Nuclear Magnetic Resonance (19F-NMR) spectroscopy was combined with site-specific labeling of a distal surface residue (S171C of the FG-loop), one residue of the B-helix (N84C), and two proximal surface residues (T103C and T333C) with a thiol-reactive fluorine label. Adrenodoxin was used as a substitute redox protein and was found to promote a closed arrangement of the FG-loop, similar to the addition of substrate alone. Disruption of the protein-protein interface by mutagenesis of two CYP121 basic surface residues removed the allosteric effect. Moreover, 19F-NMR spectra of the proximal surface indicate that ligand-induced allostery modulates the environment at the C-helix but not the meander region of the enzyme. In light of the high degree of structural homology in this family of enzymes, we interpret the findings from this work to represent a conserved allosteric network in CYPs.
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Affiliation(s)
- Amit Kumar
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Science, University at Buffalo, Buffalo, New York, USA
| | - D Fernando Estrada
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Science, University at Buffalo, Buffalo, New York, USA.
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5
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Feng Y, Gong C, Zhu J, Liu G, Tang Y, Li W. Prediction of Sites of Metabolism of CYP3A4 Substrates Utilizing Docking-Derived Geometric Features. J Chem Inf Model 2023. [PMID: 37336765 DOI: 10.1021/acs.jcim.3c00549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
Cytochrome P450 3A4 (CYP3A4) is one of the major drug-metabolizing enzymes in the human body and is responsible for the metabolism of ∼50% of clinically used drugs. Therefore, the identification of the compound's sites of metabolism (SOMs) mediated by CYP3A4 is of utmost importance in the early stage of drug discovery and development. Herein, docking-based approaches incorporating geometric features were used for SOMs prediction of CYP3A4 substrates. The cross-docking poses of a relatively large data set containing 474 substrates were analyzed in depth, and a widely observed geometric pattern called the close proximity of SOMs was derived from the poses. On the basis of the close proximity, several structure-based models have been constructed, which demonstrated better performance than those structure-based models using the criterion of Fe-SOM distance. For further improving the prediction performance, the structure-based models were also combined with the well-known ligand-based model SMARTCyp. One combined model exhibited good performance on the SOMs prediction of an external substrate set containing kinase inhibitors, PROTACs, approved drugs, and some lead compounds.
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Affiliation(s)
- Yanjun Feng
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Changda Gong
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Jieyu Zhu
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Guixia Liu
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Yun Tang
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Weihua Li
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
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6
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Hlavica P. Key regulators in the architecture of substrate access/egress channels in mammalian cytochromes P450 governing flexibility in substrate oxyfunctionalization. J Inorg Biochem 2023; 241:112150. [PMID: 36731371 DOI: 10.1016/j.jinorgbio.2023.112150] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/21/2023] [Accepted: 01/22/2023] [Indexed: 01/31/2023]
Abstract
Cytochrome P450s (CYP) represent a superfamily of b-type hemoproteins catalyzing oxifunctionalization of a vast array of endogenous and exogenous compounds. The present review focuses on assessment of the topology of prospective determinants in substrate entry and product release channels of mammalian P450s, steering the conformational dynamics of substrate accessibility and productive ligand orientation toward the iron-oxene core. Based on a generalized, CYP3A4-related construct, the sum of critical elements from diverse target enzymes was found to cluster within the known substrate recognition sites. The majority of prevalent substrate access/egress tunnels revealed to be of fairly balanced functional importance. The hydrophobicity profile of the candidates revealed to be the most salient feature in functional interaction throughout the conduits, while bulkiness of the residues imposes steric restrictions on substrate traveling. Thus, small amino acids such as prolines and glycines serve as hinges, driving conformational flexibility in ligand passage. Similarly, bottlenecks in the tunnel architecture, being narrowest encounter points within the CYP3A4 model, have a vital function in substrate selectivity along with clusters of aromatic amino acids acting as gatekeepers. In addition, peripheral patches in conduits may house determinants modulating allosteric cooperativity between remote and central domains in the P450 structure. Remarkably, the bulk critical residues lining tunnels in the various isozymes reside in helices B'/C and F/G inclusive of their interhelical turns as well as in helix I. This suggests these regions to represent hotspots for targeted genetic engineering to tailor more sophisticated mammalian P450s exploitable in industrial, biotechnological and medicinal areas.
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Affiliation(s)
- Peter Hlavica
- Walther-Straub Institut fuer Pharmakologie und Toxikologie, Goethestrasse 33, D80336 Muenchen, Germany.
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7
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Carius Y, Hutter M, Kiss F, Bernhardt R, Lancaster CRD. Structural comparison of the cytochrome P450 enzymes CYP106A1 and CYP106A2 provides insight into their differences in steroid conversion. FEBS Lett 2022; 596:3133-3144. [PMID: 36151590 DOI: 10.1002/1873-3468.14502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/13/2022] [Accepted: 09/14/2022] [Indexed: 01/14/2023]
Abstract
Understanding the structural basis of the selectivity of steroid hydroxylation requires detailed structural and functional investigations on various steroid hydroxylases with different selectivities, such as the bacterial cytochrome P450 enzymes. Here, the crystal structure of the cytochrome P450 CYP106A1 from Priestia megaterium was solved. CYP106A1 exhibits a rare additional structural motif of a cytochrome P450, a sixth β-sheet. The protein was found in different unusual conformations corresponding to both open and closed forms even when crystallized without any known substrate. The structural comparison of CYP106A1 with the previously investigated CYP106A2, including docking studies for both isoforms with the substrate cortisol, reveals a completely different orientation of the steroid molecule in the active sites. This distinction convincingly explains the experimentally observed differences in substrate conversion and product formation by the two enzymes.
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Affiliation(s)
- Yvonne Carius
- Department of Structural Biology, Faculty of Medicine, Center of Human and Molecular Biology (ZHMB), Saarland University, Homburg, Germany
| | - Michael Hutter
- Centre for Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Flora Kiss
- Institute of Biochemistry, Saarland University, Saarbrücken, Germany
| | - Rita Bernhardt
- Institute of Biochemistry, Saarland University, Saarbrücken, Germany
| | - C Roy D Lancaster
- Department of Structural Biology, Faculty of Medicine, Center of Human and Molecular Biology (ZHMB), Saarland University, Homburg, Germany
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8
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Mokkawes T, Lim ZQ, de Visser SP. Mechanism of Melatonin Metabolism by CYP1A1: What Determines the Bifurcation Pathways of Hydroxylation versus Deformylation? J Phys Chem B 2022; 126:9591-9606. [PMID: 36380557 PMCID: PMC9706573 DOI: 10.1021/acs.jpcb.2c07200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Melatonin, a widely applied cosmetic active ingredient, has a variety of uses as a skin protector through antioxidant and anti-inflammatory functions as well as giving the body UV-induced defenses and immune system support. In the body, melatonin is synthesized from a tryptophan amino acid in a cascade of reactions, but as melatonin is toxic at high concentrations, it is metabolized in the human skin by the cytochrome P450 enzymes. The P450s are diverse heme-based mono-oxygenases that catalyze oxygen atom-transfer processes that trigger metabolism and detoxification reactions in the body. In the catalytic cycle of the P450s, a short-lived high-valent iron(IV)-oxo heme cation radical is formed that has been proposed to be the active oxidant. How and why it activates melatonin in the human body and what the origin of the product distributions is, are unknown. This encouraged us to do a detailed computational study on a typical human P450 isozyme, namely CYP1A1. We initially did a series of molecular dynamics simulations with substrate docked into several orientations. These simulations reveal a number of stable substrate-bound positions in the active site, which may lead to differences in substrate activation channels. Using tunneling analysis on the full protein structures, we show that two of the four binding conformations lead to open substrate-binding pockets. As a result, in these open pockets, the substrate is not tightly bound and can escape back into the solution. In the closed conformations, in contrast, the substrate is mainly oriented with the methoxy group pointing toward the heme, although under a different angle. We then created large quantum cluster models of the enzyme and focused on the chemical reaction mechanisms for melatonin activation, leading to competitive O-demethylation and C6-aromatic hydroxylation pathways. The calculations show that active site positioning determines the product distributions, but the bond that is activated is not necessarily closest to the heme in the enzyme-substrate complex. As such, the docking and molecular dynamics positioning of the substrate versus oxidant can give misleading predictions on product distributions. In particular, in quantum mechanics cluster model I, we observe that through a tight hydrogen bonding network, a preferential 6-hydroxylation of melatonin is obtained. However, O-demethylation becomes possible in alternative substrate-binding orientations that have the C6-aromatic ring position shielded. Finally, we investigated enzymatic and non-enzymatic O-demethylation processes and show that the hydrogen bonding network in the substrate-binding pocket can assist and perform this step prior to product release from the enzyme.
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Affiliation(s)
- Thirakorn Mokkawes
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess
Street, Manchester M1 7DN, U.K.,Department
of Chemical Engineering, The University
of Manchester, Oxford
Road, Manchester M13 9PL, U.K.
| | - Ze Qing Lim
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess
Street, Manchester M1 7DN, U.K.,Department
of Chemical Engineering, The University
of Manchester, Oxford
Road, Manchester M13 9PL, U.K.
| | - Sam P. de Visser
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess
Street, Manchester M1 7DN, U.K.,Department
of Chemical Engineering, The University
of Manchester, Oxford
Road, Manchester M13 9PL, U.K.,
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9
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Qiu M, Liang X, Deng S, Li Y, Ke Y, Wang P, Mei H. A unified GCNN model for predicting CYP450 inhibitors by using graph convolutional neural networks with attention mechanism. Comput Biol Med 2022; 150:106177. [PMID: 36242811 DOI: 10.1016/j.compbiomed.2022.106177] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 09/19/2022] [Accepted: 10/01/2022] [Indexed: 11/17/2022]
Abstract
Undesirable drug-drug interactions (DDIs) may lead to serious adverse side effects when more than two drugs are administered to a patient simultaneously. One of the most common DDIs is caused by unexpected inhibition of a specific human cytochrome P450 (CYP450), which plays a dominant role in the metabolism of the co-administered drugs. Therefore, a unified and reliable method for predicting the potential inhibitors of CYP450 family is extremely important in drug development. In this work, graph convolutional neural network (GCN) with attention mechanism and 1-D convolutional neural network (CNN) were used to extract the features of CYP ligands and the binding sites of CYP450 respectively, which were then combined to establish a unified GCN-CNN (GCNN) model for predicting the inhibitors of 5 dominant CYP isoforms, i.e., 1A2, 2C9, 2C19, 2D6, and 3A4. Overall, the established GCNN model showed good performances on the test samples and achieved better performances than the recently proposed iCYP-MFE model by using the same datasets. Based on the heat-map analysis of the resulting molecular graphs, the key structural determinants of the CYP inhibitors were further explored.
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Affiliation(s)
- Minyao Qiu
- Key Laboratory of Biorheological Science and Technology (Ministry of Education), College of Bioengineering, Chongqing University, Chongqing, 400044, China; College of Bioengineering, Chongqing University, Chongqing, 400044, China
| | - Xiaoqi Liang
- College of Bioengineering, Chongqing University, Chongqing, 400044, China
| | - Siyao Deng
- College of Bioengineering, Chongqing University, Chongqing, 400044, China
| | - Yufang Li
- College of Bioengineering, Chongqing University, Chongqing, 400044, China
| | - Yanlan Ke
- College of Bioengineering, Chongqing University, Chongqing, 400044, China
| | - Pingqing Wang
- College of Bioengineering, Chongqing University, Chongqing, 400044, China
| | - Hu Mei
- Key Laboratory of Biorheological Science and Technology (Ministry of Education), College of Bioengineering, Chongqing University, Chongqing, 400044, China; College of Bioengineering, Chongqing University, Chongqing, 400044, China.
