1
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Alvarez G, Le T, Wong N, Echave J, Pochapsky TC, Asciutto EK. Hydroxylation Regiochemistry Is Robust to Active Site Mutations in Cytochrome P450 cam (CYP101A1). Biochemistry 2022; 61:1790-1800. [PMID: 35960510 PMCID: PMC9721313 DOI: 10.1021/acs.biochem.2c00233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cytochrome P450cam (CYP101A1) catalyzes the hydroxylation of d-camphor by molecular oxygen. The enzyme-catalyzed hydroxylation exhibits a high degree of regioselectivity and stereoselectivity, with a single major product, d-5-exo-hydroxycamphor, suggesting that the substrate is oriented to facilitate this specificity. In previous work, we used an elastic network model and perturbation response scanning to show that normal deformation modes of the enzyme structure are highly responsive not only to the presence of a substrate but also to the substrate orientation. This work examines the effects of mutations near the active site on substrate localization and orientation. The investigated mutations were designed to promote a change in substrate orientation and/or location that might give rise to different hydroxylation products, while maintaining the same carbon and oxygen atom balances as in the wild type (WT) enzyme. Computational experiments and parallel in vitro site-directed mutations of CYP101A1 were used to examine reaction products and enzyme activity. 1H-15N TROSY-HSQC correlation maps were used to compare the computational results with detectable perturbations in the enzyme structure and dynamics. We found that all of the mutant enzymes retained the same regio- and stereospecificity of hydroxylation as the WT enzyme, with varying degrees of efficiency, which suggests that large portions of the enzyme have been subjected to evolutionary pressure to arrive at the appropriate sequence-structure combination for efficient 5-exo hydroxylation of camphor.
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Affiliation(s)
- Guadalupe Alvarez
- Instituto de Ciencias Físicas, Universidad Nacional de San Martín & CONICET, Campus Migueletes, 25 de Mayo y Francia, Buenos Aires 1650, Argentina
| | - Thu Le
- Department of Biochemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, United States
| | - Nathan Wong
- Department of Biochemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, United States
| | - Julian Echave
- Instituto de Ciencias Físicas, Universidad Nacional de San Martín & CONICET, Campus Migueletes, 25 de Mayo y Francia, Buenos Aires 1650, Argentina
| | - Thomas C Pochapsky
- Department of Biochemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, United States.,Department of Chemistry and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, United States
| | - Eliana K Asciutto
- Instituto de Ciencias Físicas, Universidad Nacional de San Martín & CONICET, Campus Migueletes, 25 de Mayo y Francia, Buenos Aires 1650, Argentina
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2
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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.
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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
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3
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Pochapsky TC. A dynamic understanding of cytochrome P450 structure and function through solution NMR. Curr Opin Biotechnol 2020; 69:35-42. [PMID: 33360373 DOI: 10.1016/j.copbio.2020.11.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 11/17/2020] [Indexed: 12/12/2022]
Abstract
Many economically important biosyntheses incorporate regiospecific and stereospecific oxidations at unactivated carbons. Such oxidations are commonly catalyzed by cytochrome P450 monooxygenases, heme-containing enzymes that activate molecular oxygen while selectively binding and orienting the substrate for reaction. Despite the plethora of P450-catalyzed reactions, the P450 fold is highly conserved, and static structures are often insufficient for characterizing conformational states that contribute to specificity. High-resolution solution nuclear magnetic resonance (NMR) offers insights into dynamic processes and conformational changes that are required of a P450 in order to attain the combination of specificity and efficiency required for these reactions.
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Affiliation(s)
- Thomas C Pochapsky
- Departments of Chemistry, Biochemistry and The Rosenstiel Institute for Basic Medical Research, Brandeis University, 415 South St., Waltham, MA 02454, USA.
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4
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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.
