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Maldonado-Domínguez M, Srnec M. Understanding and Predicting Post H-Atom Abstraction Selectivity through Reactive Mode Composition Factor Analysis. J Am Chem Soc 2020; 142:3947-3958. [PMID: 32000494 DOI: 10.1021/jacs.9b12800] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The selective functionalization of C-H bonds is one of the Grails of synthetic chemistry. In this work, we demonstrate that the selectivity toward fast hydroxylation or radical diffusion (known as the OH-rebound and dissociation mechanisms) following H-atom abstraction (HAA) from a substrate C-H bond by high-valent iron-oxo oxidants is already encoded in the HAA step when the post-HAA barriers are much lower than the preceding one. By applying the reactive mode composition factor (RMCF) analysis, which quantifies the kinetic energy distribution (KED) at the reactive mode (RM) of transition states, we show that reactions following the OH-rebound coordinate concentrate the RM kinetic energy on the motion of the reacting oxygen atom and the nascent substrate radical, whereas reactions following the dissociation channel localize most of their kinetic energy in H-atom motion. These motion signatures serve to predict the post-HAA selectivity, and since KED is affected by the free energy of reaction and asynchronicity (factor η) of HAA, we show that bimolecular HAA reactions in solution that are electron transfer-driven and highly exergonic have the lowest fraction of KED on the transferred H-atom and the highest chance to follow rebound hydroxylation. Finally, the RMCF analysis predicts that the H/D primary kinetic isotope effect can serve as a probe for these mechanisms, as confirmed in virtually all reported examples in the literature.
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Affiliation(s)
- Mauricio Maldonado-Domínguez
- J. Heyrovský Institute of Physical Chemistry, The Czech Academy of Sciences , Dolejškova 3 , Prague 8 18223 , Czech Republic
| | - Martin Srnec
- J. Heyrovský Institute of Physical Chemistry, The Czech Academy of Sciences , Dolejškova 3 , Prague 8 18223 , Czech Republic
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2
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Metal centers in biomolecular solid-state NMR. J Struct Biol 2018; 206:99-109. [PMID: 30502494 DOI: 10.1016/j.jsb.2018.11.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 09/25/2018] [Accepted: 11/27/2018] [Indexed: 01/03/2023]
Abstract
Solid state NMR (SSNMR) has earned a substantial success in the characterization of paramagnetic systems over the last decades. Nowadays, the resolution and sensitivity of solid state NMR in biological molecules has improved significantly and these advancements can be translated into the study of paramagnetic biomolecules. However, the electronic properties of different metal centers affect the quality of their SSNMR spectra differently, and not all systems turn out to be equally easy to approach by this technique. In this review we will try to give an overview of the properties of different paramagnetic centers and how they can be used to increase the chances of experimental success.
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3
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Mak PJ, Denisov IG. Spectroscopic studies of the cytochrome P450 reaction mechanisms. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2018; 1866:178-204. [PMID: 28668640 PMCID: PMC5709052 DOI: 10.1016/j.bbapap.2017.06.021] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 06/22/2017] [Indexed: 10/19/2022]
Abstract
The cytochrome P450 monooxygenases (P450s) are thiolate heme proteins that can, often under physiological conditions, catalyze many distinct oxidative transformations on a wide variety of molecules, including relatively simple alkanes or fatty acids, as well as more complex compounds such as steroids and exogenous pollutants. They perform such impressive chemistry utilizing a sophisticated catalytic cycle that involves a series of consecutive chemical transformations of heme prosthetic group. Each of these steps provides a unique spectral signature that reflects changes in oxidation or spin states, deformation of the porphyrin ring or alteration of dioxygen moieties. For a long time, the focus of cytochrome P450 research was to understand the underlying reaction mechanism of each enzymatic step, with the biggest challenge being identification and characterization of the powerful oxidizing intermediates. Spectroscopic methods, such as electronic absorption (UV-Vis), electron paramagnetic resonance (EPR), nuclear magnetic resonance (NMR), electron nuclear double resonance (ENDOR), Mössbauer, X-ray absorption (XAS), and resonance Raman (rR), have been useful tools in providing multifaceted and detailed mechanistic insights into the biophysics and biochemistry of these fascinating enzymes. The combination of spectroscopic techniques with novel approaches, such as cryoreduction and Nanodisc technology, allowed for generation, trapping and characterizing long sought transient intermediates, a task that has been difficult to achieve using other methods. Results obtained from the UV-Vis, rR and EPR spectroscopies are the main focus of this review, while the remaining spectroscopic techniques are briefly summarized. This article is part of a Special Issue entitled: Cytochrome P450 biodiversity and biotechnology, edited by Erika Plettner, Gianfranco Gilardi, Luet Wong, Vlada Urlacher, Jared Goldstone.
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Affiliation(s)
- Piotr J Mak
- Department of Chemistry, Saint Louis University, St. Louis, MO, United States.
| | - Ilia G Denisov
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL, United States.
