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Zhang X, Feng Y, Hua Y, Zhang C, Fang B, Long X, Pan Y, Gao B, Zhang JZH, Li L, Ni H, Zhang L. Biosynthesis of eriodictyol in citrus waster by endowing P450BM3 activity of naringenin hydroxylation. Appl Microbiol Biotechnol 2024; 108:84. [PMID: 38189953 PMCID: PMC10787690 DOI: 10.1007/s00253-023-12867-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 09/20/2023] [Accepted: 10/13/2023] [Indexed: 01/09/2024]
Abstract
The flavonoid naringenin is abundantly present in pomelo peels, and the unprocessed naringenin in wastes is not friendly for the environment once discarded directly. Fortunately, the hydroxylated product of eriodictyol from naringenin exhibits remarkable antioxidant and anticancer properties. The P450s was suggested promising for the bioconversion of the flavonoids, but less naturally existed P450s show hydroxylation activity to C3' of the naringenin. By well analyzing the catalytic mechanism and the conformations of the naringenin in P450, we proposed that the intermediate Cmpd I ((porphyrin)Fe = O) is more reasonable as key conformation for the hydrolyzation, and the distance between C3'/C5' of naringenin to the O atom of CmpdI determines the hydroxylating activity for the naringenin. Thus, the "flying kite model" that gradually drags the C-H bond of the substrate to the O atom of CmpdI was put forward for rational design. With ab initio design, we successfully endowed the self-sufficient P450-BM3 hydroxylic activity to naringenin and obtained mutant M5-5, with kcat, Km, and kcat/Km values of 230.45 min-1, 310.48 µM, and 0.742 min-1 µM-1, respectively. Furthermore, the mutant M4186 was screened with kcat/Km of 4.28-fold highly improved than the reported M13. The M4186 also exhibited 62.57% yield of eriodictyol, more suitable for the industrial application. This study provided a theoretical guide for the rational design of P450s to the nonnative compounds. KEY POINTS: •The compound I is proposed as the starting point for the rational design of the P450BM3 •"Flying kite model" is proposed based on the distance between O of Cmpd I and C3'/C5' of naringenin •Mutant M15-5 with 1.6-fold of activity than M13 was obtained by ab initio modification.
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Affiliation(s)
- Xingyi Zhang
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, 361021, China
| | - Yinghui Feng
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China
| | - Yuanzhe Hua
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, 361021, China
| | - Chuanxi Zhang
- Department of Micro/Nano Electronics, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Bohuan Fang
- Department of Micro/Nano Electronics, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiang Long
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, 361021, China
| | - Yue Pan
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China
| | - Bei Gao
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - John Z H Zhang
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, 200062, China
| | - Lijun Li
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, 361021, China
| | - Hui Ni
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, 361021, China.
| | - Lujia Zhang
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China.
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, 200062, China.
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Beech JL, Maurya AK, Rodrigues da Silva R, Akpoto E, Asundi A, Fecko JA, Yennawar NH, Sarangi R, Tassone C, Weiss TM, DuBois JL. Understanding the stability of a plastic-degrading Rieske iron oxidoreductase system. Protein Sci 2024; 33:e4997. [PMID: 38723110 PMCID: PMC11081424 DOI: 10.1002/pro.4997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 03/01/2024] [Accepted: 04/06/2024] [Indexed: 05/13/2024]
Abstract
Rieske oxygenases (ROs) are a diverse metalloenzyme class with growing potential in bioconversion and synthetic applications. We postulated that ROs are nonetheless underutilized because they are unstable. Terephthalate dioxygenase (TPADO PDB ID 7Q05) is a structurally characterized heterohexameric α3β3 RO that, with its cognate reductase (TPARED), catalyzes the first intracellular step of bacterial polyethylene terephthalate plastic bioconversion. Here, we showed that the heterologously expressed TPADO/TPARED system exhibits only ~300 total turnovers at its optimal pH and temperature. We investigated the thermal stability of the system and the unfolding pathway of TPADO through a combination of biochemical and biophysical approaches. The system's activity is thermally limited by a melting temperature (Tm) of 39.9°C for the monomeric TPARED, while the independent Tm of TPADO is 50.8°C. Differential scanning calorimetry revealed a two-step thermal decomposition pathway for TPADO with Tm values of 47.6 and 58.0°C (ΔH = 210 and 509 kcal mol-1, respectively) for each step. Temperature-dependent small-angle x-ray scattering and dynamic light scattering both detected heat-induced dissociation of TPADO subunits at 53.8°C, followed by higher-temperature loss of tertiary structure that coincided with protein aggregation. The computed enthalpies of dissociation for the monomer interfaces were most congruent with a decomposition pathway initiated by β-β interface dissociation, a pattern predicted to be widespread in ROs. As a strategy for enhancing TPADO stability, we propose prioritizing the re-engineering of the β subunit interfaces, with subsequent targeted improvements of the subunits.
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Affiliation(s)
- Jessica Lusty Beech
- Department of Chemistry and BiochemistryMontana State UniversityBozemanMontanaUSA
| | - Anjani K. Maurya
- Stanford Synchrotron Radiation LightsourceSLAC National Accelerator LaboratoryMenlo ParkCaliforniaUSA
| | | | - Emmanuel Akpoto
- Department of Chemistry and BiochemistryMontana State UniversityBozemanMontanaUSA
| | - Arun Asundi
- Stanford Synchrotron Radiation LightsourceSLAC National Accelerator LaboratoryMenlo ParkCaliforniaUSA
| | - Julia Ann Fecko
- The Huck Institutes of the Life SciencesThe Pennsylvania State University, University ParkState CollegePennsylvaniaUSA
| | - Neela H. Yennawar
- The Huck Institutes of the Life SciencesThe Pennsylvania State University, University ParkState CollegePennsylvaniaUSA
| | - Ritimukta Sarangi
- Stanford Synchrotron Radiation LightsourceSLAC National Accelerator LaboratoryMenlo ParkCaliforniaUSA
| | - Christopher Tassone
- Stanford Synchrotron Radiation LightsourceSLAC National Accelerator LaboratoryMenlo ParkCaliforniaUSA
| | - Thomas M. Weiss
- Stanford Synchrotron Radiation LightsourceSLAC National Accelerator LaboratoryMenlo ParkCaliforniaUSA
| | - Jennifer L. DuBois
- Department of Chemistry and BiochemistryMontana State UniversityBozemanMontanaUSA
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Alemany-Perna B, Tamarit J, Cabiscol E, Delaspre F, Miguela A, Huertas-Pons JM, Quiroga-Varela A, Merchan Ruiz M, López Domínguez D, Ramió I Torrentà L, Genís D, Ros J. Calcitriol Treatment Is Safe and Increases Frataxin Levels in Friedreich Ataxia Patients. Mov Disord 2024. [PMID: 38696306 DOI: 10.1002/mds.29808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 05/04/2024] Open
Abstract
BACKGROUND Calcitriol, the active form of vitamin D (also known as 1,25-dihydroxycholecalciferol), improves the phenotype and increases frataxin levels in cell models of Friedreich ataxia (FRDA). OBJECTIVES Based on these results, we aimed measuring the effects of a calcitriol dose of 0.25 mcg/24h in the neurological function and frataxin levels when administered to FRDA patients for a year. METHODS 20 FRDA patients where recluted and 15 patients completed the treatment for a year. Evaluations of neurological function changes (SARA scale, 9-HPT, 8-MWT, PATA test) and quality of life (Barthel Scale and Short Form (36) Health Survey [SF-36] quality of life questionnaire) were performed. Frataxin amounts were measured in isolated platelets obtained from these FRDA patients, from heterozygous FRDA carriers (relatives of the FA patients) and from non-heterozygous sex and age matched controls. RESULTS Although the patients did not experience any observable neurological improvement, there was a statistically significant increase in frataxin levels from initial values, 5.5 to 7.0 pg/μg after 12 months. Differences in frataxin levels referred to total protein levels were observed among sex- and age-matched controls (18.1 pg/μg), relative controls (10.1 pg/μg), and FRDA patients (5.7 pg/μg). The treatment was well tolerated by most patients, and only some of them experienced minor adverse effects at the beginning of the trial. CONCLUSIONS Calcitriol dosage used (0.25 mcg/24 h) is safe for FRDA patients, and it increases frataxin levels. We cannot rule out that higher doses administered longer could yield neurological benefits. © 2024 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Berta Alemany-Perna
- Ataxia Unit, Neurology Service, ICS/IAS, Hospital Josep Trueta/Hospital Santa Caterina, Girona/Salt, Spain
- Department of Medical Sciences, University of Girona (UdG), Girona, Spain
- Neurodegeneration and Neuroinflammacion Group, Institut d'Investigació Biomèdica de Girona (IDIBGI), Girona, Spain
| | - Jordi Tamarit
- Departament de Ciències Mèdiques Bàsiques, Institut de Recerca Biomèdica de Lleida (IRBLleida), Universitat de Lleida, Lleida, Spain
| | - Elisa Cabiscol
- Departament de Ciències Mèdiques Bàsiques, Institut de Recerca Biomèdica de Lleida (IRBLleida), Universitat de Lleida, Lleida, Spain
| | - Fabien Delaspre
- Departament de Ciències Mèdiques Bàsiques, Institut de Recerca Biomèdica de Lleida (IRBLleida), Universitat de Lleida, Lleida, Spain
| | - Albert Miguela
- Neurodegeneration and Neuroinflammacion Group, Institut d'Investigació Biomèdica de Girona (IDIBGI), Girona, Spain
| | - Joana Maria Huertas-Pons
- Neurodegeneration and Neuroinflammacion Group, Institut d'Investigació Biomèdica de Girona (IDIBGI), Girona, Spain
| | - Ana Quiroga-Varela
- Neurodegeneration and Neuroinflammacion Group, Institut d'Investigació Biomèdica de Girona (IDIBGI), Girona, Spain
| | - Miguel Merchan Ruiz
- Neurodegeneration and Neuroinflammacion Group, Institut d'Investigació Biomèdica de Girona (IDIBGI), Girona, Spain
| | - Daniel López Domínguez
- Ataxia Unit, Neurology Service, ICS/IAS, Hospital Josep Trueta/Hospital Santa Caterina, Girona/Salt, Spain
- Department of Medical Sciences, University of Girona (UdG), Girona, Spain
- Neurodegeneration and Neuroinflammacion Group, Institut d'Investigació Biomèdica de Girona (IDIBGI), Girona, Spain
| | - Lluís Ramió I Torrentà
- Department of Medical Sciences, University of Girona (UdG), Girona, Spain
- Neurology Service, ICS/IAS, Hospital Josep Trueta/Hospital Santa Caterina, Girona/Salt, Neurodegeneration and Neuroinflammacion Group (IDIBGI), Girona/Salt, Spain
| | - David Genís
- Neurodegeneration and Neuroinflammacion Group, Institut d'Investigació Biomèdica de Girona (IDIBGI), Girona, Spain
| | - Joaquim Ros
- Departament de Ciències Mèdiques Bàsiques, Institut de Recerca Biomèdica de Lleida (IRBLleida), Universitat de Lleida, Lleida, Spain
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Yadav S, Shaik S, Dubey KD. On the engineering of reductase-based-monooxygenase activity in CYP450 peroxygenases. Chem Sci 2024; 15:5174-5186. [PMID: 38577361 PMCID: PMC10988616 DOI: 10.1039/d3sc06538c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 03/06/2024] [Indexed: 04/06/2024] Open
Abstract
Recent bioengineering of CYP450OleT shows that peroxide-based CYP450OleT can be converted to a reductase-based self-sufficient enzyme, which is capable of showing efficient hydroxylation and decarboxylation activity for a wide range of substrates. The so-generated enzyme creates several mechanistic puzzles: (A) as CYP450 peroxygenases lack the conventional acid-alcohol pair, what is the source of two protons that are required to create the ultimate oxidant Cpd I? (B) Why is it only CYP450OleT that shows the reductase-based activity but no other CYP members? The present study provides a mechanistic solution to these puzzles using comprehensive MD simulations and hybrid QM/MM calculations. We show that the fusion of the reductase domain to the heme-binding domain triggers significant conformational rearrangement, which is gated by the propionate side chain, which constitutes a new water aqueduct via the carboxylate end of the substrate that ultimately participates in Cpd I formation. Importantly, such well-synchronized choreographies are controlled by remotely located Tyr359, which senses the fusion of reductase and communicates to the heme domain via non-covalent interactions. These findings provide crucial insights and a broader perspective which enables us to make a verifiable prediction: thus, the catalytic activity is not only limited to the first or second catalytic shell of an enzyme. Furthermore, it is predicted that reinstatement of tyrosine at a similar position in other members of CYP450 peroxygenases can convert these enzymes to reductase-based monooxygenases.
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Affiliation(s)
- Shalini Yadav
- Department of Chemistry, School of Natural Science, Shiv Nadar Institution of Eminence NH91 Tehsil Dadri Greater Noida Uttar Pradesh 201314 India
| | - Sason Shaik
- Institute of Chemistry, The Hebrew University Edmond J. Safra Campus at Givat Ram Jerusalem 9190401 Israel
| | - Kshatresh Dutta Dubey
- Department of Chemistry, School of Natural Science, Shiv Nadar Institution of Eminence NH91 Tehsil Dadri Greater Noida Uttar Pradesh 201314 India
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Khan S, Ansari A, Brachi M, Das D, El Housseini W, Minteer S, Miller AF. Structure, dynamics, and redox reactivity of an all-purpose flavodoxin. J Biol Chem 2024; 300:107122. [PMID: 38417793 PMCID: PMC10979112 DOI: 10.1016/j.jbc.2024.107122] [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: 12/13/2023] [Revised: 02/15/2024] [Accepted: 02/21/2024] [Indexed: 03/01/2024] Open
Abstract
The flavodoxin of Rhodopseudomonas palustris CGA009 (Rp9Fld) supplies highly reducing equivalents to crucial enzymes such as hydrogenase, especially when the organism is iron-restricted. By acquiring those electrons from photodriven electron flow via the bifurcating electron transfer flavoprotein, Rp9Fld provides solar power to vital metabolic processes. To understand Rp9Fld's ability to work with diverse partners, we solved its crystal structure. We observed the canonical flavodoxin (Fld) fold and features common to other long-chain Flds but not all the surface loops thought to recognize partner proteins. Moreover, some of the loops display alternative structures and dynamics. To advance studies of protein-protein associations and conformational consequences, we assigned the 19F NMR signals of all five tyrosines (Tyrs). Our electrochemical measurements show that incorporation of 3-19F-Tyr in place of Tyr has only a modest effect on Rp9Fld's redox properties even though Tyrs flank the flavin on both sides. Meanwhile, the 19F probes demonstrate the expected paramagnetic effect, with signals from nearby Tyrs becoming broadened beyond detection when the flavin semiquinone is formed. However, the temperature dependencies of chemical shifts and linewidths reveal dynamics affecting loops close to the flavin and regions that bind to partners in a variety of systems. These coincide with patterns of amino acid type conservation but not retention of specific residues, arguing against detailed specificity with respect to partners. We propose that the loops surrounding the flavin adopt altered conformations upon binding to partners and may even participate actively in electron transfer.
