1
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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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2
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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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3
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Frank R, Prönnecke C, Azendorf R, Jahnke HG, Beck-Sickinger AG, Robitzki AA. Advanced 96-microtiter plate based bioelectrochemical platform reveals molecular short cut of electron flow in cytochrome P450 enzyme. LAB ON A CHIP 2020; 20:1449-1460. [PMID: 32219236 DOI: 10.1039/c9lc01220f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
In bioelectrocatalysis, immobilised redox enzymes are activated in a bioelectronic interface without redox equivalents such as NADPH, thus enabling heterogeneous flow chemistry. The functional contact between enzyme and electrode requires a high degree of optimisation regarding choice of electrode material, electrode pre-treatment, enzyme immobilisation and reaction conditions. So far, however, there are no systems that can easily enable an optimisation procedure at a higher throughput. Here, we present an advanced platform with a vertical divided cell architecture in conjunction with a developed 96-multipotentiostat to be able to drive redox enzymes in 96 well microtiter plate based multielectrode arrays. This platform controls 96 independent three-electrode setups with arbitrary working electrode materials. We demonstrate its applicability in a mutation study of cytochrome P450 BM3 using indium tin oxide as electrode material and the 7-ethoxycoumarin product quantification assay. We show that the bioelectrocatalytic activity of P450 BM3 can be amplified when the cofactor FAD is erased from the enzyme by a single point mutation, so that FMN becomes the first electron entry point. Bioelectrocatalysis thus offers an approach to enzyme simplification as a remedy for the inherent instability of self-sufficient cytochrome P450 enzymes. In addition, we examined native and artificial enzyme activation with respect to ionic strength and buffer composition. The optimal conditions of the activation types differ substantially from each other and exhibit a new molecular facet in enzyme characteristics. In a proof-of-principle we demonstrate that the platform is also compatible with raw cell extracts, thus opening the door for random mutagenesis screenings.
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Affiliation(s)
- Ronny Frank
- Centre for Biotechnology and Biomedicine, Molecular biological-biochemical Processing Technology, Leipzig University, Deutscher Platz 5, D-04103 Leipzig, Germany.
| | - Christoph Prönnecke
- Centre for Biotechnology and Biomedicine, Molecular biological-biochemical Processing Technology, Leipzig University, Deutscher Platz 5, D-04103 Leipzig, Germany.
| | - Ronny Azendorf
- Centre for Biotechnology and Biomedicine, Molecular biological-biochemical Processing Technology, Leipzig University, Deutscher Platz 5, D-04103 Leipzig, Germany.
| | - Heinz-Georg Jahnke
- Centre for Biotechnology and Biomedicine, Molecular biological-biochemical Processing Technology, Leipzig University, Deutscher Platz 5, D-04103 Leipzig, Germany.
| | | | - Andrea A Robitzki
- Centre for Biotechnology and Biomedicine, Molecular biological-biochemical Processing Technology, Leipzig University, Deutscher Platz 5, D-04103 Leipzig, Germany.