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4
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Bertarello A, Schubeis T, Fuccio C, Ravera E, Fragai M, Parigi G, Emsley L, Pintacuda G, Luchinat C. Paramagnetic Properties of a Crystalline Iron–Sulfur Protein by Magic-Angle Spinning NMR Spectroscopy. Inorg Chem 2017; 56:6624-6629. [DOI: 10.1021/acs.inorgchem.7b00674] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Andrea Bertarello
- Centre de RMN à
Très Hauts Champs, Institut des Sciences Analytiques (CNRS,
ENS Lyon, UCB Lyon 1), Université de Lyon, 69100 Villeurbanne, France
| | - Tobias Schubeis
- Centre de RMN à
Très Hauts Champs, Institut des Sciences Analytiques (CNRS,
ENS Lyon, UCB Lyon 1), Université de Lyon, 69100 Villeurbanne, France
- Giotto Biotech S.R.L., Via Madonna
del Piano 6, 50019 Sesto Fiorentino, Italy
| | - Carmelo Fuccio
- Magnetic Resonance Center (CERM) and Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Enrico Ravera
- Magnetic Resonance Center (CERM) and Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Marco Fragai
- Magnetic Resonance Center (CERM) and Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Giacomo Parigi
- Magnetic Resonance Center (CERM) and Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Lyndon Emsley
- Institut
des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Guido Pintacuda
- Centre de RMN à
Très Hauts Champs, Institut des Sciences Analytiques (CNRS,
ENS Lyon, UCB Lyon 1), Université de Lyon, 69100 Villeurbanne, France
| | - Claudio Luchinat
- Giotto Biotech S.R.L., Via Madonna
del Piano 6, 50019 Sesto Fiorentino, Italy
- Magnetic Resonance Center (CERM) and Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
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5
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Banerjee S, Goyal S, Mazumdar S. Role of substituents on the reactivity and product selectivity in reactions of naphthalene derivatives catalyzed by the orphan thermostable cytochrome P450, CYP175A1. Bioorg Chem 2015; 62:94-105. [DOI: 10.1016/j.bioorg.2015.08.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2015] [Revised: 08/13/2015] [Accepted: 08/17/2015] [Indexed: 11/28/2022]
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6
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Jaroniec CP. Structural studies of proteins by paramagnetic solid-state NMR spectroscopy. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2015; 253:50-9. [PMID: 25797004 PMCID: PMC4371136 DOI: 10.1016/j.jmr.2014.12.017] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 12/17/2014] [Indexed: 05/03/2023]
Abstract
Paramagnetism-based nuclear pseudocontact shifts and spin relaxation enhancements contain a wealth of information in solid-state NMR spectra about electron-nucleus distances on the ∼20 Å length scale, far beyond that normally probed through measurements of nuclear dipolar couplings. Such data are especially vital in the context of structural studies of proteins and other biological molecules that suffer from a sparse number of experimentally-accessible atomic distances constraining their three-dimensional fold or intermolecular interactions. This perspective provides a brief overview of the recent developments and applications of paramagnetic magic-angle spinning NMR to biological systems, with primary focus on the investigations of metalloproteins and natively diamagnetic proteins modified with covalent paramagnetic tags.
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Affiliation(s)
- Christopher P Jaroniec
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH 43210, USA.
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7
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Probing the transmembrane structure and topology of microsomal cytochrome-p450 by solid-state NMR on temperature-resistant bicelles. Sci Rep 2014; 3:2556. [PMID: 23989972 PMCID: PMC3757361 DOI: 10.1038/srep02556] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Accepted: 08/15/2013] [Indexed: 01/03/2023] Open
Abstract
Though the importance of high-resolution structure and dynamics of membrane proteins has been well recognized, optimizing sample conditions to retain the native-like folding and function of membrane proteins for Nuclear Magnetic Resonance (NMR) or X-ray measurements has been a major challenge. While bicelles have been shown to stabilize the function of membrane proteins and are increasingly utilized as model membranes, the loss of their magnetic-alignment at low temperatures makes them unsuitable to study heat-sensitive membrane proteins like cytochrome-P450 and protein-protein complexes. In this study, we report temperature resistant bicelles that can magnetically-align for a broad range of temperatures and demonstrate their advantages in the structural studies of full-length microsomal cytochrome-P450 and cytochrome-b5 by solid-state NMR spectroscopy. Our results reveal that the N-terminal region of rabbit cytochromeP4502B4, that is usually cleaved off to obtain crystal structures, is helical and has a transmembrane orientation with ~17° tilt from the lipid bilayer normal.
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8
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Childers WK, Harrelson JP. Allosteric modulation of substrate motion in cytochrome P450 3A4-mediated xylene oxidation. Biochemistry 2014; 53:1018-28. [PMID: 24476063 DOI: 10.1021/bi401472p] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Many cytochrome P450 enzymes (CYPs) exhibit allosteric behavior reflecting a complex ligand-binding process involving numerous factors: conformational selection, protein-protein interactions, substrate/effector/protein structure, and multiple-ligand binding. The interplay of CYP plasticity and rigidity contributes to substrate/product selectivity and to allosterism. Detailed evidence describing how protein motion modulates product selectivity is incomplete as are descriptions of effector-induced modulation of substrate dynamics. Our intent was to discover details of allosteric behavior and CYP3A4 flexibility and rigidity by investigating substrate motion using low-molecular weight ligands. Steady state kinetics and product ratios were measured for oxidation of m-xylene-(2)H3 and p-xylene; intramolecular isotope effects were measured for m-xylene-(2)H3 oxidation as a function of m-xylene-(2)H3 and p-xylene concentration. Biphasic kinetic plots indicated homotropic cooperative behavior with xylene isomers. Selectivity for aromatic hydroxylation over benzylic hydroxylation of m-xylene-(2)H3 supports a model in which the region near the CYP3A4 active oxidizing species limits substrate dynamics. p-Xylene impedes the motion of m-xylene-(2)H3 substrates that have access to the active oxidizing species: (kH/kD)obs values for m-xylene-(2)H3 decreased with p-xylene concentration. m-Xylene-(2)H3 and p-xylene do not have simultaneous access to the active oxidizing species: deuterium-labeled and unlabeled p-xylene exhibited similar effects on the (kH/kD)obs values for m-xylene-(2)H3 oxidation. p-Xylene and m-xylene-(2)H3 bind at different sites: m-xylene-(2)H3 oxidation rates and product selectivity were consistent across the p-xylene concentration range. Overall, this study indicates that the intramolecular isotope effect experimental design provides a unique opportunity to investigate allosteric mechanisms as it provides information about substrate motion when the enzyme is primed to oxidize substrates.