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Affiliation(s)
- Sharique Khan
- Department of Chemistry, University of Kentucky, Lexington, Kentucky, USA
| | - Ahmadullah Ansari
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Monica Brachi
- Department of Chemistry, University of Utah, Salt Lake City, Utah, USA
| | - Debarati Das
- Department of Chemistry, University of Kentucky, Lexington, Kentucky, USA
| | | | - Shelley Minteer
- Department of Chemistry, University of Utah, Salt Lake City, Utah, USA; Department of Chemistry, Kummer Institute Center for Resource Sustainability, Missouri University of Science and Technology, Rolla, Missouri, USA
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Jordan S, Li B, Traore E, Wu Y, Usai R, Liu A, Xie ZR, Wang Y. Structural and spectroscopic characterization of RufO indicates a new biological role in rufomycin biosynthesis. J Biol Chem 2023; 299:105049. [PMID: 37451485 PMCID: PMC10424215 DOI: 10.1016/j.jbc.2023.105049] [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: 05/23/2023] [Revised: 06/30/2023] [Accepted: 07/10/2023] [Indexed: 07/18/2023] Open
Abstract
Rufomycins constitute a class of cyclic heptapeptides isolated from actinomycetes. They are secondary metabolites that show promising treatment against Mycobacterium tuberculosis infections by inhibiting a novel drug target. Several nonproteinogenic amino acids are integrated into rufomycins, including a conserved 3-nitro-tyrosine. RufO, a cytochrome P450 (CYP)-like enzyme, was proposed to catalyze the formation of 3-nitro-tyrosine in the presence of O2 and NO. To define its biological function, the interaction between RufO and the proposed substrate tyrosine is investigated using various spectroscopic methods that are sensitive to the structural change of a heme center. However, a low- to high-spin state transition and a dramatic increase in the redox potential that are commonly found in CYPs upon ligand binding have not been observed. Furthermore, a 1.89-Å crystal structure of RufO shows that the enzyme has flexible surface regions, a wide-open substrate access tunnel, and the heme center is largely exposed to solvent. Comparison with a closely related nitrating CYP reveals a spacious and hydrophobic distal pocket in RufO, which is incapable of stabilizing a free amino acid. Molecular docking validates the experimental data and proposes a possible substrate. Collectively, our results disfavor tyrosine as the substrate of RufO and point to the possibility that the nitration occurs during or after the assembly of the peptides. This study indicates a new function of the unique nitrating enzyme and provides insights into the biosynthesis of nonribosomal peptides.
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Affiliation(s)
- Stephanie Jordan
- Department of Chemistry, University of Georgia, Athens, Georgia, USA
| | - Bingnan Li
- Department of Chemistry, University of Georgia, Athens, Georgia, USA
| | - Ephrahime Traore
- Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas, USA
| | - Yifei Wu
- School of Electrical and Computer Engineering, University of Georgia, Athens, Georgia, USA
| | - Remigio Usai
- Department of Chemistry, University of Georgia, Athens, Georgia, USA
| | - Aimin Liu
- Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas, USA
| | - Zhong-Ru Xie
- School of Electrical and Computer Engineering, University of Georgia, Athens, Georgia, USA
| | - Yifan Wang
- Department of Chemistry, University of Georgia, Athens, Georgia, USA.
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7
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Sun Y, Huang X, Osawa Y, Chen YE, Zhang H. The Versatile Biocatalyst of Cytochrome P450 CYP102A1: Structure, Function, and Engineering. Molecules 2023; 28:5353. [PMID: 37513226 PMCID: PMC10383305 DOI: 10.3390/molecules28145353] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/07/2023] [Accepted: 07/10/2023] [Indexed: 07/30/2023] Open
Abstract
Wild-type cytochrome P450 CYP102A1 from Bacillus megaterium is a highly efficient monooxygenase for the oxidation of long-chain fatty acids. The unique features of CYP102A1, such as high catalytic activity, expression yield, regio- and stereoselectivity, and self-sufficiency in electron transfer as a fusion protein, afford the requirements for an ideal biocatalyst. In the past three decades, remarkable progress has been made in engineering CYP102A1 for applications in drug discovery, biosynthesis, and biotechnology. The repertoire of engineered CYP102A1 variants has grown tremendously, whereas the substrate repertoire is avalanched to encompass alkanes, alkenes, aromatics, organic solvents, pharmaceuticals, drugs, and many more. In this article, we highlight the major advances in the past five years in our understanding of the structure and function of CYP102A1 and the methodologies used to engineer CYP102A1 for novel applications. The objective is to provide a succinct review of the latest developments with reference to the body of CYP102A1-related literature.
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Affiliation(s)
- Yudong Sun
- Department of Pharmacology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Xiaoqiang Huang
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yoichi Osawa
- Department of Pharmacology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yuqing Eugene Chen
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Haoming Zhang
- Department of Pharmacology, University of Michigan, Ann Arbor, MI 48109, USA
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8
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Ghosh D. Structures and Functions of Human Placental Aromatase and Steroid Sulfatase, Two Key Enzymes in Estrogen Biosynthesis. Steroids 2023; 196:109249. [PMID: 37207843 DOI: 10.1016/j.steroids.2023.109249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 05/12/2023] [Accepted: 05/14/2023] [Indexed: 05/21/2023]
Abstract
Cytochrome P450 aromatase (AROM) and steroid sulfatase (STS) are the two key enzymes for the biosynthesis of estrogens in human, and maintenance of the critical balance between androgens and estrogens. Human AROM, an integral membrane protein of the endoplasmic reticulum, is a member of the cytochrome P450 superfamily. It is the only enzyme to catalyze the conversion of androgens with non-aromatic A-rings to estrogens characterized by the aromatic A-ring. Human STS, also an integral membrane protein of the endoplasmic reticulum, is a Ca2+-dependent enzyme that catalyzes the hydrolysis of sulfate esters of estrone and dehydroepiandrosterone to the unconjugated steroids, the precursors of the most potent forms of estrogens and androgens, namely, 17β-estradiol, 16α,17β-estriol, testosterone and dihydrotestosterone. Expression of these steroidogenic enzymes locally within organs and tissues of the endocrine, reproductive, and central nervous systems is the key for maintaining high levels of the reproductive steroids. The enzymes have been drug targets for the prevention and treatment of diseases associated with steroid hormone excesses, especially in breast, endometrial and prostate malignancies. Both enzymes have been the subjects of vigorous research for the past six decades. In this article, we review the important findings on their structure-function relationships, specifically, the work that began with unravelling of the closely guarded secrets, namely, the 3-D structures, active sites, mechanisms of action, origins of substrate specificity and the basis of membrane integration. Remarkably, these studies were conducted on the enzymes purified in their pristine forms from human placenta, the discarded and their most abundant source. The purification, assay, crystallization, and structure determination methodologies are described. Also reviewed are their functional quaternary organizations, post-translational modifications and the advancements made in the structure-guided inhibitor design efforts. Outstanding questions that still remain open are summarized in closing.
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Affiliation(s)
- Debashis Ghosh
- Department of Pharmacology, State University of New York Upstate Medical University, Syracuse, NY 13210.
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Yu J, Ge J, Yu H, Ye L. Improved Bioproduction of the Nylon 12 Monomer by Combining the Directed Evolution of P450 and Enhancing Heme Synthesis. Molecules 2023; 28:molecules28041758. [PMID: 36838746 PMCID: PMC9963201 DOI: 10.3390/molecules28041758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/04/2023] [Accepted: 02/08/2023] [Indexed: 02/15/2023] Open
Abstract
The nylon 12 (PA12) monomer ω-aminododecanoic acid (ω-AmDDA) could be synthesized from lauric acid (DDA) through multi-enzyme cascade transformation using engineered E. coli, with the P450 catalyzing terminal hydroxylation of DDA as a rate-limiting enzyme. Its activity is jointly determined by the heme domain and the reductase domain. To obtain a P450 mutant with higher activity, directed evolution was conducted using a colorimetric high-throughput screening (HTS) system with DDA as the real substrate. After two rounds of directed evolution, a positive double-site mutant (R14R/D629G) with 90.3% higher activity was obtained. Molecular docking analysis, kinetic parameter determination and protein electrophoresis suggested the improved soluble expression of P450 resulting from the synonymous mutation near the N-terminus and the shortened distance of the electron transfer between FMN and FAD caused by D629G mutation as the major reasons for activity improvement. The significantly increased kcat and unchanged Km provided further evidence for the increase in electron transfer efficiency. Considering the important role of heme in P450, its supply was strengthened by the metabolic engineering of the heme synthesis pathway. By combining P450-directed evolution and enhancing heme synthesis, 2.02 ± 0.03 g/L of ω-AmDDA was produced from 10 mM DDA, with a yield of 93.6%.
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Affiliation(s)
- Jiaming Yu
- Key Laboratory of Biomass Chemical Engineering (Education Ministry), College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310058, China
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310058, China
| | - Jiawei Ge
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310058, China
| | - Hongwei Yu
- Key Laboratory of Biomass Chemical Engineering (Education Ministry), College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310058, China
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310058, China
- Correspondence: (H.Y.); (L.Y.)
| | - Lidan Ye
- Key Laboratory of Biomass Chemical Engineering (Education Ministry), College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310058, China
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310058, China
- Correspondence: (H.Y.); (L.Y.)
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Marrone A, Fish RH. Bioorganometallic Chemistry at the Interface with Biocatalysis: Chemoselective Reduction of Biomimetic NAD + Cofactors with [Cp*Rh(bpy)H] +, Tandem Catalysis with 1,4-NADH-Dependent Enzymes, Chiral Synthesis, Organotin Metabolites, and DFT Mechanism Studies. Organometallics 2023. [DOI: 10.1021/acs.organomet.2c00550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Affiliation(s)
- Alessandro Marrone
- Dipartimento di Farmacia, Università “G d’Annunzio”, di Chieti-Pescara 66100, Italy
| | - Richard H. Fish
- Lawrence Berkeley National Laboratory, University of California, Berkeley, California 94720, United States
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Zhang H, Cui P, Xie D, Wang Y, Wang P, Sheng G. Axial N Ligand-Modulated Ultrahigh Activity and Selectivity Hyperoxide Activation over Single-Atoms Nanozymes. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2205681. [PMID: 36446629 PMCID: PMC9875630 DOI: 10.1002/advs.202205681] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 10/28/2022] [Indexed: 06/16/2023]
Abstract
Learning and studying the structure-activity relationship in the bio-enzymes is conducive to the design of nanozymes for energy and environmental application. Herein, Fe single-atom nanozymes (Fe-SANs) with Fe-N5 site, inspired by the structure of cytochromes P450 (CYPs), are developed and characterized. Similar to the CYPs, the hyperoxide can activate the Fe(III) center of Fe-SANs to generate Fe(IV)O intermediately, which can transfer oxygen to the substrate with ultrafast speed. Particularly, using the peroxymonosulfate (PMS)-activated Fe-SANs to oxidize sulfamethoxazole, a typical antibiotic contaminant, as the model hyperoxides activation reaction, the excellent activity within 284 min-1 g-1 (catalyst) mmol-1 (PMS) oxidation rate and 91.6% selectivity to the Fe(IV)O intermediate oxidation are demonstrated. More importantly, instead of promoting PMS adsorption, the axial N ligand modulates the electron structure of FeN5 SANs for the lower reaction energy barrier and promotes electron transfer to PMS to produce Fe(IV)O intermediate with high selectivity. The highlight of the axial N coordination in the nanozymes in this work provides deep insight to guide the design and development of nanozymes nearly to the bio-enzyme with excellent activity and selectivity.