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4
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Jeffreys LN, Pacholarz KJ, Johannissen LO, Girvan HM, Barran PE, Voice MW, Munro AW. Characterization of the structure and interactions of P450 BM3 using hybrid mass spectrometry approaches. J Biol Chem 2020; 295:7595-7607. [PMID: 32303637 PMCID: PMC7261786 DOI: 10.1074/jbc.ra119.011630] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 04/02/2020] [Indexed: 01/08/2023] Open
Abstract
The cytochrome P450 monooxygenase P450 BM3 (BM3) is a biotechnologically important and versatile enzyme capable of producing important compounds such as the medical drugs pravastatin and artemether, and the steroid hormone testosterone. BM3 is a natural fusion enzyme comprising two major domains: a cytochrome P450 (heme-binding) catalytic domain and a NADPH-cytochrome P450 reductase (CPR) domain containing FAD and FMN cofactors in distinct domains of the CPR. A crystal structure of full-length BM3 enzyme is not available in its monomeric or catalytically active dimeric state. In this study, we provide detailed insights into the protein-protein interactions that occur between domains in the BM3 enzyme and characterize molecular interactions within the BM3 dimer by using several hybrid mass spectrometry (MS) techniques, namely native ion mobility MS (IM-MS), collision-induced unfolding (CIU), and hydrogen-deuterium exchange MS (HDX-MS). These methods enable us to probe the structure, stoichiometry, and domain interactions in the ∼240 kDa BM3 dimeric complex. We obtained high-sequence coverage (88–99%) in the HDX-MS experiments for full-length BM3 and its component domains in both the ligand-free and ligand-bound states. We identified important protein interaction sites, in addition to sites corresponding to heme-CPR domain interactions at the dimeric interface. These findings bring us closer to understanding the structure and catalytic mechanism of P450 BM3.
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Affiliation(s)
- Laura N Jeffreys
- The Manchester Institute of Biotechnology, School of Natural Sciences, Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom.,Manchester Synthetic Biology Research Centre for Fine and Speciality Chemicals (SYNBIOCHEM), The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Kamila J Pacholarz
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Linus O Johannissen
- The Manchester Institute of Biotechnology, School of Natural Sciences, Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom.,Manchester Synthetic Biology Research Centre for Fine and Speciality Chemicals (SYNBIOCHEM), The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Hazel M Girvan
- The Manchester Institute of Biotechnology, School of Natural Sciences, Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom.,Manchester Synthetic Biology Research Centre for Fine and Speciality Chemicals (SYNBIOCHEM), The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Perdita E Barran
- The Manchester Institute of Biotechnology, School of Natural Sciences, Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom.,Manchester Synthetic Biology Research Centre for Fine and Speciality Chemicals (SYNBIOCHEM), The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom.,Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Michael W Voice
- Cypex Ltd., 6 Tom McDonald Avenue, Dundee, DD2 1NH, United Kingdom
| | - Andrew W Munro
- The Manchester Institute of Biotechnology, School of Natural Sciences, Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom .,Manchester Synthetic Biology Research Centre for Fine and Speciality Chemicals (SYNBIOCHEM), The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
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5
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Hussain R, Yadav R, Ahmed M, Khan TA, Kumar D, Akhter Y. Interplay between two spin states determines the hydroxylation catalyzed by P
450
monooxygenase from
Trichoderma brevicompactum. J Comput Chem 2020; 41:1330-1336. [DOI: 10.1002/jcc.26177] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Revised: 01/30/2020] [Accepted: 02/10/2020] [Indexed: 01/03/2023]
Affiliation(s)
- Razak Hussain
- Department of BotanyAligarh Muslim University Aligarh Uttar Pradesh India
| | - Rolly Yadav
- Department of Applied PhysicsSchool for Physical Sciences, Babasaheb Bhimrao Ambedkar University Lucknow Uttar Pradesh India
| | - Mushtaq Ahmed
- Centre for Molecular BiologySchool of Life Sciences, Central University of Jammu Bagla Jammu and Kashmir India
| | - Tabreiz A. Khan
- Department of BotanyAligarh Muslim University Aligarh Uttar Pradesh India
| | - Devesh Kumar
- Department of Applied PhysicsSchool for Physical Sciences, Babasaheb Bhimrao Ambedkar University Lucknow Uttar Pradesh India
| | - Yusuf Akhter
- Department of BiotechnologyBabasaheb Bhimrao Ambedkar University Lucknow Uttar Pradesh India
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Brandenberg OF, Miller DC, Markel U, Ouald Chaib A, Arnold FH. Engineering Chemoselectivity in Hemoprotein-Catalyzed Indole Amidation. ACS Catal 2019; 9:8271-8275. [PMID: 31938573 DOI: 10.1021/acscatal.9b02508] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Here we report a cytochrome P450 variant that catalyzes C2-amidation of 1-methylindoles with tosyl azide via nitrene transfer. Before evolutionary optimization the enzyme exhibited two undesired side reactivities resulting in reduction of the putative iron-nitrenoid intermediate or cycloaddition between the two substrates to form triazole products. We speculated that triazole formation was a promiscuous cycloaddition activity of the P450 heme domain, while sulfonamide formation likely arose from surplus electron transfer from the reductase domain. Directed evolution involving mutagenesis of both the heme and reductase domains delivered an enzyme providing the desired indole amidation products with up to 8400 turnovers, 90% yield, and a shift in chemoselectivity from 2:19:1 to 110:12:1 in favor of nitrene transfer over reduction or triazole formation. This work expands the substrate scope of hemoprotein nitrene transferases to heterocycles and highlights the adaptability of the P450 scaffold to solve challenging chemoselectivity problems in non-natural enzymatic catalysis.