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Affiliation(s)
- W Kurtis Childers
- Chemistry Department, Pacific University Oregon , Forest Grove, Oregon 97116, United States
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9
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Lennartson A, Christensen LU, McKenzie CJ, Nielsen UG. Solid state 13C and 2H NMR investigations of paramagnetic [Ni(II)(acac)2L2] complexes. Inorg Chem 2013; 53:399-408. [PMID: 24325293 DOI: 10.1021/ic402354r] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Nine structurally related paramagnetic acetylacetonato nickel(II) complexes: [Ni(acac)2] and trans-[Ni(acac)2(X)2]nH/D2O, X = H2O, D2O, NH3, MeOH, PMePh2, PMe2Ph, or [dppe]1/2, n = 0 or 1, dppe = 1,2-bis(diphenylphosphino)ethane, as well as cis-[Ni(F6-acac)2(D2O)2], F6-acac = hexafluoroacetylonato, have been characterized by solid state (13)C MAS NMR spectroscopy. (2)H MAS NMR was used to probe the local hydrogen bonding network in [Ni(acac)2(D2O)2]D2O and cis-[Ni(F6-acac)2(D2O)2]. The complexes serve to benchmark the paramagnetic shift, which can be associated with the resonances of atoms of the coordinated ligands. The methine (CH) and methyl (CH3) have characteristic combinations of the isotropic shift (δ) and anisotropy parameters (d, η). The size of the anisotropy (d), which is the sum of the chemical shift anisotropy (CSA) and the paramagnetic electron-nuclei dipolar coupling, is much more descriptive than the isotropic shift. Moreover, the CSA is found to constitute up to one-third of the total anisotropy and should be taken into consideration when (13)C anisotropies are used for structure determination of paramagnetic materials. The (13)C MAS NMR spectra of trans-[Ni(acac)2(PMe2Ph)2], trans-[Ni(acac)2(PMePh2)2], and the noncrystallographically characterized trans-[Ni(acac)2(dppe)]n were assigned using these correlations. The complexes with L = H2O, D2O, NH3, and MeOH can be prepared by a series of solid state desorption and sorption reactions. Crystal structures for trans-[Ni(acac)2(NH3)2] and trans-[Ni(acac)2(PMePh2)2] are reported.
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Affiliation(s)
- Anders Lennartson
- Department of Physics, Chemistry, and Pharmacy, University of Southern Denmark , Campusvej 55, 5230 Odense M, Denmark
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10
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Jaroniec CP. Solid-state nuclear magnetic resonance structural studies of proteins using paramagnetic probes. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2012; 43-44:1-13. [PMID: 22464402 DOI: 10.1016/j.ssnmr.2012.02.007] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Revised: 02/27/2012] [Accepted: 02/28/2012] [Indexed: 05/31/2023]
Abstract
Determination of three-dimensional structures of biological macromolecules by magic-angle spinning (MAS) solid-state NMR spectroscopy is hindered by the paucity of nuclear dipolar coupling-based restraints corresponding to distances exceeding 5 Å. Recent MAS NMR studies of uniformly (13)C,(15)N-enriched proteins containing paramagnetic centers have demonstrated the measurements of site-specific nuclear pseudocontact shifts and spin relaxation enhancements, which report on electron-nucleus distances up to ~20 Å. These studies pave the way for the application of such long-distance paramagnetic restraints to protein structure elucidation and analysis of protein-protein and protein-ligand interactions in the solid phase. Paramagnetic species also facilitate the rapid acquisition of high resolution and sensitivity multidimensional solid-state NMR spectra of biomacromolecules using condensed data collection schemes, and characterization of solvent-accessible surfaces of peptides and proteins. In this review we discuss some of the latest applications of magic-angle spinning NMR spectroscopy in conjunction with paramagnetic probes to the structural studies of proteins in the solid state.
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Affiliation(s)
- Christopher P Jaroniec
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH 43210, USA.
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11
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12
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Breen NF, Li K, Olsen GL, Drobny GP. Deuterium magic angle spinning NMR used to study the dynamics of peptides adsorbed onto polystyrene and functionalized polystyrene surfaces. J Phys Chem B 2011; 115:9452-60. [PMID: 21650191 DOI: 10.1021/jp1101829] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
LKα14 is a 14 amino acid peptide with a periodic sequence of leucine and lysine residues consistent with an amphipathic α-helix. This "hydrophobic periodicity" has been found to result in an α-helical secondary structure at air-water interfaces and on both polar and nonpolar solid polymer surfaces. In this paper, the dynamics of LKα14 peptides, selectively deuterated at a single leucine and adsorbed onto polystyrene and carboxylated polystyrene beads, are studied using (2)H magic angle spinning (MAS) solid state NMR over a 100 °C temperature range. We first demonstrate the sensitivity enhancement possible with (2)H MAS techniques, which in turn enables us to obtain high-quality (2)H NMR spectra for selectively deuterated peptides adsorbed onto solid polymer surfaces. The extensive literature shows that the dynamics of leucine side chains are sensitive to the local structural environment of the protein. Therefore, the degree to which the dynamics of leucine side chains and the backbone of the peptide LKα14 are influenced by surface proximity and surface chemistry is studied as a function of temperature with (2)H MAS NMR. It is found that the dynamics of the leucine side chains in LKα14 depend strongly upon the orientation of the polymer on the surface, which in turn depends on whether the LKα14 peptide adsorbs onto a polar or nonpolar surface. (2)H MAS line shapes therefore permit probes of surface orientation over a wide temperature range.
