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Wong NR, Sundar R, Kazanis S, Biswas J, Pochapsky TC. Conformational heterogeneity suggests multiple substrate binding modes in CYP106A2. J Inorg Biochem 2023; 241:112129. [PMID: 36731370 PMCID: PMC9992128 DOI: 10.1016/j.jinorgbio.2023.112129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/16/2022] [Accepted: 01/14/2023] [Indexed: 01/20/2023]
Abstract
CYP106A2 (cytochrome P450meg) is a bacterial enzyme originally isolated from B. megaterium, and has been shown to hydroxylate a wide variety of substrates, including steroids. The regio- and stereochemistry of CYP106A2 hydroxylation has been shown to be dependent on a variety of factors, and hydroxylation often occurs at more than one site and/or with lack of stereospecificity for some substrates. Comprehensive backbone 15N, 1H and 13C resonance assignments based on multidimensional nuclear magnetic resonance (NMR) experiments performed with uniform and selective isotopically labeled CYP106A2 samples are reported herein, and broadening and splitting of resonances assigned to regions of the enzyme shown to be affected by substrate binding in other P450 enzymes indicate that substrate binding does not reduce structural heterogeneity as has been observed previously in P450 enzymes CYP101A1 and MycG. Paramagnetic relaxation enhancement (PRE) due to proximity between substrate protons and the heme iron were measured for three different substrates, and the relatively uniform nature of the PREs support the proposal that multiple substrate binding modes are occupied at saturating substrate concentrations.
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Affiliation(s)
- Nathan R Wong
- Dept. of Biochemistry, Brandeis University, 415 South St., Waltham, MA 02454, United States of America
| | - Reethy Sundar
- Dept. of Biochemistry, Brandeis University, 415 South St., Waltham, MA 02454, United States of America
| | - Sophia Kazanis
- Dept. of Chemistry, Brandeis University, MS 015, 415 South St., Waltham, MA 02454, United States of America; Middlesex Community College, 33 Kearney Sq., Lowell, MA 01852, United States of America
| | - Jeetayu Biswas
- Dept. of Chemistry, Brandeis University, MS 015, 415 South St., Waltham, MA 02454, United States of America; Department of Medicine, Weill-Cornell Medicine, New York, NY, United States of America
| | - Thomas C Pochapsky
- Dept. of Biochemistry, Brandeis University, 415 South St., Waltham, MA 02454, United States of America; Dept. of Chemistry, Brandeis University, MS 015, 415 South St., Waltham, MA 02454, United States of America; Rosenstiel Center for Basic Biomedical Research, Brandeis University, 415 South St., Waltham, MA 02454, United States of America.
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2
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Podgorski MN, Coleman T, Churchman LR, Bruning JB, De Voss JJ, Bell SG. Investigating the Active Oxidants Involved in Cytochrome P450 Catalyzed Sulfoxidation Reactions. Chemistry 2022; 28:e202202428. [PMID: 36169207 PMCID: PMC10100219 DOI: 10.1002/chem.202202428] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Indexed: 12/30/2022]
Abstract
Cytochrome P450 (CYP) heme-thiolate monooxygenases catalyze the hydroxylation of the C-H bonds of organic molecules. This reaction is initiated by a ferryl-oxo heme radical cation (Cpd I). These enzymes can also catalyze sulfoxidation reactions and the ferric-hydroperoxy complex (Cpd 0) and the Fe(III)-H2 O2 complex have been proposed as alternative oxidants for this transformation. To investigate this, the oxidation of 4-alkylthiobenzoic acids and 4-methoxybenzoic acid by the CYP199A4 enzyme from Rhodopseudomonas palustris HaA2 was compared using both monooxygenase and peroxygenase pathways. By examining mutants at the mechanistically important, conserved acid alcohol-pair (D251N, T252A and T252E) the relative amounts of the reactive intermediates that would form in these reactions were disturbed. Substrate binding and X-ray crystal structures helped to understand changes in the activity and enabled an attempt to evaluate whether multiple oxidants can participate in these reactions. In peroxygenase reactions the T252E mutant had higher activity towards sulfoxidation than O-demethylation but in the monooxygenase reactions with the WT enzyme the activity of both reactions was similar. The peroxygenase activity of the T252A mutant was greater for sulfoxidation reactions than the WT enzyme, which is the reverse of the activity changes observed for O-demethylation. The monooxygenase activity and coupling efficiency of sulfoxidation and oxidative demethylation were reduced by similar degrees with the T252A mutant. These observations infer that while Cpd I is required for O-dealkylation, another oxidant may contribute to sulfoxidation. Based on the activity of the CYP199A4 mutants it is proposed that this is the Fe(III)-H2 O2 complex which would be more abundant in the peroxide-driven reactions.