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10
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Danel T, Wojtuch A, Podlewska S. Generation of new inhibitors of selected cytochrome P450 subtypes- In silico study. Comput Struct Biotechnol J 2022; 20:5639-5651. [PMID: 36284709 PMCID: PMC9582735 DOI: 10.1016/j.csbj.2022.10.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 09/30/2022] [Accepted: 10/02/2022] [Indexed: 11/16/2022] Open
Abstract
Physicochemical and pharmacokinetic compound profile has crucial impact on compound potency to become a future drug. Ligands with desired activity profile cannot be used for treatment if they are characterized by unfavourable physicochemical or ADMET properties. In the study, we consider metabolic stability and focus on selected subtypes of cytochrome P450 - proteins, which take part in the first phase of compound transformations in the organism. We develop a protocol for generation of new potential inhibitors of selected cytochrome isoforms. Its subsequent stages are composed of generation and assessment of new derivatives of known cytochrome inhibitors, docking and evaluation of the compound possible inhibition on the basis of the obtained ligand-protein complexes. Besides the library of new potential agents inhibiting particular cytochrome subtypes, we also prepare a graph neural network that predicts the change in activity for all modifications of the starting molecule. In addition, we perform a systematic statistical study on the influence of particular substitutions on the potential inhibition properties of generated compounds (both mono- and di-substitutions are considered), provide explanations of the inhibitory predictions and prepare an on-line visualization platform enabling manual inspection of the results. The developed methodology can greatly support the design of new cytochrome P450 inhibitors with the overarching goal of generation of new metabolically stable compounds. It enables instant evaluation of possible compound-cytochrome interactions and selection of ligands with the highest potential of possessing desired biological activity.
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Key Words
- CYP inhibitors
- CYP, cytochrome P450
- CYP450
- DL, deep learning
- DNNs, deep neural networks
- Docking
- Explainability
- GNN, graph neural network
- Graph neural networks
- ML, machine learning
- MSE, mean squared error
- Morgan FP, Morgan fingerprint
- New compounds generation
- On-line platform
- QSPR, quantitative structure-property relationship
- RF, random forest
- SRD, sum of ranking differences
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Affiliation(s)
- Tomasz Danel
- Faculty of Mathematics and Computer Science, Jagiellonian University, 6 Łojasiewicza Street, 30-348 Kraków, Poland
| | - Agnieszka Wojtuch
- Faculty of Mathematics and Computer Science, Jagiellonian University, 6 Łojasiewicza Street, 30-348 Kraków, Poland
| | - Sabina Podlewska
- Maj Institute of Pharmacology, Polish Academy of Sciences, Department of Medicinal Chemistry, 31-343 Kraków, Smętna Street 12, Poland,Corresponding author.
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11
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Dong YL, Chong GG, Li CX, Chen Q, Pan J, Li AT, Xu JH. Carving the Active Site of CYP153A7 Monooxygenase for Improving Terminal Hydroxylation of Medium-Chain Fatty Acids. Chembiochem 2022; 23:e202200063. [PMID: 35257464 DOI: 10.1002/cbic.202200063] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/07/2022] [Indexed: 11/10/2022]
Abstract
The P450-mediated terminal hydroxylation of non-activated C-H bonds is a chemically challenging reaction. CYP153A7 monooxygenase discovered in Sphingomonas sp. HXN200 belongs to the CYP153A subfamily and shows a pronounced terminal selectivity. Herein, we report the significantly improved terminal hydroxylation activity of CYP153A7 by redesign of the substrate binding pocket based on molecular docking of CYP153A7-C 8:0 and sequence alignments. Some of the resultant single mutants were advantageous over the wild-type enzyme with higher reaction rates, achieving a complete conversion of n- octanoic acid (C 8:0. 1 mM) in a shorter period. Especially, a single-mutation variant, D258E, showed 3.8-fold higher catalytic efficiency than the wild type toward the terminal hydroxylation of medium-chain fatty acid C 8:0 into the high value-added product 8-hydroxyoctanoic acid.
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Affiliation(s)
- Ya-Li Dong
- East China University of Science and Technology, State Key Laboratory of Bioreactor Engineering, CHINA
| | - Gang-Gang Chong
- East China University of Science and Technology, State Key Laboratory of Bioreactor Engineering, 130 Meilong Road, Shanghai 200237, China, 200237, Shanghai, CHINA
| | - Chun-Xiu Li
- East China University of Science and Technology, State Key Laboratory of Bioreactor Engineering, CHINA
| | - Qi Chen
- East China University of Science and Technology, State Key Laboratory of Bioreactor Engineering, CHINA
| | - Jiang Pan
- East China University of Science and Technology, State Key Laboratory of Bioreactor Engineering, CHINA
| | - Ai-Tao Li
- Hubei University, College of Life Science, CHINA
| | - Jian-He Xu
- East China University of Science and Technology, 130 Meilong Road, 200237, Shanghai, CHINA
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12
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Yang J, Qi Y, Blodgett JAV, Wencewicz TA. Multifunctional P450 Monooxygenase CftA Diversifies the Clifednamide Pool through Tandem C-H Bond Activations. JOURNAL OF NATURAL PRODUCTS 2022; 85:47-55. [PMID: 35086337 DOI: 10.1021/acs.jnatprod.1c00606] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Polycyclic tetramate macrolactams (PTMs) are a class of structurally complex hybrid polyketide-nonribosomal peptide (PK-NRP) natural products produced by diverse bacteria. Several PTMs display pharmaceutically interesting bioactivities, and the early stages of PTM biosynthesis involving polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) enzymology are well studied. However, the timing and mechanisms of post PKS-NRPS oxidations by P450 monooxygenases encoded in PTM biosynthetic gene clusters (BGCs) remain poorly characterized. Here we demonstrate that CftA, encoded in clifednamide-type PTM BGCs, is a multifunctional P450 monooxygenase capable of converting the C29-C30 ethyl side chain of ikarugamycin to either a C29-C30 methyl ketone or a C29-C30 hydroxymethyl ketone through C-H bond activation, resulting in the formation of clifednamide A or clifednamide C, respectively. We also report the complete structure of clifednamide C solved via multidimensional NMR (COSY, HSQC, HMBC, NOESY, and TOCSY) using material purified from an engineered Streptomyces strain optimized for production. Finally, the in vitro reconstitution of recombinant CftA catalytic activity revealed the oxidation cascade for sequential conversion of ikarugamycin to clifednamide A and clifednamide C. Our findings confirm prior genetics-based predictions on the origins of clifednamide complexity via P450s encoded in PTM BGCs and place CftA into a growing group of multifunctional P450s that tailor PTM natural products through late-stage regioselective C-H bond activation.
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Affiliation(s)
- Jinping Yang
- Department of Chemistry, Washington University in St. Louis, One Brookings Drive, St. Louis, Missouri 63130, United States
| | - Yunci Qi
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, Missouri 63130, United States
| | - Joshua A V Blodgett
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, Missouri 63130, United States
| | - Timothy A Wencewicz
- Department of Chemistry, Washington University in St. Louis, One Brookings Drive, St. Louis, Missouri 63130, United States
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13
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Montemiglio LC, Gugole E, Freda I, Exertier C, D’Auria L, Chen CG, Nardi AN, Cerutti G, Parisi G, D’Abramo M, Savino C, Vallone B. Point Mutations at a Key Site Alter the Cytochrome P450 OleP Structural Dynamics. Biomolecules 2021; 12:biom12010055. [PMID: 35053203 PMCID: PMC8774231 DOI: 10.3390/biom12010055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 12/26/2021] [Accepted: 12/29/2021] [Indexed: 12/16/2022] Open
Abstract
Substrate binding to the cytochrome P450 OleP is coupled to a large open-to-closed transition that remodels the active site, minimizing its exposure to the external solvent. When the aglycone substrate binds, a small empty cavity is formed between the I and G helices, the BC loop, and the substrate itself, where solvent molecules accumulate mediating substrate-enzyme interactions. Herein, we analyzed the role of this cavity in substrate binding to OleP by producing three mutants (E89Y, G92W, and S240Y) to decrease its volume. The crystal structures of the OleP mutants in the closed state bound to the aglycone 6DEB showed that G92W and S240Y occupied the cavity, providing additional contact points with the substrate. Conversely, mutation E89Y induces a flipped-out conformation of this amino acid side chain, that points towards the bulk, increasing the empty volume. Equilibrium titrations and molecular dynamic simulations indicate that the presence of a bulky residue within the cavity impacts the binding properties of the enzyme, perturbing the conformational space explored by the complexes. Our data highlight the relevance of this region in OleP substrate binding and suggest that it represents a key substrate-protein contact site to consider in the perspective of redirecting its activity towards alternative compounds.
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Affiliation(s)
- Linda Celeste Montemiglio
- Institute of Molecular Biology and Pathology, CNR c/o Department of Biochemical Sciences “A. Rossi Fanelli”, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy; (L.C.M.); (C.E.)
| | - Elena Gugole
- Department of Biochemical Sciences “A. Rossi Fanelli”, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy; (E.G.); (I.F.); (L.D.); (G.C.)
| | - Ida Freda
- Department of Biochemical Sciences “A. Rossi Fanelli”, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy; (E.G.); (I.F.); (L.D.); (G.C.)
| | - Cécile Exertier
- Institute of Molecular Biology and Pathology, CNR c/o Department of Biochemical Sciences “A. Rossi Fanelli”, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy; (L.C.M.); (C.E.)
| | - Lucia D’Auria
- Department of Biochemical Sciences “A. Rossi Fanelli”, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy; (E.G.); (I.F.); (L.D.); (G.C.)
| | - Cheng Giuseppe Chen
- Department of Chemistry, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy; (C.G.C.); (A.N.N.); (M.D.)
| | - Alessandro Nicola Nardi
- Department of Chemistry, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy; (C.G.C.); (A.N.N.); (M.D.)
| | - Gabriele Cerutti
- Department of Biochemical Sciences “A. Rossi Fanelli”, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy; (E.G.); (I.F.); (L.D.); (G.C.)
| | - Giacomo Parisi
- Center for Life Nano & Neuro-Science, Fondazione Istituto Italiano di Tecnologia, IIT, 00185 Rome, Italy;
| | - Marco D’Abramo
- Department of Chemistry, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy; (C.G.C.); (A.N.N.); (M.D.)
| | - Carmelinda Savino
- Institute of Molecular Biology and Pathology, CNR c/o Department of Biochemical Sciences “A. Rossi Fanelli”, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy; (L.C.M.); (C.E.)
- Correspondence: (C.S.); (B.V.); Tel.: +39-06-49910548 (C.S. & B.V.)
| | - Beatrice Vallone
- Department of Biochemical Sciences “A. Rossi Fanelli”, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy; (E.G.); (I.F.); (L.D.); (G.C.)
- Correspondence: (C.S.); (B.V.); Tel.: +39-06-49910548 (C.S. & B.V.)
