1
|
Sahil M, Singh T, Ghosh S, Mondal J. 3site Multisubstrate-Bound State of Cytochrome P450cam. J Am Chem Soc 2023; 145:23488-23502. [PMID: 37867463 DOI: 10.1021/jacs.3c06144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2023]
Abstract
We identified a multisubstrate-bound state, hereby referred as a 3site state, in cytochrome P450cam via integrating molecular dynamics simulation with nuclear magnetic resonance (NMR) pseudocontact shift measurements. The 3site state is a result of simultaneous binding of three camphor molecules in three locations around P450cam: (a) in a well-established "catalytic" site near heme, (b) in a kink-separated "waiting" site along channel-1, and (c) in a previously reported "allosteric" site at E, F, G, and H helical junctions. These three spatially distinct binding modes in the 3site state mutually communicate with each other via homotropic allostery and act cooperatively to render P450cam functional. The 3site state shows a significantly superior fit with NMR pseudo contact shift (PCS) data with a Q-score of 0.045 than previously known bound states and consists of D251 free of salt-bridges with K178 and R186, rendering the enzyme functionally primed. To date, none of the reported cocomplex of P450cam with its redox partner putidaredoxin (pdx) has been able to match solution NMR data and controversial pdx-induced opening of P450cam's channel-1 remains a matter of recurrent discourse. In this regard, inclusion of pdx to the 3site state is able to perfectly fit the NMR PCS measurement with a Q-score of 0.08 and disfavors the pdx-induced opening of channel-1, reconciling previously unexplained remarkably fast hydroxylation kinetics with a koff of 10.2 s-1. Together, our findings hint that previous experimental observations may have inadvertently captured the 3site state as an in vitro solution state, instead of the catalytic state alone, and provided a distinct departure from the conventional understanding of cytochrome P450.
Collapse
Affiliation(s)
- Mohammad Sahil
- Tata Institute of Fundamental Research, Hyderabad 500046, India
| | - Tejender Singh
- Tata Institute of Fundamental Research, Hyderabad 500046, India
| | - Soumya Ghosh
- Tata Institute of Fundamental Research, Hyderabad 500046, India
| | | |
Collapse
|
2
|
Rabe P, Walla CC, Goodyear NK, Welsh J, Southwart R, Clifton I, Linyard JDS, Tumber A, Claridge TDW, Myers WK, Schofield CJ. Spectroscopic studies reveal details of substrate-induced conformational changes distant from the active site in isopenicillin N synthase. J Biol Chem 2022; 298:102249. [PMID: 35835215 PMCID: PMC9403350 DOI: 10.1016/j.jbc.2022.102249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 11/06/2022] Open
Abstract
Isopenicillin N synthase (IPNS) catalyzes formation of the β-lactam and thiazolidine rings of isopenicillin N from its linear tripeptide l-δ-(α-aminoadipoyl)-l-cysteinyl-d-valine (ACV) substrate in an iron- and dioxygen (O2)-dependent four-electron oxidation without precedent in current synthetic chemistry. Recent X-ray free-electron laser studies including time-resolved serial femtosecond crystallography show that binding of O2 to the IPNS–Fe(II)–ACV complex induces unexpected conformational changes in α-helices on the surface of IPNS, in particular in α3 and α10. However, how substrate binding leads to conformational changes away from the active site is unknown. Here, using detailed 19F NMR and electron paramagnetic resonance experiments with labeled IPNS variants, we investigated motions in α3 and α10 induced by binding of ferrous iron, ACV, and the O2 analog nitric oxide, using the less mobile α6 for comparison. 19F NMR studies were carried out on singly and doubly labeled α3, α6, and α10 variants at different temperatures. In addition, double electron–electron resonance electron paramagnetic resonance analysis was carried out on doubly spin-labeled variants. The combined spectroscopic and crystallographic results reveal that substantial conformational changes in regions of IPNS including α3 and α10 are induced by binding of ACV and nitric oxide. Since IPNS is a member of the structural superfamily of 2-oxoglutarate-dependent oxygenases and related enzymes, related conformational changes may be of general importance in nonheme oxygenase catalysis.
Collapse
Affiliation(s)
- Patrick Rabe
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom.
| | - Carla C Walla
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Noelle K Goodyear
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Jordan Welsh
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom; Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, UK
| | - Rebecca Southwart
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Ian Clifton
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - James D S Linyard
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Anthony Tumber
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Tim D W Claridge
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - William K Myers
- Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, UK.
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom.
| |
Collapse
|
3
|
Chen H, Lin Y, Long YT, Minteer SD, Ying YL. Nanopore-based measurement of the interaction of P450cam monooxygenase and putidaredoxin at the single-molecule level. Faraday Discuss 2021; 233:295-302. [PMID: 34889330 DOI: 10.1039/d1fd00042j] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Protein-protein interactions occur in a wide range of biological processes and are of great significance to life function. Characterization of transient protein-protein interactions remains a significant barrier to our understanding of cellular processes. Nanopores provide unique nanoscale environments that accommodate single molecules from the surrounding bulk solution. This method permits label-free sensing at the single-molecule level with extremely high sensitivity. Herein, the interaction between a single P450cam monooxygenase and its redox partner putidaredoxin (Pdx) was monitored via transient ionic current by using functionalized glass nanopores. Results show that the volume of P450cam determines the blockage current while the interactions between the P450cam and Pdx give a long blockage duration. Our glass nanopore sensor with adjustable diameter could be applied for real-time sensing of protein-protein interactions between individual proteins with a wide range of molecular weight.
Collapse
Affiliation(s)
- Hui Chen
- Department of Chemistry, University of Utah, USA.
| | - Yao Lin
- Department of Chemistry, University of Utah, USA. .,State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, China.
| | - Yi-Tao Long
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, China.
| | | | - Yi-Lun Ying
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, China. .,Chemistry and Biomedicine Innovation Center, Nanjing University, China
| |
Collapse
|
4
|
Skinner SP, Follmer AH, Ubbink M, Poulos TL, Houwing-Duistermaat JJ, Paci E. Partial Opening of Cytochrome P450cam (CYP101A1) Is Driven by Allostery and Putidaredoxin Binding. Biochemistry 2021; 60:2932-2942. [PMID: 34519197 DOI: 10.1021/acs.biochem.1c00406] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Cytochrome P450cam (CYP101A1) catalyzes the regio- and stereo-specific 5-exo-hydroxylation of camphor via a multistep catalytic cycle that involves two-electron transfer steps, with an absolute requirement that the second electron be donated by the ferrodoxin, putidaredoxin (Pdx). Whether P450cam, once camphor has bound to the active site and the substrate entry channel has closed, opens up upon Pdx binding, during the second electron transfer step, or it remains closed is still a matter of debate. A potential allosteric site for camphor binding has been identified and postulated to play a role in the binding of Pdx. Here, we have revisited paramagnetic NMR spectroscopy data and determined a heterogeneous ensemble of structures that explains the data, provides a complete representation of the P450cam/Pdx complex in solution, and reconciles alternative hypotheses. The allosteric camphor binding site is always present, and the conformational changes induced by camphor binding to this site facilitates Pdx binding. We also determined that the state to which Pdx binds comprises an ensemble of structures that have features of both the open and closed state. These results demonstrate that there is a finely balanced interaction between allosteric camphor binding and the binding of Pdx at high camphor concentrations.