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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
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5
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Mikshiev VY, Pozharskii AF, Filarowski A, Novikov AS, Antonov AS, Tolstoy PM, Vovk MA, Khoroshilova OV. How Strong is Hydrogen Bonding to Amide Nitrogen? Chemphyschem 2020; 21:651-658. [PMID: 31953976 DOI: 10.1002/cphc.201901104] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 12/18/2019] [Indexed: 12/23/2022]
Abstract
The protonation of the carboxamide nitrogen atom is an essential part of in vivo and in vitro processes (cis-trans isomerization, amides hydrolysis etc). This phenomenon is well studied in geometrically strongly distorted amides, although there is little data concerning the protonation of undistorted amides. In the latter case, the participation of amide nitrogen in hydrogen bonding (which can be regarded as the incipient state of a proton transfer process) is less well-studied. Thus, it would be a worthy goal to investigate the enthalpy of this interaction. We prepared and investigated a set of peri-substituted naphthalenes containing the protonated dimethylamino group next to the amide nitrogen atom ("amide proton sponges"), which could serve as models for the study of an intramolecular hydrogen bond with the amide nitrogen atom. X-Ray analysis, NMR spectra, basicity values as well as quantum chemical calculations revealed the existence of a hydrogen bond with the amide nitrogen, that should be attributed to the borderline between moderate and weak intramolecular hydrogen bonds (2-7 kcal ⋅ mol-1 ).
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Affiliation(s)
- Vladimir Y Mikshiev
- Institute of Chemistry, St. Petersburg State University, Universitetskii pr. 26, 198504, St. Petersburg, Russian Federation
| | - Alexander F Pozharskii
- Department of Organic Chemistry, Southern Federal University, Zorge str. 7, 344090, Rostov-on-Don, Russian Federation
| | - Alexander Filarowski
- Faculty of Chemistry, Wroclaw University, F. Joliot-Curie str. 14, 50-383, Wroclaw, Poland
- Industrial University of Tyumen, Volodarskogo str. 38, 625000, Tyumen, Russian Federation
| | - Alexander S Novikov
- Institute of Chemistry, St. Petersburg State University, Universitetskii pr. 26, 198504, St. Petersburg, Russian Federation
| | - Alexander S Antonov
- Institute of Chemistry, St. Petersburg State University, Universitetskii pr. 26, 198504, St. Petersburg, Russian Federation
| | - Peter M Tolstoy
- Institute of Chemistry, St. Petersburg State University, Universitetskii pr. 26, 198504, St. Petersburg, Russian Federation
| | - Mikhail A Vovk
- Institute of Chemistry, St. Petersburg State University, Universitetskii pr. 26, 198504, St. Petersburg, Russian Federation
| | - Olesya V Khoroshilova
- Institute of Chemistry, St. Petersburg State University, Universitetskii pr. 26, 198504, St. Petersburg, Russian Federation
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6
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Abstract
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Enzyme function requires that enzyme structures be dynamic. Substrate
binding, product release, and transition state stabilization typically
involve different enzyme conformers. Furthermore, in multistep enzyme-catalyzed
reactions, more than one enzyme conformation may be important for
stabilizing different transition states. While X-ray crystallography
provides the most detailed structural information of any current methodology,
X-ray crystal structures of enzymes capture only those conformations
that fit into the crystal lattice, which may or may not be relevant
to function. Solution nuclear magnetic resonance (NMR) methods can
provide an alternative approach to characterizing enzymes under nonperturbing
and controllable conditions, allowing one to identify and localize
dynamic processes that are important to function. However, many enzymes
are too large for standard approaches to making sequential resonance
assignments, a critical first step in analyzing and interpreting the
wealth of information inherent in NMR spectra. This Account
describes our long-standing NMR-based research into
structural and dynamic aspects of function in the cytochrome P450
monooxygenase superfamily. These heme-containing enzymes typically
catalyze the oxidation of unactivated C–H and C=C bonds
in a multitude of substrates, often with complete regio- and stereospecificity.