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Affiliation(s)
- Oliver F. Brandenberg
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - David C. Miller
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Ulrich Markel
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Anissa Ouald Chaib
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Frances H. Arnold
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
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7
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Hussain R, Ahmed M, Khan TA, Akhter Y. Augmentation of cytochrome P450 monooxygenase catalysis on its interaction with NADPH-cytochrome P450 reductase FMN domain from Trichoderma brevicompactum. Int J Biochem Cell Biol 2018; 103:74-80. [DOI: 10.1016/j.biocel.2018.08.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 08/08/2018] [Accepted: 08/16/2018] [Indexed: 12/23/2022]
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8
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Frauenkron-Machedjou VJ, Fulton A, Zhao J, Weber L, Jaeger KE, Schwaneberg U, Zhu L. Exploring the full natural diversity of single amino acid exchange reveals that 40–60% of BSLA positions improve organic solvents resistance. BIORESOUR BIOPROCESS 2018. [DOI: 10.1186/s40643-017-0188-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
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9
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Dubey KD, Shaik S. Choreography of the Reductase and P450 BM3 Domains Toward Electron Transfer Is Instigated by the Substrate. J Am Chem Soc 2018; 140:683-690. [PMID: 29277994 DOI: 10.1021/jacs.7b10072] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The driving force for the electron transfer (ET) step in the catalytic cycle of cytochrome P450BM3 is investigated using three sets of 1 μs molecular dynamic simulations for the resting state of P450 in complex with the flavin (FMN) in the reductase domain. These sets involve the following: (i) substrate-free (SF), (ii) substrate (N-palmitoyl glycine, i.e., NPG)-bound (SB), and (iii) SB with the semiquinone radical anion (SQ-) of FMN. Starting from the X-ray structure of the SF heme domain, we observe that the α1-helix (of the reductase) and the C-helix (of the heme) undergo reorientation to a parallel orientation, which is the thermochemically stable form. The reorientation of the helices pushes away the FMN to a distance of 18.4 Å from the heme's center. When the substrate binds it causes the I-helix of the heme domain to kink and push the C-helix toward the α1-helix, thereby locking the latter two into a stabilized perpendicular conformation, wherein the FMN-heme distance is 12 Å. The distance drops further in the SQ- form, and upon QM/MM geometry optimization the two moieties approach 8.8 Å, which enhances the ET rate (by 104-106 fold) to the heme's Fe3+ ion. These motions are driven by hydrogen bond strengthening between the C- and the α1-helices. Finally, substrate binding leads to formation of an organized water chain connecting the FMN and heme moieties. The water channel assists the ET and couples it to the proton transfer steps that should activate O2 and create the oxo-iron active species.