Collapse
Affiliation(s)
- Simon P Skinner
- School of Molecular and Cell Biology and Astbury Centre, University of Leeds, Leeds LS2 9JT, U.K
| | - Alec H Follmer
- Department of Chemistry, University of California, Irvine, California 92697-3900, United States
| | - Marcellus Ubbink
- Leiden University, Institute of Chemistry, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Thomas L Poulos
- Department of Chemistry, University of California, Irvine, California 92697-3900, United States.,Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3900, United States.,Department of Pharmaceutical Sciences, University of California, Irvine, California 92697-3900, United States
| | | | - Emanuele Paci
- School of Molecular and Cell Biology and Astbury Centre, University of Leeds, Leeds LS2 9JT, U.K
| |
Collapse
|
5
|
Schröder GC, Meilleur F. Metalloprotein catalysis: structural and mechanistic insights into oxidoreductases from neutron protein crystallography. Acta Crystallogr D Struct Biol 2021; 77:1251-1269. [PMID: 34605429 PMCID: PMC8489226 DOI: 10.1107/s2059798321009025] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 08/31/2021] [Indexed: 11/11/2022] Open
Abstract
Metalloproteins catalyze a range of reactions, with enhanced chemical functionality due to their metal cofactor. The reaction mechanisms of metalloproteins have been experimentally characterized by spectroscopy, macromolecular crystallography and cryo-electron microscopy. An important caveat in structural studies of metalloproteins remains the artefacts that can be introduced by radiation damage. Photoreduction, radiolysis and ionization deriving from the electromagnetic beam used to probe the structure complicate structural and mechanistic interpretation. Neutron protein diffraction remains the only structural probe that leaves protein samples devoid of radiation damage, even when data are collected at room temperature. Additionally, neutron protein crystallography provides information on the positions of light atoms such as hydrogen and deuterium, allowing the characterization of protonation states and hydrogen-bonding networks. Neutron protein crystallography has further been used in conjunction with experimental and computational techniques to gain insight into the structures and reaction mechanisms of several transition-state metal oxidoreductases with iron, copper and manganese cofactors. Here, the contribution of neutron protein crystallography towards elucidating the reaction mechanism of metalloproteins is reviewed.
Collapse
Affiliation(s)
- Gabriela C. Schröder
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Flora Meilleur
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| |
Collapse
|
6
|
Mammoser CC, Ramos S, Thielges MC. Active Site Hydrogen Bonding Induced in Cytochrome P450cam by Effector Putidaredoxin. Biochemistry 2021; 60:1699-1707. [PMID: 34006086 DOI: 10.1021/acs.biochem.1c00075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cytochrome P450s are diverse and powerful catalysts that can activate molecular oxygen to oxidize a wide variety of substrates. Catalysis relies on effective uptake of two electrons and two protons. For cytochrome P450cam, an archetypal member of the superfamily, the second electron must be supplied by the redox partner putidaredoxin (Pdx). Pdx also plays an effector role beyond electron transfer, but after decades the mechanism remains under investigation. We applied infrared spectroscopy to heme-ligated CN- to examine the influence of Pdx binding. The results indicate that Pdx induces the population of a conformation wherein the CN- ligand forms a strong hydrogen bond to a solvent water molecule, experimentally corroborating the formation of a proposed proton delivery network. Further, characterization of T252A P450cam implicates the side chain of Thr252 in regulating the population equilibrium of hydrogen-bonded states within the P450cam/Pdx complex, which could underlie its role in directing activated oxygen toward product formation and preventing reaction uncoupling through peroxide release.
Collapse
Affiliation(s)
- Claire C Mammoser
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Sashary Ramos
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Megan C Thielges
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| |
Collapse
|
7
|
Ramos S, Mammoser CC, Thibodeau KE, Thielges MC. Dynamics underlying hydroxylation selectivity of cytochrome P450cam. Biophys J 2021; 120:912-923. [PMID: 33545101 PMCID: PMC8008267 DOI: 10.1016/j.bpj.2021.01.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 01/18/2021] [Accepted: 01/27/2021] [Indexed: 10/22/2022] Open
Abstract
Structural heterogeneity and the dynamics of the complexes of enzymes with substrates can determine the selectivity of catalysis; however, fully characterizing how remains challenging as heterogeneity and dynamics can vary at the spatial level of an amino acid residue and involve rapid timescales. We demonstrate the nascent approach of site-specific two-dimensional infrared (IR) spectroscopy to investigate the archetypical cytochrome P450, P450cam, to better delineate the mechanism of the lower regioselectivity of hydroxylation of the substrate norcamphor in comparison to the native substrate camphor. Specific locations are targeted throughout the enzyme by selectively introducing cyano groups that have frequencies in a spectrally isolated region of the protein IR spectrum as local vibrational probes. Linear and two-dimensional IR spectroscopy were applied to measure the heterogeneity and dynamics at each probe and investigate how they differentiate camphor and norcamphor recognition. The IR data indicate that the norcamphor complex does not fully induce a large-scale conformational change to a closed state of the enzyme adopted in the camphor complex. Additionally, a probe directed at the bound substrate experiences rapidly interconverting states in the norcamphor complex that explain the hydroxylation product distribution. Altogether, the study reveals large- and small-scale structural heterogeneity and dynamics that could contribute to selectivity of a cytochrome P450 and illustrates the approach of site-selective IR spectroscopy to elucidate protein dynamics.