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Affiliation(s)
- Matthew N Podgorski
- Department of Chemistry, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Tom Coleman
- Department of Chemistry, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Luke R Churchman
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Qld, 4072, Australia
| | - John B Bruning
- School of Biological Sciences, University of Adelaide, Adelaide, SA, 5005, Australia
| | - James J De Voss
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Qld, 4072, Australia
| | - Stephen G Bell
- Department of Chemistry, University of Adelaide, Adelaide, SA, 5005, Australia
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3
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Wang S, Huang Q. A spectroscopic approach to identifying the out-of-plane conformations of Ni(II) meso-tetraphenylporphyrin in solution. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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4
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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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5
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Abstract
This review examines low-frequency vibrational modes of proteins and their coupling to enzyme catalytic sites. That protein motions are critical to enzyme function is clear, but the kinds of motions present in proteins and how they are involved in function remain unclear. Several models of enzyme-catalyzed reaction suggest that protein dynamics may be involved in the chemical step of the catalyzed reaction, but the evidence in support of such models is indirect. Spectroscopic studies of low-frequency protein vibrations consistently show that there are underdamped modes of the protein with frequencies in the tens of wavenumbers where overdamped behavior would be expected. Recent studies even show that such underdamped vibrations modulate enzyme active sites. These observations suggest that increasingly sophisticated spectroscopic methods will be able to unravel the link between low-frequency protein vibrations and enzyme function.
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6
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Charkhesht A, Regmi CK, Mitchell-Koch KR, Cheng S, Vinh NQ. High-Precision Megahertz-to-Terahertz Dielectric Spectroscopy of Protein Collective Motions and Hydration Dynamics. J Phys Chem B 2018; 122:6341-6350. [PMID: 29791154 DOI: 10.1021/acs.jpcb.8b02872] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The low-frequency collective vibrational modes in proteins as well as the protein-water interface have been suggested as dominant factors controlling the efficiency of biochemical reactions and biological energy transport. It is thus crucial to uncover the mystery of the hydration structure and dynamics as well as their coupling to collective motions of proteins in aqueous solutions. Here, we report dielectric properties of aqueous bovine serum albumin protein solutions as a model system using an extremely sensitive dielectric spectrometer with frequencies spanning from megahertz to terahertz. The dielectric relaxation spectra reveal several polarization mechanisms at the molecular level with different time constants and dielectric strengths, reflecting the complexity of protein-water interactions. Combining the effective-medium approximation and molecular dynamics simulations, we have determined collective vibrational modes at terahertz frequencies and the number of water molecules in the tightly bound and loosely bound hydration layers. High-precision measurements of the number of hydration water molecules indicate that the dynamical influence of proteins extends beyond the first solvation layer, to around 7 Å distance from the protein surface, with the largest slowdown arising from water molecules directly hydrogen-bonded to the protein. Our results reveal critical information of protein dynamics and protein-water interfaces, which determine biochemical functions and reactivity of proteins.