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Affiliation(s)
- Kshatresh Dutta Dubey
- Institute of Chemistry, The Hebrew University of Jerusalem , 9190400 Jerusalem, Israel
| | - Sason Shaik
- Institute of Chemistry, The Hebrew University of Jerusalem , 9190400 Jerusalem, Israel
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10
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Darimont D, Weissenborn MJ, Nebel BA, Hauer B. Modulating proposed electron transfer pathways in P450 BM3 led to improved activity and coupling efficiency. Bioelectrochemistry 2017; 119:119-123. [PMID: 28965071 DOI: 10.1016/j.bioelechem.2017.08.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 08/23/2017] [Accepted: 08/24/2017] [Indexed: 10/18/2022]
Abstract
Electrochemical in vitro reduction of P450 enzymes is a promising alternative to in vivo applications. Previously we presented three engineered P450BM3 variants for aniline hydroxylation, equipped with a carbon nanotube binding-peptide (CNT-tag) for self-assembly on CNT electrodes. Compared to wildtype P450BM3 the NADPH-dependent activity was enhanced, but the coupling efficiency remained low. For P450BM3 Verma, Schwaneberg and Roccatano (2014, Biopolymers 101, 197-209) calculated putative electron transfer pathways (eTPs) by MD simulations. We hypothesised that knockouts of these transfer pathways would alter the coupling efficiency of the system. The results revealed no improved system for the electrically-driven P450s. For the NADPH-driven P450s, however, the most active eTP-mutant showed a 13-fold increased activity and a 32-fold elevated coupling efficiency using NADPH as reducing equivalent. This suggests an alternative principle of electron transport for the reduction by NADPH and an electrode, respectively. The work presents moreover a tool to improve the coupling and activity of P450s with non-natural substrates.
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Affiliation(s)
- Dominique Darimont
- Institute of Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Martin J Weissenborn
- Leibniz-Institute of Plant Biochemistry (IPB), Weinberg 3, 06120 Halle (Saale), Germany; Martin-Luther-University Halle-Wittenberg, Institute of Chemistry, Germany
| | - Bernd A Nebel
- Institute of Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Bernhard Hauer
- Institute of Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany.
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11
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Panneerselvam S, Shehzad A, Mueller-Dieckmann J, Wilmanns M, Bocola M, Davari MD, Schwaneberg U. Crystallographic insights into a cobalt (III) sepulchrate based alternative cofactor system of P450 BM3 monooxygenase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1866:134-140. [PMID: 28739446 DOI: 10.1016/j.bbapap.2017.07.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 07/15/2017] [Accepted: 07/18/2017] [Indexed: 12/26/2022]
Abstract
P450 BM3 is a multi-domain heme-containing soluble bacterial monooxygenase. P450 BM3 and variants are known to oxidize structurally diverse substrates. Crystal structures of individual domains of P450 BM3 are available. However, the spatial organization of the full-length protein is unknown. In this study, crystal structures of the P450 BM3 M7 heme domain variant with and without cobalt (III) sepulchrate are reported. Cobalt (III) sepulchrate acts as an electron shuttle in an alternative cofactor system employing zinc dust as the electron source. The crystal structure shows a binding site for the mediator cobalt (III) sepulchrate at the entrance of the substrate access channel. The mediator occupies an unusual position which is far from the active site and distinct from the binding of the natural redox partner (FAD/NADPH binding domain).
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Affiliation(s)
| | - Aamir Shehzad
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany; Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology, Kohat, Khyber Pakhtunkhwa, Pakistan
| | | | - Matthias Wilmanns
- European Molecular Biology Laboratory-Hamburg, c/o DESY, Hamburg, Germany
| | - Marco Bocola
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Mehdi D Davari
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Ulrich Schwaneberg
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany; DWI-Leibniz Institut für Interaktive Materialien, Forckenbeckstraße 50, 52056 Aachen, Germany.