Collapse
Affiliation(s)
- Sashary Ramos
- Department of Chemistry, Indiana University, Bloomington, Indiana
| | | | | | - Megan C Thielges
- Department of Chemistry, Indiana University, Bloomington, Indiana.
| |
Collapse
|
8
|
Di Nardo G, Zhang C, Marcelli AG, Gilardi G. Molecular and Structural Evolution of Cytochrome P450 Aromatase. Int J Mol Sci 2021; 22:E631. [PMID: 33435208 PMCID: PMC7827799 DOI: 10.3390/ijms22020631] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/06/2021] [Accepted: 01/07/2021] [Indexed: 12/22/2022] Open
Abstract
Aromatase is the cytochrome P450 enzyme converting androgens into estrogen in the last phase of steroidogenesis. As estrogens are crucial in reproductive biology, aromatase is found in vertebrates and the invertebrates of the genus Branchiostoma, where it carries out the aromatization reaction of the A-ring of androgens that produces estrogens. Here, we investigate the molecular evolution of this unique and highly substrate-selective enzyme by means of structural, sequence alignment, and homology modeling, shedding light on its key role in species conservation. The alignments led to the identification of a core structure that, together with key and unique amino acids located in the active site and the substrate recognition sites, has been well conserved during evolution. Structural analysis shows what their roles are and the reason why they have been preserved. Moreover, the residues involved in the interaction with the redox partner and some phosphorylation sites appeared late during evolution. These data reveal how highly substrate-selective cytochrome P450 has evolved, indicating that the driving forces for evolution have been the optimization of the interaction with the redox partner and the introduction of phosphorylation sites that give the possibility of modulating its activity in a rapid way.
Collapse
Affiliation(s)
- Giovanna Di Nardo
- Department of Life Sciences and Systems Biology, University of Torino, via Accademia Albertina 13, 1023 Torino, Italy; (C.Z.); (A.G.M.)
| | | | | | - Gianfranco Gilardi
- Department of Life Sciences and Systems Biology, University of Torino, via Accademia Albertina 13, 1023 Torino, Italy; (C.Z.); (A.G.M.)
| |
Collapse
|
9
|
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.
Collapse
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.
| |
Collapse
|
10
|
Murarka VC, Batabyal D, Amaya JA, Sevrioukova IF, Poulos TL. Unexpected Differences between Two Closely Related Bacterial P450 Camphor Monooxygenases. Biochemistry 2020; 59:2743-2750. [PMID: 32551522 DOI: 10.1021/acs.biochem.0c00366] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The bacterial cytochrome P450cam catalyzes the oxidation of camphor to 5-exo-hydroxycamphor as the first step in the oxidative assimilation of camphor as a carbon/energy source. CYP101D1 is another bacterial P450 that catalyzes the same reaction. A third P450 (P450tcu) has recently been discovered that has ≈86% sequence identity to P450cam as well as very similar enzymatic properties. P450tcu, however, exhibits three unusual features not found in P450cam. First, we observe product in at least two orientations in the X-ray structure that indicates that, unlike the case for P450cam, X-ray-generated reducing equivalents can drive substrate hydroxylation in crystallo. We postulate, on the basis of molecular dynamics simulations, that greater flexibility in P450tcu enables easier access of protons to the active site and, together with X-ray driven reduction, results in O2 activation and substrate hydroxylation. Second, the characteristic low-spin to high-spin transition when camphor binds occurs immediately with P450cam but is very slow in P450tcu. Third, isothermal titration calorimetry shows that in P450cam substrate binding is entropically driven with a ΔH of >0 while in P450tcu with a ΔH of <0 with a more modest change in -TΔS. These results indicate that despite nearly identical structures and enzymatic properties, these two P450s exhibit quite different properties most likely related to differences in conformational dynamics.
Collapse
Affiliation(s)
- Vidhi C Murarka
- Departments of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and Chemistry, University of California, Irvine, California 92697-3900, United States
| | - Dipanwita Batabyal
- Departments of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and Chemistry, University of California, Irvine, California 92697-3900, United States
| | - Jose A Amaya
- Departments of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and Chemistry, University of California, Irvine, California 92697-3900, United States
| | - Irina F Sevrioukova
- Departments of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and Chemistry, University of California, Irvine, California 92697-3900, United States
| | - Thomas L Poulos
- Departments of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and Chemistry, University of California, Irvine, California 92697-3900, United States
| |
Collapse
|
11
|
Liou SH, Chuo SW, Qiu Y, Wang LP, Goodin DB. Linkage between Proximal and Distal Movements of P450cam Induced by Putidaredoxin. Biochemistry 2020; 59:2012-2021. [PMID: 32369344 PMCID: PMC9749489 DOI: 10.1021/acs.biochem.0c00294] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Putidaredoxin (Pdx) is the exclusive reductase and a structural effector for P450cam (CYP101A1). However, the mechanism of how Pdx modulates the conformational states of P450cam remains elusive. Here we report a putative communication pathway for the Pdx-induced conformational change in P450cam using results of double electron-electron resonance (DEER) spectroscopy and molecular dynamics simulations. Use of solution state DEER measurements allows us to observe subtle conformational changes in the internal helices in P450cam among closed, open, and P450cam-Pdx complex states. Molecular dynamics simulations and dynamic network analysis suggest that Pdx binding is coupled to small coordinated movements of several regions of P450cam, including helices C, B', I, G, and F. These changes provide a linkage between the Pdx binding site on the proximal side of the enzyme and helices F/G on the distal side and the site of the largest movement resulting from the Pdx-induced closed-to-open transition. This study provides a detailed rationale for how Pdx exerts its long-recognized effector function at the active site from its binding site on the opposite face of the enzyme.
Collapse
Affiliation(s)
| | | | - Yudong Qiu
- Department of Chemistry, University of California, Davis, Davis, California 95616, United States
| | - Lee-Ping Wang
- Department of Chemistry, University of California, Davis, Davis, California 95616, United States
| | - David B. Goodin
- Department of Chemistry, University of California, Davis, Davis, California 95616, United States
| |
Collapse
|
12
|
Shi X, Chuo SW, Liou SH, Goodin DB. Double Electron–Electron Resonance Shows That the Substrate but Not the Inhibitors Causes Disorder in the F/G Loop of CYP119 in Solution. Biochemistry 2020; 59:1823-1831. [DOI: 10.1021/acs.biochem.0c00171] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Xiaoxiao Shi
- Department of Chemistry, University of California, One Shields Avenue, Davis, California 95616, United States
- Department of Plant Sciences, University of California, One Shields Avenue, Davis, California 95616, United States
| | - Shih-Wei Chuo
- Department of Chemistry, University of California, One Shields Avenue, Davis, California 95616, United States
| | - Shu-Hao Liou
- Department of Chemistry, University of California, One Shields Avenue, Davis, California 95616, United States
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - David B. Goodin
- Department of Chemistry, University of California, One Shields Avenue, Davis, California 95616, United States
| |
Collapse
|
13
|
Chuo SW, Liou SH, Wang LP, Britt RD, Poulos TL, Sevrioukova IF, Goodin DB. Conformational Response of N-Terminally Truncated Cytochrome P450 3A4 to Ligand Binding in Solution. Biochemistry 2019; 58:3903-3910. [PMID: 31456404 DOI: 10.1021/acs.biochem.9b00620] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Human cytochrome P450 3A4 (CYP3A4) is a membrane-associated monooxygenase that is responsible for metabolizing >50% of the pharmaceuticals in the current market, so studying its chemical mechanism and structural changes upon ligand binding will help provide deeper insights into drug metabolism and further drug development. The best-characterized cytochrome P450 is a bacterial form, P450cam, which undergoes significant conformational changes upon binding substrate and its redox partner, putidaredoxin. In contrast, most crystal structures of CYP3A4 with or without ligands have shown few changes, although allosteric effects and multiple-substrate binding in solution are well-documented. In this study, we use double electron-electron resonance (DEER) to measure distances between spatially separated spin-labels on CYP3A4 and molecular dynamics to interpret the DEER data. These methods were applied to a soluble N-terminally truncated CYP3A4 form, and the results show that there are few changes in the average structure upon binding ketoconazole, ritonavir, or midazolam. However, binding of midazolam, but not ketoconazole or ritonavir, resulted in a significant change in the motion and/or disorder in the F/G helix region near the substrate binding pocket. These results suggest that soluble CYP3A4 behaves in a unique way in response to inhibitor and substrate binding.