Over 600 000 genes in GenBank have been assigned to P450s,
yet all known P450 structures exhibit a highly conserved and unique
fold. This combination of functional and structural conservation with
a vast substrate clientele, each substrate having multiple possible
sites for oxidation, makes the P450s a unique target for understanding
the role of enzyme structure and dynamics in determining a particular
substrate–product combination. P450s are large by solution
NMR standards, requiring us to develop specialized approaches for
making sequential resonance assignments and interpreting the spectral
changes that occur as a function of changing conditions (e.g., oxidation
and spin state changes, ligand, substrate or effector binding). Solution
conformations are characterized by the fitting of residual dipolar
couplings (RDCs) measured for sequence-specifically assigned amide
N–H correlations to alignment tensors optimized in the course
of restrained molecular dynamics (MD) simulations. The conformational
ensembles obtained by such RDC-restrained simulations, which we call
“soft annealing”, are then tested by site-directed mutation
and spectroscopic and activity assays for relevance. These efforts
have gained us insights into cryptic conformational changes associated
with substrate and redox partner binding that were not suspected from
crystal structures, but were shown by subsequent work to be relevant
to function. Furthermore, it appears that many of these changes can
be generalized to P450s besides those that we have characterized,
providing guidance for enzyme engineering efforts. While past research
was primarily directed at the more tractable prokaryotic P450s, our
current efforts are aimed at medically relevant human enzymes, including
CYP17A1, CYP2D6, and CYP3A4.
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7
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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.
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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
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8
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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.
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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
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9
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Asciutto EK, Pochapsky TC. Some Surprising Implications of NMR-directed Simulations of Substrate Recognition and Binding by Cytochrome P450 cam (CYP101A1). J Mol Biol 2018; 430:1295-1310. [PMID: 29596916 DOI: 10.1016/j.jmb.2018.03.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 03/19/2018] [Accepted: 03/19/2018] [Indexed: 02/05/2023]
Abstract
Cytochrome P450cam (CYP101A1) catalyzes the stereospecific 5-exo hydroxylation of d-camphor by molecular oxygen. Previously, residual dipolar couplings measured for backbone amide 1H-15N correlations in both substrate-free and bound forms of CYP101A1 were used as restraints in soft annealing molecular dynamic simulations in order to identify average conformations of the enzyme with and without substrate bound. Multiple substrate-dependent conformational changes remote from the enzyme active site were identified, and site-directed mutagenesis and activity assays confirmed the importance of these changes in substrate recognition. The current work makes use of perturbation response scanning (PRS) and umbrella sampling molecular dynamic of the residual dipolar coupling-derived CYP101A1 structures to probe the roles of remote structural features in enforcing the regio- and stereospecific nature of the hydroxylation reaction catalyzed by CYP101A1. An improper dihedral angle Ψ was defined and used to maintain substrate orientation in the CYP101A1 active site, and it was observed that different values of Ψ result in different PRS response maps. Umbrella sampling methods show that the free energy of the system is sensitive to Ψ, and bound substrate forms an important mechanical link in the transmission of mechanical coupling through the enzyme structure. Finally, a qualitative approach to interpreting PRS maps in terms of the roles of secondary structural features is proposed.
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Affiliation(s)
- Eliana K Asciutto
- School of Science and Technology, UNSAM and CONICET, Campus Migueletes, 25 de Mayo y Francia, Buenos Aires, Argentina
| | - Thomas C Pochapsky
- Department of Chemistry and Rosenstiel Basic Biomedical Sciences Research Institute, MS 015, Brandeis University, 415 South St., Waltham, MA 02454-9110, USA.
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10
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Tietz DR, Colthart AM, Sondej Pochapsky S, Pochapsky TC. Substrate recognition by two different P450s: Evidence for conserved roles in a common fold. Sci Rep 2017; 7:13581. [PMID: 29051575 PMCID: PMC5648816 DOI: 10.1038/s41598-017-14011-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 10/04/2017] [Indexed: 11/17/2022] Open
Abstract
Cytochrome P450 monooxygenases CYP101A1 and MycG catalyze regio- and stereospecific oxidations of their respective substrates, d-camphor and mycinamicin IV. Despite the low sequence homology between the two enzymes (29% identity) and differences in size and hydrophobicity of their substrates, the conformational changes that occur upon substrate binding in both enzymes as determined by solution NMR methods show some striking similarities. Many of the same secondary structural features in both enzymes are perturbed, suggesting the existence of a common mechanism for substrate binding and recognition in the P450 superfamily.