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Affiliation(s)
- Nicholas F Breen
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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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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14
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The structure of CYP101D2 unveils a potential path for substrate entry into the active site. Biochem J 2011; 433:85-93. [PMID: 20950270 DOI: 10.1042/bj20101017] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The cytochrome P450 CYP101D2 from Novosphingobium aromaticivorans DSM12444 is closely related to CYP101D1 from the same bacterium and to P450cam (CYP101A1) from Pseudomonas putida. All three are capable of oxidizing camphor stereoselectively to 5-exo-hydroxycamphor. The crystal structure of CYP101D2 revealed that the likely ferredoxin-binding site on the proximal face is largely positively charged, similar to that of CYP101D1. However, both the native and camphor-soaked forms of CYP101D2 had open conformations with an access channel. In the active site of the camphor-soaked form, the camphor carbonyl interacted with the haem-iron-bound water. Two other potential camphor-binding sites were also identified from electron densities in the camphor-soaked structure: one located in the access channel, flanked by the B/C and F/G loops and the I helix, and the other in a cavity on the surface of the enzyme near the F helix side of the F/G loop. The observed open structures may be conformers of the CYP101D2 enzyme that enable the substrate to enter the buried active site via a conformational selection mechanism. The second and third binding sites may be intermediate locations of substrate entry and translocation into the active site, and provide insight into a multi-step substrate-binding mechanism.
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15
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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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16
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Bach RD. The rate-limiting step in P450 hydroxylation of hydrocarbons a direct comparison of the "somersault" versus the "consensus" mechanism involving compound I. J Phys Chem A 2010; 114:9319-32. [PMID: 20690650 DOI: 10.1021/jp1045518] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Model theoretical quantum mechanical (QM) calculations are described for the P-450 hydroxylation of methane, isobutane, and camphor that compare the concerted somersault H-abstraction mechanism with the oxidation step involving Cpd I. Special emphasis has been placed on maintaining a balanced basis set in the oxidation step. QM calculations, employing the 6-311+G(d,p) basis set on the Fe atom and all of the key surrounding atoms involved in the C-H abstraction step, reaffirm a mechanism involving rearrangement of the iron hydroperoxide group (FeO-OH --> FeO...HO(*)) in concert with hydrogen abstraction from the C-H bond of the substrate by the incipient bound hydroxyl radical HO(*). The barrier for the somersault rearrangement of model Cpd 0 (FeO-OH) is calculated to be 21.4 kcal/mol in the absence of substrate. The overall activation energy for the oxidation of camphor involving the somersault motion of the FeO-OH group of P450 model porphyrin iron(III) hydroperoxide [Por(SH)Fe(III)-OOH(-)] --> [Por(SH)Fe(III)-O....HO(-)] in concert with hydrogen abstraction is DeltaE(++) = 12.4 kcal/mol. The corresponding abstraction of the hydrogen atom from the C-H bond of camphor by Cpd I has an activation barrier of 17.6 kcal/mol. Arguments are presented that the somersault rearrangement is induced by steric compression at the active site. Kinetic isotope effect data are discussed that provides compelling evidence for a rate-limiting step involving C-H bond cleavage.
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Affiliation(s)
- Robert D Bach
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA.
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17
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Site of metabolism prediction on cytochrome P450 2C9: a knowledge-based docking approach. J Comput Aided Mol Des 2010; 24:399-408. [PMID: 20361237 DOI: 10.1007/s10822-010-9347-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2009] [Accepted: 03/18/2010] [Indexed: 01/21/2023]
Abstract
A novel structure-based approach for site of metabolism prediction has been developed. This knowledge-based method consists of three steps: (1) generation of possible metabolites, (2) docking the predicted metabolites to the CYP binding site and (3) selection of the most probable metabolites based on their complementarity to the binding site. As a proof of concept we evaluated our method by using MetabolExpert for metabolite generation and Glide for docking into the binding site of the CYP2C9 crystal structure. Our method could identify the correct metabolite among the three best-ranked compounds in 69% of the cases. The predictive power of our knowledge-based method was compared to that achieved by substrate docking and two alternative literature approaches.
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18
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Bertini I, Bhaumik A, De Paëpe G, Griffin RG, Lelli M, Lewandowski JR, Luchinat C. High-resolution solid-state NMR structure of a 17.6 kDa protein. J Am Chem Soc 2010; 132:1032-40. [PMID: 20041641 DOI: 10.1021/ja906426p] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The use of pseudocontact shifts arising from paramagnetic metal ions in a microcrystalline protein sample is proposed as a strategy to obtain unambiguous signal assignments in solid-state NMR spectra enabling distance extraction for protein structure calculation. With this strategy, 777 unambiguous (281 sequential, 217 medium-range, and 279 long-range) distance restraints could be obtained from PDSD, DARR, CHHC, and the recently introduced PAR and PAIN-CP solid-state experiments for the cobalt(II)-substituted catalytic domain of matrix metalloproteinase 12 (159 amino acids, 17.6 kDa). The obtained structure is a high resolution one, with backbone rmsd of 1.0 +/- 0.2 A, and is in good agreement with the X-ray structure (rmsd to X-ray 1.3 A). The proposed strategy, which may be generalized for nonmetalloproteins with the use of paramagnetic tags, represents a significant step ahead in protein structure determination using solid-state NMR.