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Affiliation(s)
- Han‐Chao Zhang
- CAS Key Laboratory of Urban Pollutant ConversionDepartment of Environmental Science and EngineeringUniversity of Science and Technology of ChinaHefei230026China
- Department of Civil & Environmental EngineeringThe Hong Kong Polytechnic UniversityKowloonHong Kong999077China
| | - Pei‐Xin Cui
- Key Laboratory of Soil Environment and Pollution RemediationInstitute of Soil ScienceChinese Academy of SciencesNanjing210008China
| | - Dong‐Hua Xie
- CAS Key Laboratory of Urban Pollutant ConversionDepartment of Environmental Science and EngineeringUniversity of Science and Technology of ChinaHefei230026China
| | - Yu‐Jun Wang
- Key Laboratory of Soil Environment and Pollution RemediationInstitute of Soil ScienceChinese Academy of SciencesNanjing210008China
| | - Peng Wang
- Department of Civil & Environmental EngineeringThe Hong Kong Polytechnic UniversityKowloonHong Kong999077China
| | - Guo‐Ping Sheng
- CAS Key Laboratory of Urban Pollutant ConversionDepartment of Environmental Science and EngineeringUniversity of Science and Technology of ChinaHefei230026China
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12
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Meng S, Ji Y, Zhu L, Dhoke GV, Davari MD, Schwaneberg U. The molecular basis and enzyme engineering strategies for improvement of coupling efficiency in cytochrome P450s. Biotechnol Adv 2022; 61:108051. [DOI: 10.1016/j.biotechadv.2022.108051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 09/26/2022] [Accepted: 10/13/2022] [Indexed: 11/28/2022]
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13
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Dixit VA, Murty US, Bajaj P, Blumberger J, de Visser SP. Mechanisms of Electron Transfer Rate Modulations in Cytochrome P450 BM3. J Phys Chem B 2022; 126:9737-9747. [PMID: 36384294 DOI: 10.1021/acs.jpcb.2c03967] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Bacterial cytochromes P450 BM3 (CYP450 BM3) catalyze reactions of industrial importance. Despite many successful biotransformations, robust (re)design for novel applications remains challenging. Rational design and evolutionary approaches are not always successful, highlighting a lack of complete understanding of the mechanisms of electron transfer (ET) modulations. Thus, the full potential of CYP450 reactions remains under-exploited. In this work, we report the first molecular dynamics (MD)-based explicit prediction of BM3 ET parameters (reorganization energies; λ and ET free energies; ΔG°), and log ET rates (log kET) using the Marcus theory. Overall, the calculated ET rates for the BM3 wild-type (WT), mutants (F393 and L86), ligand-bound state, and ion concentrations agree well with experimental data. In ligand-free (LF) BM3, mutations modulate kET via ET ΔG°. Simulations show that the experimental ET rate enhancement is due to increased driving force (more negative ΔG°) upon ligation. This increase is related to the protein reorganization required to accommodate the ligand in the binding pocket rather than binding interactions with the ligand. Our methodology (CYPWare 1.0) automates all the stages of the MD simulation step-up, energy calculations, and estimation of ET parameters. CYPWare 1.0 and this work thus represent an important advancement in the CYP450 ET rate predictions, which has the potential to guide the redesign of ET enzymes. This program and a Web tool are available on GitHub for academic research.
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Affiliation(s)
- Vaibhav A Dixit
- Department of Medicinal Chemistry, Department of Pharmaceuticals, Ministry of Chemicals & Fertilizers,, National Institute of Pharmaceutical Education and Research, Guwahati, (NIPER Guwahati) Govt. of India, Sila Katamur (Halugurisuk), P.O.: Changsari, Dist: Kamrup, 781101Guwahati, Assam, India
| | - Upadhyayula Suryanarayana Murty
- Department of Medicinal Chemistry, Department of Pharmaceuticals, Ministry of Chemicals & Fertilizers,, National Institute of Pharmaceutical Education and Research, Guwahati, (NIPER Guwahati) Govt. of India, Sila Katamur (Halugurisuk), P.O.: Changsari, Dist: Kamrup, 781101Guwahati, Assam, India
| | - Priyanka Bajaj
- National Institute of Pharmaceutical Education and Research, Hyderabad (NIPER Hyderabad), NH-9, Balanagar Main Road, Kukatpally Industrial Estate, Balanagar, Hyderabad500037, Telangana, India
| | - Jochen Blumberger
- Department of Physics and Astronomy, and Thomas Young Centre, University College London, Gower Street, LondonWC1E 6BT, U.K
| | - Sam P de Visser
- Manchester Institute of Biotechnology and Department of Chemical Engineering, The University of Manchester, 131 Princess Street, ManchesterM17DN, U.K
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14
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Hargrove TY, Lamb DC, Smith JA, Wawrzak Z, Kelly SL, Lepesheva GI. Unravelling the role of transient redox partner complexes in P450 electron transfer mechanics. Sci Rep 2022; 12:16232. [PMID: 36171457 PMCID: PMC9519919 DOI: 10.1038/s41598-022-20671-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 09/16/2022] [Indexed: 01/05/2023] Open
Abstract
The molecular evolution of cytochromes P450 and associated redox-driven oxidative catalysis remains a mystery in biology. It is widely believed that sterol 14α-demethylase (CYP51), an essential enzyme of sterol biosynthesis, is the ancestor of the whole P450 superfamily given its conservation across species in different biological kingdoms. Herein we have utilized X-ray crystallography, molecular dynamics simulations, phylogenetics and electron transfer measurements to interrogate the nature of P450-redox partner binding using the naturally occurring fusion protein, CYP51-ferredoxin found in the sterol-producing bacterium Methylococcus capsulatus. Our data advocates that the electron transfer mechanics in the M. capsulatus CYP51-ferredoxin fusion protein involves an ensemble of ferredoxin molecules in various orientations and the interactions are transient. Close proximity of ferredoxin, however, is required to complete the substrate-induced large-scale structural switch in the P450 domain that enables proton-coupled electron transfer and subsequent oxygen scission and catalysis. These results have fundamental implications regarding the early evolution of electron transfer proteins and for the redox reactions in the early steps of sterol biosynthesis. They also shed new light on redox protein mechanics and the subsequent diversification of the P450 electron transfer machinery in nature.
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Affiliation(s)
- Tatiana Y Hargrove
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - David C Lamb
- Faculty of Medicine, Health and Life Science, Swansea University, Swansea, SA2 8PP, UK
| | - Jarrod A Smith
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA.,Center for Structural Biology, Vanderbilt University, Nashville, TN, 37232, USA
| | - Zdzislaw Wawrzak
- Synchrotron Research Center, Life Science Collaborative Access Team, Northwestern University, Argonne, IL, 60439, USA
| | - Steven L Kelly
- Faculty of Medicine, Health and Life Science, Swansea University, Swansea, SA2 8PP, UK
| | - Galina I Lepesheva
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA. .,Center for Structural Biology, Vanderbilt University, Nashville, TN, 37232, USA.
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15
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Urban P, Pompon D. Confrontation of AlphaFold models with experimental structures enlightens conformational dynamics supporting CYP102A1 functions. Sci Rep 2022; 12:15982. [PMID: 36155638 PMCID: PMC9510131 DOI: 10.1038/s41598-022-20390-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 09/13/2022] [Indexed: 11/16/2022] Open
Abstract
Conformational dynamics plays a critical role for the function of multidomain electron transfer complexes. While crystallographic or NMR approaches allow detailed insight into structures, lower resolution methods like cryo-electron microscopy can provide more information on dynamics. In silico structure modelling using AlphaFold was recently successfully extended to the prediction of protein complexes but its capability to address large conformational changes involved in catalysis remained obscure. We used bacterial CYP102A1 monooxygenase homodimer as a test case to design a competitive modelling approach (CMA) for assessing alternate conformations of multi-domain complexes. Predictions were confronted with published crystallographic and cryo-EM data, evidencing consistencies but also permitting some reinterpretation of experimental data. Structural determinants stabilising the new type of domain connectivity evidenced in this bacterial self-sufficient monooxygenase were analysed by CMA and used for in silico retro-engineering applied to its eukaryotic bi-component counterparts.
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16
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Li C, Yang J, Yang K, Wu H, Chen H, Wu Q, Zhao H. Tartary buckwheat FtF3'H1 as a metabolic branch switch to increase anthocyanin content in transgenic plant. FRONTIERS IN PLANT SCIENCE 2022; 13:959698. [PMID: 36092410 PMCID: PMC9452690 DOI: 10.3389/fpls.2022.959698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 08/08/2022] [Indexed: 06/15/2023]
Abstract
Tartary buckwheat (TB) is a pseudocereal rich in flavonoids, mainly including flavonols and anthocyanins. The flavonoid 3'-hydroxylase (F3'H) is a key enzyme in flavonoid biosynthesis and is encoded by two copies in TB genome. However, its biological function and effects on flavonol and anthocyanin synthesis in TB have not been well validated yet. In this study, we cloned the full-length FtF3'H1 gene highly expressed in all tissues (compared with FtF3'H2) according to TB flowering transcriptome data. The corresponding FtF3'H1 protein contains 534 amino acids with the molecular properties of the typical plant F3'H and belongs to the CYP75B family. During the flowering stage, the FtF3'H1 expression was highest in flowers, and its expression pattern showed a significant and positive correlation with the total flavonoids (R 2 > 0.95). The overexpression of FtF3'H1 in Arabidopsis thaliana, Nicotiana tabacum and TB hairy roots resulted in a significant increase in anthocyanin contents (p < 0.05) but a decrease in rutin (p < 0.05). The average anthocyanin contents were 2.94 mg/g (fresh weight, FW) in A. thaliana (about 135% increase), 1.18 mg/g (FW) in tobacco (about 17% increase), and 1.56 mg/g (FW) TB hairy roots (about 44% increase), and the rutin contents were dropped to about 53.85, 14.99, 46.31%, respectively. However, the expression of genes involved in anthocyanin (DFRs and ANSs) and flavonol (FLSs) synthesis pathways were significantly upregulated (p < 0.05). In particular, the expression level of DFR, a key enzyme that enters the anthocyanin branch, was upregulated thousand-fold in A. thaliana and in N. tabacum. These results might be attributed to FtF3'H1 protein with a higher substrate preference for anthocyanin synthesis substrates. Altogether, we identified the basic biochemical activity of FtF3'H1 in vivo and investigated its involvement in anthocyanin and flavonol metabolism in plant.
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17
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Smeets E, Huang S, Lee XY, Van Nieuwenhove E, Helsen C, Handle F, Moris L, El Kharraz S, Eerlings R, Devlies W, Willemsen M, Bücken L, Prezzemolo T, Humblet-Baron S, Voet A, Rochtus A, Van Schepdael A, de Zegher F, Claessens F. A disease-associated missense mutation in CYP4F3 affects the metabolism of leukotriene B4 via disruption of electron transfer. J Cachexia Sarcopenia Muscle 2022; 13:2242-2253. [PMID: 35686338 PMCID: PMC9397552 DOI: 10.1002/jcsm.13022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/19/2022] [Accepted: 05/09/2022] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Cytochrome P450 4F3 (CYP4F3) is an ω-hydroxylase that oxidizes leukotriene B4 (LTB4), prostaglandins, and fatty acid epoxides. LTB4 is synthesized by leukocytes and acts as a chemoattractant for neutrophils, making it an essential component of the innate immune system. Recently, involvement of the LTB4 pathway was reported in various immunological disorders such as asthma, arthritis, and inflammatory bowel disease. We report a 26-year-old female with a complex immune phenotype, mainly marked by exhaustion, muscle weakness, and inflammation-related conditions. The molecular cause is unknown, and symptoms have been aggravating over the years. METHODS Whole exome sequencing was performed and validated; flow cytometry and enzyme-linked immunosorbent assay were used to describe patient's phenotype. Function and impact of the mutation were investigated using molecular analysis: co-immunoprecipitation, western blot, and enzyme-linked immunosorbent assay. Capillary electrophoresis with ultraviolet detection was used to detect LTB4 and its metabolite and in silico modelling provided structural information. RESULTS We present the first report of a patient with a heterozygous de novo missense mutation c.C1123 > G;p.L375V in CYP4F3 that severely impairs its activity by 50% (P < 0.0001), leading to reduced metabolization of the pro-inflammatory LTB4. Systemic LTB4 levels (1034.0 ± 75.9 pg/mL) are significantly increased compared with healthy subjects (305.6 ± 57.0 pg/mL, P < 0.001), and immune phenotyping shows increased total CD19+ CD27- naive B cells (25%) and decreased total CD19+ CD27+ IgD- switched memory B cells (19%). The mutant CYP4F3 protein is stable and binding with its electron donors POR and Cytb5 is unaffected (P > 0.9 for both co-immunoprecipitation with POR and Cytb5). In silico modelling of CYP4F3 in complex with POR and Cytb5 suggests that the loss of catalytic activity of the mutant CYP4F3 is explained by a disruption of an α-helix that is crucial for the electron shuffling between the electron carriers and CYP4F3. Interestingly, zileuton still inhibits ex vivo LTB4 production in patient's whole blood to 2% of control (P < 0.0001), while montelukast and fluticasone do not (99% and 114% of control, respectively). CONCLUSIONS A point mutation in the catalytic domain of CYP4F3 is associated with high leukotriene B4 plasma levels and features of a more naive adaptive immune response. Our data provide evidence for the pathogenicity of the CYP4F3 variant as a cause for the observed clinical features in the patient. Inhibitors of the LTB4 pathway such as zileuton show promising effects in blocking LTB4 production and might be used as a future treatment strategy.