Collapse
Affiliation(s)
- Shih-Wei Chuo
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
| | - Shu-Hao Liou
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States.,Department of Anatomy and Structural Biology , Albert Einstein College of Medicine , Bronx , New York 10461 , United States
| | - Lee-Ping Wang
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
| | - R David Britt
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
| | - Thomas L Poulos
- Department of Molecular Biology and Biochemistry , University of California , Irvine , California 92697-3900 , United States.,Department of Chemistry , University of California , Irvine , California 92697-3900 , United States.,Department of Pharmaceutical Sciences , University of California , Irvine , California 92697-3900 , United States
| | - Irina F Sevrioukova
- Department of Molecular Biology and Biochemistry , University of California , Irvine , California 92697-3900 , United States
| | - David B Goodin
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
| |
Collapse
|
14
|
Crystal structure of bacterial CYP116B5 heme domain: New insights on class VII P450s structural flexibility and peroxygenase activity. Int J Biol Macromol 2019; 140:577-587. [PMID: 31430491 DOI: 10.1016/j.ijbiomac.2019.08.141] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 08/16/2019] [Accepted: 08/16/2019] [Indexed: 11/22/2022]
Abstract
Class VII cytochromes P450 are self-sufficient enzymes carrying a phthalate family oxygenase-like reductase domain and a P450 domain fused in a single polypeptide chain. The biocatalytic applications of CYP116B members are limited by the need of the NADPH cofactor and the lack of crystal structures as a starting point for protein engineering. Nevertheless, we demonstrated that the heme domain of CYP116B5 can use hydrogen peroxide as electron donor bypassing the need of NADPH. Here, we report the crystal structure of CYP116B5 heme domain in complex with histidine at 2.6 Å of resolution. The structure reveals the typical P450 fold and a closed conformation with an active site cavity of 284 Å3 in volume, accommodating a histidine molecule forming a hydrogen bond with the water molecule present as 6th heme iron ligand. MD simulations in the absence of any ligand revealed the opening of a tunnel connecting the active site to the protein surface through the movement of F-, G- and H-helices. A structural alignment with bacterial cytochromes P450 allowed the identification of amino acids in the proximal heme site potentially involved in peroxygenase activity. The availability of the crystal structure provides the bases for the structure-guided design of new biocatalysts.
Collapse
|
15
|
Guengerich FP, Wilkey CJ, Glass SM, Reddish MJ. Conformational selection dominates binding of steroids to human cytochrome P450 17A1. J Biol Chem 2019; 294:10028-10041. [PMID: 31072872 DOI: 10.1074/jbc.ra119.008860] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 05/06/2019] [Indexed: 12/17/2022] Open
Abstract
Cytochrome P450 (P450, CYP) enzymes are the major catalysts involved in the oxidation of steroids as well as many other compounds. Their versatility has been explained in part by flexibility of the proteins and complexity of the binding mechanisms. However, whether these proteins bind their substrates via induced fit or conformational selection is not understood. P450 17A1 has a major role in steroidogenesis, catalyzing the two-step oxidations of progesterone and pregnenolone to androstenedione and dehydroepiandrosterone, respectively, via 17α-hydroxy (OH) intermediates. We examined the interaction of P450 17A1 with its steroid substrates by analyzing progress curves (UV-visible spectroscopy), revealing that the rates of binding of any of these substrates decreased with increasing substrate concentration, a hallmark of conformational selection. Further, when the concentration of 17α-OH pregnenolone was held constant and the P450 concentration increased, the binding rate increased, and such opposite patterns are also diagnostic of conformational selection. Kinetic simulation modeling was also more consistent with conformational selection than with an induced-fit mechanism. Cytochrome b 5 partially enhances P450 17A1 lyase activity by altering the P450 17A1 conformation but did not measurably alter the binding of 17α-OH pregnenolone or 17α-OH progesterone, as judged by the apparent Kd and binding kinetics. The P450 17A1 inhibitor abiraterone also bound to P450 17A1 in a multistep manner, and modeling indicated that the selective inhibition of the two P450 17A1 steps by the drug orteronel can be rationalized only by a multiple-conformation model. In conclusion, P450 17A1 binds its steroid substrates via conformational selection.
Collapse
Affiliation(s)
- F Peter Guengerich
- From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146
| | - Clayton J Wilkey
- From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146
| | - Sarah M Glass
- From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146
| | - Michael J Reddish
- From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146
| |
Collapse
|
16
|
Chuo SW, Wang LP, Britt RD, Goodin DB. An Intermediate Conformational State of Cytochrome P450cam-CN in Complex with Putidaredoxin. Biochemistry 2019; 58:2353-2361. [PMID: 30994334 DOI: 10.1021/acs.biochem.9b00192] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Cytochrome P450cam is an archetypal example of the vast family of heme monooxygenases and serves as a model for an enzyme that is highly specific for both its substrate and reductase. During catalysis, it undergoes significant conformational changes of the F and G helices upon binding its substrate and redox partner, putidaredoxin (Pdx). Recent studies have shown that Pdx binding to the closed camphor-bound form of ferric P450cam results in its conversion to a fully open state. However, during catalytic turnover, it remains unclear whether this same conformational change also occurs or whether it is coupled to the formation of the critical compound I intermediate. Here, we have examined P450cam bound simultaneously by camphor, CN-, and Pdx as a mimic of the catalytically competent ferrous oxy-P450cam-Pdx state. The combined use of double electron-electron resonance and molecular dynamics showed direct observation of intermediate conformational states of the enzyme upon CN- and subsequent Pdx binding. This state is coupled to the movement of the I helix and residues at the active site, including Arg-186, Asp-251, and Thr-252. These movements enable occupation of a water molecule that has been implicated in proton delivery and peroxy bond cleavage to give compound I. These findings provide a detailed understanding of how the Pdx-induced conformational change may sequentially promote compound I formation followed by product release, while retaining stereoselective hydroxylation of the substrate of this highly specific monooxygenase.