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14
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Davydov DR, Prasad B. Assembling the P450 puzzle: on the sources of nonadditivity in drug metabolism. Trends Pharmacol Sci 2021; 42:988-997. [PMID: 34602306 DOI: 10.1016/j.tips.2021.09.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 09/04/2021] [Accepted: 09/06/2021] [Indexed: 01/04/2023]
Abstract
There is an increasing number of indications of an oversimplification in the premise that the cumulative properties of the human drug-metabolizing ensemble represent a simple aggregate of the properties of the constituting enzymes. Recent studies of the functional effects of hetero-association of multiple cytochrome P450 species and their interactions with metabolically related enzymes revealed a tight integration in the drug-metabolizing ensemble. In our opinion, the sources of interindividual variability in drug metabolism can be elucidated only when considering this ensemble as a multienzyme system, the functional parameters of which are determined by interactions between its constituents. In this article, we present a conceptual model providing a mechanistic explanation for the functional effects of the interactions between multiple P450 species and propose a clue to understanding the nonadditive behavior of the drug-metabolizing ensemble.
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Affiliation(s)
- Dmitri R Davydov
- Department of Chemistry, Washington State University, Pullman, WA 99164, USA.
| | - Bhagwat Prasad
- Department of Pharmaceutical Sciences, Washington State University, Spokane, WA 99202, USA
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15
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Wojtuch A, Jankowski R, Podlewska S. How can SHAP values help to shape metabolic stability of chemical compounds? J Cheminform 2021; 13:74. [PMID: 34579792 PMCID: PMC8477573 DOI: 10.1186/s13321-021-00542-y] [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: 05/03/2021] [Accepted: 08/15/2021] [Indexed: 12/31/2022] Open
Abstract
Background Computational methods support nowadays each stage of drug design campaigns. They assist not only in the process of identification of new active compounds towards particular biological target, but also help in the evaluation and optimization of their physicochemical and pharmacokinetic properties. Such features are not less important in terms of the possible turn of a compound into a future drug than its desired affinity profile towards considered proteins. In the study, we focus on metabolic stability, which determines the time that the compound can act in the organism and play its role as a drug. Due to great complexity of xenobiotic transformation pathways in the living organisms, evaluation and optimization of metabolic stability remains a big challenge. Results Here, we present a novel methodology for the evaluation and analysis of structural features influencing metabolic stability. To this end, we use a well-established explainability method called SHAP. We built several predictive models and analyse their predictions with the SHAP values to reveal how particular compound substructures influence the model’s prediction. The method can be widely applied by users thanks to the web service, which accompanies the article. It allows a detailed analysis of SHAP values obtained for compounds from the ChEMBL database, as well as their determination and analysis for any compound submitted by a user. Moreover, the service enables manual analysis of the possible structural modifications via the provision of analogous analysis for the most similar compound from the ChEMBL dataset. Conclusions To our knowledge, this is the first attempt to employ SHAP to reveal which substructural features are utilized by machine learning models when evaluating compound metabolic stability. The accompanying web service for metabolic stability evaluation can be of great help for medicinal chemists. Its significant usefulness is related not only to the possibility of assessing compound stability, but also to the provision of information about substructures influencing this parameter. It can assist in the design of new ligands with improved metabolic stability, helping in the detection of privileged and unfavourable chemical moieties during stability optimization. The tool is available at https://metstab-shap.matinf.uj.edu.pl/.
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Affiliation(s)
- Agnieszka Wojtuch
- Faculty of Mathematics and Computer Science, Jagiellonian University, 6 S. Łojasiewicza Street, 30-348, Kraków, Poland
| | - Rafał Jankowski
- Faculty of Mathematics and Computer Science, Jagiellonian University, 6 S. Łojasiewicza Street, 30-348, Kraków, Poland
| | - Sabina Podlewska
- Maj Institute of Pharmacology, Polish Academy of Sciences, 12 Smętna Street, 31-343, Kraków, Poland. .,Department of Technology and Biotechnology of Drugs, Faculty of Pharmacy, Jagiellonian University Medical College, 9 Medyczna Street, 30-688, Kraków, Poland.
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16
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Hameduh T, Mokry M, Miller AD, Adam V, Heger Z, Haddad Y. A rotamer relay information system in the epidermal growth factor receptor-drug complexes reveals clues to new paradigm in protein conformational change. Comput Struct Biotechnol J 2021; 19:5443-5454. [PMID: 34667537 PMCID: PMC8511715 DOI: 10.1016/j.csbj.2021.09.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 09/13/2021] [Accepted: 09/24/2021] [Indexed: 11/04/2022] Open
Abstract
Cancer cells can escape the effects of chemotherapy through mutations and upregulation of a tyrosine kinase protein called the epidermal growth factor receptor (EGFR). In the past two decades, four generations of tyrosine kinase inhibitors targeting EGFR have been developed. Using comparative structure analysis of 116 EGFR-drug complex crystal structures, cluster analysis produces two clans of 73 and 43 structures, respectively. The first clan of 73 structures is larger and is comprised mostly of the C-helix-IN conformation while the second clan of 43 structures correlates with the C-helix-OUT conformation. A deep rotamer analysis identifies 43 residues (18%) of the total of 237 residues spanning the kinase structures under investigation with significant rotamer variations between the C-helix-IN and C-helix-OUT clans. The locations of these rotamer variations take on the appearance of side chain conformational relays extending out from points of EGFR mutation to different regions of the EGFR kinase. Accordingly, we propose that key EGFR mutations act singly or together to induce drug resistant conformational changes in EGFR that are communicated via these side chain conformational relays. Accordingly, these side chain conformational relays appear to play a significant role in the development of tumour resistance. This phenomenon also suggests a new paradigm in protein conformational change that is mediated by supportive relays of rotamers on the protein surface, rather than through conventional backbone movements.
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Affiliation(s)
- Tareq Hameduh
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic
| | - Michal Mokry
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic
- Central European Institute of Technology, Brno University of Technology, Purkynova 656/123, 612 00 Brno, Czech Republic
| | - Andrew D. Miller
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic
- Veterinary Research Institute, Hudcova 70, CZ-62100 Brno, Czech Republic
- KP Therapeutics (Europe) s.r.o., Purkyňova 649/127, Brno CZ-61200, Czech Republic
| | - Vojtech Adam
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic
- Central European Institute of Technology, Brno University of Technology, Purkynova 656/123, 612 00 Brno, Czech Republic
| | - Zbynek Heger
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic
- Central European Institute of Technology, Brno University of Technology, Purkynova 656/123, 612 00 Brno, Czech Republic
| | - Yazan Haddad
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic
- Central European Institute of Technology, Brno University of Technology, Purkynova 656/123, 612 00 Brno, Czech Republic
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17
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Functional Characterization of 21 Rare Allelic CYP1A2 Variants Identified in a Population of 4773 Japanese Individuals by Assessing Phenacetin O-Deethylation. J Pers Med 2021; 11:jpm11080690. [PMID: 34442334 PMCID: PMC8401128 DOI: 10.3390/jpm11080690] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 07/16/2021] [Accepted: 07/20/2021] [Indexed: 11/16/2022] Open
Abstract
Cytochrome P450 1A2 (CYP1A2), which accounts for approximately 13% of the total hepatic cytochrome content, catalyzes the metabolic reactions of approximately 9% of frequently used drugs, including theophylline and olanzapine. Substantial inter-individual differences in enzymatic activity have been observed among patients, which could be caused by genetic polymorphisms. Therefore, we functionally characterized 21 novel CYP1A2 variants identified in 4773 Japanese individuals by determining the kinetic parameters of phenacetin O-deethylation. Our results showed that most of the evaluated variants exhibited decreased or no enzymatic activity, which may be attributed to potential structural alterations. Notably, the Leu98Gln, Gly233Arg, Ser380del Gly454Asp, and Arg457Trp variants did not exhibit quantifiable enzymatic activity. Additionally, three-dimensional (3D) docking analyses were performed to further understand the underlying mechanisms behind variant pharmacokinetics. Our data further suggest that despite mutations occurring on the protein surface, accumulating interactions could result in the impairment of protein function through the destabilization of binding regions and changes in protein folding. Therefore, our findings provide additional information regarding rare CYP1A2 genetic variants and how their underlying effects could clarify discrepancies noted in previous phenotypical studies. This would allow the improvement of personalized therapeutics and highlight the importance of identifying and characterizing rare variants.
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18
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Di Nardo G, Di Venere A, Zhang C, Nicolai E, Castrignanò S, Di Paola L, Gilardi G, Mei G. Polymorphism on human aromatase affects protein dynamics and substrate binding: spectroscopic evidence. Biol Direct 2021; 16:8. [PMID: 33902660 PMCID: PMC8073906 DOI: 10.1186/s13062-021-00292-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 04/08/2021] [Indexed: 01/07/2023] Open
Abstract
Human aromatase is a member of the cytochrome P450 superfamily, involved in steroid hormones biosynthesis. In particular, it converts androgen into estrogens being therefore responsible for the correct sex steroids balance. Due to its capacity in producing estrogens it has also been considered as a promising target for breast cancer therapy. Two single-nucleotide polymorphisms (R264C and R264H) have been shown to alter aromatase activity and they have been associated to an increased or decreased risk for estrogen-dependent pathologies. Here, the effect of these mutations on the protein dynamics is investigated by UV/FTIR and time resolved fluorescence spectroscopy. H/D exchange rates were measured by FTIR for the three proteins in the ligand-free, substrate- and inhibitor-bound forms and the data indicate that the wild-type enzyme undergoes a conformational change leading to a more compact tertiary structure upon substrate or inhibitor binding. Indeed, the H/D exchange rates are decreased when a ligand is present. In the variants, the exchange rates in the ligand-free and -bound forms are similar, indicating that a structural change is lacking, despite the single amino acid substitution is located in the peripheral shell of the protein molecule. Moreover, the fluorescence lifetimes data show that the quenching effect on tryptophan-224 observed upon ligand binding in the wild-type, is absent in both variants. Since this residue is located in the catalytic pocket, these findings suggest that substrate entrance and/or retention in the active site is partially compromised in both mutants. A contact network analysis demonstrates that the protein structure is organized in two main clusters, whose connectivity is altered by ligand binding, especially in correspondence of helix-G, where the amino acid substitutions occur. Our findings demonstrate that SNPs resulting in mutations on aromatase surface modify the protein flexibility that is required for substrate binding and catalysis. The cluster analysis provides a rationale for such effect, suggesting helix G as a possible target for aromatase inhibition.
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Affiliation(s)
- Giovanna Di Nardo
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, Via Accademia Albertina 13, 10123, Turin, Italy
| | - Almerinda Di Venere
- Dipartimento di Medicina Sperimentale, Università di Roma Tor Vergata, Via Montpellier 1, 00133, Rome, Italy
| | - Chao Zhang
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, Via Accademia Albertina 13, 10123, Turin, Italy
| | - Eleonora Nicolai
- Dipartimento di Medicina Sperimentale, Università di Roma Tor Vergata, Via Montpellier 1, 00133, Rome, Italy
| | - Silvia Castrignanò
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, Via Accademia Albertina 13, 10123, Turin, Italy
| | - Luisa Di Paola
- Dipartimento di Ingegneria, Unità di Fondamenti Chimico-Fisici dell'Ingegneria Chimica, Università Campus Bio-Medico di Roma, via Álvaro del Portillo 21, 00128, Rome, Italy
| | - Gianfranco Gilardi
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, Via Accademia Albertina 13, 10123, Turin, Italy.
| | - Giampiero Mei
- Dipartimento di Medicina Sperimentale, Università di Roma Tor Vergata, Via Montpellier 1, 00133, Rome, Italy.