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Affiliation(s)
| | | | - Katie R Mitchell-Koch
- Department of Chemistry , Wichita State University , Wichita , Kansas 67260 , United States
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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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8
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Pochapsky TC, Wong N, Zhuang Y, Futcher J, Pandelia ME, Teitz DR, Colthart AM. NADH reduction of nitroaromatics as a probe for residual ferric form high-spin in a cytochrome P450. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1866:126-133. [PMID: 28473297 DOI: 10.1016/j.bbapap.2017.04.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Revised: 04/19/2017] [Accepted: 04/29/2017] [Indexed: 10/19/2022]
Abstract
The existence of a substrate-sensitive equilibrium between high spin (S=5/2) and low spin (S=1/2) ferric iron is a well-established phenomenon in the cytochrome P450 (CYP) superfamily, although its origins are still a subject of discussion. A series of mutations that strongly perturb the spin state equilibrium in the camphor hydroxylase CYP101A1 were recently described (Colthart et al., Sci. Rep. 6, 22035 (2016)). Wild type CYP101A1 as well as some CYP101A1 mutants are herein shown to be capable of catalyzing the reduction of nitroacetophenones by NADH to the corresponding anilino compounds (nitroreductase or NRase activity). The distinguishing characteristic between those mutants that catalyze the reduction and those that cannot appears to be the extent to which residual high spin form exists in the absence of the native substrate d-camphor, with those showing the largest spin state shifts upon camphor binding also exhibiting NRase activity. Optical and EPR spectroscopy was used to further examine these phenomena. These results suggest that reduction of nitroaromatics may provide a useful probe of residual high spin states in the CYP superfamily. 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)
- Thomas C Pochapsky
- Department of Chemistry, Brandeis University, 415 South St., Waltham, MA 02454-9110, USA.
| | - Nathan Wong
- Department of Biochemistry, Brandeis University, 415 South St., Waltham, MA 02454-9110, USA
| | - Yihao Zhuang
- Department of Biochemistry, Brandeis University, 415 South St., Waltham, MA 02454-9110, USA
| | - Jeffrey Futcher
- Department of Chemistry, Brandeis University, 415 South St., Waltham, MA 02454-9110, USA
| | - Maria-Eirini Pandelia
- Department of Biochemistry, Brandeis University, 415 South St., Waltham, MA 02454-9110, USA
| | - Drew R Teitz
- Department of Chemistry, Brandeis University, 415 South St., Waltham, MA 02454-9110, USA
| | - Allison M Colthart
- Department of Biochemistry, Brandeis University, 415 South St., Waltham, MA 02454-9110, USA
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9
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Batabyal D, Lewis-Ballester A, Yeh SR, Poulos TL. A Comparative Analysis of the Effector Role of Redox Partner Binding in Bacterial P450s. Biochemistry 2016; 55:6517-6523. [PMID: 27808504 DOI: 10.1021/acs.biochem.6b00913] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The camphor monooxygenase, cytochrome P450cam, exhibits a strict requirement for its own redox partner, putidaredoxin (Pdx), a two-iron-sulfur ferredoxin. The closest homologue to P450cam, CYP101D1, is structurally very similar, uses a similar redox partner, and exhibits nearly identical enzymatic properties in the monooxygenation of camphor to give the same single 5-exo-hydroxy camphor product. However, CYP101D1 does not strictly require its own ferredoxin (Arx) for activity because Pdx can support CYP101D1 catalysis but Arx cannot support P450cam catalysis. We have further examined the differences between these two P450s by determining the effect of spin equilibrium, redox properties, and stability of oxygen complexes. We find that Arx shifts the spin state equilibrium toward high-spin, which is the opposite of the effect of Pdx on P450cam. In both P450s, redox partner binding destabilizes the oxy-P450 complex but this effect is much weaker with CYP101D1. In addition, resonance Raman data show that structural perturbations observed in P450cam upon addition of Pdx are absent in CYP101D1. These data indicate that Arx does not play the same effector role in catalysis as Pdx does with P450cam. The most relevant structural difference between these two P450s centers on a catalytically important Asp residue required for proton-coupled electron transfer. We postulate that with P450cam larger Pdx-assisted motions are required to free this Asp for catalysis while the smaller number of restrictions in CYP101D1 precludes the need for redox partner-assisted structural changes.