Collapse
Affiliation(s)
- Shih-Wei Chuo
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
| | - Lee-Ping Wang
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
| | - R David Britt
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
| | - David B Goodin
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
| |
Collapse
|
17
|
Ramos S, Thielges MC. Site-Specific 1D and 2D IR Spectroscopy to Characterize the Conformations and Dynamics of Protein Molecular Recognition. J Phys Chem B 2019; 123:3551-3566. [PMID: 30848912 DOI: 10.1021/acs.jpcb.9b00969] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Proteins exist as ensembles of interconverting states on a complex energy landscape. A complete, molecular-level understanding of their function requires knowledge of the populated states and thus the experimental tools to characterize them. Infrared (IR) spectroscopy has an inherently fast time scale that can capture all states and their dynamics with, in principle, bond-specific spatial resolution, and 2D IR methods that provide richer information are becoming more routine. Although application of IR spectroscopy for investigation of proteins is challenged by spectral congestion, the issue can be overcome by site-specific introduction of amino acid side chains that have IR probe groups with frequency-resolved absorptions, which furthermore enables selective characterization of different locations in proteins. Here, we briefly introduce the biophysical methods and summarize the current progress toward the study of proteins. We then describe our efforts to apply site-specific 1D and 2D IR spectroscopy toward elucidation of protein conformations and dynamics to investigate their involvement in protein molecular recognition, in particular mediated by dynamic complexes: plastocyanin and its binding partner cytochrome f, cytochrome P450s and substrates or redox partners, and Src homology 3 domains and proline-rich peptide motifs. We highlight the advantages of frequency-resolved probes to characterize specific, local sites in proteins and uncover variation among different locations, as well as the advantage of the fast time scale of IR spectroscopy to detect rapidly interconverting states. In addition, we illustrate the greater insight provided by 2D methods and discuss potential routes for further advancement of the field of biomolecular 2D IR spectroscopy.
Collapse
Affiliation(s)
- Sashary Ramos
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405 , United States
| | - Megan C Thielges
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405 , United States
| |
Collapse
|
18
|
Follmer AH, Tripathi S, Poulos TL. Ligand and Redox Partner Binding Generates a New Conformational State in Cytochrome P450cam (CYP101A1). J Am Chem Soc 2019; 141:2678-2683. [PMID: 30672701 DOI: 10.1021/jacs.8b13079] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
It has become increasingly clear that cytochromes P450 can cycle back and forth between two extreme conformational states termed the closed and open states. In the well-studied cytochrome P450cam, the binding of its redox partner, putidaredoxin (Pdx), shifts P450cam toward the open state. Shifting to the open state is thought to be important in the formation of a proton relay network essential for O-O bond cleavage and formation of the active Fe(IV)═O intermediate. Another important intermediate is the oxy-P450cam complex when bound to Pdx. Trapping this intermediate in crystallo is challenging owing to its instability, but the CN- complex is both stable and an excellent mimic of the O2 complex. Here we present the P450cam-Pdx structure complexed with CN-. CN- results in large conformational changes including cis/trans isomerization of proline residues. Changes include large rearrangements of active-site residues and the formation of new active-site access channel that we have termed channel 2. The formation of channel 2 has also been observed in our previous molecular dynamics simulations wherein substrate binding to an allosteric site remote from the active site opens up channel 2. This new structure supports an extensive amount of previous work showing that distant regions of the structure are dynamically coupled and underscores the potentially important role that large conformational changes and dynamics play in P450 catalysis.
Collapse
Affiliation(s)
- Alec H Follmer
- Departments of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and Chemistry , University of California , Irvine , California 92697-3900 , United States
| | - Sarvind Tripathi
- Department of Chemistry & Biochemistry , University of California , Santa Cruz , California 95064 , United States
| | - Thomas L Poulos
- Departments of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and Chemistry , University of California , Irvine , California 92697-3900 , United States
| |
Collapse
|
19
|
Ahalawat N, Mondal J. Mapping the Substrate Recognition Pathway in Cytochrome P450. J Am Chem Soc 2018; 140:17743-17752. [PMID: 30479124 DOI: 10.1021/jacs.8b10840] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Cytochrome P450s are ubiquitous metalloenzymes involved in the metabolism and detoxification of foreign components via catalysis of the hydroxylation reactions of a vast array of organic substrates. However, the mechanism underlying the pharmaceutically critical process of substrate access to the catalytic center of cytochrome P450 is a long-standing puzzle, further complicated by the crystallographic evidence of a closed catalytic center in both substrate-free and substrate-bound cytochrome P450. Here, we address a crucial question whether the conformational heterogeneity prevalent in cytochrome P450 translates to heterogeneous pathways for substrate access to the catalytic center of these metalloenzymes. By atomistically capturing the full process of spontaneous substrate association from bulk solvent to the occluded catalytic center of an archetypal system P450cam in multi-microsecond-long continuous unbiased molecular dynamics simulations, we here demonstrate that the substrate recognition in P450cam always occurs through a single well-defined dominant pathway. The simulated final bound pose resulting from these unguided simulations is in striking resemblance with the crystallographic bound pose. Each individual binding trajectory reveals that the substrate, initially placed at random locations in bulk solvent, spontaneously lands on a single key channel on the protein-surface of P450cam and resides there for an uncharacteristically long period, before correctly identifying the occluded target-binding cavity. Surprisingly, the passage of substrate to the closed catalytic center is not accompanied by any large-scale opening in protein. Rather, the unbiased simulated trajectories (∼57 μs) and underlying Markov state model, in combination with free-energy analysis, unequivocally show that the substrate recognition process in P450cam needs a substrate-induced side-chain displacement coupled with a complex array of dynamical interconversions of multiple metastable substrate conformations. Further, the work reconciles multiple precedent experimental and theoretical observations on P450cam and establishes a comprehensive view of substrate-recognition in cytochrome P450 that only occurs via substrate-induced structural rearrangements.