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Affiliation(s)
- Ivano Bertini
- Magnetic Resonance Center, CERM, University of Florence, Via L. Sacconi, 6-50019 Sesto Fiorentino, Italy.
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Nadaud PS, Helmus JJ, Kall SL, Jaroniec CP. Paramagnetic Ions Enable Tuning of Nuclear Relaxation Rates and Provide Long-Range Structural Restraints in Solid-State NMR of Proteins. J Am Chem Soc 2009; 131:8108-20. [DOI: 10.1021/ja900224z] [Citation(s) in RCA: 116] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Philippe S. Nadaud
- Department of Chemistry, The Ohio State University, Columbus, Ohio 43210
| | - Jonathan J. Helmus
- Department of Chemistry, The Ohio State University, Columbus, Ohio 43210
| | - Stefanie L. Kall
- Department of Chemistry, The Ohio State University, Columbus, Ohio 43210
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Paramagnetic shifts in solid-state NMR of proteins to elicit structural information. Proc Natl Acad Sci U S A 2008; 105:17284-9. [PMID: 18988744 DOI: 10.1073/pnas.0708460105] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The recent observation of pseudocontact shifts (pcs) in (13)C high-resolution solid-state NMR of paramagnetic proteins opens the way to their application as structural restraints. Here, by investigating a microcrystalline sample of cobalt(II)-substituted matrix metalloproteinase 12 [CoMMP-12 (159 AA, 17.5 kDa)], it is shown that a combined strategy of protein labeling and dilution of the paramagnetic species (i.e., (13)C-,(15)N-labeled CoMMP-12 diluted in unlabeled ZnMMP-12, and (13)C-,(15)N-labeled ZnMMP-12 diluted in unlabeled CoMMP-12) allows one to easily separate the pcs contributions originated from the protein internal metal (intramolecular pcs) from those due to the metals in neighboring proteins in the crystal lattice (intermolecular pcs) and that both can be used for structural purposes. It is demonstrated that intramolecular pcs are significant structural restraints helpful in increasing both precision and accuracy of the structure, which is a need in solid-state structural biology nowadays. Furthermore, intermolecular pcs provide unique information on positions and orientations of neighboring protein molecules in the solid phase.
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21
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Isin EM, Guengerich FP. Substrate binding to cytochromes P450. Anal Bioanal Chem 2008; 392:1019-30. [PMID: 18622598 DOI: 10.1007/s00216-008-2244-0] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2008] [Revised: 06/10/2008] [Accepted: 06/11/2008] [Indexed: 01/08/2023]
Abstract
P450s have attracted tremendous attention owing to not only their involvement in the metabolism of drug molecules and endogenous substrates but also the unusual nature of the reaction they catalyze, namely, the oxidation of unactivated C-H bonds. The binding of substrates to P450s, which is usually viewed as the first step in the catalytic cycle, has been studied extensively via a variety of biochemical and biophysical approaches. These studies were directed towards answering different questions related to P450s, including mechanism of oxidation, substrate properties, unusual substrate oxidation kinetics, function, and active-site features. Some of the substrate binding studies extending over a period of more than 40 years of dedicated work have been summarized in this review and categorized by the techniques employed in the binding studies.
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Affiliation(s)
- Emre M Isin
- Biotransformation Section, Department of Discovery DMPK & Bioanalytical Chemistry, AstraZeneca R & D Mölndal, 431 83, Mölndal, Sweden.
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Harrelson JP, Atkins WM, Nelson SD. Multiple-ligand binding in CYP2A6: probing mechanisms of cytochrome P450 cooperativity by assessing substrate dynamics. Biochemistry 2008; 47:2978-88. [PMID: 18247580 DOI: 10.1021/bi702020y] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The contribution of ligand dynamics to CYP allosterism has not been considered in detail. On the basis of a previous study, we hypothesized that CYP2A6 and CYP2E1 accommodate multiple xylene ligands. As a result, the intramolecular ( k H/ k D) obs values observed for some xylene isomers are expected to be dependent on ligand concentration with contributions from [CYP.xylene] and [CYP.xylene.xylene], etc. To explore this possibility and the utility of kinetic isotope effects in characterizing allosteric CYP behavior, steady state kinetics, product ratios, and ( k H/ k D) obs values for CYP2E1 and CYP2A6 oxidation of m-xylene-alpha- (2)H 3 and p-xylene-alpha- (2)H 3 were determined. Evidence is presented that CYP2A6 accommodates multiple ligands and that intramolecular isotope effect experiments can provide insight into the mechanisms of multiple-ligand binding. CYP2A6 exhibited cooperative kinetics for m-xylene-alpha- (2)H 3 oxidation and a concentration-dependent decrease in the m-methylbenzylalcohol:2,4-dimethylphenol product ratio (9.8 +/- 0.1 and 4.8 +/- 0.3 at 2.5 microM and 1 mM, respectively). Heterotropic effects were observed as well, as incubations containing both 15 microM m-xylene-alpha- (2)H 3 and 200 microM p-xylene resulted in further reduction of the product ratio (2.4 +/- 0.2). When p-xylene (60 microM) was replaced with deuterium-labeled d 6- p-xylene (60 microM), an intermolecular competitive inverse isotope effect on 2,4-dimethylphenol formation [( k H/ k D) obs = 0.49] was observed, indicating that p-xylene exerts heterotropic effects by residing in the active site simultaneously with m-xylene. The data indicate that there is a concentration-dependent decrease in the reorientation rate of m-xylene, as no increase in ( k H/ k D) obs was observed in the presence of an increased level of metabolic switching. That is, the accommodation of a second xylene molecule in the active site leads to a decrease in substrate dynamics.