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Madsen JJ, Olsen OH. Conformational Plasticity-Rigidity Axis of the Coagulation Factor VII Zymogen Elucidated by Atomistic Simulations of the N-Terminally Truncated Factor VIIa Protease Domain. Biomolecules 2021; 11:549. [PMID: 33917935 PMCID: PMC8068379 DOI: 10.3390/biom11040549] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 04/02/2021] [Accepted: 04/06/2021] [Indexed: 11/22/2022] Open
Abstract
The vast majority of coagulation factor VII (FVII), a trypsin-like protease, circulates as the inactive zymogen. Activated FVII (FVIIa) is formed upon proteolytic activation of FVII, where it remains in a zymogen-like state and it is fully activated only when bound to tissue factor (TF). The catalytic domains of trypsin-like proteases adopt strikingly similar structures in their fully active forms. However, the dynamics and structures of the available corresponding zymogens reveal remarkable conformational plasticity of the protease domain prior to activation in many cases. Exactly how ligands and cofactors modulate the conformational dynamics and function of these proteases is not entirely understood. Here, we employ atomistic simulations of FVIIa (and variants hereof, including a TF-independent variant and N-terminally truncated variants) to provide fundamental insights with atomistic resolution into the plasticity-rigidity interplay of the protease domain conformations that appears to govern the functional response to proteolytic and allosteric activation. We argue that these findings are relevant to the FVII zymogen, whose structure has remained elusive despite substantial efforts. Our results shed light on the nature of FVII and demonstrate how conformational dynamics has played a crucial role in the evolutionary adaptation of regulatory mechanisms that were not present in the ancestral trypsin. Exploiting this knowledge could lead to engineering of protease variants for use as next-generation hemostatic therapeutics.
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Affiliation(s)
- Jesper J. Madsen
- Global and Planetary Health, College of Public Health, University of South Florida, Tampa, FL 33612, USA
| | - Ole H. Olsen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Section for Metabolic Receptology, University of Copenhagen, Blegdamsvej 3b, DK-2200 Copenhagen, Denmark
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20
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Surface hydrophobics mediate functional dimerization of CYP121A1 of Mycobacterium tuberculosis. Sci Rep 2021; 11:394. [PMID: 33431984 PMCID: PMC7801616 DOI: 10.1038/s41598-020-79545-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 12/09/2020] [Indexed: 11/28/2022] Open
Abstract
Tuberculosis is caused by the pathogenic bacterium Mycobacterium tuberculosis (Mtb) and remains the leading cause of death by infection world-wide. The Mtb genome encodes a disproportionate number of twenty cytochrome P450 enzymes, of which the essential enzyme cytochrome P450 121A1 (CYP121A1) remains a target of drug design efforts. CYP121A1 mediates a phenol coupling reaction of the tyrosine dipeptide cyclo-L-Tyr-L-Tyr (cYY). In this work, a structure and function investigation of dimerization was performed as an overlooked feature of CYP121A1 function. This investigation showed that CYP121A1 dimers form via intermolecular contacts on the distal surface and are mediated by a network of solvent-exposed hydrophobic residues. Disruption of CYP121A1 dimers by site-directed mutagenesis leads to a partial loss of specificity for cYY, resulting in an approximate 75% decrease in catalysis. 19F labeling and nuclear magnetic resonance of the enzyme FG-loop was also combined with protein docking to develop a working model of a functional CYP121A1 dimer. The results obtained suggest that participation of a homodimer interface in substrate selectivity represents a novel paradigm of substrate binding in CYPs, while also providing important mechanistic insight regarding a relevant drug target in the development of novel anti-tuberculosis agents.
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21
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Pochapsky TC. A dynamic understanding of cytochrome P450 structure and function through solution NMR. Curr Opin Biotechnol 2020; 69:35-42. [PMID: 33360373 DOI: 10.1016/j.copbio.2020.11.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 11/17/2020] [Indexed: 12/12/2022]
Abstract
Many economically important biosyntheses incorporate regiospecific and stereospecific oxidations at unactivated carbons. Such oxidations are commonly catalyzed by cytochrome P450 monooxygenases, heme-containing enzymes that activate molecular oxygen while selectively binding and orienting the substrate for reaction. Despite the plethora of P450-catalyzed reactions, the P450 fold is highly conserved, and static structures are often insufficient for characterizing conformational states that contribute to specificity. High-resolution solution nuclear magnetic resonance (NMR) offers insights into dynamic processes and conformational changes that are required of a P450 in order to attain the combination of specificity and efficiency required for these reactions.
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Affiliation(s)
- Thomas C Pochapsky
- Departments of Chemistry, Biochemistry and The Rosenstiel Institute for Basic Medical Research, Brandeis University, 415 South St., Waltham, MA 02454, USA.
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22
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Li J, Zhou Y, Tang Y, Li W, Tu Y. Dissecting the Structural Plasticity and Dynamics of Cytochrome P450 2B4 by Molecular Dynamics Simulations. J Chem Inf Model 2020; 60:5026-5035. [PMID: 32808774 DOI: 10.1021/acs.jcim.0c00482] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The plasticity of cytochromes P450 (P450s) is known to contribute significantly to their catalytic capacity of metabolizing various substrates. Although numerous studies have been performed, factors governing the plasticity and dynamics of P450s are still not fully understood. In this study, taking CYP2B4 as an example, we dissect the protein plasticity and dynamics in different environments. CYP2B4 is featured by a high degree of plasticity, which exhibits open, closed, and intermediate states. By analyzing the CYP2B4 crystal structures, we identified the structural features for the closed, open, and intermediate states. Interestingly, formation of the dimer structure was found in the open and intermediate states. The subsequent molecular dynamics (MD) simulations of the open structure in water confirmed the importance of the dimer form in stabilizing the open conformations. MD simulations of the closed and open structures in the membrane environment and the free energies for opening the F-G cassette obtained from the umbrella sampling calculations indicate that the membrane environment is important for stabilizing the F-G cassette. The dynamical network analysis indicates that Asp105 on the B-C loop plays an important role in transiting the structure from the open to the intermediate state. Our results thus unveil the mechanisms of dimer formation and open-to-intermediate transition for CYP2B4 in the water and membrane environments.
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Affiliation(s)
- Junhao Li
- Department of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Yang Zhou
- Department of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Yun Tang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Weihua Li
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Yaoquan Tu
- Department of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
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23
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Zhang B, Lewis KM, Abril A, Davydov DR, Vermerris W, Sattler SE, Kang C. Structure and Function of the Cytochrome P450 Monooxygenase Cinnamate 4-hydroxylase from Sorghum bicolor. PLANT PHYSIOLOGY 2020; 183:957-973. [PMID: 32332088 PMCID: PMC7333690 DOI: 10.1104/pp.20.00406] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 04/09/2020] [Indexed: 05/02/2023]
Abstract
Cinnamate 4-hydroxylase (C4H; CYP73A) is a cytochrome P450 monooxygenase associated externally with the endoplasmic reticulum of plant cells. The enzyme uses NADPH-cytochrome P450 reductase as a donor of electrons and hydroxylates cinnamic acid to form 4-coumaric acid in phenylpropanoid metabolism. In order to better understand the structure and function of this unique class of plant P450 enzymes, we have characterized the enzyme C4H1 from lignifying tissues of sorghum (Sorghum bicolor), encoded by Sobic.002G126600 Here we report the 1.7 Å resolution crystal structure of CYP73A33. The obtained structural information, along with the results of the steady-state kinetic analysis and the absorption spectroscopy titration, displays a high degree of similarity of the structural and functional features of C4H to those of other P450 proteins. Our data also suggest the presence of a putative allosteric substrate-binding site in a hydrophobic pocket on the enzyme surface. In addition, comparing the newly resolved structure with those of well-investigated cytochromes P450 from mammals and bacteria enabled us to identify those residues of critical functional importance and revealed a unique sequence signature that is potentially responsible for substrate specificity and catalytic selectivity of C4H.
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Affiliation(s)
- Bixia Zhang
- Department of Chemistry, Washington State University, Pullman, Washington 99164
| | - Kevin M Lewis
- Department of Chemistry, Washington State University, Pullman, Washington 99164
| | - Alejandra Abril
- Plant Molecular and Cellular Biology Graduate Program, University of Florida, Gainesville, Florida 32610
| | - Dmitri R Davydov
- Department of Chemistry, Washington State University, Pullman, Washington 99164
| | - Wilfred Vermerris
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida 32610
- University of Florida Genetics Institute, Gainesville, Florida 32610
- Florida Center for Renewable Chemicals and Fuels, University of Florida, Gainesville, Florida 32610
| | - Scott E Sattler
- U.S. Department of Agriculture-Agricultural Research Service, Wheat, Sorghum and Forage Research Unit, Lincoln, Nebraska 68583
| | - ChulHee Kang
- Department of Chemistry, Washington State University, Pullman, Washington 99164
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24
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Ji L, Zhao Y, Tao M, Wang H, Niu D, Ouyang G, Xia A, Liu M. Dimension-Tunable Circularly Polarized Luminescent Nanoassemblies with Emerging Selective Chirality and Energy Transfer. ACS NANO 2020; 14:2373-2384. [PMID: 32027478 DOI: 10.1021/acsnano.9b09584] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
The selective interplay between dimensional morphology transition and signal transfer is an important feature for both nanomaterials and biosystems. While most of those reported examples considered either dimensional transition or signal transfer, the integrated interplay or selectivity for these two aspects in single self-assembled system has been rarely studied. Here, we report that a positively charged chiral π-building block could self-assemble into multidimensional nanostructures, which showed tunable circularly polarized luminescence (CPL). Impressively, when these CPL-active multidimensional structures interacted with two achiral dyes (positively charged ThT and negatively charged CNA), 3D nanocubes and 0D nanospheres showed neither chirality transfer nor energy transfer, while 2D nanoplates could successfully trigger a selective chirality or energy transfer depending on the charge type of acceptor dyes, which then emitted an enhanced CPL signal. This work demonstrated rational design of charged π-building block for the construction of dimension controllable and selective signal transfer self-assembly system, which might deepen the understanding the interplay of dimensional structures and signal transfer functions in natural and nano systems.