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Affiliation(s)
- Elien Smeets
- Department of Cellular and Molecular Medicine, Molecular Endocrinology Laboratory, KU Leuven, Leuven, Belgium
| | - Shengyun Huang
- Department of Pharmaceutical and Pharmacological Sciences, Pharmaceutical Analysis Laboratory, KU Leuven, Leuven, Belgium
| | - Xiao Yin Lee
- Department of Cellular and Molecular Medicine, Molecular Endocrinology Laboratory, KU Leuven, Leuven, Belgium
| | - Erika Van Nieuwenhove
- Department of Microbiology, Immunology and Transplantation, Laboratory of Adaptive Immunity, KU Leuven, Leuven, Belgium.,Department of Pediatrics, University Hospitals Leuven, Leuven, Belgium
| | - Christine Helsen
- Department of Cellular and Molecular Medicine, Molecular Endocrinology Laboratory, KU Leuven, Leuven, Belgium
| | - Florian Handle
- Department of Cellular and Molecular Medicine, Molecular Endocrinology Laboratory, KU Leuven, Leuven, Belgium
| | - Lisa Moris
- Department of Cellular and Molecular Medicine, Molecular Endocrinology Laboratory, KU Leuven, Leuven, Belgium
| | - Sarah El Kharraz
- Department of Cellular and Molecular Medicine, Molecular Endocrinology Laboratory, KU Leuven, Leuven, Belgium
| | - Roy Eerlings
- Department of Cellular and Molecular Medicine, Molecular Endocrinology Laboratory, KU Leuven, Leuven, Belgium
| | - Wout Devlies
- Department of Cellular and Molecular Medicine, Molecular Endocrinology Laboratory, KU Leuven, Leuven, Belgium
| | - Mathijs Willemsen
- Department of Microbiology, Immunology and Transplantation, Laboratory of Adaptive Immunity, KU Leuven, Leuven, Belgium
| | - Leoni Bücken
- Department of Microbiology, Immunology and Transplantation, Laboratory of Adaptive Immunity, KU Leuven, Leuven, Belgium
| | - Teresa Prezzemolo
- Department of Microbiology, Immunology and Transplantation, Laboratory of Adaptive Immunity, KU Leuven, Leuven, Belgium
| | - Stephanie Humblet-Baron
- Department of Microbiology, Immunology and Transplantation, Laboratory of Adaptive Immunity, KU Leuven, Leuven, Belgium
| | - Arnout Voet
- Department of Chemistry, Biochemistry, Molecular and Structural Biology Section Laboratory, KU Leuven, Leuven, Belgium
| | - Anne Rochtus
- Department of Pediatrics, University Hospitals Leuven, Leuven, Belgium
| | - Ann Van Schepdael
- Department of Pharmaceutical and Pharmacological Sciences, Pharmaceutical Analysis Laboratory, KU Leuven, Leuven, Belgium
| | - Francis de Zegher
- Department of Pediatrics, University Hospitals Leuven, Leuven, Belgium
| | - Frank Claessens
- Department of Cellular and Molecular Medicine, Molecular Endocrinology Laboratory, KU Leuven, Leuven, Belgium
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18
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Van Stappen C, Deng Y, Liu Y, Heidari H, Wang JX, Zhou Y, Ledray AP, Lu Y. Designing Artificial Metalloenzymes by Tuning of the Environment beyond the Primary Coordination Sphere. Chem Rev 2022; 122:11974-12045. [PMID: 35816578 DOI: 10.1021/acs.chemrev.2c00106] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Metalloenzymes catalyze a variety of reactions using a limited number of natural amino acids and metallocofactors. Therefore, the environment beyond the primary coordination sphere must play an important role in both conferring and tuning their phenomenal catalytic properties, enabling active sites with otherwise similar primary coordination environments to perform a diverse array of biological functions. However, since the interactions beyond the primary coordination sphere are numerous and weak, it has been difficult to pinpoint structural features responsible for the tuning of activities of native enzymes. Designing artificial metalloenzymes (ArMs) offers an excellent basis to elucidate the roles of these interactions and to further develop practical biological catalysts. In this review, we highlight how the secondary coordination spheres of ArMs influence metal binding and catalysis, with particular focus on the use of native protein scaffolds as templates for the design of ArMs by either rational design aided by computational modeling, directed evolution, or a combination of both approaches. In describing successes in designing heme, nonheme Fe, and Cu metalloenzymes, heteronuclear metalloenzymes containing heme, and those ArMs containing other metal centers (including those with non-native metal ions and metallocofactors), we have summarized insights gained on how careful controls of the interactions in the secondary coordination sphere, including hydrophobic and hydrogen bonding interactions, allow the generation and tuning of these respective systems to approach, rival, and, in a few cases, exceed those of native enzymes. We have also provided an outlook on the remaining challenges in the field and future directions that will allow for a deeper understanding of the secondary coordination sphere a deeper understanding of the secondary coordintion sphere to be gained, and in turn to guide the design of a broader and more efficient variety of ArMs.
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Affiliation(s)
- Casey Van Stappen
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yunling Deng
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yiwei Liu
- Department of Chemistry, University of Illinois, Urbana-Champaign, 505 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Hirbod Heidari
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Jing-Xiang Wang
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yu Zhou
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Aaron P Ledray
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yi Lu
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States.,Department of Chemistry, University of Illinois, Urbana-Champaign, 505 South Mathews Avenue, Urbana, Illinois 61801, United States
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19
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Meng S, Ji Y, Liu L, Davari MD, Schwaneberg U. Modulating the Coupling Efficiency of P450 BM3 by Controlling Water Diffusion through Access Tunnel Engineering. CHEMSUSCHEM 2022; 15:e202102434. [PMID: 34936208 PMCID: PMC9302676 DOI: 10.1002/cssc.202102434] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/19/2021] [Indexed: 06/03/2023]
Abstract
Cytochromes P450 have gained much interest for their broad substrate scope in the catalysis of oxidation reactions for pharmaceuticals, plastics, and hormones. However, achieving high coupling efficiency by the engineering of P450s is still a big challenge. The presence of extra water around the active site is deemed to be related to uncoupling. In this study, the access tunnels of P450 BM3 from Bacillus megaterium are engineered to control water access from bulk solvent to the active site. Nine residues located in tunnels are investigated by site-saturation mutagenesis to reduce water diffusion, thereby improving the coupling efficiency. The recombined variant N319L/T411V/T436A shows improved coupling efficiency (from 31.2 % to 52.6 %). Tunnel polarity analysis and molecular dynamics simulation further indicate that reduced water molecules around the active site lead to higher coupling efficiency. Overall, this study provides valuable insight on improving coupling efficiency by controlling water diffusion through tunnel engineering.
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Affiliation(s)
- Shuaiqi Meng
- Institute of BiotechnologyRWTH Aachen UniversityWorringerweg 352074AachenGermany
| | - Yu Ji
- Institute of BiotechnologyRWTH Aachen UniversityWorringerweg 352074AachenGermany
| | - Luo Liu
- Beijing Bioprocess Key LaboratoryBeijing University of Chemical TechnologyBeisanhuan East Road 15Beijing10029P. R. China
| | - Mehdi D. Davari
- Department of Bioorganic ChemistryLeibniz Institute of Plant BiochemistryWeinberg 306120HalleGermany
| | - Ulrich Schwaneberg
- Institute of BiotechnologyRWTH Aachen UniversityWorringerweg 352074AachenGermany
- DWI-Leibniz Institute for Interactive MaterialsForckenbeckstraße 5052074AachenGermany
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20
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Mahor D, Cong Z, Weissenborn MJ, Hollmann F, Zhang W. Valorization of Small Alkanes by Biocatalytic Oxyfunctionalization. CHEMSUSCHEM 2022; 15:e202101116. [PMID: 34288540 DOI: 10.1002/cssc.202101116] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 07/18/2021] [Indexed: 06/13/2023]
Abstract
The oxidation of alkanes into valuable chemical products is a vital reaction in organic synthesis. This reaction, however, is challenging, owing to the inertness of C-H bonds. Transition metal catalysts for C-H functionalization are frequently explored. Despite chemical alternatives, nature has also evolved powerful oxidative enzymes (e. g., methane monooxygenases, cytochrome P450 oxygenases, peroxygenases) that are capable of transforming C-H bonds under very mild conditions, with only the use of molecular oxygen or hydrogen peroxide as electron acceptors. Although progress in alkane oxidation has been reviewed extensively, little attention has been paid to small alkane oxidation. The latter holds great potential for the manufacture of chemicals. This Minireview provides a concise overview of the most relevant enzyme classes capable of small alkanes (C<6 ) oxyfunctionalization, describes the essentials of the catalytic mechanisms, and critically outlines the current state-of-the-art in preparative applications.
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Affiliation(s)
- Durga Mahor
- National Innovation Center for Synthetic Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, P. R. China
- Indian Institute of Science Education and Research Berhampur, Odisha, 760010, India
| | - Zhiqi Cong
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology Chinese Academy of Sciences, Qingdao, Shandong, 266101, P. R. China
| | - Martin J Weissenborn
- Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle, Saale), Germany
| | - Frank Hollmann
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ, Delft, The Netherlands
| | - Wuyuan Zhang
- National Innovation Center for Synthetic Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, P. R. China
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21
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Ivanov YD, Malsagova KA, Bukharina NS, Vesnin SG, Usanov SA, Tatur VY, Lukyanitsa AA, Ivanova ND, Konev VA, Ziborov VS. Radiothermometric Study of the Effect of Amino Acid Mutation on the Characteristics of the Enzymatic System. Diagnostics (Basel) 2022; 12:diagnostics12040943. [PMID: 35453991 PMCID: PMC9024681 DOI: 10.3390/diagnostics12040943] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 04/05/2022] [Accepted: 04/08/2022] [Indexed: 11/16/2022] Open
Abstract
The radiothermometry (RTM) study of a cytochrome-containing system (CYP102 A1) has been conducted in order to demonstrate the applicability of RTM for monitoring changes in the functional activity of an enzyme in case of its point mutation. The study has been performed with the example of the wild-type cytochrome (WT) and its mutant type A264K. CYP102 A1 is a nanoscale protein-enzymatic system of about 10 nm in size. RTM uses a radio detector and can record the corresponding brightness temperature (Tbr) of the nanoscale enzyme solution within the 3.4–4.2 GHz frequency range during enzyme functioning. It was found that the enzymatic reaction during the lauric acid hydroxylation at the wild-type CYP102 A1 (WT) concentration of ~10−9 M is accompanied by Tbr fluctuations of ~0.5–1 °C. At the same time, no Tbr fluctuations are observed for the mutated forms of the enzyme CYP102 A1 (A264K), where one amino acid was replaced. We know that the activity of CYP102 A1 (WT) is ~4 orders of magnitude higher than that of CYP102 A1 (A264K). We therefore concluded that the disappearance of the fluctuation of Tbr CYP102 A1 (A264K) is associated with a decrease in the activity of the enzyme. This effect can be used to develop new methods for testing the activity of the enzyme that do not require additional labels and expensive equipment, in comparison with calorimetry and spectral methods. The RTM is beginning to find application in the diagnosis of oncological diseases and for the analysis of biochemical processes.
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Affiliation(s)
- Yuri D. Ivanov
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, Pogodinskaya St. 10 Build. 8, 119121 Moscow, Russia; (N.S.B.); (V.S.Z.)
- Laboratory of Shock Wave Impacts, Joint Institute for High Temperatures of Russian Academy of Sciences, Izhorskaya St. 13 Build. 2, 125412 Moscow, Russia
- Correspondence: (Y.D.I.); (K.A.M.); Tel.: +7-(499)-246-37-61 (Y.D.I.)
| | - Kristina A. Malsagova
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, Pogodinskaya St. 10 Build. 8, 119121 Moscow, Russia; (N.S.B.); (V.S.Z.)
- Correspondence: (Y.D.I.); (K.A.M.); Tel.: +7-(499)-246-37-61 (Y.D.I.)
| | - Natalia S. Bukharina
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, Pogodinskaya St. 10 Build. 8, 119121 Moscow, Russia; (N.S.B.); (V.S.Z.)
| | | | - Sergey A. Usanov
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Academician V.F. Kuprevich 5 Build. 2, 220141 Minsk, Belarus;
| | - Vadim Yu. Tatur
- Foundation of Perspective Technologies and Novations, Shipilovskaya St. 64, 115682 Moscow, Russia; (V.Y.T.); (A.A.L.)
| | - Andrei A. Lukyanitsa
- Foundation of Perspective Technologies and Novations, Shipilovskaya St. 64, 115682 Moscow, Russia; (V.Y.T.); (A.A.L.)
| | - Nina D. Ivanova
- Skryabin Moscow State Academy of Veterinary Medicine and Biotechnology, Academician Skryabin St. 23, 109472 Moscow, Russia;
| | - Vladimir A. Konev
- Department of Infectious Diseases in Children, Faculty of Pediatrics, Pirogov Russian National Research Medical University, Ostrovityanov St. 1, 117997 Moscow, Russia;
| | - Vadim S. Ziborov
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, Pogodinskaya St. 10 Build. 8, 119121 Moscow, Russia; (N.S.B.); (V.S.Z.)
- Laboratory of Shock Wave Impacts, Joint Institute for High Temperatures of Russian Academy of Sciences, Izhorskaya St. 13 Build. 2, 125412 Moscow, Russia
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22
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Catucci G, Ciaramella A, Di Nardo G, Zhang C, Castrignanò S, Gilardi G. Molecular Lego of Human Cytochrome P450: The Key Role of Heme Domain Flexibility for the Activity of the Chimeric Proteins. Int J Mol Sci 2022; 23:ijms23073618. [PMID: 35408976 PMCID: PMC8998974 DOI: 10.3390/ijms23073618] [Citation(s) in RCA: 4] [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] [Received: 12/27/2021] [Revised: 03/22/2022] [Accepted: 03/24/2022] [Indexed: 02/04/2023] Open
Abstract
The cytochrome P450 superfamily are heme-thiolate enzymes able to carry out monooxygenase reactions. Several studies have demonstrated the feasibility of using a soluble bacterial reductase from Bacillus megaterium, BMR, as an artificial electron transfer partner fused to the human P450 domain in a single polypeptide chain in an approach known as ‘molecular Lego’. The 3A4-BMR chimera has been deeply characterized biochemically for its activity, coupling efficiency, and flexibility by many different biophysical techniques leading to the conclusion that an extension of five glycines in the loop that connects the two domains improves all the catalytic parameters due to improved flexibility of the system. In this work, we extend the characterization of 3A4-BMR chimeras using differential scanning calorimetry to evaluate stabilizing role of BMR. We apply the ‘molecular Lego’ approach also to CYP19A1 (aromatase) and the data show that the activity of the chimeras is very low (<0.003 min−1) for all the constructs tested with a different linker loop length: ARO-BMR, ARO-BMR-3GLY, and ARO-BMR-5GLY. Nevertheless, the fusion to BMR shows a remarkable effect on thermal stability studied by differential scanning calorimetry as indicated by the increase in Tonset by 10 °C and the presence of a cooperative unfolding process driven by the BMR protein domain. Previously characterized 3A4-BMR constructs show the same behavior of ARO-BMR constructs in terms of thermal stabilization but a higher activity as a function of the loop length. A comparison of the ARO-BMR system to 3A4-BMR indicates that the design of each P450-BMR chimera should be carefully evaluated not only in terms of electron transfer, but also for the biophysical constraints that cannot always be overcome by chimerization.