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Affiliation(s)
- Drew R Tietz
- Department of Chemistry, Brandeis University, MS 015, 415 South St, Waltham, MA, 02453, USA
| | - Allison M Colthart
- Department of Biochemistry and the Rosenstiel Basic Medical Sciences Research Institute, Brandeis University, 415 South St., Waltham, MA, 02453, USA
| | - Susan Sondej Pochapsky
- Department of Chemistry, Brandeis University, MS 015, 415 South St, Waltham, MA, 02453, USA
| | - Thomas C Pochapsky
- Department of Chemistry, Brandeis University, MS 015, 415 South St, Waltham, MA, 02453, USA. .,Department of Biochemistry and the Rosenstiel Basic Medical Sciences Research Institute, Brandeis University, 415 South St., Waltham, MA, 02453, USA.
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11
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Tietz DR, Podust LM, Sherman DH, Pochapsky TC. Solution Conformations and Dynamics of Substrate-Bound Cytochrome P450 MycG. Biochemistry 2017; 56:2701-2714. [PMID: 28488849 DOI: 10.1021/acs.biochem.7b00291] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
MycG is a P450 monooxygenase that catalyzes the sequential hydroxylation and epoxidation of mycinamicin IV (M-IV), the last two steps in the biosynthesis of mycinamicin II, a macrolide antibiotic isolated from Micromonospora griseorubida. The crystal structure of MycG with M-IV bound was previously determined but showed the bound substrate in an orientation that did not rationalize the observed regiochemistry of M-IV hydroxylation. Nuclear magnetic resonance paramagnetic relaxation enhancements provided evidence of an orientation of M-IV in the MycG active site more compatible with the observed chemistry, but substrate-induced changes in the enzyme structure were not characterized. We now describe the use of amide 1H-15N residual dipolar couplings as experimental restraints in solvated "soft annealing" molecular dynamics simulations to generate solution structural ensembles of M-IV-bound MycG. Chemical shift perturbations, hydrogen-deuterium exchange, and 15N relaxation behavior provide insight into the dynamic and electronic perturbations in the MycG structure in response to M-IV binding. The solution and crystallographic structures are compared, and the possibility that the crystallographic orientation of bound M-IV represents an inhibitory mode is discussed.
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Affiliation(s)
| | - Larissa M Podust
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California , San Diego, California 92093, United States
| | - David H Sherman
- Life Sciences Institute, University of Michigan , Ann Arbor, Michigan 48109-2216, United States
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12
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Colthart AM, Tietz DR, Ni Y, Friedman JL, Dang M, Pochapsky TC. Detection of substrate-dependent conformational changes in the P450 fold by nuclear magnetic resonance. Sci Rep 2016; 6:22035. [PMID: 26911901 PMCID: PMC4766564 DOI: 10.1038/srep22035] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 02/03/2016] [Indexed: 01/23/2023] Open
Abstract
Cytochrome P450 monooxygenases typically catalyze the insertion of one atom of oxygen from O2 into unactivated carbon-hydrogen and carbon-carbon bonds, with concomitant reduction of the other oxygen atom to H2O by NAD(P)H. Comparison of the average structures of the camphor hydroxylase cytochrome P450(cam) (CYP101) obtained from residual dipolar coupling (RDC)-restrained molecular dynamics (MD) in the presence and absence of substrate camphor shows structural displacements resulting from the essential collapse of the active site upon substrate removal. This collapse has conformational consequences that extend across the protein structure, none of which were observed in analogous crystallographic structures. Mutations were made to test the involvement of the observed conformational changes in substrate binding and recognition. All of the mutations performed based upon the NMR-detected perturbations, even those remote from the active site, resulted in modified substrate selectivity, enzyme efficiency and/or haem iron spin state. The results demonstrate that solution NMR can provide insights into enzyme structure-function relationships that are difficult to obtain by other methods.