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Affiliation(s)
- John P Harrelson
- School of Pharmacy, Pacific University, HPC-Ste 451, Hillsboro, Oregon 97123, USA.
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Dürr UH, Waskell L, Ramamoorthy A. The cytochromes P450 and b5 and their reductases—Promising targets for structural studies by advanced solid-state NMR spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2007; 1768:3235-59. [DOI: 10.1016/j.bbamem.2007.08.007] [Citation(s) in RCA: 105] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2007] [Accepted: 08/08/2007] [Indexed: 02/02/2023]
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Mizuno M, Suzuki Y, Endo K, Murakami M, Tansho M, Shimizu T. Molecular Dynamics in Paramagnetic Materials as Studied by Magic-Angle Spinning 2H NMR Spectra. J Phys Chem A 2007; 111:12954-60. [DOI: 10.1021/jp075405l] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Motohiro Mizuno
- Department of Chemistry, Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan, and National Institute for Materials Science, 3-13 Sakura, Tsukuba, Ibaraki 305-0003, Japan
| | - You Suzuki
- Department of Chemistry, Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan, and National Institute for Materials Science, 3-13 Sakura, Tsukuba, Ibaraki 305-0003, Japan
| | - Kazunaka Endo
- Department of Chemistry, Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan, and National Institute for Materials Science, 3-13 Sakura, Tsukuba, Ibaraki 305-0003, Japan
| | - Miwa Murakami
- Department of Chemistry, Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan, and National Institute for Materials Science, 3-13 Sakura, Tsukuba, Ibaraki 305-0003, Japan
| | - Masataka Tansho
- Department of Chemistry, Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan, and National Institute for Materials Science, 3-13 Sakura, Tsukuba, Ibaraki 305-0003, Japan
| | - Tadashi Shimizu
- Department of Chemistry, Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan, and National Institute for Materials Science, 3-13 Sakura, Tsukuba, Ibaraki 305-0003, Japan
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25
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Yao H, McCullough CR, Costache AD, Pullela PK, Sem DS. Structural evidence for a functionally relevant second camphor binding site in P450cam: model for substrate entry into a P450 active site. Proteins 2007; 69:125-38. [PMID: 17598143 DOI: 10.1002/prot.21508] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
P450cam has long served as a prototype for the cytochrome P450 (CYP) gene family. But, little is known about how substrate enters its active site pocket, and how access is achieved in a way that minimizes exposure of the reactive heme. We hypothesize that P450cam may first bind substrate transiently near the mobile F-G helix that covers the active site pocket. Such a two-step binding process is kinetically required if P450cam rarely populates an open conformation-as suggested by previous literature and the inability to obtain a crystal structure of P450cam in an open conformation. Such a mechanism would minimize exposure of the heme by allowing P450cam to stay in a closed conformation as long as possible, since only brief flexing into an open conformation would be required to allow substrate entry. To test this model, we have attempted to dock a second camphor molecule into the crystal structure of camphor-bound P450cam. The docking identified only one potential entry site pocket, a well-defined cavity on the F-helix side of the F-G flap, 16 A from the heme iron. Location of this entry site pocket is consistent with our NMR T1 relaxation-based measurements of distances for a camphor that binds in fast exchange (active site camphor is known to bind in slow exchange). Presence of a second camphor binding site is also confirmed with [(1)H-(13)C] HSQC titrations of (13)CH3-threonine labeled P450cam. To confirm that camphor can bind outside of the active site pocket, (13)CH3-S-pyridine was bound to the heme iron to physically block the active site, and to serve as an NMR chemical shift probe. Titration of this P450cam-pyridine complex confirms that camphor can bind to a site outside the active site pocket, with an estimated Kd of 43 microM. The two-site binding model that is proposed based on these data is analogous to that recently proposed for CYP3A4, and is consistent with recent crystal structures of P450cam bound to tethered-substrates, which force a partially opened conformation.
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Affiliation(s)
- Huili Yao
- Department of Chemistry, Marquette University, Milwaukee, Wisconsin 53201, USA
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26
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Pintacuda G, Giraud N, Pierattelli R, Böckmann A, Bertini I, Emsley L. Solid-State NMR Spectroscopy of a Paramagnetic Protein: Assignment and Study of Human Dimeric Oxidized CuII–ZnII Superoxide Dismutase (SOD). Angew Chem Int Ed Engl 2007; 46:1079-82. [PMID: 17191298 DOI: 10.1002/anie.200603093] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Guido Pintacuda
- Laboratoire de Chimie, UMR 5182 CNRS-ENS Lyon, Ecole Normale Supérieure de Lyon, 46 allée d'Italie, 69364 Lyon, France
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27
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Pintacuda G, Giraud N, Pierattelli R, Böckmann A, Bertini I, Emsley L. Solid-State NMR Spectroscopy of a Paramagnetic Protein: Assignment and Study of Human Dimeric Oxidized CuII–ZnII Superoxide Dismutase (SOD). Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200603093] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Antonijevic S, Persson E. Study of water dynamics and distances in paramagnetic solids by variable-temperature two-dimensional H2 NMR spectroscopy. J Chem Phys 2007; 126:014504. [PMID: 17212497 DOI: 10.1063/1.2424701] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A recently proposed two-dimensional (2)H NMR experiment is used to measure the (2)H (spin I=1) quadrupolar and paramagnetic shift anisotropy interactions in powdered CuCl(2).2D(2)O as a function of temperature. The principal components of the quadrupolar and paramagnetic shift anisotropy tensors and the Euler angles describing the orientations of the tensors in the molecular frame are determined at each temperature. For this purpose an analytical approach is introduced to extract desired parameters from motionally averaged two-dimensional line shapes where the averaging is introduced by rapid 180 degrees flips around C(2) axes of D(2)O molecules. This approach can be readily applied to study various materials containing water of crystallization. It is also clearly shown that the rapid continuous rotation of D(2)O molecules around their C(2) axes is not taking place in the studied solid in the range of temperatures between 209 and 344 K. Once the paramagnetic shift anisotropy of a deuterium atom is measured accurately it is used to estimate the distance between deuterium and the nearest copper atom bearing an unpaired electron. Excellent agreement is found between structural parameters obtained in this study and those provided by neutron and x-ray diffraction, showing that the paramagnetic shift anisotropy is a sensitive probe of distances in paramagnetic solids.