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23
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Zhang B, Munske GR, Timokhin VI, Ralph J, Davydov DR, Vermerris W, Sattler SE, Kang C. Functional and structural insight into the flexibility of cytochrome P450 reductases from Sorghum bicolor and its implications for lignin composition. J Biol Chem 2022; 298:101761. [PMID: 35202651 PMCID: PMC8942828 DOI: 10.1016/j.jbc.2022.101761] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 02/17/2022] [Accepted: 02/18/2022] [Indexed: 11/17/2022] Open
Abstract
Plant NADPH-dependent cytochrome P450 reductase (CPR) is a multidomain enzyme that donates electrons for hydroxylation reactions catalyzed by class II cytochrome P450 monooxygenases involved in the synthesis of many primary and secondary metabolites. These P450 enzymes include trans-cinnamate-4-hydroxylase, p-coumarate-3′-hydroxylase, and ferulate-5-hydroxylase involved in monolignol biosynthesis. Because of its role in monolignol biosynthesis, alterations in CPR activity could change the composition and overall output of lignin. Therefore, to understand the structure and function of three CPR subunits from sorghum, recombinant subunits SbCPR2a, SbCPR2b, and SbCPR2c were subjected to X-ray crystallography and kinetic assays. Steady-state kinetic analyses demonstrated that all three CPR subunits supported the oxidation reactions catalyzed by SbC4H1 (CYP73A33) and SbC3′H (CYP98A1). Furthermore, comparing the SbCPR2b structure with the well-investigated CPRs from mammals enabled us to identify critical residues of functional importance and suggested that the plant flavin mononucleotide–binding domain might be more flexible than mammalian homologs. In addition, the elucidated structure of SbCPR2b included the first observation of NADP+ in a native CPR. Overall, we conclude that the connecting domain of SbCPR2, especially its hinge region, could serve as a target to alter biomass composition in bioenergy and forage sorghums through protein engineering.
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Affiliation(s)
- Bixia Zhang
- Department of Chemistry, Washington State University, Pullman, Washington, USA
| | - Gerhard R Munske
- School of Molecular Biosciences, Washington State University, Pullman, Washington, USA
| | - Vitaliy I Timokhin
- Department of Biochemistry and Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin, USA
| | - John Ralph
- Department of Biochemistry and Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin, USA
| | - Dmitri R Davydov
- Department of Chemistry, Washington State University, Pullman, Washington, USA
| | - Wilfred Vermerris
- Department of Microbiology & Cell Science and UF Genetics Institute, University of Florida, Gainesville, Florida, USA
| | - Scott E Sattler
- U.S. Department of Agriculture - Agricultural Research Service, Wheat, Sorghum and Forage Research Unit, Lincoln, Nebraska, USA
| | - ChulHee Kang
- Department of Chemistry, Washington State University, Pullman, Washington, USA.
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24
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Prediction of Monomeric and Dimeric Structures of CYP102A1 Using AlphaFold2 and AlphaFold Multimer and Assessment of Point Mutation Effect on the Efficiency of Intra- and Interprotein Electron Transfer. Molecules 2022; 27:molecules27041386. [PMID: 35209175 PMCID: PMC8874714 DOI: 10.3390/molecules27041386] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 02/08/2022] [Accepted: 02/11/2022] [Indexed: 02/01/2023] Open
Abstract
The three-dimensional structure of monomers and homodimers of CYP102A1/WT (wild-type) proteins and their A83F and A83I mutant forms was predicted using the AlphaFold2 (AF2) and AlphaFold Multimer (AFMultimer) programs, which were compared with the rate constants of hydroxylation reactions of these enzyme forms to determine the efficiency of intra- and interprotein electron transport in the CYP102A1 hydroxylase system. The electron transfer rate constants (ket), which determine the rate of indole hydroxylation by the CYP102A1 system, were calculated based on the distances (R) between donor-acceptor prosthetic groups (PG) FAD→FMN→HEME of these proteins using factor β, which describes an exponential decay from R the speed of electron transport (ET) according to the tunnelling mechanism. It was shown that the structure of monomers in the homodimer, calculated using the AlpfaFold Multimer program, is in good agreement with the experimental structures of globular domains (HEME-, FMN-, and FAD-domains) in CYP102A1/WT obtained by X-ray structural analysis, and the structure of isolated monomers predicted in AF2 does not coincide with the structure of monomers in the homodimer, although a high level of similarity in individual domains remains. The structures of monomers and homodimers of A83F and A83I mutants were also calculated, and their structures were compared with the wild-type protein. Significant differences in the structure of all isolated monomers with respect to the structures of monomers in homodimers were also found for them, and at the same time, insignificant differences were revealed for all homodimers. Comparative analysis for CYP102A1/WT between the calculated intra- and interprotein distances FAD→FMN→HEME and the rate constants of hydroxylation in these proteins showed that the distance between prosthetic groups both in the monomer and in the dimer allows the implementation of electron transfer between PGs, which is consistent with experimental literature data about kcat. For the mutant form of monomer A83I, an increase in the distance between PGs was obtained, which can restrict electron transportation compared to WT; however, for the dimer of this protein, a decrease in the distance between PGs was observed compared to the WT form, which can lead to an increase in the electron transfer rate constant and, accordingly, kcat. For the monomer and homodimer of the A83F mutant, the calculations showed an increase in the distance between the PGs compared to the WT form, which should have led to a decrease in the electron transfer rate, but at the same time, for the homodimer, the approach of the aromatic group F262 with heme can speed up transportation for this form and, accordingly, the rate of hydroxylation.
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25
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Poulos TL, Follmer AH. Updating the Paradigm: Redox Partner Binding and Conformational Dynamics in Cytochromes P450. Acc Chem Res 2022; 55:373-380. [PMID: 34965086 PMCID: PMC8959394 DOI: 10.1021/acs.accounts.1c00632] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
This Account summarizes recent findings centered on the role that redox partner binding, allostery, and conformational dynamics plays in cytochrome P450 proton coupled electron transfer. P450s are one of Nature's largest enzyme families and it is not uncommon to find a P450 wherever substrate oxidation is required in the formation of essential molecules critical to the life of the organism or in xenobiotic detoxification. P450s can operate on a remarkably large range of substrates from the very small to the very large, yet the overall P450 three-dimensional structure is conserved. Given this conservation of structure, it is generally assumed that the basic catalytic mechanism is conserved. In nearly all P450s, the O2 O-O bond must be cleaved heterolytically enabling one oxygen atom, the distal oxygen, to depart as water and leave behind a heme iron-linked O atom as the powerful oxidant that is used to activate the nearby substrate. For this process to proceed efficiently, externally supplied electrons and protons are required. Two protons must be added to the departing O atom while an electron is transferred from a redox partner that typically contains either a Fe2S2 or FMN redox center. The paradigm P450 used to unravel the details of these mechanisms has been the bacterial CYP101A1 or P450cam. P450cam is specific for its own Fe2S2 redox partner, putidaredoxin or Pdx, and it has long been postulated that Pdx plays an effector/allosteric role by possibly switching P450cam to an active conformation. Crystal structures, spectroscopic data, and direct binding experiments of the P450cam-Pdx complex provide some answers. Pdx shifts the conformation of P450cam to a more open state, a transition that is postulated to trigger the proton relay network required for O2 activation. An essential part of this proton relay network is a highly conserved Asp (sometimes Glu) that is known to be critical for activity in a number of P450s. How this Asp and proton delivery networks are connected to redox partner binding is quite simple. In the closed state, this Asp is tied down by salt bridges, but these salt bridges are ruptured when Pdx binds, leaving the Asp free to serve its role in proton transfer. An alternative hypothesis suggests that a specific proton relay network is not really necessary. In this scenario, the Asp plays a structural role in the open/close transition and merely opening the active site access channel is sufficient to enable solvent protons in for O2 protonation. Experiments designed to test these various hypotheses have revealed some surprises in both P450cam and other bacterial P450s. Molecular dynamics and crystallography show that P450cam can undergo rather significant conformational gymnastics that result in a large restructuring of the active site requiring multiple cis/trans proline isomerizations. It also has been found that X-ray driven substrate hydroxylation is a useful tool for better understanding the role that the essential Asp and surrounding residues play in catalysis. Here we summarize these recent results which provide a much more dynamic picture of P450 catalysis.
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Affiliation(s)
- Thomas L. Poulos
- Departments of Molecular Biology & Biochemistry, Pharmaceutical Sciences, and Chemistry, University of California, Irvine, Irvine, California 92697-3900, United States
| | - Alec H. Follmer
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
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26
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Raju DR, Kumar A, BK N, Shetty A, PS A, Kumar RP, Lalitha R, Sigamani G. Extensive modelling and quantum chemical study of sterol C-22 desaturase mechanism: A commercially important cytochrome P450 family. Catal Today 2021. [DOI: 10.1016/j.cattod.2021.12.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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27
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28
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Darragh K, Nelson DR, Ramírez SR. The Birth-and-Death Evolution of Cytochrome P450 Genes in Bees. Genome Biol Evol 2021; 13:evab261. [PMID: 34850870 PMCID: PMC8670302 DOI: 10.1093/gbe/evab261] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/20/2021] [Indexed: 12/13/2022] Open
Abstract
The birth-and-death model of multigene family evolution describes how gene families evolve and diversify through duplication and deletion. The cytochrome P450s are one of the most diverse and well-studied multigene families, involved in both physiological and xenobiotic functions. Extensive studies of insect P450 genes have demonstrated their role in insecticide resistance. Bees are thought to experience toxin exposure through their diet of nectar and pollen, as well as the resin-collecting behavior exhibited by some species. Here, we describe the repertoire of P450 genes in the orchid bee Euglossa dilemma. Male orchid bees form perfume bouquets used in courtship displays by collecting volatile compounds, resulting in exposure to compounds known to be toxic. In addition, we conducted phylogenetic and selection analyses across ten bee species encompassing three bee families. We find that social behavior and resin collection are not correlated with the repertoire of P450 present in a bee species. However, our analyses revealed that P450 clades can be classified as stable and unstable, and that genes involved in xenobiotic metabolism are more likely to belong to unstable clades. Furthermore, we find that unstable clades are under more dynamic evolutionary pressures and exhibit signals of adaptive evolution. This work highlights the complexity of multigene family evolution, revealing that multiple factors contribute to the diversification, stability, and dynamics of this gene family. Furthermore, we provide a resource for future detailed studies investigating the function of different P450s in economically important bee species.
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Affiliation(s)
- Kathy Darragh
- Department of Evolution and Ecology, University of California, Davis, California, USA
| | - David R Nelson
- Department of Molecular Sciences, University of Tennessee, Memphis, Tennessee, USA
| | - Santiago R Ramírez
- Department of Evolution and Ecology, University of California, Davis, California, USA
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29
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Nowrouzi B, Rios-Solis L. Redox metabolism for improving whole-cell P450-catalysed terpenoid biosynthesis. Crit Rev Biotechnol 2021; 42:1213-1237. [PMID: 34749553 DOI: 10.1080/07388551.2021.1990210] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The growing preference for producing cytochrome P450-mediated natural products in microbial systems stems from the challenging nature of the organic chemistry approaches. The P450 enzymes are redox-dependent proteins, through which they source electrons from reducing cofactors to drive their activities. Widely researched in biochemistry, most of the previous studies have extensively utilised expensive cell-free assays to reveal mechanistic insights into P450 functionalities in presence of commercial redox partners. However, in the context of microbial bioproduction, the synergic activity of P450- reductase proteins in microbial systems have not been largely investigated. This is mainly due to limited knowledge about their mutual interactions in the context of complex systems. Hence, manipulating the redox potential for natural product synthesis in microbial chassis has been limited. As the potential of redox state as crucial regulator of P450 biocatalysis has been greatly underestimated by the scientific community, in this review, we re-emphasize their pivotal role in modulating the in vivo P450 activity through affecting the product profile and yield. Particularly, we discuss the applications of widely used in vivo redox engineering methodologies for natural product synthesis to provide further suggestions for patterning on P450-based terpenoids production in microbial platforms.
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Affiliation(s)
- Behnaz Nowrouzi
- Institute for Bioengineering, School of Engineering, The University of Edinburgh, Edinburgh, UK.,Centre for Synthetic and Systems Biology (SynthSys), The University of Edinburgh, Edinburgh, UK
| | - Leonardo Rios-Solis
- Institute for Bioengineering, School of Engineering, The University of Edinburgh, Edinburgh, UK.,Centre for Synthetic and Systems Biology (SynthSys), The University of Edinburgh, Edinburgh, UK
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30
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Cardellini A, Jiménez-Ángeles F, Asinari P, Olvera de la Cruz M. A Modeling-Based Design to Engineering Protein Hydrogels with Random Copolymers. ACS NANO 2021; 15:16139-16148. [PMID: 34644059 DOI: 10.1021/acsnano.1c04955] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Protein enzymes have shown great potential in numerous technological applications. However, the design of supporting materials is needed to preserve protein functionality outside their native environment. Direct enzyme-polymer self-assembly offers a promising alternative to immobilize proteins in an aqueous solution, achieving higher control of their stability and enzymatic activity in industrial applications. Herein, we propose a modeling-based design to engineering hydrogels of cytochrome P450 and of PETase with styrene/2-vinylpyridine (2VP) random copolymers. By tuning the copolymer fraction of polar groups and of charged groups via quaternization of 2VP for coassembly with cytochrome P450 and via sulfonation of styrene for coassembly with PETase, we provide quantitative guidelines to select either a protein-polymer hydrogel structure or a single-protein encapsulation. The results highlight that, regardless of the protein surface domains, the presence of polar interactions and hydration effects promote the formation of a more elongated enzyme-polymer complex, suggesting a membrane-like coassembly. On the other hand, the effectiveness of a single-protein encapsulation is reached by decreasing the fraction of polar groups and by increasing the charge fraction up to 15%. Our computational analysis demonstrates that the enzyme-polymer assemblies are first promoted by the hydrophobic interactions which lead the protein nonpolar residues to achieve the maximum coverage and to play the role of the most robust contact points. The mechanisms of coassembly are unveiled in the light of both protein and polymer physical-chemistry, providing bioconjugate phase diagrams for the optimal material design.