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Affiliation(s)
- Dipanwita Batabyal
- Departments of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California , Irvine, California 92697, United States
| | - Ariel Lewis-Ballester
- Department of Physiology and Biophysics, Albert Einstein College of Medicine , 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Syun-Ru Yeh
- Department of Physiology and Biophysics, Albert Einstein College of Medicine , 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Thomas L Poulos
- Departments of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California , Irvine, California 92697, United States
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10
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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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12
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Kim SY, Joo T. Coherent Nuclear Wave Packets in Q States by Ultrafast Internal Conversions in Free Base Tetraphenylporphyrin. J Phys Chem Lett 2015; 6:2993-2998. [PMID: 26267193 DOI: 10.1021/acs.jpclett.5b01188] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Persistence of vibrational coherence in electronic transition has been noted especially in biochemical systems. Here, we report the dynamics between electronic excited states in free base tetraphenylporphyrin (H2TPP) by time-resolved fluorescence with high time resolution. Following the photoexcitation of the B state, ultrafast internal conversion occurs to the Qx state directly as well as via the Qy state. Unique and distinct coherent nuclear wave packet motions in the Qx and Qy states are observed through the modulation of the fluorescence intensity in time. The instant, serial internal conversions from the B to the Qy and Qx states generate the coherent wave packets. Theory and experiment show that the observed vibrational modes involve the out-of-plane vibrations of the porphyrin ring that are strongly coupled to the internal conversion of H2TPP.
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Affiliation(s)
- So Young Kim
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
| | - Taiha Joo
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
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13
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Maiuri M, Delfino I, Cerullo G, Manzoni C, Pelmenschikov V, Guo Y, Wang H, Gee LB, Dapper CH, Newton WE, Cramer SP. Low frequency dynamics of the nitrogenase MoFe protein via femtosecond pump probe spectroscopy - Observation of a candidate promoting vibration. J Inorg Biochem 2015; 153:128-135. [PMID: 26343576 DOI: 10.1016/j.jinorgbio.2015.07.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 06/18/2015] [Accepted: 07/09/2015] [Indexed: 11/28/2022]
Abstract
We have used femtosecond pump-probe spectroscopy (FPPS) to study the FeMo-cofactor within the nitrogenase (N2ase) MoFe protein from Azotobacter vinelandii. A sub-20-fs visible laser pulse was used to pump the sample to an excited electronic state, and a second sub-10-fs pulse was used to probe changes in transmission as a function of probe wavelength and delay time. The excited protein relaxes to the ground state with a ~1.2ps time constant. With the short laser pulse we coherently excited the vibrational modes associated with the FeMo-cofactor active site, which are then observed in the time domain. Superimposed on the relaxation dynamics, we distinguished a variety of oscillation frequencies with the strongest band peaks at ~84, 116, 189, and 226cm(-1). Comparison with data from nuclear resonance vibrational spectroscopy (NRVS) shows that the latter pair of signals comes predominantly from the FeMo-cofactor. The frequencies obtained from the FPPS experiment were interpreted with normal mode calculations using both an empirical force field (EFF) and density functional theory (DFT). The FPPS data were also compared with the first reported resonance Raman (RR) spectrum of the N2ase MoFe protein. This approach allows us to outline and assign vibrational modes having relevance to the catalytic activity of N2ase. In particular, the 226cm(-1) band is assigned as a potential 'promoting vibration' in the H-atom transfer (or proton-coupled electron transfer) processes that are an essential feature of N2ase catalysis. The results demonstrate that high-quality room-temperature solution data can be obtained on the MoFe protein by the FPPS technique and that these data provide added insight to the motions and possible operation of this protein and its catalytic prosthetic group.
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Affiliation(s)
- Margherita Maiuri
- IFN-CNR, Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
| | - Ines Delfino
- Dipartimento di Scienze Ecologiche e Biologiche, Università della Tuscia, Largo dell'Università, I-01100 Viterbo, Italy
| | - Giulio Cerullo
- IFN-CNR, Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
| | - Cristian Manzoni
- IFN-CNR, Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
| | - Vladimir Pelmenschikov
- Institut für Chemie, Technische Universität Berlin, Strasse des 17 Juni 135, 10623 Berlin, Germany
| | - Yisong Guo
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA 15213, United States
| | - Hongxin Wang
- Department of Chemistry, University of California, Davis, CA 95616, United States
| | - Leland B Gee
- Department of Chemistry, University of California, Davis, CA 95616, United States
| | - Christie H Dapper
- Department of Biochemistry, Virginia Polytechnic Institute & State University, Blacksburg, VA 24061, United States
| | - William E Newton
- Department of Biochemistry, Virginia Polytechnic Institute & State University, Blacksburg, VA 24061, United States
| | - Stephen P Cramer
- Department of Chemistry, University of California, Davis, CA 95616, United States; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States.