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Affiliation(s)
- Allison M. Colthart
- Departments of Chemistry and Biochemistry Brandeis University, 415 South St., Waltham MA 02454-9110, USA
| | - Drew R. Tietz
- Departments of Chemistry and Biochemistry Brandeis University, 415 South St., Waltham MA 02454-9110, USA
| | - Yuhua Ni
- Departments of Chemistry and Biochemistry Brandeis University, 415 South St., Waltham MA 02454-9110, USA
| | - Jessica L. Friedman
- Departments of Chemistry and Biochemistry Brandeis University, 415 South St., Waltham MA 02454-9110, USA
| | - Marina Dang
- Departments of Chemistry and Biochemistry Brandeis University, 415 South St., Waltham MA 02454-9110, USA
| | - Thomas C. Pochapsky
- Departments of Chemistry and Biochemistry Brandeis University, 415 South St., Waltham MA 02454-9110, USA
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13
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Abstract
The energy landscapes of proteins are highly complex and can be influenced by changes in physical and chemical conditions under which the protein is studied. The redox enzyme cytochrome P450cam undergoes a multistep catalytic cycle wherein two electrons are transferred to the heme group and the enzyme visits several conformational states. Using paramagnetic NMR spectroscopy with a lanthanoid tag, we show that the enzyme bound to its redox partner, putidaredoxin, is in a closed state at ambient temperature in solution. This result contrasts with recent crystal structures of the complex, which suggest that the enzyme opens up when bound to its partner. The closed state supports a model of catalysis in which the substrate is locked in the active site pocket and the enzyme acts as an insulator for the reactive intermediates of the reaction.
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14
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Hiruma Y, Gupta A, Kloosterman A, Olijve C, Ölmez B, Hass MAS, Ubbink M. Hot-Spot Residues in the Cytochrome P450cam-Putidaredoxin Binding Interface. Chembiochem 2013; 15:80-6. [DOI: 10.1002/cbic.201300582] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Indexed: 11/09/2022]
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15
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Kaur R, Bren KL. Redox state dependence of axial ligand dynamics in Nitrosomonas europaea cytochrome c552. J Phys Chem B 2013; 117:15720-8. [PMID: 23909651 DOI: 10.1021/jp4064577] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Analysis of NMR spectra reveals that the heme axial Met ligand orientation and dynamics in Nitrosomonas europaea cytochrome c552 (Ne cyt c) are dependent on the heme redox state. In the oxidized state, the heme axial Met is fluxional, interconverting between two conformers related to each other by inversion through the Met δS atom. In the reduced state, there is no evidence of fluxionality, with the Met occupying one conformation similar to that seen in the homologous Pseudomonas aeruginosa cytochrome c551. Comparison of the observed and calculated pseudocontact shifts for oxidized Ne cyt c using the reduced protein structure as a reference structure reveals a redox-dependent change in the structure of the loop bearing the axial Met (loop 3). Analysis of nuclear Overhauser effects (NOEs) and existing structural data provides further support for the redox state dependence of the loop 3 structure. Implications for electron transfer function are discussed.