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12
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Verma R, Mitchell-Koch K. In Silico Studies of Small Molecule Interactions with Enzymes Reveal Aspects of Catalytic Function. Catalysts 2017; 7:212. [PMID: 30464857 PMCID: PMC6241538 DOI: 10.3390/catal7070212] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Small molecules, such as solvent, substrate, and cofactor molecules, are key players in enzyme catalysis. Computational methods are powerful tools for exploring the dynamics and thermodynamics of these small molecules as they participate in or contribute to enzymatic processes. In-depth knowledge of how small molecule interactions and dynamics influence protein conformational dynamics and function is critical for progress in the field of enzyme catalysis. Although numerous computational studies have focused on enzyme-substrate complexes to gain insight into catalytic mechanisms, transition states and reaction rates, the dynamics of solvents, substrates, and cofactors are generally less well studied. Also, solvent dynamics within the biomolecular solvation layer play an important part in enzyme catalysis, but a full understanding of its role is hampered by its complexity. Moreover, passive substrate transport has been identified in certain enzymes, and the underlying principles of molecular recognition are an area of active investigation. Enzymes are highly dynamic entities that undergo different conformational changes, which range from side chain rearrangement of a residue to larger-scale conformational dynamics involving domains. These events may happen nearby or far away from the catalytic site, and may occur on different time scales, yet many are related to biological and catalytic function. Computational studies, primarily molecular dynamics (MD) simulations, provide atomistic-level insight and site-specific information on small molecule interactions, and their role in conformational pre-reorganization and dynamics in enzyme catalysis. The review is focused on MD simulation studies of small molecule interactions and dynamics to characterize and comprehend protein dynamics and function in catalyzed reactions. Experimental and theoretical methods available to complement and expand insight from MD simulations are discussed briefly.
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Affiliation(s)
- Rajni Verma
- Department of Chemistry, McKinley Hall, Wichita State University, 1845 Fairmount, Wichita, KS 67260-0051, USA
| | - Katie Mitchell-Koch
- Department of Chemistry, McKinley Hall, Wichita State University, 1845 Fairmount, Wichita, KS 67260-0051, USA
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Spradlin J, Lee D, Mahadevan S, Mahomed M, Tang L, Lam Q, Colbert A, Shafaat OS, Goodin D, Kloos M, Kato M, Cheruzel LE. Insights into an efficient light-driven hybrid P450 BM3 enzyme from crystallographic, spectroscopic and biochemical studies. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:1732-1738. [PMID: 27639964 DOI: 10.1016/j.bbapap.2016.09.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 09/09/2016] [Accepted: 09/13/2016] [Indexed: 12/31/2022]
Abstract
BACKGROUND In order to perform selective CH functionalization upon visible light irradiation, Ru(II)-diimine functionalized P450 heme enzymes have been developed. The sL407C-1 enzyme containing the Ru(bpy)2PhenA (bpy=2,2'-bipyridine and PhenA=5-acetamido-1,10-phenanthroline) photosensitizer (1) covalently attached to the non-native single cysteine L407C of the P450BM3 heme domain mutant, displays high photocatalytic activity in the selective CH bond hydroxylation of several substrates. METHODS A combination of X-ray crystallography, site-directed mutagenesis, transient absorption measurements and enzymatic assays was used to gain insights into its photocatalytic activity and electron transfer pathway. RESULTS The crystal structure of the sL407C-1 enzyme was solved in the open and closed conformations revealing a through-space electron transfer pathway involving highly conserved, F393 and Q403, residues. Several mutations of these residues (F393A, F393W or Q403W) were introduced to probe their roles in the overall reaction. Transient absorption measurements confirm rapid electron transfer as heme reduction is observed in all four hybrid enzymes. Compared to the parent sL407C-1, photocatalytic activity was negligible in the dF393A-1 enzyme while 60% increase in activity with total turnover numbers of 420 and 90% product conversion was observed with the dQ403W-1 mutant. CONCLUSIONS In the sL407C-1 enzyme, the photosensitizer is ideally located to rapidly deliver electrons, using the naturally occurring electron transfer pathway, to the heme center in order to activate molecular dioxygen and sustain photocatalytic activity. GENERAL SIGNIFICANCE The results shed light on the design of efficient light-driven biocatalysts and the approach can be generalized to other members of the P450 superfamily.