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Affiliation(s)
- Sasa Antonijevic
- Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland.
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29
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Harrelson JP, Henne KR, Alonso DOV, Nelson SD. A comparison of substrate dynamics in human CYP2E1 and CYP2A6. Biochem Biophys Res Commun 2006; 352:843-9. [PMID: 17156750 PMCID: PMC2728047 DOI: 10.1016/j.bbrc.2006.11.071] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2006] [Accepted: 11/11/2006] [Indexed: 11/26/2022]
Abstract
Considering the dynamic nature of CYPs, methods that reveal information about substrate and enzyme dynamics are necessary to generate predictive models. To compare substrate dynamics in CYP2E1 and CYP2A6, intramolecular isotope effect experiments were conducted, using deuterium labeled substrates: o-xylene, m-xylene, p-xylene, 2,6-dimethylnaphthalene, and 4,4'-dimethylbiphenyl. Competitive intermolecular experiments were also conducted using d(0)- and d(6)-labeled p-xylene. Both CYP2E1 and CYP2A6 displayed full isotope effect expression for o-xylene oxidation and almost complete suppression for dimethylbiphenyl. Interestingly, (k(H)/k(D))(obs) for d(3)-p-xylene oxidation ((k(H)/k(D))(obs)=6.04 and (k(H)/k(D))(obs)=5.53 for CYP2E1 and CYP2A6, respectively) was only slightly higher than (k(H)/k(D))(obs) for d(3)-dimethylnaphthalene ((k(H)/k(D))(obs)=5.50 and (k(H)/k(D))(obs)=4.96, respectively). One explanation is that in some instances (k(H)/k(D))(obs) values are generated by the presence of two substrates-bound simultaneously to the CYP. Speculatively, if this explanation is valid, then intramolecular isotope effect experiments should be useful in the mechanistic investigation of P450 cooperativity.
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Affiliation(s)
- John P Harrelson
- Department of Medicinal Chemistry, University of Washington, Box 357610, Seattle, WA 98195, USA.
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30
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Shaik S, Kumar D, de Visser SP, Altun A, Thiel W. Theoretical Perspective on the Structure and Mechanism of Cytochrome P450 Enzymes. Chem Rev 2005; 105:2279-328. [PMID: 15941215 DOI: 10.1021/cr030722j] [Citation(s) in RCA: 958] [Impact Index Per Article: 50.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sason Shaik
- Department of Organic Chemistry and the Lise-Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, Israel.
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31
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Straus SK. Recent developments in solid-state magic-angle spinning, nuclear magnetic resonance of fully and significantly isotopically labelled peptides and proteins. Philos Trans R Soc Lond B Biol Sci 2004; 359:997-1008. [PMID: 15306412 PMCID: PMC1693383 DOI: 10.1098/rstb.2003.1398] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In recent years, a large number of solid-state nuclear magnetic resonance (NMR) techniques have been developed and applied to the study of fully or significantly isotopically labelled ((13)C, (15)N or (13)C/(15)N) biomolecules. In the past few years, the first structures of (13)C/(15)N-labelled peptides, Gly-Ile and Met-Leu-Phe, and a protein, Src-homology 3 domain, were solved using magic-angle spinning NMR, without recourse to any structural information obtained from other methods. This progress has been made possible by the development of NMR experiments to assign solid-state spectra and experiments to extract distance and orientational information. Another key aspect to the success of solid-state NMR is the advances made in sample preparation. These improvements will be reviewed in this contribution. Future prospects for the application of solid-state NMR to interesting biological questions will also briefly be discussed.
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Affiliation(s)
- Suzana K Straus
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada.
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32
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Meunier B, de Visser SP, Shaik S. Mechanism of Oxidation Reactions Catalyzed by Cytochrome P450 Enzymes. Chem Rev 2004; 104:3947-80. [PMID: 15352783 DOI: 10.1021/cr020443g] [Citation(s) in RCA: 1723] [Impact Index Per Article: 86.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Bernard Meunier
- Laboratoire de Chimie de Coordination du CNRS, 205 route de Narbonne, 31077 Toulouse Cedex 4, France.