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Affiliation(s)
- Ravinder Kaur
- Center for Infectious Disease and Immunology, Research Institute, Rochester General Hospital , Rochester, New York 14621, United States
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16
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Myers WK, Lee YT, Britt RD, Goodin DB. The conformation of P450cam in complex with putidaredoxin is dependent on oxidation state. J Am Chem Soc 2013; 135:11732-5. [PMID: 23901883 DOI: 10.1021/ja405751z] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Double electron-electron resonance (DEER) spectroscopy was used to determine the conformational state in solution for the heme monooxygenase P450cam when bound to its natural redox partner, putidaredoxin (Pdx). When oxidized Pdx was titrated into substrate-bound ferric P450cam, the enzyme shifted from the closed to the open conformation. In sharp contrast, however, the enzyme remained in the closed conformation when ferrous-CO P450cam was titrated with reduced Pdx. This result fully supports the proposal that binding of oxidized Pdx to P450cam opposes the open-to-closed transition induced by substrate binding. However, the data strongly suggest that in solution, binding of reduced Pdx to P450cam does not favor the open conformation. This supports a model in which substrate recognition is associated with the open-to-closed transition and electron transfer from Pdx occurs in the closed conformation. The opening of the enzyme in the ferric-hydroperoxo state following electron transfer from Pdx would provide for efficient O2 bond activation, substrate oxidation, and product release.
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Affiliation(s)
- William K Myers
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, USA
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17
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Asciutto EK, Young MJ, Madura J, Pochapsky SS, Pochapsky TC. Solution structural ensembles of substrate-free cytochrome P450(cam). Biochemistry 2012; 51:3383-93. [PMID: 22468842 DOI: 10.1021/bi300007r] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Removal of substrate (+)-camphor from the active site of cytochrome P450(cam) (CYP101A1) results in nuclear magnetic resonance-detected perturbations in multiple regions of the enzyme. The (1)H-(15)N correlation map of substrate-free diamagnetic Fe(II) CO-bound CYP101A permits these perturbations to be mapped onto the solution structure of the enzyme. Residual dipolar couplings (RDCs) were measured for (15)N-(1)H amide pairs in two independent alignment media for the substrate-free enzyme and used as restraints in solvated molecular dynamics (MD) simulations to generate an ensemble of best-fit structures of the substrate-free enzyme in solution. Nuclear magnetic resonance-detected chemical shift perturbations reflect changes in the electronic environment of the NH pairs, such as hydrogen bonding and ring current shifts, and are observed for residues in the active site as well as in hinge regions between secondary structural features. RDCs provide information about relative orientations of secondary structures, and RDC-restrained MD simulations indicate that portions of a β-rich region adjacent to the active site shift so as to partially occupy the vacancy left by removal of the substrate. The accessible volume of the active site is reduced in the substrate-free enzyme relative to the substrate-bound structure calculated using the same methods. Both symmetric and asymmetric broadening of multiple resonances observed upon substrate removal as well as localized increased errors in RDC fits suggest that an ensemble of enzyme conformations are present in the substrate-free form.
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Affiliation(s)
- Eliana K Asciutto
- Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, PA 15282-1530, USA
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18
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Tian JM, Ou-Yang SS, Zhang X, Di YT, Jiang HL, Li HL, Dai WX, Chen KY, Liu ML, Hao XJ, Shen YH, Luo C, Zhang WD. Experimental and computational insights into the conformations of tunicyclin E, a new cycloheptapeptide from Psammosilene tunicoides. RSC Adv 2012. [DOI: 10.1039/c1ra00593f] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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19
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Abstract
A hydrogen bond network has been identified that adjusts protein-substrate contacts in cytochrome P450(cam) (CYP101A1). Replacing the native substrate camphor with adamantanone or norcamphor causes perturbations in NMR-detected NH correlations assigned to the network, which includes portions of a β sheet and an adjacent helix that is remote from the active site. A mutation in this helix reduces enzyme efficiency and perturbs the extent of substrate-induced spin state changes at the haem iron that accompany substrate binding. In turn, the magnitude of the spin state changes induced by alternate substrate binding parallel the NMR-detected perturbations observed near the haem in the enzyme active site.