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Affiliation(s)
- Annalisa Cardellini
- Politecnico di Torino, Torino 10129, Italy
- Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Felipe Jiménez-Ángeles
- Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Pietro Asinari
- Politecnico di Torino, Torino 10129, Italy
- Istituto Nazionale di Ricerca Metrologica, 10135 Torino, Italy
| | - Monica Olvera de la Cruz
- Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
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31
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Coin G, Latour JM. Nitrene transfers mediated by natural and artificial iron enzymes. J Inorg Biochem 2021; 225:111613. [PMID: 34634542 DOI: 10.1016/j.jinorgbio.2021.111613] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/30/2021] [Accepted: 09/13/2021] [Indexed: 12/19/2022]
Abstract
Amines are ubiquitous in biology and pharmacy. As a consequence, introducing N functionalities in organic molecules is attracting strong continuous interest. The past decade has witnessed the emergence of very efficient and selective catalytic systems achieving this goal thanks to engineered hemoproteins. In this review, we examine how these enzymes have been engineered focusing rather on the rationale behind it than the methodology employed. These studies are put in perspective with respect to in vitro and in vivo nitrene transfer processes performed by cytochromes P450. An emphasis is put on mechanistic aspects which are confronted to current molecular knowledge of these reactions. Forthcoming developments are delineated.
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Affiliation(s)
- Guillaume Coin
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, DIESE, LCBM, pmb, F-38000 Grenoble, France; Univ. Grenoble Alpes, CNRS UMR 5250, DCM, CIRE, F-38000 Grenoble, France
| | - Jean-Marc Latour
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, DIESE, LCBM, pmb, F-38000 Grenoble, France.
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Ikebe J, Suzuki M, Komori A, Kobayashi K, Kameda T. Enzyme modification using mutation site prediction method for enhancing the regioselectivity of substrate reaction sites. Sci Rep 2021; 11:19004. [PMID: 34602611 PMCID: PMC8488038 DOI: 10.1038/s41598-021-98433-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 09/02/2021] [Indexed: 11/16/2022] Open
Abstract
Enzymes with low regioselectivity of substrate reaction sites may produce multiple products from a single substrate. When a target product is produced industrially using these enzymes, the production of non-target products (byproducts) causes adverse effects such as increased processing costs for purification and the amount of raw material. Thus it is required the development of modified enzymes to reduce the amount of byproducts’ production. In this paper, we report a method called mutation site prediction for enhancing the regioselectivity of substrate reaction sites (MSPER). MSPER takes conformational data for docking poses of an enzyme and a substrate as input and automatically generates a ranked list of mutation sites to destabilize docking poses for byproducts while maintaining those for target products in silico. We applied MSPER to the enzyme cytochrome P450 CYP102A1 (BM3) and the two substrates to enhance the regioselectivity for four target products with different reaction sites. The 13 of the total 14 top-ranked mutation sites predicted by MSPER for the four target products succeeded in selectively enhancing the regioselectivity up to 6.4-fold. The results indicate that MSPER can distinguish differences of substrate structures and the reaction sites, and can accurately predict mutation sites to enhance regioselectivity without selection by directed evolution screening.
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Affiliation(s)
- Jinzen Ikebe
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Munenori Suzuki
- KNC Bio-Research Center, KNC Laboratories Co., Ltd., 1-1-1 Murotani, Nishi-ku, Kobe, Hyogo, 651-2241, Japan
| | - Aya Komori
- KNC Bio-Research Center, KNC Laboratories Co., Ltd., 1-1-1 Murotani, Nishi-ku, Kobe, Hyogo, 651-2241, Japan
| | - Kaito Kobayashi
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Tomoshi Kameda
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan.
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33
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Structure-based virtual screening of CYP1A1 inhibitors: towards rapid tier-one assessment of potential developmental toxicants. Arch Toxicol 2021; 95:3031-3048. [PMID: 34181028 PMCID: PMC8380238 DOI: 10.1007/s00204-021-03111-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 06/17/2021] [Indexed: 10/26/2022]
Abstract
Cytochrome P450 1A1 (CYP1A1) metabolizes estrogens, melatonin, and other key endogenous signaling molecules critical for embryonic/fetal development. The enzyme has increasing expression during pregnancy, and its inhibition or knockout increases embryonic/fetal lethality and/or developmental problems. Here, we present a virtual screening model for CYP1A1 inhibitors based on the orthosteric and predicted allosteric sites of the enzyme. Using 1001 reference compounds with CYP1A1 activity data, we optimized the decision thresholds of our model and classified the training compounds with 68.3% balanced accuracy (91.0% sensitivity and 45.7% specificity). We applied our final model to 11 known CYP1A1 orthosteric binders and related compounds, and found that our ranking of the known orthosteric binders generally agrees with the relative activity of CYP1A1 in metabolizing these compounds. We also applied the model to 22 new test compounds with unknown/unclear CYP1A1 inhibitory activity, and predicted 16 of them are CYP1A1 inhibitors. The CYP1A1 potency and modes of inhibition of these 22 compounds were experimentally determined. We confirmed that most predicted inhibitors, including drugs contraindicated during pregnancy (amiodarone, bicalutamide, cyproterone acetate, ketoconazole, and tamoxifen) and environmental agents suspected to be endocrine disruptors (bisphenol A, diethyl and dibutyl phthalates, and zearalenone), are indeed potent inhibitors of CYP1A1. Our results suggest that virtual screening may be used as a rapid tier-one method to screen for potential CYP1A1 inhibitors, and flag them out for further experimental evaluations.
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34
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Belsare KD, Ruff AJ, Martinez R, Schwaneberg U. Insights on intermolecular FMN-heme domain interaction and the role of linker length in cytochrome P450cin fusion proteins. Biol Chem 2021; 401:1249-1255. [PMID: 32549121 DOI: 10.1515/hsz-2020-0134] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 05/25/2020] [Indexed: 11/15/2022]
Abstract
Cytochrome P450s are an important group of enzymes catalyzing hydroxylation, and epoxidations reactions. In this work we describe the characterization of the CinA-CinC fusion enzyme system of a previously reported P450 using genetically fused heme (CinA) and FMN (CinC) enzyme domains from Citrobacter braaki. We observed that mixing individually inactivated heme (-) with FMN (-) domain in the CinA-10aa linker - CinC fusion constructs results in recovered activity and the formation of (2S)-2β-hydroxy,1,8-cineole (174 µM), a similar amount when compared to the fully functional fusion protein (176 µM). We also studied the effect of the fusion linker length in the activity complementation assay. Our results suggests an intermolecular interaction between heme and FMN parts from different CinA-CinC fusion protein similar to proposed mechanisms for P450 BM3 on the other hand, linker length plays a crucial influence on the activity of the fusion constructs. However, complementation assays show that inactive constructs with shorter linker lengths have functional subunits, and that the lack of activity might be due to incorrect interaction between fused enzymes.
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Affiliation(s)
- Ketaki D Belsare
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, Aachen, D-52074, Germany
- University of California at San Francisco, 555 Mission Bay Blvd South, San Francisco, 94158, CA, USA
| | - Anna Joëlle Ruff
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, Aachen, D-52074, Germany
| | - Ronny Martinez
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, Aachen, D-52074, Germany
- Departamento de Ingeniería en Alimentos, Universidad de La Serena, Av. Raúl Bitrán 1305, La Serena, 1720010, Chile
| | - Ulrich Schwaneberg
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, Aachen, D-52074, Germany
- DWI - Leibniz Institut für Interaktive Materialien, Forckenbeckstraße 50, Aachen, D-52074, Germany
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Midlik A, Navrátilová V, Moturu TR, Koča J, Svobodová R, Berka K. Uncovering of cytochrome P450 anatomy by SecStrAnnotator. Sci Rep 2021; 11:12345. [PMID: 34117311 PMCID: PMC8196199 DOI: 10.1038/s41598-021-91494-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 05/21/2021] [Indexed: 12/25/2022] Open
Abstract
Protein structural families are groups of homologous proteins defined by the organization of secondary structure elements (SSEs). Nowadays, many families contain vast numbers of structures, and the SSEs can help to orient within them. Communities around specific protein families have even developed specialized SSE annotations, always assigning the same name to the equivalent SSEs in homologous proteins. A detailed analysis of the groups of equivalent SSEs provides an overview of the studied family and enriches the analysis of any particular protein at hand. We developed a workflow for the analysis of the secondary structure anatomy of a protein family. We applied this analysis to the model family of cytochromes P450 (CYPs)-a family of important biotransformation enzymes with a community-wide used SSE annotation. We report the occurrence, typical length and amino acid sequence for the equivalent SSE groups, the conservation/variability of these properties and relationship to the substrate recognition sites. We also suggest a generic residue numbering scheme for the CYP family. Comparing the bacterial and eukaryotic part of the family highlights the significant differences and reveals a well-known anomalous group of bacterial CYPs with some typically eukaryotic features. Our workflow for SSE annotation for CYP and other families can be freely used at address https://sestra.ncbr.muni.cz .
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Affiliation(s)
- Adam Midlik
- CEITEC - Central European Institute of Technology, Masaryk University, Brno, 625 00, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, 625 00, Czech Republic
| | - Veronika Navrátilová
- Department of Physical Chemistry, Faculty of Science, Palacký University, Olomouc, 771 46, Czech Republic
| | - Taraka Ramji Moturu
- CEITEC - Central European Institute of Technology, Masaryk University, Brno, 625 00, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, 625 00, Czech Republic
| | - Jaroslav Koča
- CEITEC - Central European Institute of Technology, Masaryk University, Brno, 625 00, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, 625 00, Czech Republic
| | - Radka Svobodová
- CEITEC - Central European Institute of Technology, Masaryk University, Brno, 625 00, Czech Republic.
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, 625 00, Czech Republic.
| | - Karel Berka
- Department of Physical Chemistry, Faculty of Science, Palacký University, Olomouc, 771 46, Czech Republic.
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Structural Basis for the Diminished Ligand Binding and Catalytic Ability of Human Fetal-Specific CYP3A7. Int J Mol Sci 2021; 22:ijms22115831. [PMID: 34072457 PMCID: PMC8198134 DOI: 10.3390/ijms22115831] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/19/2021] [Accepted: 05/26/2021] [Indexed: 02/07/2023] Open
Abstract
Cytochrome P450 3A7 (CYP3A7) is a fetal/neonatal liver enzyme that participates in estriol synthesis, clearance of all-trans retinoic acid, and xenobiotic metabolism. Compared to the closely related major drug-metabolizing enzyme in adult liver, CYP3A4, the ligand binding and catalytic capacity of CYP3A7 are substantially reduced. To better understand the structural basis for these functional differences, the 2.15 Å crystal structure of CYP3A7 has been solved. Comparative analysis of CYP3A enzymes shows that decreased structural plasticity rather than the active site microenvironment defines the ligand binding ability of CYP3A7. In particular, a rotameric switch in the gatekeeping amino acid F304 triggers local and long-range rearrangements that transmit to the F-G fragment and alter its interactions with the I-E-D-helical core, resulting in a more rigid structure. Elongation of the β3-β4 strands, H-bond linkage in the substrate channel, and steric constraints in the C-terminal loop further increase the active site rigidity and limit conformational ensemble. Collectively, these structural distinctions lower protein plasticity and change the heme environment, which, in turn, could impede the spin-state transition essential for optimal reactivity and oxidation of substrates.
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Felker D, Zhang H, Bo Z, Lau M, Morishima Y, Schnell S, Osawa Y. Mapping protein-protein interactions in homodimeric CYP102A1 by crosslinking and mass spectrometry. Biophys Chem 2021; 274:106590. [PMID: 33894563 DOI: 10.1016/j.bpc.2021.106590] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 04/05/2021] [Accepted: 04/06/2021] [Indexed: 11/28/2022]
Abstract
Covalent crosslinking and mass spectrometry techniques hold great potential in the study of multiprotein complexes, but a major challenge is the inability to differentiate intra- and inter- protein crosslinks in homomeric complexes. In the current study we use CYP102A1, a well-characterized homodimeric P450, to examine a subtractive method that utilizes limited crosslinking with disuccinimidyl dibutyric urea (DSBU) and isolation of the monomer, in addition to the crosslinked dimer, to identify inter-monomer crosslinks. The utility of this approach was examined with the use of MS-cleavable crosslinker DSBU and recently published cryo-EM based structures of the CYP102A1 homodimer. Of the 31 unique crosslinks found, 26 could be fit to the reported structures whereas 5 exceeded the spatial constraints. Not only did these crosslinks validate the cryo-EM structure, they point to new conformations of CYP102A1 that bring the flavins in closer proximity to the heme.
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Affiliation(s)
- Dana Felker
- Department of Pharmacology, University of Michigan Medical School, 1301 MSRB III, 1150 W. Medical Center Dr., Ann Arbor, MI 48109-5632, USA.
| | - Haoming Zhang
- Department of Pharmacology, University of Michigan Medical School, 1301 MSRB III, 1150 W. Medical Center Dr., Ann Arbor, MI 48109-5632, USA.
| | - Zhiyuan Bo
- Department of Pharmacology, University of Michigan Medical School, 1301 MSRB III, 1150 W. Medical Center Dr., Ann Arbor, MI 48109-5632, USA.
| | - Miranda Lau
- Department of Pharmacology, University of Michigan Medical School, 1301 MSRB III, 1150 W. Medical Center Dr., Ann Arbor, MI 48109-5632, USA.
| | - Yoshihiro Morishima
- Department of Pharmacology, University of Michigan Medical School, 1301 MSRB III, 1150 W. Medical Center Dr., Ann Arbor, MI 48109-5632, USA.
| | - Santiago Schnell
- Department of Molecular & Integrative Physiology, 7744 MS II, 1137 E. Catherine St., Ann Arbor, MI 48109-5622, USA.
| | - Yoichi Osawa
- Department of Pharmacology, University of Michigan Medical School, 1301 MSRB III, 1150 W. Medical Center Dr., Ann Arbor, MI 48109-5632, USA.