Collapse
Affiliation(s)
- Navjeet Ahalawat
- Tata Institute of Fundamental Research, Center for Interdisciplinary Sciences , Hyderabad 500107 , India
| | - Jagannath Mondal
- Tata Institute of Fundamental Research, Center for Interdisciplinary Sciences , Hyderabad 500107 , India
| |
Collapse
|
20
|
Abstract
Enzymes are complex biological catalysts and are critical to life. Most oxidations of chemicals are catalyzed by cytochrome P450 (P450, CYP) enzymes, which generally utilize mixed-function oxidase stoichiometry, utilizing pyridine nucleotides as electron donors: NAD(P)H + O2 + R → NAD(P)+ + RO + H2O (where R is a carbon substrate and RO is an oxidized product). The catalysis of oxidations is largely understood in the context of the heme iron-oxygen complex generally referred to as Compound I, formally FeO3+, whose basis was in peroxidase chemistry. Many X-ray crystal structures of P450s are now available (≥ 822 structures from ≥146 different P450s) and have helped in understanding catalytic specificity. In addition to hydroxylations, P450s catalyze more complex oxidations, including C-C bond formation and cleavage. Enzymes derived from P450s by directed evolution can even catalyze more unusual reactions, e.g. cyclopropanation. Current P450 questions under investigation include the potential role of the intermediate Compound 0 (formally FeIII-O2 -) in catalysis of some reactions, the roles of high- and low-spin forms of Compound I, the mechanism of desaturation, the roles of open and closed structures of P450s in catalysis, the extent of processivity in multi-step oxidations, and the role of the accessory protein cytochrome b 5. More global questions include exactly how structure drives function, prediction of catalysis, and roles of multiple protein conformations.
Collapse
Affiliation(s)
- F. Peter Guengerich
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, United States
| |
Collapse
|
21
|
Ramos S, Basom EJ, Thielges MC. Conformational Change Induced by Putidaredoxin Binding to Ferrous CO-ligated Cytochrome P450cam Characterized by 2D IR Spectroscopy. Front Mol Biosci 2018; 5:94. [PMID: 30483514 PMCID: PMC6243089 DOI: 10.3389/fmolb.2018.00094] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 10/22/2018] [Indexed: 11/16/2022] Open
Abstract
The importance of conformational dynamics to protein function is now well-appreciated. An outstanding question is whether they are involved in the effector role played by putidaredoxin (Pdx) in its reduction of the O2 complex of cytochrome P450cam (P450cam), an archetypical member of the cytochrome P450 superfamily. Recent studies have reported that binding of Pdx induces a conformational change from a closed to an open state of ferric P450cam, but a similar conformational change does not appear to occur for the ferrous, CO-ligated enzyme. To better understand the effector role of Pdx when binding the ferrous, CO-ligated P450cam, we applied 2D IR spectroscopy to compare the conformations and dynamics of the wild-type (wt) enzyme in the absence and presence of Pdx, as well as of L358P P450cam (L358P), which has served as a putative model for the Pdx complex. The CO vibrations of the Pdx complex and L358P report population of two conformational states in which the CO experiences distinct environments. The dynamics among the CO frequencies indicate that the energy landscape of substates within one conformation are reflective of the closed state of P450cam, and for the other conformation, differ from the free wt enzyme, but are equivalent between the Pdx complex and L358P. The two states co-populated by the Pdx complex are postulated to reflect a loosely bound encounter complex and a more tightly bound state, as is commonly observed for the dynamic complexes of redox partners. Significantly, this study shows that the binding of Pdx to ferrous, CO-ligated P450cam does perturb the conformational ensemble in a way that might underlie the effector role of Pdx.
Collapse
Affiliation(s)
- Sashary Ramos
- Department of Chemistry, Indiana University, Bloomington, IN, United States
| | - Edward J Basom
- Department of Chemistry, Indiana University, Bloomington, IN, United States
| | - Megan C Thielges
- Department of Chemistry, Indiana University, Bloomington, IN, United States
| |
Collapse
|
22
|
Goodin DB, Chuo SW, Liou SH. Conformational Changes in Cytochrome P450cam and the Effector Role of Putidaredoxin. DIOXYGEN-DEPENDENT HEME ENZYMES 2018. [DOI: 10.1039/9781788012911-00292] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The cytochromes P450 form an enormous family of over 20 000 enzyme variants found in all branches of life. They catalyze the O2 dependent monooxygenation of a wide range of substrates in reactions important to drug metabolism, biosynthesis and energy utilization. Understanding how they function is important for biomedical science and requires a full description of their notorious propensity for specificity and promiscuity. The bacterial P450cam is an unusual example, having the most well characterized chemical mechanism of all of the forms. It also undergoes an increasingly well characterized structural change upon substrate binding, which may be similar to to that displayed by some, but not all forms of P450. Finally, P450cam is one of the rare forms that have a strict requirement for a particular electron donor, putidaredoxin (pdx). Pdx provides the required electrons for enzyme turnover, but it also induces specific changes in the enzyme to allow enzyme turnover, long known as its effector role. This review summarizes recent crystallographic and double electron–electron resonance studies that have revealed the effects of substrate and pdx binding on the structure of P450cam. We describe an emerging idea for how pdx exerts its effector function by inducing a conformational change in the enzyme. This change then propagates to the active site to enable cleavage of the ferric–hydroperoxy bond during catalysis, and appears to provide a very elegant approach for P450cam to attain both high efficiency and protection from oxidative damage.
Collapse
Affiliation(s)
- David B. Goodin
- University of California Davis, Department of Chemistry One Shields Ave Davis CA 95616 USA
| | - Shih-Wei Chuo
- University of California Davis, Department of Chemistry One Shields Ave Davis CA 95616 USA
| | - Shu-Hao Liou
- Research Group EPR Spectroscopy, Max-Planck-Institute for Biophysical Chemistry Göttingen 37077 Germany
| |
Collapse
|
23
|
Haga T, Hirakawa H, Nagamune T. Artificial Self‐Sufficient Cytochrome P450 Containing Multiple Auxiliary Proteins Demonstrates Improved Monooxygenase Activity. Biotechnol J 2018; 13:e1800088. [DOI: 10.1002/biot.201800088] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 07/18/2018] [Indexed: 02/04/2023]
Affiliation(s)
- Tomoaki Haga
- Department of Chemistry and BiotechnologySchool of EngineeringThe University of TokyoTokyo 113‐8656Japan
| | - Hidehiko Hirakawa
- Department of Chemistry and BiotechnologySchool of EngineeringThe University of TokyoTokyo 113‐8656Japan
| | - Teruyuki Nagamune
- Department of Chemistry and BiotechnologySchool of EngineeringThe University of TokyoTokyo 113‐8656Japan
| |
Collapse
|
24
|
Batabyal D, Poulos TL. Effect of redox partner binding on CYP101D1 conformational dynamics. J Inorg Biochem 2018; 183:179-183. [PMID: 29550100 PMCID: PMC5976445 DOI: 10.1016/j.jinorgbio.2018.02.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Revised: 02/13/2018] [Accepted: 02/18/2018] [Indexed: 11/27/2022]
Abstract
We have compared the thermodynamics of substrate and redox partner binding of P450cam to its close homologue, CYP101D1, using isothermal titration calorimetry (ITC). CYP101D1 binds camphor about 10-fold more weakly than P450cam which is consistent with the inability of camphor to cause a complete low- to high-spin shift in CYP101D1. Even so molecular dynamics simulations show that camphor is very stable in the CYP101D1 active site similar to P450cam. ITC data on the binding of the CYP101D1 ferredoxin redox partner (abbreviated Arx) shows that the substrate-bound closed state of CYP101D1 binds Arx more tightly than the substrate-free open form. This is just the opposite to P450cam where Pdx (ferredoxin redox partner of P450cam) favors binding to the P450cam open state. In addition, CYP101D1-Arx binding has a large negative ΔS while the P450cam-Pdx has a much smaller ΔS indicating that interactions at the docking interface are different. The most obvious difference is that PDXD38 which forms an important ion pair with P450camR112 at the center of the interface is ArxL39 in Arx. This suggests that Arx may adopt a different orientation than Pdx in order to optimize nonpolar interactions with ArxL39.