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14
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Adamczyk K, Simpson N, Greetham GM, Gumiero A, Walsh MA, Towrie M, Parker AW, Hunt NT. Ultrafast infrared spectroscopy reveals water-mediated coherent dynamics in an enzyme active site. Chem Sci 2014; 6:505-516. [PMID: 28936306 PMCID: PMC5588449 DOI: 10.1039/c4sc02752c] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 10/22/2014] [Indexed: 11/24/2022] Open
Abstract
Ultrafast infrared spectroscopy provides insights into the dynamic nature of water in the active sites of catalase and peroxidase enzymes.
Understanding the impact of fast dynamics upon the chemical processes occurring within the active sites of proteins and enzymes is a key challenge that continues to attract significant interest, though direct experimental insight in the solution phase remains sparse. Similar gaps in our knowledge exist in understanding the role played by water, either as a solvent or as a structural/dynamic component of the active site. In order to investigate further the potential biological roles of water, we have employed ultrafast multidimensional infrared spectroscopy experiments that directly probe the structural and vibrational dynamics of NO bound to the ferric haem of the catalase enzyme from Corynebacterium glutamicum in both H2O and D2O. Despite catalases having what is believed to be a solvent-inaccessible active site, an isotopic dependence of the spectral diffusion and vibrational lifetime parameters of the NO stretching vibration are observed, indicating that water molecules interact directly with the haem ligand. Furthermore, IR pump–probe data feature oscillations originating from the preparation of a coherent superposition of low-frequency vibrational modes in the active site of catalase that are coupled to the haem ligand stretching vibration. Comparisons with an exemplar of the closely-related peroxidase enzyme family shows that they too exhibit solvent-dependent active-site dynamics, supporting the presence of interactions between the haem ligand and water molecules in the active sites of both catalases and peroxidases that may be linked to proton transfer events leading to the formation of the ferryl intermediate Compound I. In addition, a strong, water-mediated, hydrogen bonding structure is suggested to occur in catalase that is not replicated in peroxidase; an observation that may shed light on the origins of the different functions of the two enzymes.
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Affiliation(s)
- Katrin Adamczyk
- Department of Physics , University of Strathclyde , SUPA , 107 Rottenrow East , Glasgow , G4 0NG , UK .
| | - Niall Simpson
- Department of Physics , University of Strathclyde , SUPA , 107 Rottenrow East , Glasgow , G4 0NG , UK .
| | - Gregory M Greetham
- Central Laser Facility , Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Harwell Oxford , Didcot, Oxon , OX11 0QX , UK
| | - Andrea Gumiero
- Diamond Light Source , Diamond House, Harwell Science and Innovation Campus , Didcot, Oxfordshire , OX11 0DE , UK
| | - Martin A Walsh
- Diamond Light Source , Diamond House, Harwell Science and Innovation Campus , Didcot, Oxfordshire , OX11 0DE , UK
| | - Michael Towrie
- Central Laser Facility , Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Harwell Oxford , Didcot, Oxon , OX11 0QX , UK
| | - Anthony W Parker
- Central Laser Facility , Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Harwell Oxford , Didcot, Oxon , OX11 0QX , UK
| | - Neil T Hunt
- Department of Physics , University of Strathclyde , SUPA , 107 Rottenrow East , Glasgow , G4 0NG , UK .
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15
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Terahertz underdamped vibrational motion governs protein-ligand binding in solution. Nat Commun 2014; 5:3999. [PMID: 24893252 DOI: 10.1038/ncomms4999] [Citation(s) in RCA: 119] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Accepted: 04/29/2014] [Indexed: 11/08/2022] Open
Abstract
Low-frequency collective vibrational modes in proteins have been proposed as being responsible for efficiently directing biochemical reactions and biological energy transport. However, evidence of the existence of delocalized vibrational modes is scarce and proof of their involvement in biological function absent. Here we apply extremely sensitive femtosecond optical Kerr-effect spectroscopy to study the depolarized Raman spectra of lysozyme and its complex with the inhibitor triacetylchitotriose in solution. Underdamped delocalized vibrational modes in the terahertz frequency domain are identified and shown to blue-shift and strengthen upon inhibitor binding. This demonstrates that the ligand-binding coordinate in proteins is underdamped and not simply solvent-controlled as previously assumed. The presence of such underdamped delocalized modes in proteins may have significant implications for the understanding of the efficiency of ligand binding and protein-molecule interactions, and has wider implications for biochemical reactivity and biological function.