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Vincent T, Gaillet B, Garnier A. Optimisation of Cytochrome P450 BM3 Assisted by Consensus-Guided Evolution. Appl Biochem Biotechnol 2021; 193:2893-2914. [PMID: 33860879 DOI: 10.1007/s12010-021-03573-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 04/08/2021] [Indexed: 10/21/2022]
Abstract
Cytochrome P450 enzymes have attracted much interest over the years given their ability to insert oxygen into saturated carbon-hydrogen bonds, a difficult feat to accomplish by traditional chemistry. Much of the activity in this field has centered on the bacterial enzyme CYP102A1, or BM3, from Bacillus megaterium, as it has shown itself capable of hydroxylating/acting upon a wide range of substrates, thereby producing industrially relevant pharmaceuticals, fine chemicals, and hormones. In addition, unlike most cytochromes, BM3 is both soluble and fused to its natural redox partner, thus facilitating its use. The industrial use of BM3 is however stifled by its instability and its requirement for the expensive NADPH cofactor. In this work, we added several mutations to the BM3 mutant R966D/W1046S that enhanced the turnover number achievable with the inexpensive cofactors NADH and NBAH. These new mutations, A769S, S847G, S850R, E852P, and V978L, are localized on the reductase domain of BM3 thus leaving the oxidase domain intact. For NBAH-driven reactions by new mutant NTD5, this led to a 5.24-fold increase in total product output when compared to the BM3 mutant R966D/W1046S. For reactions driven by NADH by new mutant NTD6, this enhanced total product output by as much as 2.3-fold when compared to the BM3 mutant R966D/W1046S. We also demonstrated that reactions driven by NADH with the NTD6 mutant not only surpassed total product output achievable by wild-type BM3 with NADPH but also retained the ability to use this latter cofactor with greater total product output as well.
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Affiliation(s)
- Thierry Vincent
- Department of Chemical Engineering, Université Laval, Québec, Québec, G1V 0A6, Canada
| | - Bruno Gaillet
- Department of Chemical Engineering, Université Laval, Québec, Québec, G1V 0A6, Canada
| | - Alain Garnier
- Department of Chemical Engineering, Université Laval, Québec, Québec, G1V 0A6, Canada.
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Correddu D, Di Nardo G, Gilardi G. Self-Sufficient Class VII Cytochromes P450: From Full-Length Structure to Synthetic Biology Applications. Trends Biotechnol 2021; 39:1184-1207. [PMID: 33610332 DOI: 10.1016/j.tibtech.2021.01.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/25/2021] [Accepted: 01/26/2021] [Indexed: 11/25/2022]
Abstract
Members of class VII cytochromes P450 are catalytically self-sufficient enzymes containing a phthalate dioxygenase reductase-like domain fused to the P450 catalytic domain. Among these, CYP116B46 is the first enzyme for which the 3D structure of the whole polypeptide chain has been solved, shedding light on the interaction between its domains, which is crucial for catalysis. Most of these enzymes have been isolated from extremophiles or detoxifying bacteria that can carry out regio- and enantioselective oxidation of compounds of biotechnological interest. Protein engineering has generated mutants that can perform challenging organic reactions such as the anti-Markovnikov alkene oxidation. This potential, combined with the detailed 3D structure, forms the basis for further directed evolution studies aimed at widening their biotechnological exploitation.
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Affiliation(s)
- Danilo Correddu
- Department of Life Sciences and Systems Biology, University of Torino, Via Accademia Albertina 13, 10123, Torino, Italy
| | - Giovanna Di Nardo
- Department of Life Sciences and Systems Biology, University of Torino, Via Accademia Albertina 13, 10123, Torino, Italy
| | - Gianfranco Gilardi
- Department of Life Sciences and Systems Biology, University of Torino, Via Accademia Albertina 13, 10123, Torino, Italy.
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Xu C, Zou H, Zhao Z, Zheng Z, Kwok RTK, Lam JWY, Sung HHY, Williams ID, Chen S, Zheng L, Tang BZ. Turning on Light Emission of a Dark Pro‐Aggregation‐Induced Emission Luminogen in Aqueous Media Through Reductase‐Modulated Derotation. ADVANCED NANOBIOMED RESEARCH 2021. [DOI: 10.1002/anbr.202000080] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Affiliation(s)
- Changhuo Xu
- Department of Chemistry The Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction Department of Chemical and Biomedical Engineering, Institute for Advanced Study The Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong China
| | - Hang Zou
- Department of Chemistry The Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction Department of Chemical and Biomedical Engineering, Institute for Advanced Study The Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong China
- Department of Laboratory Medicine Nanfang Hospital Southern Medical University Guangzhou 510515 China
| | - Zheng Zhao
- School of Chemistry and Chemical Engineering Southeast University Nanjing China
| | - Zheng Zheng
- Department of Chemistry The Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction Department of Chemical and Biomedical Engineering, Institute for Advanced Study The Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong China
| | - Ryan T. K. Kwok
- Department of Chemistry The Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction Department of Chemical and Biomedical Engineering, Institute for Advanced Study The Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong China
| | - Jacky W. Y. Lam
- Department of Chemistry The Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction Department of Chemical and Biomedical Engineering, Institute for Advanced Study The Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong China
| | - Herman H. Y. Sung
- Department of Chemistry The Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction Department of Chemical and Biomedical Engineering, Institute for Advanced Study The Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong China
| | - Ian D Williams
- Department of Chemistry The Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction Department of Chemical and Biomedical Engineering, Institute for Advanced Study The Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong China
| | - Sijie Chen
- Ming Wai Lau Centre for Reparative Medicine Karolinska Institutet Sha Tin Hong Kong China
| | - Lei Zheng
- Department of Laboratory Medicine Nanfang Hospital Southern Medical University Guangzhou 510515 China
| | - Ben Zhong Tang
- Department of Chemistry The Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction Department of Chemical and Biomedical Engineering, Institute for Advanced Study The Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong China
- Center for Aggregation-Induced Emission SCUT-HKUST Joint Research Institute State Key Laboratory of Luminescent Materials and Devices South China University of Technology Guangzhou 510640 China
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41
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Sellner M, Fischer A, Don CG, Smieško M. Conformational Landscape of Cytochrome P450 Reductase Interactions. Int J Mol Sci 2021; 22:1023. [PMID: 33498551 PMCID: PMC7864194 DOI: 10.3390/ijms22031023] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/15/2021] [Accepted: 01/18/2021] [Indexed: 01/05/2023] Open
Abstract
Oxidative reactions catalyzed by Cytochrome P450 enzymes (CYPs), which constitute the most relevant group of drug-metabolizing enzymes, are enabled by their redox partner Cytochrome P450 reductase (CPR). Both proteins are anchored to the membrane of the endoplasmic reticulum and the CPR undergoes a conformational change in order to interact with the respective CYP and transfer electrons. Here, we conducted over 22 microseconds of molecular dynamics (MD) simulations in combination with protein-protein docking to investigate the conformational changes necessary for the formation of the CPR-CYP complex. While some structural features of the CPR and the CPR-CYP2D6 complex that we highlighted confirmed previous observations, our simulations revealed additional mechanisms for the conformational transition of the CPR. Unbiased simulations exposed a movement of the whole protein relative to the membrane, potentially to facilitate interactions with its diverse set of redox partners. Further, we present a structural mechanism for the susceptibility of the CPR to different redox states based on the flip of a glycine residue disrupting the local interaction network that maintains inter-domain proximity. Simulations of the CPR-CYP2D6 complex pointed toward an additional interaction surface of the FAD domain and the proximal side of CYP2D6. Altogether, this study provides novel structural insight into the mechanism of CPR-CYP interactions and underlying conformational changes, improving our understanding of this complex machinery Cytochrome P450 reductase; CPR; conformational; dynamicsrelevant for drug metabolism.
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Affiliation(s)
| | | | | | - Martin Smieško
- Computational Pharmacy, Departement of Pharmaceutical Sciences, University of Basel, 4056 Basel, Switzerland; (M.S.); (A.F.); (C.G.D.)
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42
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Britti E, Delaspre F, Sanz-Alcázar A, Medina-Carbonero M, Llovera M, Purroy R, Mincheva-Tasheva S, Tamarit J, Ros J. Calcitriol increases frataxin levels and restores mitochondrial function in cell models of Friedreich Ataxia. Biochem J 2021; 478:1-20. [PMID: 33305808 DOI: 10.1042/bcj20200331] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 11/30/2020] [Accepted: 12/07/2020] [Indexed: 12/17/2023]
Abstract
Friedreich ataxia (FA) is a neurodegenerative disease caused by the deficiency of frataxin, a mitochondrial protein. In primary cultures of dorsal root ganglia neurons, we showed that frataxin depletion resulted in decreased levels of the mitochondrial calcium exchanger NCLX, neurite degeneration and apoptotic cell death. Here, we describe that frataxin-deficient dorsal root ganglia neurons display low levels of ferredoxin 1 (FDX1), a mitochondrial Fe/S cluster-containing protein that interacts with frataxin and, interestingly, is essential for the synthesis of calcitriol, the active form of vitamin D. We provide data that calcitriol supplementation, used at nanomolar concentrations, is able to reverse the molecular and cellular markers altered in DRG neurons. Calcitriol is able to recover both FDX1 and NCLX levels and restores mitochondrial membrane potential indicating an overall mitochondrial function improvement. Accordingly, reduction in apoptotic markers and neurite degeneration was observed and, as a result, cell survival was also recovered. All these beneficial effects would be explained by the finding that calcitriol is able to increase the mature frataxin levels in both, frataxin-deficient DRG neurons and cardiomyocytes; remarkably, this increase also occurs in lymphoblastoid cell lines derived from FA patients. In conclusion, these results provide molecular bases to consider calcitriol for an easy and affordable therapeutic approach for FA patients.
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Affiliation(s)
- Elena Britti
- Dept. Ciències Mèdiques Bàsiques, Universitat de Lleida, IRBLleida, AV. Rovira Roure 80, 25198 Lleida, Spain
| | - Fabien Delaspre
- Dept. Ciències Mèdiques Bàsiques, Universitat de Lleida, IRBLleida, AV. Rovira Roure 80, 25198 Lleida, Spain
| | - A Sanz-Alcázar
- Dept. Ciències Mèdiques Bàsiques, Universitat de Lleida, IRBLleida, AV. Rovira Roure 80, 25198 Lleida, Spain
| | - Marta Medina-Carbonero
- Dept. Ciències Mèdiques Bàsiques, Universitat de Lleida, IRBLleida, AV. Rovira Roure 80, 25198 Lleida, Spain
| | - Marta Llovera
- Dept. Ciències Mèdiques Bàsiques, Universitat de Lleida, IRBLleida, AV. Rovira Roure 80, 25198 Lleida, Spain
| | - Rosa Purroy
- Dept. Ciències Mèdiques Bàsiques, Universitat de Lleida, IRBLleida, AV. Rovira Roure 80, 25198 Lleida, Spain
| | - Stefka Mincheva-Tasheva
- Dept. Ciències Mèdiques Bàsiques, Universitat de Lleida, IRBLleida, AV. Rovira Roure 80, 25198 Lleida, Spain
| | - Jordi Tamarit
- Dept. Ciències Mèdiques Bàsiques, Universitat de Lleida, IRBLleida, AV. Rovira Roure 80, 25198 Lleida, Spain
| | - Joaquim Ros
- Dept. Ciències Mèdiques Bàsiques, Universitat de Lleida, IRBLleida, AV. Rovira Roure 80, 25198 Lleida, Spain
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Ivanov YD, Pleshakova TO, Shumov ID, Kozlov AF, Valueva AA, Ivanova IA, Ershova MO, Larionov DI, Repnikov VV, Ivanova ND, Tatur VY, Stepanov IN, Ziborov VS. AFM and FTIR Investigation of the Effect of Water Flow on Horseradish Peroxidase. Molecules 2021; 26:E306. [PMID: 33435278 PMCID: PMC7826892 DOI: 10.3390/molecules26020306] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/04/2021] [Accepted: 01/05/2021] [Indexed: 11/17/2022] Open
Abstract
Atomic force microscopy (AFM)-based fishing is a promising method for the detection of low-abundant proteins. This method is based on the capturing of the target proteins from the analyzed solution onto a solid substrate, with subsequent counting of the captured protein molecules on the substrate surface by AFM. Protein adsorption onto the substrate surface represents one of the key factors determining the capturing efficiency. Accordingly, studying the factors influencing the protein adsorbability onto the substrate surface represents an actual direction in biomedical research. Herein, the influence of water motion in a flow-based system on the protein adsorbability and on its enzymatic activity has been studied with an example of horseradish peroxidase (HRP) enzyme by AFM, attenuated total reflection Fourier-transform infrared spectroscopy (ATR-FTIR) and conventional spectrophotometry. In the experiments, HRP solution was incubated in a setup modeling the flow section of a biosensor communication. The measuring cell with the protein solution was placed near a coiled silicone pipe, through which water was pumped. The adsorbability of the protein onto the surface of the mica substrate has been studied by AFM. It has been demonstrated that incubation of the HRP solution near the coiled silicone pipe with flowing water leads to an increase in its adsorbability onto mica. This is accompanied by a change in the enzyme's secondary structure, as has been revealed by ATR-FTIR. At the same time, its enzymatic activity remains unchanged. The results reported herein can be useful in the development of models describing the influence of liquid flow on the properties of enzymes and other proteins. The latter is particularly important for the development of biosensors for biomedical applications-particularly for serological analysis, which is intended for the early diagnosis of various types of cancer and infectious diseases. Our results should also be taken into account in studies of the effects of protein aggregation on hemodynamics, which plays a key role in human body functioning.