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Affiliation(s)
- Lukang Ji
- Beijing National Laboratory for Molecular Science (BNLMS), CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics , Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190 , P.R. China
- University of Chinese Academy of Sciences , Beijing 100049 , P.R. China
| | - Yang Zhao
- Beijing National Laboratory for Molecular Science (BNLMS), CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics , Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190 , P.R. China
- College of Pharmacy , Hebei University , Baoding 071002 , P.R. China
| | - Min Tao
- University of Chinese Academy of Sciences , Beijing 100049 , P.R. China
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Photochemistry , Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190 , P.R. China
| | - Hanxiao Wang
- Beijing National Laboratory for Molecular Science (BNLMS), CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics , Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190 , P.R. China
| | - Dian Niu
- Beijing National Laboratory for Molecular Science (BNLMS), CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics , Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190 , P.R. China
- University of Chinese Academy of Sciences , Beijing 100049 , P.R. China
| | - Guanghui Ouyang
- Beijing National Laboratory for Molecular Science (BNLMS), CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics , Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190 , P.R. China
| | - Andong Xia
- University of Chinese Academy of Sciences , Beijing 100049 , P.R. China
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Photochemistry , Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190 , P.R. China
| | - Minghua Liu
- Beijing National Laboratory for Molecular Science (BNLMS), CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics , Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190 , P.R. China
- University of Chinese Academy of Sciences , Beijing 100049 , P.R. China
- Collaborative Innovation Centre of Chemical Science and Engineering , Nankai University , Tianjin 300072 , P.R. China
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25
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Hajeyah AA, Griffiths WJ, Wang Y, Finch AJ, O’Donnell VB. The Biosynthesis of Enzymatically Oxidized Lipids. Front Endocrinol (Lausanne) 2020; 11:591819. [PMID: 33329396 PMCID: PMC7711093 DOI: 10.3389/fendo.2020.591819] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 10/26/2020] [Indexed: 12/14/2022] Open
Abstract
Enzymatically oxidized lipids are a specific group of biomolecules that function as key signaling mediators and hormones, regulating various cellular and physiological processes from metabolism and cell death to inflammation and the immune response. They are broadly categorized as either polyunsaturated fatty acid (PUFA) containing (free acid oxygenated PUFA "oxylipins", endocannabinoids, oxidized phospholipids) or cholesterol derivatives (oxysterols, steroid hormones, and bile acids). Their biosynthesis is accomplished by families of enzymes that include lipoxygenases (LOX), cyclooxygenases (COX), cytochrome P450s (CYP), and aldo-keto reductases (AKR). In contrast, non-enzymatically oxidized lipids are produced by uncontrolled oxidation and are broadly considered to be harmful. Here, we provide an overview of the biochemistry and enzymology of LOXs, COXs, CYPs, and AKRs in humans. Next, we present biosynthetic pathways for oxylipins, oxidized phospholipids, oxysterols, bile acids and steroid hormones. Last, we address gaps in knowledge and suggest directions for future work.
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Affiliation(s)
- Ali A. Hajeyah
- Systems Immunity Research Institute and Division of Infection and Immunity, Cardiff University, Cardiff, United Kingdom
- *Correspondence: Ali A. Hajeyah,
| | - William J. Griffiths
- Institute of Life Science, Swansea University Medical School, Swansea, United Kingdom
| | - Yuqin Wang
- Institute of Life Science, Swansea University Medical School, Swansea, United Kingdom
| | - Andrew J. Finch
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Valerie B. O’Donnell
- Systems Immunity Research Institute and Division of Infection and Immunity, Cardiff University, Cardiff, United Kingdom
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26
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DeMars MD, Samora NL, Yang S, Garcia-Borràs M, Sanders JN, Houk KN, Podust LM, Sherman DH. Exploring the molecular basis for substrate specificity in homologous macrolide biosynthetic cytochromes P450. J Biol Chem 2019; 294:15947-15961. [PMID: 31488542 PMCID: PMC6827315 DOI: 10.1074/jbc.ra119.010352] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 08/30/2019] [Indexed: 11/06/2022] Open
Abstract
Cytochromes P450 (P450s) are nature's catalysts of choice for performing demanding and physiologically vital oxidation reactions. Biochemical characterization of these enzymes over the past decades has provided detailed mechanistic insight and highlighted the diversity of substrates P450s accommodate and the spectrum of oxidative transformations they catalyze. Previously, we discovered that the bacterial P450 MycCI from the mycinamicin biosynthetic pathway in Micromonospora griseorubida possesses an unusually broad substrate scope, whereas the homologous P450 from tylosin-producing Streptomyces fradiae (TylHI) exhibits a high degree of specificity for its native substrate. Here, using biochemical, structural, and computational approaches, we aimed to understand the molecular basis for the disparate reactivity profiles of these two P450s. Turnover and equilibrium binding experiments with substrate analogs revealed that TylHI strictly prefers 16-membered ring macrolides bearing the deoxyamino sugar mycaminose. To help rationalize these results, we solved the X-ray crystal structure of TylHI in complex with its native substrate at 1.99-Å resolution and assayed several site-directed mutants. We also conducted molecular dynamics simulations of TylHI and MycCI and biochemically characterized a third P450 homolog from the chalcomycin biosynthetic pathway in Streptomyces bikiniensis These studies provided a basis for constructing P450 chimeras to gain further insight into the features dictating the differences in reaction profile among these structurally and functionally related enzymes, ultimately unveiling the central roles of key loop regions in influencing substrate binding and turnover. Our work highlights the complex nature of P450/substrate interactions and raises interesting questions regarding the evolution of functional diversity among biosynthetic enzymes.
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Affiliation(s)
- Matthew D DeMars
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109
| | - Nathan L Samora
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California 92093
| | - Song Yang
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
| | - Marc Garcia-Borràs
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
| | - Jacob N Sanders
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
| | - K N Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
| | - Larissa M Podust
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California 92093
| | - David H Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan 48109
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan 48109
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27
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Santos GDA, Dhoke GV, Davari MD, Ruff AJ, Schwaneberg U. Directed Evolution of P450 BM3 towards Functionalization of Aromatic O-Heterocycles. Int J Mol Sci 2019; 20:E3353. [PMID: 31288417 PMCID: PMC6651506 DOI: 10.3390/ijms20133353] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 06/28/2019] [Accepted: 07/01/2019] [Indexed: 02/04/2023] Open
Abstract
The O-heterocycles, benzo-1,4-dioxane, phthalan, isochroman, 2,3-dihydrobenzofuran, benzofuran, and dibenzofuran are important building blocks with considerable medical application for the production of pharmaceuticals. Cytochrome P450 monooxygenase (P450) Bacillus megaterium 3 (BM3) wild type (WT) from Bacillus megaterium has low to no conversion of the six O-heterocycles. Screening of in-house libraries for active variants yielded P450 BM3 CM1 (R255P/P329H), which was subjected to directed evolution and site saturation mutagenesis of four positions. The latter led to the identification of position R255, which when introduced in the P450 BM3 WT, outperformed all other variants. The initial oxidation rate of nicotinamide adenine dinucleotide phosphate (NADPH) consumption increased ≈140-fold (WT: 8.3 ± 1.3 min-1; R255L: 1168 ± 163 min-1), total turnover number (TTN) increased ≈21-fold (WT: 40 ± 3; R255L: 860 ± 15), and coupling efficiency, ≈2.9-fold (WT: 8.8 ± 0.1%; R255L: 25.7 ± 1.0%). Computational analysis showed that substitution R255L (distant from the heme-cofactor) does not have the salt bridge formed with D217 in WT, which introduces flexibility into the I-helix and leads to a heme rearrangement allowing for efficient hydroxylation.
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Affiliation(s)
| | - Gaurao V Dhoke
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Mehdi D Davari
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Anna Joëlle Ruff
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Ulrich Schwaneberg
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
- DWI-Leibniz-Institut für Interaktive Materialien e.V., Forckenbeckstraße 50, 52074 Aachen, Germany.
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28
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Abstract
![]()
Enzyme function requires that enzyme structures be dynamic. Substrate
binding, product release, and transition state stabilization typically
involve different enzyme conformers. Furthermore, in multistep enzyme-catalyzed
reactions, more than one enzyme conformation may be important for
stabilizing different transition states. While X-ray crystallography
provides the most detailed structural information of any current methodology,
X-ray crystal structures of enzymes capture only those conformations
that fit into the crystal lattice, which may or may not be relevant
to function. Solution nuclear magnetic resonance (NMR) methods can
provide an alternative approach to characterizing enzymes under nonperturbing
and controllable conditions, allowing one to identify and localize
dynamic processes that are important to function. However, many enzymes
are too large for standard approaches to making sequential resonance
assignments, a critical first step in analyzing and interpreting the
wealth of information inherent in NMR spectra. This Account
describes our long-standing NMR-based research into
structural and dynamic aspects of function in the cytochrome P450
monooxygenase superfamily. These heme-containing enzymes typically
catalyze the oxidation of unactivated C–H and C=C bonds
in a multitude of substrates, often with complete regio- and stereospecificity.
Over 600 000 genes in GenBank have been assigned to P450s,
yet all known P450 structures exhibit a highly conserved and unique
fold. This combination of functional and structural conservation with
a vast substrate clientele, each substrate having multiple possible
sites for oxidation, makes the P450s a unique target for understanding
the role of enzyme structure and dynamics in determining a particular
substrate–product combination. P450s are large by solution
NMR standards, requiring us to develop specialized approaches for
making sequential resonance assignments and interpreting the spectral
changes that occur as a function of changing conditions (e.g., oxidation
and spin state changes, ligand, substrate or effector binding). Solution
conformations are characterized by the fitting of residual dipolar
couplings (RDCs) measured for sequence-specifically assigned amide
N–H correlations to alignment tensors optimized in the course
of restrained molecular dynamics (MD) simulations. The conformational
ensembles obtained by such RDC-restrained simulations, which we call
“soft annealing”, are then tested by site-directed mutation
and spectroscopic and activity assays for relevance. These efforts
have gained us insights into cryptic conformational changes associated
with substrate and redox partner binding that were not suspected from
crystal structures, but were shown by subsequent work to be relevant
to function. Furthermore, it appears that many of these changes can
be generalized to P450s besides those that we have characterized,
providing guidance for enzyme engineering efforts. While past research
was primarily directed at the more tractable prokaryotic P450s, our
current efforts are aimed at medically relevant human enzymes, including
CYP17A1, CYP2D6, and CYP3A4.
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29
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Child SA, Flint KL, Bruning JB, Bell SG. The characterisation of two members of the cytochrome P450 CYP150 family: CYP150A5 and CYP150A6 from Mycobacterium marinum. Biochim Biophys Acta Gen Subj 2019; 1863:925-934. [PMID: 30826435 DOI: 10.1016/j.bbagen.2019.02.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 02/20/2019] [Accepted: 02/27/2019] [Indexed: 12/25/2022]
Abstract
BACKGROUND Actinobacteria, including the Mycobacteria, have a large component of cytochrome P450 family monooxygenases. This includes Mycobacterium tuberculosis, M. ulcerans and M. marinum, and M. vanbaalenii. These enzymes can abstract CH bonds and have important roles in natural product biosynthesis. METHODS Two members of the bacterial CYP150 family, CYP150A5 and CYP150A6 from M. marinum, were produced, purified and characterised. The potential substrate ranges of both enzymes were analysed and the monooxygenase activity of CYP150A5 was reconstituted using a physiological electron transfer partner system. CYP150A6 was structurally characterised by X-ray crystallography. RESULTS CYP150A5 was shown to bind various norisoprenoids and terpenoids. It could regioselectively hydroxylate β-ionol. The X-ray crystal structure of substrate-free CYP150A6 was solved to 1.5 Å. This displayed an open conformation with short F and G helices, an unresolved F-G loop region and exposed active site pocket. The active site residues could be identified and important variations were found among the CYP150A enzymes. Haem-binding azole inhibitors were identified for both enzymes. CONCLUSIONS The structure of CYP150A6 will facilitate the identification of physiological substrates and the design of better inhibitors for members of this P450 family. Based on the observed differences in substrate binding preference and sequence variations among the active site residues, their roles are predicted to be different. GENERAL SIGNIFICANCE Multiple CYP150 family members were found in many bacteria and are prevalent in the Mycobacteria including several human pathogens. Inhibition and structural data are reported here for these enzymes for the first time.