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Affiliation(s)
- Marina Dang
- Dept. of Chemistry, MS 015, Brandeis University, 415 South St., Waltham, MA 02454-9110 USA
| | - Susan Sondej Pochapsky
- Dept. of Chemistry, MS 015, Brandeis University, 415 South St., Waltham, MA 02454-9110 USA
| | - Thomas C. Pochapsky
- Dept. of Chemistry, MS 015, Brandeis University, 415 South St., Waltham, MA 02454-9110 USA
- Rosenstiel Basic Medical Sciences Research Institute, Brandeis University, Waltham, MA 02454-9110 USA
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20
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Asciutto EK, Dang M, Pochapsky SS, Madura JD, Pochapsky TC. Experimentally restrained molecular dynamics simulations for characterizing the open states of cytochrome P450cam. Biochemistry 2011; 50:1664-71. [PMID: 21265500 DOI: 10.1021/bi101820d] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Residual dipolar couplings (RDCs) were used as restraints in fully solvated molecular dynamics simulations of reduced substrate- and carbonmonoxy-bound cytochrome P450(cam) (CYP101A1), a 414-residue soluble monomeric heme-containing camphor monooxygenase from the soil bacterium Pseudomonas putida. The (1)D(NH) residual dipolar couplings used as restraints were measured in two independent alignment media. A soft annealing protocol was used to heat the starting structures while incorporating the RDC restraints. After production dynamics, structures with the lowest total violation energies for RDC restraints were extracted to identify ensembles of conformers accessible to the enzyme in solution. The simulations result in substrate orientations different from that seen in crystallographic structures and a more open and accessible enzyme active site and largely support previously reported differences between the open and closed states of CYP101A1.
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Affiliation(s)
- Eliana K Asciutto
- Department of Chemistry and Biochemistry, Center for Computational Sciences, Duquesne University, Pittsburgh, Pennsylvania 15282, United States
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21
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Lee YT, Glazer EC, Wilson RF, Stout CD, Goodin DB. Three clusters of conformational states in p450cam reveal a multistep pathway for closing of the substrate access channel. Biochemistry 2011; 50:693-703. [PMID: 21171581 DOI: 10.1021/bi101726d] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Conformational changes in the substrate access channel have been observed for several forms of cytochrome P450, but the extent of conformational plasticity exhibited by a given isozyme has not been completely characterized. Here we present crystal structures of P450cam bound to a library of 12 active site probes containing a substrate analogue tethered to a variable linker. The structures provide a unique view of the range of protein conformations accessible during substrate binding. Principal component analysis of a total of 30 structures reveals three discrete clusters of conformations: closed (P450cam-C), intermediate (P450cam-I), and fully open (P450cam-O). Relative to P450cam-C, the P450cam-I state results predominantly from a retraction of helix F, while both helices F and G move in concert to reach the fully open P450cam-O state. Both P450cam-C and P450cam-I are well-defined states, while P450cam-O shows evidence of a somewhat broader distribution of conformations and includes the open form recently seen in the absence of substrate. The observed clustering of protein conformations over a wide range of ligand variants suggests a multistep closure of the enzyme around the substrate that begins by conformational selection from an ensemble of open conformations and proceeds through a well-defined intermediate, P450cam-I, before full closure to the P450cam-C state in the presence of small substrates. This multistep pathway may have significant implications for a full understanding of substrate specificity, kinetics, and coupling of substrate binding to P450 function.
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Affiliation(s)
- Young-Tae Lee
- Department of Molecular Biology, 10550 North Torrey Pines Road, The Scripps Research Institute, La Jolla, California 92037, United States
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22
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Luthra A, Denisov IG, Sligar SG. Spectroscopic features of cytochrome P450 reaction intermediates. Arch Biochem Biophys 2010; 507:26-35. [PMID: 21167809 DOI: 10.1016/j.abb.2010.12.008] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2010] [Revised: 12/06/2010] [Accepted: 12/07/2010] [Indexed: 11/24/2022]
Abstract
Cytochromes P450 constitute a broad class of heme monooxygenase enzymes with more than 11,500 isozymes which have been identified in organisms from all biological kingdoms [1]. These enzymes are responsible for catalyzing dozens chemical oxidative transformations such as hydroxylation, epoxidation, N-demethylation, etc., with very broad range of substrates [2,3]. Historically these enzymes received their name from 'pigment 450' due to the unusual position of the Soret band in UV-vis absorption spectra of the reduced CO-saturated state [4,5]. Despite detailed biochemical characterization of many isozymes, as well as later discoveries of other 'P450-like heme enzymes' such as nitric oxide synthase and chloroperoxidase, the phenomenological term 'cytochrome P450' is still commonly used as indicating an essential spectroscopic feature of the functionally active protein which is now known to be due to the presence of a thiolate ligand to the heme iron [6]. Heme proteins with an imidazole ligand such as myoglobin and hemoglobin as well as an inactive form of P450 are characterized by Soret maxima at 420nm [7]. This historical perspective highlights the importance of spectroscopic methods for biochemical studies in general, and especially for heme enzymes, where the presence of the heme iron and porphyrin macrocycle provides rich variety of specific spectroscopic markers available for monitoring chemical transformations and transitions between active intermediates of catalytic cycle.