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Affiliation(s)
- Yuri D. Ivanov
- Institute of Biomedical Chemistry, Moscow 119121, Russia; (T.O.P.); (I.D.S.); (A.F.K.); (A.A.V.); (I.A.I.); (M.O.E.); (D.I.L.); (V.S.Z.)
| | - Tatyana O. Pleshakova
- Institute of Biomedical Chemistry, Moscow 119121, Russia; (T.O.P.); (I.D.S.); (A.F.K.); (A.A.V.); (I.A.I.); (M.O.E.); (D.I.L.); (V.S.Z.)
| | - Ivan D. Shumov
- Institute of Biomedical Chemistry, Moscow 119121, Russia; (T.O.P.); (I.D.S.); (A.F.K.); (A.A.V.); (I.A.I.); (M.O.E.); (D.I.L.); (V.S.Z.)
| | - Andrey F. Kozlov
- Institute of Biomedical Chemistry, Moscow 119121, Russia; (T.O.P.); (I.D.S.); (A.F.K.); (A.A.V.); (I.A.I.); (M.O.E.); (D.I.L.); (V.S.Z.)
| | - Anastasia A. Valueva
- Institute of Biomedical Chemistry, Moscow 119121, Russia; (T.O.P.); (I.D.S.); (A.F.K.); (A.A.V.); (I.A.I.); (M.O.E.); (D.I.L.); (V.S.Z.)
| | - Irina A. Ivanova
- Institute of Biomedical Chemistry, Moscow 119121, Russia; (T.O.P.); (I.D.S.); (A.F.K.); (A.A.V.); (I.A.I.); (M.O.E.); (D.I.L.); (V.S.Z.)
| | - Maria O. Ershova
- Institute of Biomedical Chemistry, Moscow 119121, Russia; (T.O.P.); (I.D.S.); (A.F.K.); (A.A.V.); (I.A.I.); (M.O.E.); (D.I.L.); (V.S.Z.)
| | - Dmitry I. Larionov
- Institute of Biomedical Chemistry, Moscow 119121, Russia; (T.O.P.); (I.D.S.); (A.F.K.); (A.A.V.); (I.A.I.); (M.O.E.); (D.I.L.); (V.S.Z.)
| | | | - Nina D. Ivanova
- Skryabin Moscow State Academy of Veterinary Medicine and Biotechnology, Moscow 109472, Russia;
| | - Vadim Yu. Tatur
- Foundation of Perspective Technologies and Novations, Moscow 115682, Russia; (V.Y.T.); (I.N.S.)
| | - Igor N. Stepanov
- Foundation of Perspective Technologies and Novations, Moscow 115682, Russia; (V.Y.T.); (I.N.S.)
| | - Vadim S. Ziborov
- Institute of Biomedical Chemistry, Moscow 119121, Russia; (T.O.P.); (I.D.S.); (A.F.K.); (A.A.V.); (I.A.I.); (M.O.E.); (D.I.L.); (V.S.Z.)
- Joint Institute for High Temperatures of the Russian Academy of Sciences, Moscow 125412, Russia
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An electron transfer competent structural ensemble of membrane-bound cytochrome P450 1A1 and cytochrome P450 oxidoreductase. Commun Biol 2021; 4:55. [PMID: 33420418 PMCID: PMC7794467 DOI: 10.1038/s42003-020-01568-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 12/06/2020] [Indexed: 01/29/2023] Open
Abstract
Cytochrome P450 (CYP) heme monooxygenases require two electrons for their catalytic cycle. For mammalian microsomal CYPs, key enzymes for xenobiotic metabolism and steroidogenesis and important drug targets and biocatalysts, the electrons are transferred by NADPH-cytochrome P450 oxidoreductase (CPR). No structure of a mammalian CYP-CPR complex has been solved experimentally, hindering understanding of the determinants of electron transfer (ET), which is often rate-limiting for CYP reactions. Here, we investigated the interactions between membrane-bound CYP 1A1, an antitumor drug target, and CPR by a multiresolution computational approach. We find that upon binding to CPR, the CYP 1A1 catalytic domain becomes less embedded in the membrane and reorients, indicating that CPR may affect ligand passage to the CYP active site. Despite the constraints imposed by membrane binding, we identify several arrangements of CPR around CYP 1A1 that are compatible with ET. In the complexes, the interactions of the CPR FMN domain with the proximal side of CYP 1A1 are supplemented by more transient interactions of the CPR NADP domain with the distal side of CYP 1A1. Computed ET rates and pathways agree well with available experimental data and suggest why the CYP-CPR ET rates are low compared to those of soluble bacterial CYPs.
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45
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Chen CC, Min J, Zhang L, Yang Y, Yu X, Guo RT. Advanced Understanding of the Electron Transfer Pathway of Cytochrome P450s. Chembiochem 2020; 22:1317-1328. [PMID: 33232569 DOI: 10.1002/cbic.202000705] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 11/24/2020] [Indexed: 11/08/2022]
Abstract
Cytochrome P450s are heme-thiolate enzymes that participate in carbon source assimilation, natural compound biosynthesis and xenobiotic metabolism in all kingdoms of life. P450s can catalyze various reactions by using a wide range of organic compounds, thus exhibiting great potential in biotechnological applications. The catalytic reactions of P450s are driven by electron equivalents that are sourced from pyridine nucleotides and delivered by cognate or matching redox partners (RPs). The electron transfer (ET) route from RPs to P450s involves one or more redox center-containing domains. As the rate of ET is one of the main determinants of P450 efficacy, an in-depth understanding of the P450 ET pathway should increase our knowledge of these important enzymes and benefit their further applications. Here, the various P450 RP systems along with current understanding of their ET routes will be reviewed. Notably, state-of-the-art structural studies of the two main types of self-sufficient P450 will also be summarized.
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Affiliation(s)
- Chun-Chi Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources Hubei Key Laboratory of Industrial Biotechnology School of Life Sciences, Hubei University, Wuhan, Hubei, 430062, P. R. China
| | - Jian Min
- State Key Laboratory of Biocatalysis and Enzyme Engineering Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources Hubei Key Laboratory of Industrial Biotechnology School of Life Sciences, Hubei University, Wuhan, Hubei, 430062, P. R. China
| | - Lilan Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources Hubei Key Laboratory of Industrial Biotechnology School of Life Sciences, Hubei University, Wuhan, Hubei, 430062, P. R. China
| | - Yu Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources Hubei Key Laboratory of Industrial Biotechnology School of Life Sciences, Hubei University, Wuhan, Hubei, 430062, P. R. China
| | - Xuejing Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources Hubei Key Laboratory of Industrial Biotechnology School of Life Sciences, Hubei University, Wuhan, Hubei, 430062, P. R. China
| | - Rey-Ting Guo
- State Key Laboratory of Biocatalysis and Enzyme Engineering Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources Hubei Key Laboratory of Industrial Biotechnology School of Life Sciences, Hubei University, Wuhan, Hubei, 430062, P. R. China
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Li Y, Zhang R, Xu Y. Structure-based mechanisms: On the way to apply alcohol dehydrogenases/reductases to organic-aqueous systems. Int J Biol Macromol 2020; 168:412-427. [PMID: 33316337 DOI: 10.1016/j.ijbiomac.2020.12.068] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 12/08/2020] [Accepted: 12/08/2020] [Indexed: 12/20/2022]
Abstract
Alcohol dehydrogenases/reductases catalyze enantioselective syntheses of versatile chiral compounds relying on direct hydride transfer from cofactor to substrates, or to an intermediate and then to substrates. Since most of the substrates catalyzed by alcohol dehydrogenases/reductases are insoluble in aqueous solutions, increasing interest has been turning to organic-aqueous systems. However, alcohol dehydrogenases/reductases are normally instable in organic solvents, leading to the unsatisfied enantioselective synthesis efficiency. The behaviors of these enzymes in organic solvents at an atomic level are unclear, thus it is of great importance to understand its structure-based mechanisms in organic-aqueous systems to improve their relative stability. Here, we summarized the accessible structures of alcohol dehydrogenases/reductases in Protein Data Bank crystallized in organic-aqueous systems, and compared the structures of alcohol dehydrogenases/reductases which have different tolerance towards organic solvents. By understanding the catalytic behaviors and mechanisms of these enzymes in organic-aqueous systems, the efficient enantioselective syntheses mediated by alcohol dehydrogenases/reductases and further challenges are also discussed through solvent engineering and enzyme-immobilization in the last decade.
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Affiliation(s)
- Yaohui Li
- Key Laboratory of Industrial Biotechnology of Ministry of Education & School of Biotechnology, Jiangnan University, Wuxi 214122, PR China; Department of Biological Science, Columbia University, New York, NY 10025, United States
| | - Rongzhen Zhang
- Key Laboratory of Industrial Biotechnology of Ministry of Education & School of Biotechnology, Jiangnan University, Wuxi 214122, PR China.
| | - Yan Xu
- Key Laboratory of Industrial Biotechnology of Ministry of Education & School of Biotechnology, Jiangnan University, Wuxi 214122, PR China.
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Eidenschenk C, Cheruzel L. Ru(II)-diimine complexes and cytochrome P450 working hand-in-hand. J Inorg Biochem 2020; 213:111254. [PMID: 32979791 PMCID: PMC7686262 DOI: 10.1016/j.jinorgbio.2020.111254] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/19/2020] [Accepted: 09/06/2020] [Indexed: 10/23/2022]
Abstract
With a growing interest in utilizing visible light to drive biocatalytic processes, several light-harvesting units and approaches have been employed to harness the synthetic potential of heme monooxygenases and carry out selective oxyfunctionalization of a wide range of substrates. While the fields of cytochrome P450 and Ru(II) photochemistry have separately been prolific, it is not until the turn of the 21st century that they converged. Non-covalent and subsequently covalently attached Ru(II) complexes were used to promote rapid intramolecular electron transfer in bacterial P450 enzymes. Photocatalytic activity with Ru(II)-modified P450 enzymes was achieved under reductive conditions with a judicious choice of a sacrificial electron donor. The initial concept of Ru(II)-modified P450 enzymes was further improved using protein engineering, photosensitizer functionalization and was successfully applied to other P450 enzymes. In this review, we wish to present the recent contributions from our group and others in utilizing Ru(II) complexes coupled with P450 enzymes in the broad context of photobiocatalysis, protein assemblies and chemoenzymatic reactions. The merging of chemical catalysts with the synthetic potential of P450 enzymes has led to the development of several chemoenzymatic approaches. Moreover, strained Ru(II) compounds have been shown to selectively inhibit P450 enzymes by releasing aromatic heterocycle containing molecules upon visible light excitation taking advantage of the rapid ligand loss feature in those complexes.
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Affiliation(s)
- Celine Eidenschenk
- Department Biochemical and Cellular Pharmacology, Genentech, One DNA Way, South San Francisco, CA 94080, USA
| | - Lionel Cheruzel
- San José State University, Department of Chemistry, One Washington Square, San José, CA 95192-0101, USA.
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48
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Li Y, Qiao B, Olvera de la Cruz M. Protein Surface Printer for Exploring Protein Domains. J Chem Inf Model 2020; 60:5255-5264. [PMID: 32846088 DOI: 10.1021/acs.jcim.0c00582] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The surface of proteins is vital in determining protein functions. Herein, a program, Protein Surface Printer (PSP), is built that performs multiple functions in quantifying protein surface domains. Two proteins, PETase and cytochrome P450, are used to validate that the program supports atomistic simulations with different combinations of programs and force fields. A case study is conducted on the structural analysis of the spike proteins of SARS-CoV-2 and SARS-CoV and the human cell receptor ACE2. Although the surface domains of both spike proteins are highly similar, their receptor-binding domains (RBDs) and the O-linked glycan domains are structurally different. The O-linked glycan domain of SARS-CoV-2 is highly positively charged, which may promote binding to negatively charged human cells.
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Affiliation(s)
- Yang Li
- Department of Chemical Engineering, Northwestern University, Evanston, Illinois 60201, United States
| | - Baofu Qiao
- Department of Material Science and Engineering, Northwestern University, Evanston, Illinois 60201, United States
| | - Monica Olvera de la Cruz
- Department of Chemical Engineering, Northwestern University, Evanston, Illinois 60201, United States.,Department of Material Science and Engineering, Northwestern University, Evanston, Illinois 60201, United States.,Department of Chemistry, Northwestern University, Evanston, Illinois 60201, United States
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Dunham NP, Arnold FH. Nature's Machinery, Repurposed: Expanding the Repertoire of Iron-Dependent Oxygenases. ACS Catal 2020; 10:12239-12255. [PMID: 33282461 PMCID: PMC7710332 DOI: 10.1021/acscatal.0c03606] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Iron is an especially important redox-active cofactor in biology because of its ability to mediate reactions with atmospheric O2. Iron-dependent oxygenases exploit this earth-abundant transition metal for the insertion of oxygen atoms into organic compounds. Throughout the astounding diversity of transformations catalyzed by these enzymes, the protein framework directs reactive intermediates toward the precise formation of products, which, in many cases, necessitates the cleavage of strong C-H bonds. In recent years, members of several iron-dependent oxygenase families have been engineered for new-to-nature transformations that offer advantages over conventional synthetic methods. In this Perspective, we first explore what is known about the reactivity of heme-dependent cytochrome P450 oxygenases and nonheme iron-dependent oxygenases bearing the 2-His-1-carboxylate facial triad by reviewing mechanistic studies with an emphasis on how the protein scaffold maximizes the catalytic potential of the iron-heme and iron cofactors. We then review how these cofactors have been repurposed for abiological transformations by engineering the protein frameworks of these enzymes. Finally, we discuss contemporary challenges associated with engineering these platforms and comment on their roles in biocatalysis moving forward.
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Affiliation(s)
- Noah P. Dunham
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, MC 210-41, Pasadena, California 91125, United States
| | - Frances H. Arnold
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, MC 210-41, Pasadena, California 91125, United States
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50
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New frontiers: harnessing pivotal advances in microbial engineering for the biosynthesis of plant-derived terpenoids. Curr Opin Biotechnol 2020; 65:88-93. [DOI: 10.1016/j.copbio.2020.02.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 01/30/2020] [Accepted: 02/02/2020] [Indexed: 01/01/2023]
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