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Affiliation(s)
- Stella A Child
- Department of Chemistry, University of Adelaide, SA 5005, Australia
| | - Kate L Flint
- Department of Chemistry, University of Adelaide, SA 5005, Australia
| | - John B Bruning
- School of Biological Sciences, University of Adelaide, SA 5005, Australia
| | - Stephen G Bell
- Department of Chemistry, University of Adelaide, SA 5005, Australia.
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30
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Busta L, Yim WC, LaBrant EW, Wang P, Grimes L, Malyszka K, Cushman JC, Santos P, Kosma DK, Cahoon EB. Identification of Genes Encoding Enzymes Catalyzing the Early Steps of Carrot Polyacetylene Biosynthesis. PLANT PHYSIOLOGY 2018; 178:1507-1521. [PMID: 30333150 PMCID: PMC6288749 DOI: 10.1104/pp.18.01195] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 10/11/2018] [Indexed: 05/24/2023]
Abstract
Polyacetylenic lipids accumulate in various Apiaceae species after pathogen attack, suggesting that these compounds are naturally occurring pesticides and potentially valuable resources for crop improvement. These compounds also promote human health and slow tumor growth. Even though polyacetylenic lipids were discovered decades ago, the biosynthetic pathway underlying their production is largely unknown. To begin filling this gap and ultimately enable polyacetylene engineering, we studied polyacetylenes and their biosynthesis in the major Apiaceae crop carrot (Daucus carota subsp. sativus). Using gas chromatography and mass spectrometry, we identified three known polyacetylenes and assigned provisional structures to two novel polyacetylenes. We also quantified these compounds in carrot leaf, petiole, root xylem, root phloem, and root periderm extracts. Falcarindiol and falcarinol predominated and accumulated primarily in the root periderm. Since the multiple double and triple carbon-carbon bonds that distinguish polyacetylenes from ubiquitous fatty acids are often introduced by Δ12 oleic acid desaturase (FAD2)-type enzymes, we mined the carrot genome for FAD2 genes. We identified a FAD2 family with an unprecedented 24 members and analyzed public, tissue-specific carrot RNA-Seq data to identify coexpressed members with root periderm-enhanced expression. Six candidate genes were heterologously expressed individually and in combination in yeast and Arabidopsis (Arabidopsis thaliana), resulting in the identification of one canonical FAD2 that converts oleic to linoleic acid, three divergent FAD2-like acetylenases that convert linoleic into crepenynic acid, and two bifunctional FAD2s with Δ12 and Δ14 desaturase activity that convert crepenynic into the further desaturated dehydrocrepenynic acid, a polyacetylene pathway intermediate. These genes can now be used as a basis for discovering other steps of falcarin-type polyacetylene biosynthesis, to modulate polyacetylene levels in plants, and to test the in planta function of these molecules.
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Affiliation(s)
- Lucas Busta
- Center for Plant Science Innovation and Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588
| | - Won Cheol Yim
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada 89557
| | - Evan William LaBrant
- Center for Plant Science Innovation and Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588
| | - Peng Wang
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, Hainan 571737, China
| | - Lindsey Grimes
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada 89557
| | - Kiah Malyszka
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada 89557
| | - John C Cushman
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada 89557
| | - Patricia Santos
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada 89557
| | - Dylan K Kosma
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada 89557
| | - Edgar B Cahoon
- Center for Plant Science Innovation and Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588
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31
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Entropic contribution to enhanced thermal stability in the thermostable P450 CYP119. Proc Natl Acad Sci U S A 2018; 115:E10049-E10058. [PMID: 30297413 PMCID: PMC6205451 DOI: 10.1073/pnas.1807473115] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The enhanced thermostability of thermophilic proteins with respect to their mesophilic counterparts is often attributed to the enthalpy effect, arising from strong interactions between protein residues. Intuitively, these strong interresidue interactions will rigidify the biomolecules. However, the present work utilizing neutron scattering and solution NMR spectroscopy measurements demonstrates a contrary example that the thermophilic cytochrome P450, CYP119, is much more flexible than its mesophilic counterpart, CYP101A1, something which is not apparent just from structural comparison of the two proteins. A mechanism to explain this apparent contradiction is that higher flexibility in the folded state of CYP119 increases its conformational entropy and thereby reduces the entropy gain during denaturation, which will increase the free energy needed for unfolding and thus stabilize the protein. This scenario is supported by thermodynamic data on the temperature dependence of unfolding free energy, which shows a significant entropic contribution to the thermostability of CYP119 and lends an added dimension to enhanced stability, previously attributed only to presence of aromatic stacking interactions and salt bridge networks. Our experimental data also support the notion that highly thermophilic P450s such as CYP119 may use a mechanism that partitions flexibility differently from mesophilic P450s between ligand binding and thermal stability.
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32
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Parisi G, Montemiglio LC, Giuffrè A, Macone A, Scaglione A, Cerutti G, Exertier C, Savino C, Vallone B. Substrate-induced conformational change in cytochrome P450 OleP. FASEB J 2018; 33:1787-1800. [PMID: 30207799 DOI: 10.1096/fj.201800450rr] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The regulation of cytochrome P450 activity is often achieved by structural transitions induced by substrate binding. We describe the conformational transition experienced upon binding by the P450 OleP, an epoxygenase involved in oleandomycin biosynthesis. OleP bound to the substrate analog 6DEB crystallized in 2 forms: one with an ensemble of open and closed conformations in the asymmetric unit and another with only the closed conformation. Characterization of OleP-6DEB binding kinetics, also using the P450 inhibitor clotrimazole, unveiled a complex binding mechanism that involves slow conformational rearrangement with the accumulation of a spectroscopically detectable intermediate where 6DEB is bound to open OleP. Data reported herein provide structural snapshots of key precatalytic steps in the OleP reaction and explain how structural rearrangements induced by substrate binding regulate activity.-Parisi, G., Montemiglio, L. C., Giuffrè, A., Macone, A., Scaglione, A., Cerutti, G., Exertier, C., Savino, C., Vallone, B. Substrate-induced conformational change in cytochrome P450 OleP.
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Affiliation(s)
- Giacomo Parisi
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche A. Rossi Fanelli, Sapienza Università di Roma, Rome, Italy.,Dipartimento di Scienze Biochimiche A. Rossi Fanelli, Sapienza Università di Roma, Rome, Italy
| | - Linda Celeste Montemiglio
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche A. Rossi Fanelli, Sapienza Università di Roma, Rome, Italy.,Dipartimento di Scienze Biochimiche A. Rossi Fanelli, Sapienza Università di Roma, Rome, Italy.,Institute of Molecular Biology and Pathology, National Research Council, Rome, Italy
| | - Alessandro Giuffrè
- Institute of Molecular Biology and Pathology, National Research Council, Rome, Italy
| | - Alberto Macone
- Dipartimento di Scienze Biochimiche A. Rossi Fanelli, Sapienza Università di Roma, Rome, Italy
| | - Antonella Scaglione
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche A. Rossi Fanelli, Sapienza Università di Roma, Rome, Italy.,Dipartimento di Scienze Biochimiche A. Rossi Fanelli, Sapienza Università di Roma, Rome, Italy
| | - Gabriele Cerutti
- Dipartimento di Scienze Biochimiche A. Rossi Fanelli, Sapienza Università di Roma, Rome, Italy
| | - Cécile Exertier
- Dipartimento di Scienze Biochimiche A. Rossi Fanelli, Sapienza Università di Roma, Rome, Italy
| | - Carmelinda Savino
- Institute of Molecular Biology and Pathology, National Research Council, Rome, Italy
| | - Beatrice Vallone
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche A. Rossi Fanelli, Sapienza Università di Roma, Rome, Italy.,Dipartimento di Scienze Biochimiche A. Rossi Fanelli, Sapienza Università di Roma, Rome, Italy.,Institute of Molecular Biology and Pathology, National Research Council, Rome, Italy
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33
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Kuzikov AV, Masamrekh RA, Archakov AI, Shumyantseva VV. Methods for Determination of Functional Activity of Cytochrome P450 Isoenzymes. BIOCHEMISTRY MOSCOW-SUPPLEMENT SERIES B-BIOMEDICAL CHEMISTRY 2018. [DOI: 10.1134/s1990750818030046] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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34
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Wong NR, Liu X, Lloyd H, Colthart AM, Ferrazzoli AE, Cooper DL, Zhuang Y, Esquea P, Futcher J, Pochapsky TM, Matthews JM, Pochapsky TC. A new approach to understanding structure-function relationships in cytochromes P450 by targeting terpene metabolism in the wild. J Inorg Biochem 2018; 188:96-101. [PMID: 30170307 DOI: 10.1016/j.jinorgbio.2018.08.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 07/24/2018] [Accepted: 08/03/2018] [Indexed: 01/30/2023]
Abstract
A strategy for elucidating sequence determinants of function in the class of cytochrome P450 (CYP) enzymes that catalyze the first steps of terpene metabolism in wild microbiomes is described. Wild organisms that can use camphor, terpineol, pinene and limonene were isolated from soils rich in coniferous waste. Cell free extracts and growth beers were analyzed by gas chromatography/mass spectrometry to identify primary oxidative metabolites. For one organism, Pseudomonas nitroreducens TPJM, a cytochrome P450 (CYP108B1) isolated from cell free extracts was demonstrated to catalyze the oxidation of α-terpineol in assays combining the native ferredoxin and putidaredoxin reductase, and the resulting oxidation products identified by gas chromatography/mass spectrometry. Shotgun sequencing of PnTPJM identified four candidate P450 genes, including an apparently fragmentary gene with a high degree of homology with the known enzyme CYP108 (P450terp).
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Affiliation(s)
- Nathan R Wong
- Department of Biochemistry, Brandeis University, 415 South St., Waltham, MA 02454-9110, United States of America
| | - Xinyue Liu
- Department of Chemistry, Brandeis University, 415 South St., Waltham, MA 02454-9110, United States of America
| | - Hannah Lloyd
- Department of Biology, Brandeis University, 415 South St., Waltham, MA 02454-9110, United States of America
| | - Allison M Colthart
- Department of Biochemistry, Brandeis University, 415 South St., Waltham, MA 02454-9110, United States of America
| | - Alexander E Ferrazzoli
- Department of Biology, Brandeis University, 415 South St., Waltham, MA 02454-9110, United States of America
| | - Deani L Cooper
- Department of Biology, Brandeis University, 415 South St., Waltham, MA 02454-9110, United States of America
| | - Yihao Zhuang
- Department of Biochemistry, Brandeis University, 415 South St., Waltham, MA 02454-9110, United States of America
| | - Phillix Esquea
- Department of Chemistry, Brandeis University, 415 South St., Waltham, MA 02454-9110, United States of America
| | - Jeffrey Futcher
- Department of Chemistry, Brandeis University, 415 South St., Waltham, MA 02454-9110, United States of America
| | - Theodore M Pochapsky
- Malden Catholic High School, 90 Crystal St., Malden, MA 02148, United States of America
| | - Jeffrey M Matthews
- Malden Catholic High School, 90 Crystal St., Malden, MA 02148, United States of America
| | - Thomas C Pochapsky
- Department of Biochemistry, Brandeis University, 415 South St., Waltham, MA 02454-9110, United States of America; Department of Chemistry, Brandeis University, 415 South St., Waltham, MA 02454-9110, United States of America.