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16
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Karunakaran V, Sun Y, Benabbas A, Champion PM. Investigations of the low frequency modes of ferric cytochrome c using vibrational coherence spectroscopy. J Phys Chem B 2014; 118:6062-70. [PMID: 24823442 PMCID: PMC4059251 DOI: 10.1021/jp501298c] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
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Femtosecond vibrational coherence
spectroscopy is used to investigate
the low frequency vibrational dynamics of the electron transfer heme
protein, cytochrome c (cyt c). The
vibrational coherence spectra of ferric cyt c have
been measured as a function of excitation wavelength within the Soret
band. Vibrational coherence spectra obtained with excitation between
412 and 421 nm display a strong mode at ∼44 cm–1 that has been assigned to have a significant contribution from heme
ruffling motion in the electronic ground state. This assignment is
based partially on the presence of a large heme ruffling distortion
in the normal coordinate structural decomposition (NSD) analysis of
the X-ray crystal structures. When the excitation wavelength is moved
into the ∼421–435 nm region, the transient absorption
increases along with the relative intensity of two modes near ∼55
and 30 cm–1. The intensity of the mode near 44 cm–1 appears to minimize in this region and then recover
(but with an opposite phase compared to the blue excitation) when
the laser is tuned to 443 nm. These observations are consistent with
the superposition of both ground and excited state coherence in the
421–435 nm region due to the excitation of a weak porphyrin-to-iron
charge transfer (CT) state, which has a lifetime long enough to observe
vibrational coherence. The mode near 55 cm–1 is
suggested to arise from ruffling in a transient CT state that has
a less ruffled heme due to its iron d6 configuration.
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Affiliation(s)
- Venugopal Karunakaran
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University , Boston, Massachusetts 02115, United States
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17
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Thompson LM, Lasoroski A, Champion PM, Sage JT, Frisch MJ, van Thor JJ, Bearpark MJ. Analytical Harmonic Vibrational Frequencies for the Green Fluorescent Protein Computed with ONIOM: Chromophore Mode Character and Its Response to Environment. J Chem Theory Comput 2014; 10:751-66. [DOI: 10.1021/ct400664p] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Lee M. Thompson
- Department
of Chemistry, Imperial College, London SW7 2AZ, United Kingdom
| | - Aurélie Lasoroski
- Department
of Chemistry, Imperial College, London SW7 2AZ, United Kingdom
- Ecole Normale
Supérieure, Département de Chimie, ENS-CNRS-UPMC UMR8640, 75005 Paris, France
| | - Paul M. Champion
- Department
of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115, United States
| | - J. Timothy Sage
- Department
of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115, United States
| | - Michael J. Frisch
- Gaussian, Inc., 340 Quinnipiac Street, Building 40, Wallingford, Connecticut 06492, United States
| | - Jasper J. van Thor
- Division
of Molecular Biosciences, Imperial College, London SW7 2AZ, United Kingdom
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18
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Saito K, Umena Y, Kawakami K, Shen JR, Kamiya N, Ishikita H. Deformation of Chlorin Rings in the Photosystem II Crystal Structure. Biochemistry 2012; 51:4290-9. [DOI: 10.1021/bi300428s] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Keisuke Saito
- 202 Building E, Career-Path
Promotion Unit for Young Life Scientists, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto
606-8501, Japan
| | - Yasufumi Umena
- The OCU
Advanced Research Institute
for Natural Science and Technology (OCARINA)/Graduate School of Science, Osaka City University, Sumiyoshi, Osaka 558-8585, Japan
- Japan Science and Technology Agency (JST), Precursory Research for Embryonic
Science and Technology, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012,
Japan
| | - Keisuke Kawakami
- The OCU
Advanced Research Institute
for Natural Science and Technology (OCARINA)/Graduate School of Science, Osaka City University, Sumiyoshi, Osaka 558-8585, Japan
| | - Jian-Ren Shen
- Division of Bioscience,
Graduate
School of Natural Science and Technology/Faculty of Science, Okayama University, Okayama 700-8530, Japan
| | - Nobuo Kamiya
- The OCU
Advanced Research Institute