Collapse
Affiliation(s)
- Dipanwita Batabyal
- Departments of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and Chemistry, University of California, Irvine, CA 92697-3900, USA
| | - Thomas L Poulos
- Departments of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and Chemistry, University of California, Irvine, CA 92697-3900, USA.
| |
Collapse
|
25
|
Bowen AM, Johnson EOD, Mercuri F, Hoskins NJ, Qiao R, McCullagh JSO, Lovett JE, Bell SG, Zhou W, Timmel CR, Wong LL, Harmer JR. A Structural Model of a P450-Ferredoxin Complex from Orientation-Selective Double Electron-Electron Resonance Spectroscopy. J Am Chem Soc 2018; 140:2514-2527. [PMID: 29266939 DOI: 10.1021/jacs.7b11056] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Cytochrome P450 (CYP) monooxygenases catalyze the oxidation of chemically inert carbon-hydrogen bonds in diverse endogenous and exogenous organic compounds by atmospheric oxygen. This C-H bond oxy-functionalization activity has huge potential in biotechnological applications. Class I CYPs receive the two electrons required for oxygen activation from NAD(P)H via a ferredoxin reductase and ferredoxin. The interaction of Class I CYPs with their cognate ferredoxin is specific. In order to reconstitute the activity of diverse CYPs, structural characterization of CYP-ferredoxin complexes is necessary, but little structural information is available. Here we report a structural model of such a complex (CYP199A2-HaPux) in frozen solution derived from distance and orientation restraints gathered by the EPR technique of orientation-selective double electron-electron resonance (os-DEER). The long-lived oscillations in the os-DEER spectra were well modeled by a single orientation of the CYP199A2-HaPux complex. The structure is different from the two known Class I CYP-Fdx structures: CYP11A1-Adx and CYP101A1-Pdx. At the protein interface, HaPux residues in the [Fe2S2] cluster-binding loop and the α3 helix and the C-terminus residue interact with CYP199A2 residues in the proximal loop and the C helix. These residue contacts are consistent with biochemical data on CYP199A2-ferredoxin binding and electron transfer. Electron-tunneling calculations indicate an efficient electron-transfer pathway from the [Fe2S2] cluster to the heme. This new structural model of a CYP-Fdx complex provides the basis for tailoring CYP enzymes for which the cognate ferredoxin is not known, to accept electrons from HaPux and display monooxygenase activity.
Collapse
Affiliation(s)
- Alice M Bowen
- Centre for Applied Electron Spin Resonance, Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford , South Parks Road, Oxford OX1 3QR, U.K
| | - Eachan O D Johnson
- Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford , South Parks Road, Oxford OX1 3QR, U.K
| | - Francesco Mercuri
- Consiglio Nazionale delle Ricerche (CNR), Istituto per lo Studio dei Materiali Nanostrutturati (ISMN) Via P. Gobetti 101, 40129 Bologna, Italy
| | - Nicola J Hoskins
- Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford , South Parks Road, Oxford OX1 3QR, U.K
| | - Ruihong Qiao
- College of Life Sciences, Nankai University , Tianjin 300071, China
| | - James S O McCullagh
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford , Mansfield Road, Oxford OX1 3TA, U.K
| | - Janet E Lovett
- Centre for Applied Electron Spin Resonance, Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford , South Parks Road, Oxford OX1 3QR, U.K
| | - Stephen G Bell
- Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford , South Parks Road, Oxford OX1 3QR, U.K
| | - Weihong Zhou
- College of Life Sciences, Nankai University , Tianjin 300071, China
| | - Christiane R Timmel
- Centre for Applied Electron Spin Resonance, Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford , South Parks Road, Oxford OX1 3QR, U.K
| | - Luet Lok Wong
- Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford , South Parks Road, Oxford OX1 3QR, U.K
| | - Jeffrey R Harmer
- Centre for Applied Electron Spin Resonance, Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford , South Parks Road, Oxford OX1 3QR, U.K
| |
Collapse
|
26
|
Batabyal D, Richards LS, Poulos TL. Effect of Redox Partner Binding on Cytochrome P450 Conformational Dynamics. J Am Chem Soc 2017; 139:13193-13199. [PMID: 28823160 DOI: 10.1021/jacs.7b07656] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Previous crystal structures of cytochrome P450cam complexed with its redox partner, putidaredoxin (Pdx), shows that P450cam adopts the open conformation. It has been hypothesized that the Pdx-induced shift toward the open state frees the essential Asp251 from salt bridges with Arg186 and Lys178 so that Asp251 can participate in a proton relay network required for O2 activation. This in part explains why P450cam has such a strict requirement for Pdx. One problem with this view is that looser substrate-protein interactions in the open state may not be compatible with the observed regio- and stereoselective hydroxylation. In the present study, molecular dynamics simulations show that Pdx binding favors a conformation that stabilizes the active site and decreases camphor mobility yet retains a partially open conformation compatible with the required proton relay network. The R186A mutant which frees Asp251 in the absence of Pdx retains good enzyme activity, and the crystal structure shows that product, 5-exo-hydroxycamphor, is bound. This indicates that rupture of the Asp251-Arg186 relaxes selectivity with respect to source of electrons and enables X-ray generated reducing equivalents to support substrate hydroxylation. These combined computational and experimental results are consistent with the proposed role of Pdx in assisting the release of Asp251 from ion pairs so that it can participate in proton-coupled electron transfer.