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35
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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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Li X, Xu Y, Lai L, Pei J. Prediction of Human Cytochrome P450 Inhibition Using a Multitask Deep Autoencoder Neural Network. Mol Pharm 2018; 15:4336-4345. [DOI: 10.1021/acs.molpharmaceut.8b00110] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Xiang Li
- Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
- BNLMS, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Youjun Xu
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Luhua Lai
- Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
- BNLMS, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Jianfeng Pei
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
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Tavanti M, Porter JL, Levy CW, Gómez Castellanos JR, Flitsch SL, Turner NJ. The crystal structure of P450-TT heme-domain provides the first structural insights into the versatile class VII P450s. Biochem Biophys Res Commun 2018; 501:846-850. [PMID: 29738765 DOI: 10.1016/j.bbrc.2018.05.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 05/02/2018] [Indexed: 02/06/2023]
Abstract
The first crystal structure of a class VII P450, CYP116B46 from Tepidiphilus thermophilus, has been solved at 1.9 Å resolution. The structure reveals overall conservation of the P450-fold and a water conduit around the I-helix. Active site residues have been identified and sequence comparisons have been made with other class VII enzymes. A structure similarity search demonstrated that the P450-TT structure is similar to enzymes capable of oxy-functionalization of fatty acids, terpenes, macrolides, steroids and statins. The insight gained from solving this structure will provide a guideline for future engineering and modelling studies on this catalytically promiscuous class of enzymes.
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Affiliation(s)
- Michele Tavanti
- Manchester Institute of Biotechnology (MIB), School of Chemistry, The University of Manchester, 131Princess Street, M1 7DN, Manchester, United Kingdom
| | - Joanne L Porter
- Manchester Institute of Biotechnology (MIB), School of Chemistry, The University of Manchester, 131Princess Street, M1 7DN, Manchester, United Kingdom
| | - Colin W Levy
- Manchester Institute of Biotechnology (MIB), School of Chemistry, The University of Manchester, 131Princess Street, M1 7DN, Manchester, United Kingdom
| | - J Rubén Gómez Castellanos
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Via Ferrata 9, 27100, Pavia, Italy
| | - Sabine L Flitsch
- Manchester Institute of Biotechnology (MIB), School of Chemistry, The University of Manchester, 131Princess Street, M1 7DN, Manchester, United Kingdom.
| | - Nicholas J Turner
- Manchester Institute of Biotechnology (MIB), School of Chemistry, The University of Manchester, 131Princess Street, M1 7DN, Manchester, United Kingdom.
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38
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Kuzikov AV, Masamrekh RA, Archakov AI, Shumyantseva VV. [Methods for determining of cytochrome P450 isozymes functional activity]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2018; 64:149-168. [PMID: 29723145 DOI: 10.18097/pbmc20186402149] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The review is dedicated to modern methods and technologies for determining of cytochrome P450 isozymes functional activity, such as absorbance and fluorescent spectroscopy, electron paramagnetic resonance (EPR), nuclear magnetic resonance (NMR), Raman, Mossbauer, and X-ray spectroscopy, surface plasmon resonance (SPR), atomic force microscopy (AFM). Methods of molecular genetic analysis were reviewed from personalized medicine point of view. The use of chromate-mass-spectrometric methods for cytochrome P450-dependent catalytic reactions' products was discussed. The review covers modern electrochemical systems based on cytochrome P450 isozymes for their catalytic activity analysis, their use in practice and further development perspectives for experimental pharmacology, biotechnology and translational medicine.
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Affiliation(s)
- A V Kuzikov
- Institute of Biomedical Chemistry, Moscow, Russia; Pirogov Russian National Research Medical University (RNRMU), Moscow, Russia
| | - R A Masamrekh
- Institute of Biomedical Chemistry, Moscow, Russia; Pirogov Russian National Research Medical University (RNRMU), Moscow, Russia
| | - A I Archakov
- Institute of Biomedical Chemistry, Moscow, Russia; Pirogov Russian National Research Medical University (RNRMU), Moscow, Russia
| | - V V Shumyantseva
- Institute of Biomedical Chemistry, Moscow, Russia; Pirogov Russian National Research Medical University (RNRMU), Moscow, Russia
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39
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Asciutto EK, Pochapsky TC. Some Surprising Implications of NMR-directed Simulations of Substrate Recognition and Binding by Cytochrome P450 cam (CYP101A1). J Mol Biol 2018; 430:1295-1310. [PMID: 29596916 DOI: 10.1016/j.jmb.2018.03.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 03/19/2018] [Accepted: 03/19/2018] [Indexed: 02/05/2023]
Abstract
Cytochrome P450cam (CYP101A1) catalyzes the stereospecific 5-exo hydroxylation of d-camphor by molecular oxygen. Previously, residual dipolar couplings measured for backbone amide 1H-15N correlations in both substrate-free and bound forms of CYP101A1 were used as restraints in soft annealing molecular dynamic simulations in order to identify average conformations of the enzyme with and without substrate bound. Multiple substrate-dependent conformational changes remote from the enzyme active site were identified, and site-directed mutagenesis and activity assays confirmed the importance of these changes in substrate recognition. The current work makes use of perturbation response scanning (PRS) and umbrella sampling molecular dynamic of the residual dipolar coupling-derived CYP101A1 structures to probe the roles of remote structural features in enforcing the regio- and stereospecific nature of the hydroxylation reaction catalyzed by CYP101A1. An improper dihedral angle Ψ was defined and used to maintain substrate orientation in the CYP101A1 active site, and it was observed that different values of Ψ result in different PRS response maps. Umbrella sampling methods show that the free energy of the system is sensitive to Ψ, and bound substrate forms an important mechanical link in the transmission of mechanical coupling through the enzyme structure. Finally, a qualitative approach to interpreting PRS maps in terms of the roles of secondary structural features is proposed.
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Affiliation(s)
- Eliana K Asciutto
- School of Science and Technology, UNSAM and CONICET, Campus Migueletes, 25 de Mayo y Francia, Buenos Aires, Argentina
| | - Thomas C Pochapsky
- Department of Chemistry and Rosenstiel Basic Biomedical Sciences Research Institute, MS 015, Brandeis University, 415 South St., Waltham, MA 02454-9110, USA.
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40
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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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41
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Tietz DR, Colthart AM, Sondej Pochapsky S, Pochapsky TC. Substrate recognition by two different P450s: Evidence for conserved roles in a common fold. Sci Rep 2017; 7:13581. [PMID: 29051575 PMCID: PMC5648816 DOI: 10.1038/s41598-017-14011-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 10/04/2017] [Indexed: 11/17/2022] Open
Abstract
Cytochrome P450 monooxygenases CYP101A1 and MycG catalyze regio- and stereospecific oxidations of their respective substrates, d-camphor and mycinamicin IV. Despite the low sequence homology between the two enzymes (29% identity) and differences in size and hydrophobicity of their substrates, the conformational changes that occur upon substrate binding in both enzymes as determined by solution NMR methods show some striking similarities. Many of the same secondary structural features in both enzymes are perturbed, suggesting the existence of a common mechanism for substrate binding and recognition in the P450 superfamily.
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Affiliation(s)
- Drew R Tietz
- Department of Chemistry, Brandeis University, MS 015, 415 South St, Waltham, MA, 02453, USA
| | - Allison M Colthart
- Department of Biochemistry and the Rosenstiel Basic Medical Sciences Research Institute, Brandeis University, 415 South St., Waltham, MA, 02453, USA
| | - Susan Sondej Pochapsky
- Department of Chemistry, Brandeis University, MS 015, 415 South St, Waltham, MA, 02453, USA
| | - Thomas C Pochapsky
- Department of Chemistry, Brandeis University, MS 015, 415 South St, Waltham, MA, 02453, USA. .,Department of Biochemistry and the Rosenstiel Basic Medical Sciences Research Institute, Brandeis University, 415 South St., Waltham, MA, 02453, USA.
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42
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Tabassum R. Molecular cloning and 3D model of first cytochrome P450 from CYP3A subfamily in saltwater crocodile (Crocodylus porosus). Biochem Biophys Res Commun 2017; 516:1046-1052. [PMID: 29054410 DOI: 10.1016/j.bbrc.2017.10.079] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 10/15/2017] [Indexed: 10/18/2022]
Abstract
Cytochrome P450s (CYPs) play critical role in oxidative metabolism of numerous xenobiotics and endogenous compounds. The first CYP3A subfamily member in saltwater crocodile has been cloned and modelled for three-dimensional (3D) structure. The full-length cDNA was obtained employing reverse transcription polymerase chain reaction (RT-PCR) strategy and rapid amplification of cDNA ends (RACE). The cDNA sequence of 1659 nucleotides includes 132 nucleotides from 5' untranslated region (UTR), an open reading frame of 1527 nucleotides encoding 509 amino acids designated as CYP3A163. The alignment of CYP3A163 sequence with CYP3A subfamily across the lineages exhibit the loss of 1 residue in birds and 7 residues in mammals in comparison to reptiles suggesting the adaptation processes during evolution. The amino acid identity of CYP3A163 with Alligator mississippiensis CYP3A77 and Homo sapiens CYP3A4 is 91% and 62% respectively. The 3D structure of CYP3A163 modelled using human CYP3A4 structure as a template with Phyre2 software, represents high similarity with its functionally important motifs and catalytic domain. Both sequence and structure of CYP3A163 display the common and conserved features of CYP3A subfamily. Overall, this study provides primary molecular and structural data of CYP3A163 required to investigate the xenobiotic metabolism in saltwater crocodiles.
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Affiliation(s)
- Rabia Tabassum
- Faculty of Engineering, Health, Science and Environment, Charles Darwin University, Darwin, NT, 0909 Australia.