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Affiliation(s)
- Abhinav Luthra
- Department of Biochemistry, School of Molecular and Cellular Biology, University of Illinois, Urbana, IL 61801, USA
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23
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Pochapsky TC, Kazanis S, Dang M. Conformational plasticity and structure/function relationships in cytochromes P450. Antioxid Redox Signal 2010; 13:1273-96. [PMID: 20446763 PMCID: PMC2959183 DOI: 10.1089/ars.2010.3109] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The cytochrome P450s are a superfamily of enzymes that are found in all kingdoms of living organisms, and typically catalyze the oxidative addition of atomic oxygen to an unactivated C-C or C-H bond. Over 8000 nonredundant sequences of putative and confirmed P450 enzymes have been identified, but three-dimensional structures have been determined for only a small fraction of these. While all P450 enzymes for which structures have been determined share a common global fold, the flexibility and modularity of structure around the active site account for the ability of P450 enzymes to accommodate a vast number of structurally dissimilar substrates and support a wide range of selective oxidations. In this review, known P450 structures are compared, and some structural criteria for prediction of substrate selectivity and reaction type are suggested. The importance of dynamic processes such as redox-dependent and effector-induced conformational changes in determining catalytic competence and regio- and stereoselectivity is discussed, and noncrystallographic methods for characterizing P450 structures and dynamics, in particular, mass spectrometry and nuclear magnetic resonance spectroscopy are reviewed.
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Affiliation(s)
- Thomas C Pochapsky
- Department of Chemistry, Brandeis University, Waltham, Massachusetts 02454-9110, USA.
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24
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Lampe JN, Brandman R, Sivaramakrishnan S, de Montellano PRO. Two-dimensional NMR and all-atom molecular dynamics of cytochrome P450 CYP119 reveal hidden conformational substates. J Biol Chem 2010; 285:9594-9603. [PMID: 20097757 DOI: 10.1074/jbc.m109.087593] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cytochrome P450 enzymes are versatile catalysts involved in a wide variety of biological processes from hormonal regulation and antibiotic synthesis to drug metabolism. A hallmark of their versatility is their promiscuous nature, allowing them to recognize a wide variety of chemically diverse substrates. However, the molecular details of this promiscuity have remained elusive. Here, we have utilized two-dimensional heteronuclear single quantum coherence NMR spectroscopy to examine a series of mutants site-specific labeled with the unnatural amino acid, [(13)C]p-methoxyphenylalanine, in conjunction with all-atom molecular dynamics simulations to examine substrate and inhibitor binding to CYP119, a P450 from Sulfolobus acidocaldarius. The results suggest that tight binding hydrophobic ligands tend to lock the enzyme into a single conformational substate, whereas weak binding low affinity ligands bind loosely in the active site, resulting in a distribution of localized conformers. Furthermore, the molecular dynamics simulations suggest that the ligand-free enzyme samples ligand-bound conformations of the enzyme and, therefore, that ligand binding may proceed largely through a process of conformational selection rather than induced fit.
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Affiliation(s)
- Jed N Lampe
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158-2517
| | | | - Santhosh Sivaramakrishnan
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158-2517
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