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33
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Shaik S, Cohen S, de Visser S, Sharma P, Kumar D, Kozuch S, Ogliaro F, Danovich D. The “Rebound Controversy”: An Overview and Theoretical Modeling of the Rebound Step in C−H Hydroxylation by Cytochrome P450. Eur J Inorg Chem 2004. [DOI: 10.1002/ejic.200300448] [Citation(s) in RCA: 137] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Sason Shaik
- Department of Organic Chemistry and the Lise Meitner‐Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, Givat Ram Campus, 91904 Jerusalem, Israel Fax: (internat.) + 972‐2‐658‐4680
| | - Shimrit Cohen
- Department of Organic Chemistry and the Lise Meitner‐Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, Givat Ram Campus, 91904 Jerusalem, Israel Fax: (internat.) + 972‐2‐658‐4680
| | - Samuël P. de Visser
- Department of Organic Chemistry and the Lise Meitner‐Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, Givat Ram Campus, 91904 Jerusalem, Israel Fax: (internat.) + 972‐2‐658‐4680
| | - Pankaz K. Sharma
- Department of Organic Chemistry and the Lise Meitner‐Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, Givat Ram Campus, 91904 Jerusalem, Israel Fax: (internat.) + 972‐2‐658‐4680
| | - Devesh Kumar
- Department of Organic Chemistry and the Lise Meitner‐Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, Givat Ram Campus, 91904 Jerusalem, Israel Fax: (internat.) + 972‐2‐658‐4680
| | - Sebastian Kozuch
- Department of Organic Chemistry and the Lise Meitner‐Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, Givat Ram Campus, 91904 Jerusalem, Israel Fax: (internat.) + 972‐2‐658‐4680
| | - François Ogliaro
- Department of Organic Chemistry and the Lise Meitner‐Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, Givat Ram Campus, 91904 Jerusalem, Israel Fax: (internat.) + 972‐2‐658‐4680
| | - David Danovich
- Department of Organic Chemistry and the Lise Meitner‐Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, Givat Ram Campus, 91904 Jerusalem, Israel Fax: (internat.) + 972‐2‐658‐4680
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Abstract
Over the last decades, NMR spectroscopy has grown into an indispensable tool for chemical analysis, structure determination, and the study of dynamics in organic, inorganic, and biological systems. It is commonly used for a wide range of applications from the characterization of synthetic products to the study of molecular structures of systems such as catalysts, polymers, and proteins. Although most NMR experiments are performed on liquid-state samples, solid-state NMR is rapidly emerging as a powerful method for the study of solid samples and materials. This Review outlines some of the developments of solid-state NMR spectroscopy, including techniques such as cross-polarization, magic-angle spinning, multiple-pulse sequences, homo- and heteronuclear decoupling and recoupling techniques, multiple-quantum spectroscopy, and dynamic angle spinning, as well as their applications to structure determination. Modern solid-state NMR spectroscopic techniques not only produce spectra with a resolution close to that of liquid-state spectra, but also capitalize on anisotropic interactions, which are often unavailable for liquid samples. With this background, the future of solid-state NMR spectroscopy in chemistry appears to be promising, indeed.
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Affiliation(s)
- David D Laws
- Materials Sciences Division, Lawrence Berkeley National Laboratory and Department of Chemistry, University of California at Berkeley, Berkeley, CA 94720, USA
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Xiang H, Tschirret-Guth RA, Ortiz De Montellano PR. An A245T mutation conveys on cytochrome P450eryF the ability to oxidize alternative substrates. J Biol Chem 2000; 275:35999-6006. [PMID: 10956654 DOI: 10.1074/jbc.m005811200] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cytochrome P450(eryF) (CYP107A1), which hydroxylates deoxyerythronolide B in erythromycin biosynthesis, lacks the otherwise highly conserved threonine that is thought to promote O-O bond scission. The role of this threonine is satisfied in P450(eryF) by a substrate hydroxyl group, making deoxyerythronolide B the only acceptable substrate. As shown here, replacement of Ala(245) by a threonine enables the oxidation of alternative substrates using either H(2)O(2) or O(2)/spinach ferredoxin/ferredoxin reductase as the source of oxidizing equivalents. Testosterone is oxidized to 1-, 11alpha-, 12-, and 16alpha-hydroxytestosterone. A kinetic solvent isotope effect of 2.2 indicates that the A245T mutation facilitates dioxygen bond cleavage. This gain-of-function evidence confirms the role of the conserved threonine in P450 catalysis. Furthermore, a Hill coefficient of 1.3 and dependence of the product distribution on the testosterone concentration suggest that two testosterone molecules bind in the active site, in accord with a published structure of the P450(eryF)-androstenedione complex. P450(eryF) is thus a structurally defined model for the catalytic turnover of multiply bound substrates proposed to occur with CYP3A4. In view of its large active site and defined structure, catalytically active P450(eryF) mutants are also attractive templates for the engineering of novel P450 activities.
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Affiliation(s)
- H Xiang
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143-0446, USA
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Das B, Helms V, Lounnas V, Wade RC. Multicopy molecular dynamics simulations suggest how to reconcile crystallographic and product formation data for camphor enantiomers bound to cytochrome P-450cam. J Inorg Biochem 2000; 81:121-31. [PMID: 11051557 DOI: 10.1016/s0162-0134(00)00095-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Multiple ligand binding modes are possible in many enzyme active sites; their presence in cytochrome P450cam (P450cam) is evident from crystallographic studies of the binding of thiocamphor and phenylimidazoles. Here, we use multicopy molecular dynamics simulations to compare the binding modes of (1R)- and (1S)-camphor in the active site of P450cam. Simulations with (1R)-camphor, the natural substrate, serve to calibrate our protocol: 19 out of 20 copies of (1R)-camphor converged to coordinates very close to those observed for (1R)-camphor in its crystallographic complex with P450cam during the simulations. Simulations with the (1S)-camphor enantiomer showed greater mobility of the substrate, consistent with spectroscopic data, and resulted in 3 major binding modes. One of these is similar to the major conformation (of the two conformations assigned) in a recently determined crystal structure, but this conformation is not correctly oriented for regiospecific hydroxylation at C-5. The simulations, however, provide evidence for reorientation of (1S)-camphor upon formation of the reactive Fe-O intermediate to an orientation suitable for hydroxylation. The simulations thus permit rationalisation of the apparent inconsistency between the crystal structure and the reaction products.
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Affiliation(s)
- B Das
- CSIT, Florida State University, Tallahassee 32306, USA
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