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43
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Pochapsky TC, Wong N, Zhuang Y, Futcher J, Pandelia ME, Teitz DR, Colthart AM. NADH reduction of nitroaromatics as a probe for residual ferric form high-spin in a cytochrome P450. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1866:126-133. [PMID: 28473297 DOI: 10.1016/j.bbapap.2017.04.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Revised: 04/19/2017] [Accepted: 04/29/2017] [Indexed: 10/19/2022]
Abstract
The existence of a substrate-sensitive equilibrium between high spin (S=5/2) and low spin (S=1/2) ferric iron is a well-established phenomenon in the cytochrome P450 (CYP) superfamily, although its origins are still a subject of discussion. A series of mutations that strongly perturb the spin state equilibrium in the camphor hydroxylase CYP101A1 were recently described (Colthart et al., Sci. Rep. 6, 22035 (2016)). Wild type CYP101A1 as well as some CYP101A1 mutants are herein shown to be capable of catalyzing the reduction of nitroacetophenones by NADH to the corresponding anilino compounds (nitroreductase or NRase activity). The distinguishing characteristic between those mutants that catalyze the reduction and those that cannot appears to be the extent to which residual high spin form exists in the absence of the native substrate d-camphor, with those showing the largest spin state shifts upon camphor binding also exhibiting NRase activity. Optical and EPR spectroscopy was used to further examine these phenomena. These results suggest that reduction of nitroaromatics may provide a useful probe of residual high spin states in the CYP superfamily. 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)
- Thomas C Pochapsky
- Department of Chemistry, Brandeis University, 415 South St., Waltham, MA 02454-9110, USA.
| | - Nathan Wong
- Department of Biochemistry, Brandeis University, 415 South St., Waltham, MA 02454-9110, USA
| | - Yihao Zhuang
- Department of Biochemistry, Brandeis University, 415 South St., Waltham, MA 02454-9110, USA
| | - Jeffrey Futcher
- Department of Chemistry, Brandeis University, 415 South St., Waltham, MA 02454-9110, USA
| | - Maria-Eirini Pandelia
- Department of Biochemistry, Brandeis University, 415 South St., Waltham, MA 02454-9110, USA
| | - Drew R Teitz
- Department of Chemistry, Brandeis University, 415 South St., Waltham, MA 02454-9110, USA
| | - Allison M Colthart
- Department of Biochemistry, Brandeis University, 415 South St., Waltham, MA 02454-9110, USA
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Yadav R, Petrunak EM, Estrada DF, Scott EE. Structural insights into the function of steroidogenic cytochrome P450 17A1. Mol Cell Endocrinol 2017; 441:68-75. [PMID: 27566228 PMCID: PMC5235955 DOI: 10.1016/j.mce.2016.08.035] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 08/19/2016] [Accepted: 08/22/2016] [Indexed: 12/12/2022]
Abstract
Cytochrome P450 17A1 (CYP17A1) operates at the core of human steroidogenesis, directing precursors into mineralocorticoids, glucocorticoids, or sex steroids. Although the 17α-hydroxylase and 17,20-lyase activities of this dual function enzyme have been investigated extensively, until recently no CYP17A1 structures were available to inform our understanding. Structures of CYP17A1 with a range of steroidal inhibitors and substrates are now available. This review relates functional knowledge of this enzyme to structural features defining the selective differentiation between its various substrates. While both hydroxylase and lyase substrates have similar orientations with respect to the heme, subtle differences in hydrogen bonding between CYP17A1 and the C3 substituent at the opposite end of ligands appear to correlate with differential substrate utilization and product formation. Complementary structural information from solution NMR supports cytochrome b5 allosteric modulation of the lyase reaction, implicating regions involved in ligand access to the otherwise buried active site.
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Affiliation(s)
- Rahul Yadav
- Department of Medicinal Chemistry, 1251 Wescoe Hall Dr., The University of Kansas, Lawrence, KS 66045, USA
| | - Elyse M Petrunak
- Department of Medicinal Chemistry, 1251 Wescoe Hall Dr., The University of Kansas, Lawrence, KS 66045, USA
| | - D Fernando Estrada
- Department of Medicinal Chemistry, 1251 Wescoe Hall Dr., The University of Kansas, Lawrence, KS 66045, USA
| | - Emily E Scott
- Department of Medicinal Chemistry, 1251 Wescoe Hall Dr., The University of Kansas, Lawrence, KS 66045, USA.
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45
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Reed JR, Backes WL. Physical Studies of P450-P450 Interactions: Predicting Quaternary Structures of P450 Complexes in Membranes from Their X-ray Crystal Structures. Front Pharmacol 2017; 8:28. [PMID: 28194112 PMCID: PMC5276844 DOI: 10.3389/fphar.2017.00028] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 01/16/2017] [Indexed: 01/15/2023] Open
Abstract
Cytochrome P450 enzymes, which catalyze oxygenation reactions of both exogenous and endogenous chemicals, are membrane bound proteins that require interaction with their redox partners in order to function. Those responsible for drug and foreign compound metabolism are localized primarily in the endoplasmic reticulum of liver, lung, intestine, and other tissues. More recently, the potential for P450 enzymes to exist as supramolecular complexes has been shown by the demonstration of both homomeric and heteromeric complexes. The P450 units in these complexes are heterogeneous with respect to their distribution and function, and the interaction of different P450s can influence P450-specific metabolism. The goal of this review is to examine the evidence supporting the existence of physical complexes among P450 enzymes. Additionally, the review examines the crystal lattices of different P450 enzymes derived from X-ray diffraction data to make assumptions regarding possible quaternary structures in membranes and in turn, to predict how the quaternary structures could influence metabolism and explain the functional effects of specific P450-P450 interactions.
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Affiliation(s)
- James R Reed
- Department of Pharmacology and Experimental Therapeutics, Louisiana State University Health Sciences Center New Orleans LA, USA
| | - Wayne L Backes
- Department of Pharmacology and Experimental Therapeutics, Louisiana State University Health Sciences Center New Orleans LA, USA
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46
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Davydov DR, Yang Z, Davydova N, Halpert JR, Hubbell WL. Conformational Mobility in Cytochrome P450 3A4 Explored by Pressure-Perturbation EPR Spectroscopy. Biophys J 2016; 110:1485-1498. [PMID: 27074675 DOI: 10.1016/j.bpj.2016.02.026] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Revised: 12/04/2015] [Accepted: 02/15/2016] [Indexed: 11/18/2022] Open
Abstract
We used high hydrostatic pressure as a tool for exploring the conformational landscape of human cytochrome P450 3A4 (CYP3A4) by electron paramagnetic resonance and fluorescence spectroscopy. Site-directed incorporation of a luminescence resonance energy transfer donor-acceptor pair allowed us to identify a pressure-dependent equilibrium between two states of the enzyme, where an increase in pressure increased the spatial separation between the two distantly located fluorophores. This transition is characterized by volume change (ΔV°) and P1/2 values of -36.8 ± 5.0 mL/mol and 1.45 ± 0.33 kbar, respectively, which corresponds to a Keq° of 0.13 ± 0.06, so that only 15% of the enzyme adopts the pressure-promoted conformation at ambient pressure. This pressure-promoted displacement of the equilibrium is eliminated by the addition of testosterone, an allosteric activator. Using site-directed spin labeling, we demonstrated that the pressure- and testosterone-sensitive transition is also revealed by pressure-induced changes in the electron paramagnetic resonance spectra of a nitroxide side chain placed at position 85 or 409 of the enzyme. Furthermore, we observed a pressure-induced displacement of the emission maxima of a solvatochromic fluorophore (7-diethylamino-3-((((2-maleimidyl)ethyl)amino)carbonyl) coumarin) placed at the same positions, which suggests a relocation to a more polar environment. Taken together, the results reveal an effector-dependent conformational equilibrium between open and closed states of CYP3A4 that involves a pronounced change at the interface between the region of α-helices A/A' and the meander loop of the enzyme, where residues 85 and 409 are located. Our study demonstrates the high potential of pressure-perturbation strategies for studying protein conformational landscapes.
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Affiliation(s)
- Dmitri R Davydov
- Department of Chemistry, Washington State University, Pullman, Washington; V. N. Orekhovich Institute of Biomedical Chemistry, Russian Academy of Medical Sciences, Moscow, Russia.
| | - Zhongyu Yang
- Jules Stein Eye Institute, University of California, Los Angeles, Los Angeles, California; Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California
| | - Nadezhda Davydova
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California
| | - James R Halpert
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California
| | - Wayne L Hubbell
- Jules Stein Eye Institute, University of California, Los Angeles, Los Angeles, California; Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California
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47
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Hoffmann SM, Danesh-Azari HR, Spandolf C, Weissenborn MJ, Grogan G, Hauer B. Structure-Guided Redesign of CYP153AM.aqfor the Improved Terminal Hydroxylation of Fatty Acids. ChemCatChem 2016. [DOI: 10.1002/cctc.201600680] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Sara M. Hoffmann
- Institute of Technical Biochemistry; Universität Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Hamid-Reza Danesh-Azari
- York Structural Biology Laboratory; Department of Chemistry; University of York; YO10 5DD York United Kingdom
| | - Claudia Spandolf
- York Structural Biology Laboratory; Department of Chemistry; University of York; YO10 5DD York United Kingdom
| | - Martin J. Weissenborn
- Institute of Technical Biochemistry; Universität Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Gideon Grogan
- York Structural Biology Laboratory; Department of Chemistry; University of York; YO10 5DD York United Kingdom
| | - Bernhard Hauer
- Institute of Technical Biochemistry; Universität Stuttgart; Allmandring 31 70569 Stuttgart Germany
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48
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Ordered chimerogenesis applied to CYP2B P450 enzymes. Biochim Biophys Acta Gen Subj 2016; 1860:1395-403. [DOI: 10.1016/j.bbagen.2016.03.028] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 02/12/2016] [Accepted: 03/20/2016] [Indexed: 12/11/2022]
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Almeida D, Maldonado E, Khan I, Silva L, Gilbert MTP, Zhang G, Jarvis ED, O'Brien SJ, Johnson WE, Antunes A. Whole-Genome Identification, Phylogeny, and Evolution of the Cytochrome P450 Family 2 (CYP2) Subfamilies in Birds. Genome Biol Evol 2016; 8:1115-31. [PMID: 26979796 PMCID: PMC4860681 DOI: 10.1093/gbe/evw041] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/27/2016] [Indexed: 12/19/2022] Open
Abstract
The cytochrome P450 (CYP) superfamily defends organisms from endogenous and noxious environmental compounds, and thus is crucial for survival. However, beyond mammals the molecular evolution of CYP2 subfamilies is poorly understood. Here, we characterized the CYP2 family across 48 avian whole genomes representing all major extant bird clades. Overall, 12 CYP2 subfamilies were identified, including the first description of the CYP2F, CYP2G, and several CYP2AF genes in avian genomes. Some of the CYP2 genes previously described as being lineage-specific, such as CYP2K and CYP2W, are ubiquitous to all avian groups. Furthermore, we identified a large number of CYP2J copies, which have been associated previously with water reabsorption. We detected positive selection in the avian CYP2C, CYP2D, CYP2H, CYP2J, CYP2K, and CYP2AC subfamilies. Moreover, we identified new substrate recognition sites (SRS0, SRS2_SRS3, and SRS3.1) and heme binding areas that influence CYP2 structure and function of functional importance as under significant positive selection. Some of the positively selected sites in avian CYP2D are located within the same SRS1 region that was previously linked with the metabolism of plant toxins. Additionally, we find that selective constraint variations in some avian CYP2 subfamilies are consistently associated with different feeding habits (CYP2H and CYP2J), habitats (CYP2D, CYP2H, CYP2J, and CYP2K), and migratory behaviors (CYP2D, CYP2H, and CYP2J). Overall, our findings indicate that there has been active enzyme site selection on CYP2 subfamilies and differential selection associated with different life history traits among birds.
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Affiliation(s)
- Daniela Almeida
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Portugal Department of Biology, Faculty of Sciences, University of Porto, Portugal
| | - Emanuel Maldonado
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Portugal
| | - Imran Khan
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Portugal Department of Biology, Faculty of Sciences, University of Porto, Portugal
| | - Liliana Silva
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Portugal Department of Biology, Faculty of Sciences, University of Porto, Portugal
| | - M Thomas P Gilbert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Guojie Zhang
- China National GeneBank, BGI-Shenzhen, Shenzen, China Centre for Social Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Erich D Jarvis
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark Howard Hughes Medical Institute, Chevy Chase, Maryland
| | - Stephen J O'Brien
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, Russia Oceanographic Center, Nova Southeastern University, Ft Lauderdale
| | - Warren E Johnson
- National Zoological Park, Smithsonian Conservation Biology Institute, Washington DC
| | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Portugal Department of Biology, Faculty of Sciences, University of Porto, Portugal
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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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