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Affiliation(s)
- Jessica Spradlin
- San José State University, Department of Chemistry, One Washington Square, San José, CA, United States
| | - Diana Lee
- San José State University, Department of Chemistry, One Washington Square, San José, CA, United States
| | - Sruthi Mahadevan
- San José State University, Department of Chemistry, One Washington Square, San José, CA, United States
| | - Mavish Mahomed
- Department of Chemistry, One Shields Ave., University of California Davis, Davis, CA, United States
| | - Lawrence Tang
- San José State University, Department of Chemistry, One Washington Square, San José, CA, United States
| | - Quan Lam
- San José State University, Department of Chemistry, One Washington Square, San José, CA, United States
| | - Alexander Colbert
- San José State University, Department of Chemistry, One Washington Square, San José, CA, United States
| | - Oliver S Shafaat
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, United States
| | - David Goodin
- Department of Chemistry, One Shields Ave., University of California Davis, Davis, CA, United States
| | - Marco Kloos
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Mallory Kato
- San José State University, Department of Chemistry, One Washington Square, San José, CA, United States
| | - Lionel E Cheruzel
- San José State University, Department of Chemistry, One Washington Square, San José, CA, United States.
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14
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Durairaj P, Hur JS, Yun H. Versatile biocatalysis of fungal cytochrome P450 monooxygenases. Microb Cell Fact 2016; 15:125. [PMID: 27431996 PMCID: PMC4950769 DOI: 10.1186/s12934-016-0523-6] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 07/10/2016] [Indexed: 11/19/2022] Open
Abstract
Cytochrome P450 (CYP) monooxygenases, the nature’s most versatile biological catalysts have unique ability to catalyse regio-, chemo-, and stereospecific oxidation of a wide range of substrates under mild reaction conditions, thereby addressing a significant challenge in chemocatalysis. Though CYP enzymes are ubiquitous in all biological kingdoms, the divergence of CYPs in fungal kingdom is manifold. The CYP enzymes play pivotal roles in various fungal metabolisms starting from housekeeping biochemical reactions, detoxification of chemicals, and adaptation to hostile surroundings. Considering the versatile catalytic potentials, fungal CYPs has gained wide range of attraction among researchers and various remarkable strategies have been accomplished to enhance their biocatalytic properties. Numerous fungal CYPs with multispecialty features have been identified and the number of characterized fungal CYPs is constantly increasing. Literature reveals ample reviews on mammalian, plant and bacterial CYPs, however, modest reports on fungal CYPs urges a comprehensive review highlighting their novel catalytic potentials and functional significances. In this review, we focus on the diversification and functional diversity of fungal CYPs and recapitulate their unique and versatile biocatalytic properties. As such, this review emphasizes the crucial issues of fungal CYP systems, and the factors influencing efficient biocatalysis.
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Affiliation(s)
- Pradeepraj Durairaj
- Korean Lichen Research Institute, Sunchon National University, Suncheon, South Korea
| | - Jae-Seoun Hur
- Korean Lichen Research Institute, Sunchon National University, Suncheon, South Korea
| | - Hyungdon Yun
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, South Korea.