for Natural Science and Technology (OCARINA)/Graduate School of Science, Osaka City University, Sumiyoshi, Osaka 558-8585, Japan
- Graduate School of Science, Osaka City University, Sumiyoshi, Osaka 558-8585, Japan
| | - Hiroshi Ishikita
- 202 Building E, Career-Path
Promotion Unit for Young Life Scientists, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto
606-8501, Japan
- Japan Science and Technology Agency (JST), Precursory Research for Embryonic
Science and Technology, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012,
Japan
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19
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Gussem ED, Bultinck P, Feledziak M, Marchand-Brynaert J, Stevens CV, Herrebout W. Vibrational Circular Dichroism versus Optical Rotation Dispersion and Electronic Circular Dichroism for diastereomers: the stereochemistry of 3-(1′-hydroxyethyl)-1-(3′-phenylpropanoyl)-azetidin-2-one. Phys Chem Chem Phys 2012; 14:8562-71. [DOI: 10.1039/c2cp40617a] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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20
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Karunakaran V, Benabbas A, Youn H, Champion PM. Vibrational coherence spectroscopy of the heme domain in the CO-sensing transcriptional activator CooA. J Am Chem Soc 2011; 133:18816-27. [PMID: 21961804 DOI: 10.1021/ja206152m] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Femtosecond vibrational coherence spectroscopy was used to investigate the low-frequency vibrational dynamics of the heme in the carbon monoxide oxidation activator protein (CooA) from the thermophilic anaerobic bacterium Carboxydothermus hydrogenoformans (Ch-CooA). Low frequency vibrational modes are important because they are excited by the ambient thermal bath (k(B)T = 200 cm(-1)) and participate in thermally activated barrier crossing events. However, such modes are nearly impossible to detect in the aqueous phase using traditional spectroscopic methods. Here, we present the low frequency coherence spectra of the ferric, ferrous, and CO-bound forms of Ch-CooA in order to compare the protein-induced heme distortions in its active and inactive states. Distortions take place predominantly along the coordinates of low-frequency modes because of their weak force constants, and such distortions are reflected in the intensity of the vibrational coherence signals. A strong mode near ~90 cm(-1) in the ferrous form of Ch-CooA is suggested to contain a large component of heme ruffling, consistent with the imidazole-bound ferrous heme crystal structure, which shows a significant protein-induced heme distortion along this coordinate. A mode observed at ~228 cm(-1) in the six-coordinate ferrous state is proposed to be the ν(Fe-His) stretching vibration. The observation of the Fe-His mode indicates that photolysis of the N-terminal α-amino axial ligand takes place. This is followed by a rapid (~8.5 ps) transient absorption recovery, analogous to methionine rebinding in photolyzed ferrous cytochrome c. We have also studied CO photolysis in CooA, which revealed very strong photoproduct state coherent oscillations. The observation of heme-CO photoproduct oscillations is unusual because most other heme systems have CO rebinding kinetics that are too slow to make the measurement possible. The low frequency coherence spectrum of the CO-bound form of Ch-CooA shows a strong vibration at ~230 cm(-1) that is broadened and up-shifted compared to the ν(Fe-His) of Rr-CooA (216 cm(-1)). We propose that the stronger Fe-His bond is related to the enhanced thermal stability of Ch-CooA and that there is a smaller (time dependent) tilt of the histidine ring with respect to the heme plane in Ch-CooA. The appearance of strong modes at ~48 cm(-1) in both the ferrous and CO-bound forms of Ch-CooA is consistent with coupling of the heme doming distortion to the photolysis reaction in both samples. Upon CO binding and protein activation, a heme mode near 112 ± 5 cm(-1) disappears, probably indicating a decreased heme saddling distortion. This reflects changes in the heme environment and geometry that must be associated with the conformational transition activating the DNA-binding domain. Protein-specific DNA binding to the CO-bound form of Ch-CooA was also investigated, and although the CO rebinding kinetics are significantly perturbed, there are negligible changes in the low-frequency vibrational spectrum of the heme.
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Affiliation(s)
- Venugopal Karunakaran
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115, USA
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