Collapse
Affiliation(s)
- Dipanwita Batabyal
- Departments of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and Chemistry, University of California , Irvine, California 92697-3900, United States
| | - Logan S Richards
- Departments of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and Chemistry, University of California , Irvine, California 92697-3900, United States
| | - Thomas L Poulos
- Departments of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and Chemistry, University of California , Irvine, California 92697-3900, United States
| |
Collapse
|
27
|
Thermodynamics of camphor migration in cytochrome P450cam by atomistic simulations. Sci Rep 2017; 7:7736. [PMID: 28798338 PMCID: PMC5552751 DOI: 10.1038/s41598-017-07993-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 07/05/2017] [Indexed: 01/12/2023] Open
Abstract
Understanding the mechanisms of ligand binding to enzymes is of paramount importance for the design of new drugs. Here, we report on the use of a novel biased molecular dynamics (MD) methodology to study the mechanism of camphor binding to cytochrome P450cam. Microsecond-long MD simulations allowed us to observe reaction coordinates characterizing ligand diffusion from the active site of cytochrome P450cam to solvent via three egress routes. These atomistic simulations were used to estimate thermodynamic quantities along the reaction coordinates and indicate diverse binding configurations. The results suggest that the diffusion of camphor along the pathway near the substrate recognition site (SRS) is thermodynamically preferred. In addition, we show that the diffusion near the SRS is triggered by a transition from a heterogeneous collection of closed ligand-bound conformers to the basin comprising the open conformations of cytochrome P450cam. The conformational change accompanying this switch is characterized by the retraction of the F and G helices and the disorder of the B' helix. These results are corroborated by experimental studies and provide detailed insight into ligand binding and conformational behavior of the cytochrome family. The presented methodology is general and can be applied to other ligand-protein systems.
Collapse
|
28
|
Liou SH, Myers WK, Oswald JD, Britt RD, Goodin DB. Putidaredoxin Binds to the Same Site on Cytochrome P450cam in the Open and Closed Conformation. Biochemistry 2017; 56:4371-4378. [DOI: 10.1021/acs.biochem.7b00564] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Shu-Hao Liou
- Department
of Chemistry, University of California, Davis, California 95616, United States
- Research
Group EPR Spectroscopy, Max-Planck-Institute for Biophysical Chemistry, Göttingen 37077, Germany
| | - William K. Myers
- Centre
for Advanced Electron Spin Resonance, Inorganic Chemistry Laboratory, University of Oxford, Oxford OX1 3QR, United Kingdom
| | - Jason D. Oswald
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - R. David Britt
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - David B. Goodin
- Department
of Chemistry, University of California, Davis, California 95616, United States
| |
Collapse
|
29
|
Basom EJ, Manifold BA, Thielges MC. Conformational Heterogeneity and the Affinity of Substrate Molecular Recognition by Cytochrome P450cam. Biochemistry 2017; 56:3248-3256. [PMID: 28581729 DOI: 10.1021/acs.biochem.7b00238] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The broad and variable substrate specificity of cytochrome P450 enzymes makes them a model system for studying the determinants of protein molecular recognition. The archetypal cytochrome P450cam (P450cam) is a relatively specific P450, a feature once attributed to the high rigidity of its active site. However, increasingly studies have provided evidence of the importance of conformational changes to P450cam activity. Here we used infrared (IR) spectroscopy to investigate the molecular recognition of P450cam. Toward this goal, and to assess the influence of a hydrogen bond (H-bond) between active site residue Y96 and substrates, two variants in which Y96 is replaced by a cyanophenyl (Y96CNF) or phenyl (Y96F) group were characterized in complexes with the substrates camphor, isoborneol, and camphane. These combinations allow for a comparison of complexes in which the moieties on both the protein and substrate can serve as a H-bond donor, acceptor, or neither. The IR spectra of heme-bound CO and the site-specifically incorporated CN of Y96CNF were analyzed to characterize the number and nature of environments in each protein, both in the free and bound states. Although the IR spectra do not support the idea that protein-substrate H-bonding is central to P450cam recognition, the data altogether suggest that the differing conformational heterogeneity in the active site of the P450cam variants and changes in heterogeneity upon binding of different substrates likely contribute to their variable affinities via a conformational selection mechanism. This study further extends our understanding of the molecular recognition of archetypal P450cam and demonstrates the application of IR spectroscopy combined with selective protein modification to delineate protein-ligand interactions.
Collapse
Affiliation(s)
- Edward J Basom
- Department of Chemistry, Indiana University , 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Bryce A Manifold
- Department of Chemistry, Indiana University , 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Megan C Thielges
- Department of Chemistry, Indiana University , 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| |
Collapse
|
30
|
Identification of productive and futile encounters in an electron transfer protein complex. Proc Natl Acad Sci U S A 2017; 114:E1840-E1847. [PMID: 28223532 DOI: 10.1073/pnas.1616813114] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Well-defined, stereospecific states in protein complexes are often in exchange with an ensemble of more dynamic orientations: the encounter states. The structure of the stereospecific complex between cytochrome P450cam and putidaredoxin was solved recently by X-ray diffraction as well as paramagnetic NMR spectroscopy. Other than the stereospecific complex, the NMR data clearly show the presence of additional states in the complex in solution. In these encounter states, populated for a small percentage of the time, putidaredoxin assumes multiple orientations and samples a large part of the surface of cytochrome P450cam. To characterize the nature of the encounter states, an extensive paramagnetic NMR dataset has been analyzed using the Maximum Occurrence of Regions methodology. The analysis reveals the location and maximal spatial extent of the additional states needed to fully explain the NMR data. Under the assumption of sparsity of the size of the conformational ensemble, several minor states can be located quite precisely. The distribution of these minor states correlates with the electrostatic potential map around cytochrome P450cam. Whereas some minor states are on isolated positively charged patches, others are connected to the stereospecific site via positively charged paths. The existence of electrostatically favorable pathways between the stereospecific interaction site and the different minor states or lack thereof suggests a means to discriminate between productive and futile encounter states.
Collapse
|
31
|
Raven EL. A short history of heme dioxygenases: rise, fall and rise again. J Biol Inorg Chem 2016; 22:175-183. [PMID: 27909919 PMCID: PMC5350241 DOI: 10.1007/s00775-016-1412-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 11/10/2016] [Indexed: 01/20/2023]
Abstract
It is well established that there are two different classes of enzymes—tryptophan 2,3-dioxygenase (TDO) and indoleamine 2,3-dioxygenase (IDO)—that catalyse the O2-dependent oxidation of l-tryptophan to N-formylkynurenine. But it was not always so. This perspective presents a short history of the early TDO and IDO literature, the people that were involved in creating it, and the legacy that this left for the future.
Collapse
Affiliation(s)
- Emma L Raven
- Department of Chemistry, University of Leicester, University Road, Leicester, LE1 7RH, UK.
| |
Collapse
|