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15
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Verma R, Schwaneberg U, Holtmann D, Roccatano D. Unraveling Binding Effects of Cobalt(II) Sepulchrate with the Monooxygenase P450 BM-3 Heme Domain Using Molecular Dynamics Simulations. J Chem Theory Comput 2015; 12:353-63. [DOI: 10.1021/acs.jctc.5b00290] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Rajni Verma
- Department
of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Ulrich Schwaneberg
- Department
of Biotechnology, RWTH Aachen University, Worringer Weg 1, 52074 Aachen, Germany
| | - Dirk Holtmann
- Biochemical
Engineering Group, DECHEMA-Forschungsinstitut, Theodor-Heuss-Allee 25, 60486 Frankfurt am Main, Germany
| | - Danilo Roccatano
- School
of Mathematics and Physics, University of Lincoln, Brayford Pool, Lincoln LN6 7TS, United Kingdom
- School
of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
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16
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Roccatano D. Structure, dynamics, and function of the monooxygenase P450 BM-3: insights from computer simulations studies. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2015; 27:273102. [PMID: 26061496 DOI: 10.1088/0953-8984/27/27/273102] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The monooxygenase P450 BM-3 is a NADPH-dependent fatty acid hydroxylase enzyme isolated from soil bacterium Bacillus megaterium. As a pivotal member of cytochrome P450 superfamily, it has been intensely studied for the comprehension of structure-dynamics-function relationships in this class of enzymes. In addition, due to its peculiar properties, it is also a promising enzyme for biochemical and biomedical applications. However, despite the efforts, the full understanding of the enzyme structure and dynamics is not yet achieved. Computational studies, particularly molecular dynamics (MD) simulations, have importantly contributed to this endeavor by providing new insights at an atomic level regarding the correlations between structure, dynamics, and function of the protein. This topical review summarizes computational studies based on MD simulations of the cytochrome P450 BM-3 and gives an outlook on future directions.
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Affiliation(s)
- Danilo Roccatano
- School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
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17
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Cui YL, Zheng QC, Zhang JL, Zhang HX. Molecular basis of the recognition of arachidonic acid by cytochrome P450 2E1 along major access tunnel. Biopolymers 2014; 103:53-66. [DOI: 10.1002/bip.22567] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 09/23/2014] [Indexed: 01/09/2023]
Affiliation(s)
- Ying-Lu Cui
- State Key Laboratory of Theoretical and Computational Chemistry; Institute of Theoretical Chemistry, Jilin University; Changchun People's Republic of China
| | - Qing-Chuan Zheng
- State Key Laboratory of Theoretical and Computational Chemistry; Institute of Theoretical Chemistry, Jilin University; Changchun People's Republic of China
| | - Ji-Long Zhang
- State Key Laboratory of Theoretical and Computational Chemistry; Institute of Theoretical Chemistry, Jilin University; Changchun People's Republic of China
| | - Hong-Xing Zhang
- State Key Laboratory of Theoretical and Computational Chemistry; Institute of Theoretical Chemistry, Jilin University; Changchun People's Republic of China
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18
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Bernhardt R, Urlacher VB. Cytochromes P450 as promising catalysts for biotechnological application: chances and limitations. Appl Microbiol Biotechnol 2014; 98:6185-203. [PMID: 24848420 DOI: 10.1007/s00253-014-5767-7] [Citation(s) in RCA: 248] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2014] [Revised: 04/08/2014] [Accepted: 04/09/2014] [Indexed: 01/08/2023]
Abstract
Cytochromes P450 (CYPs) belong to the superfamily of heme b containing monooxygenases with currently more than 21,000 members. These enzymes accept a vast range of organic molecules and catalyze diverse reactions. These extraordinary capabilities of CYP systems that are unmet by other enzymes make them attractive for biotechnology. However, the complexity of these systems due to the need of electron transfer from nicotinamide adenine dinucleotide (phosphate) (NAD(P)H) via redox partner proteins for the initial hydroxylation step limits a broader technical implementation of CYP enzymes. There have been several reviews during the past years tackling the potential CYPs for synthetic application. The aim of this review is to give a critical overview about possibilities and chances for application of these interesting catalysts as well as to discuss drawbacks and problems related to their use. Solutions to overcome these limitations will be demonstrated, and several selected examples of successful CYP applications under industrial conditions will be reviewed.
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Affiliation(s)
- Rita Bernhardt
- Institute of Biochemistry, Saarland University, 66123, Saarbrücken, Germany,
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