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Buhrke D, Hildebrandt P. Probing Structure and Reaction Dynamics of Proteins Using Time-Resolved Resonance Raman Spectroscopy. Chem Rev 2019; 120:3577-3630. [PMID: 31814387 DOI: 10.1021/acs.chemrev.9b00429] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The mechanistic understanding of protein functions requires insight into the structural and reaction dynamics. To elucidate these processes, a variety of experimental approaches are employed. Among them, time-resolved (TR) resonance Raman (RR) is a particularly versatile tool to probe processes of proteins harboring cofactors with electronic transitions in the visible range, such as retinal or heme proteins. TR RR spectroscopy offers the advantage of simultaneously providing molecular structure and kinetic information. The various TR RR spectroscopic methods can cover a wide dynamic range down to the femtosecond time regime and have been employed in monitoring photoinduced reaction cascades, ligand binding and dissociation, electron transfer, enzymatic reactions, and protein un- and refolding. In this account, we review the achievements of TR RR spectroscopy of nearly 50 years of research in this field, which also illustrates how the role of TR RR spectroscopy in molecular life science has changed from the beginning until now. We outline the various methodological approaches and developments and point out current limitations and potential perspectives.
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Affiliation(s)
- David Buhrke
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17, Juni 135, D-10623 Berlin, Germany
| | - Peter Hildebrandt
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17, Juni 135, D-10623 Berlin, Germany
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2
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Watanabe A, Takakusa H, Kimura T, Inoue SI, Kusuhara H, Ando O. Difference in Mechanism-Based Inhibition of Cytochrome P450 3A4 and 3A5 by a Series of Fluoroquinolone Antibacterial Agents. Drug Metab Dispos 2016; 45:336-341. [PMID: 27974381 DOI: 10.1124/dmd.116.073783] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2016] [Accepted: 12/13/2016] [Indexed: 11/22/2022] Open
Abstract
A series of fluoroquinolone antibacterial compounds were found to be irreversible (compounds 1-5) and quasi-irreversible (compounds 6-9) inhibitors of CYP3A4. The purpose of this study was to evaluate their mechanism-based inhibition (MBI) potency against CYP3A5. Compounds 1-5 were also irreversible inhibitors of CYP3A5, whereas compounds 6-9 showed neither irreversible nor quasi-irreversible inhibition of CYP3A5. Compounds 6 and 8 did not form a metabolite-intermediate complex with the heme of CYP3A5 during incubation. The structural analysis of the metabolites after incubation of compounds 1 and 6 with CYP3A5 revealed that their metabolites were identical to those produced by CYP3A4, including the precursors of which are speculated to account for the MBI of CYP3A4. The homology modeling of CYP3A5 suggests that four residues around the nitroso intermediate of compound 6 in the substrate-binding pocket of CYP3A4 correspond with the bulkier residues in CYP3A5-especially Phe210 in CYP3A5-which might contribute to the steric hindrance with the nitroso intermediate of compound 6. The substrate-binding pocket structure of CYP3A5 might prevent the nitroso intermediate from coordinate binding with the heme, thereby preventing quasi-irreversible inhibition. Our study may provide new insights into the observable differences between the inhibition of CYP3A4 and CYP3A5.
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Affiliation(s)
- Akiko Watanabe
- Drug Metabolism and Pharmacokinetics Research Laboratories, Daiichi Sankyo Company, Ltd., Tokyo, Japan (A.W., H.T., S.I., O.A.); Structural Biology Group, Biological Research Department, Daiichi Sankyo RD Novare Company, Ltd., Tokyo, Japan (T.K.); and Laboratory of Molecular Pharmacokinetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan (H.K.)
| | - Hideo Takakusa
- Drug Metabolism and Pharmacokinetics Research Laboratories, Daiichi Sankyo Company, Ltd., Tokyo, Japan (A.W., H.T., S.I., O.A.); Structural Biology Group, Biological Research Department, Daiichi Sankyo RD Novare Company, Ltd., Tokyo, Japan (T.K.); and Laboratory of Molecular Pharmacokinetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan (H.K.)
| | - Takako Kimura
- Drug Metabolism and Pharmacokinetics Research Laboratories, Daiichi Sankyo Company, Ltd., Tokyo, Japan (A.W., H.T., S.I., O.A.); Structural Biology Group, Biological Research Department, Daiichi Sankyo RD Novare Company, Ltd., Tokyo, Japan (T.K.); and Laboratory of Molecular Pharmacokinetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan (H.K.)
| | - Shin-Ichi Inoue
- Drug Metabolism and Pharmacokinetics Research Laboratories, Daiichi Sankyo Company, Ltd., Tokyo, Japan (A.W., H.T., S.I., O.A.); Structural Biology Group, Biological Research Department, Daiichi Sankyo RD Novare Company, Ltd., Tokyo, Japan (T.K.); and Laboratory of Molecular Pharmacokinetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan (H.K.)
| | - Hiroyuki Kusuhara
- Drug Metabolism and Pharmacokinetics Research Laboratories, Daiichi Sankyo Company, Ltd., Tokyo, Japan (A.W., H.T., S.I., O.A.); Structural Biology Group, Biological Research Department, Daiichi Sankyo RD Novare Company, Ltd., Tokyo, Japan (T.K.); and Laboratory of Molecular Pharmacokinetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan (H.K.)
| | - Osamu Ando
- Drug Metabolism and Pharmacokinetics Research Laboratories, Daiichi Sankyo Company, Ltd., Tokyo, Japan (A.W., H.T., S.I., O.A.); Structural Biology Group, Biological Research Department, Daiichi Sankyo RD Novare Company, Ltd., Tokyo, Japan (T.K.); and Laboratory of Molecular Pharmacokinetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan (H.K.)
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3
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Watanabe A, Takakusa H, Kimura T, Inoue SI, Kusuhara H, Ando O. Analysis of Mechanism-Based Inhibition of CYP 3A4 by a Series of Fluoroquinolone Antibacterial Agents. Drug Metab Dispos 2016; 44:1608-16. [DOI: 10.1124/dmd.116.071654] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 07/27/2016] [Indexed: 11/22/2022] Open
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4
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NO binding kinetics in myoglobin investigated by picosecond Fe K-edge absorption spectroscopy. Proc Natl Acad Sci U S A 2015; 112:12922-7. [PMID: 26438842 DOI: 10.1073/pnas.1424446112] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Diatomic ligands in hemoproteins and the way they bind to the active center are central to the protein's function. Using picosecond Fe K-edge X-ray absorption spectroscopy, we probe the NO-heme recombination kinetics with direct sensitivity to the Fe-NO binding after 532-nm photoexcitation of nitrosylmyoglobin (MbNO) in physiological solutions. The transients at 70 and 300 ps are identical, but they deviate from the difference between the static spectra of deoxymyoglobin and MbNO, showing the formation of an intermediate species. We propose the latter to be a six-coordinated domed species that is populated on a timescale of ∼ 200 ps by recombination with NO ligands. This work shows the feasibility of ultrafast pump-probe X-ray spectroscopic studies of proteins in physiological media, delivering insight into the electronic and geometric structure of the active center.
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Ramos-Alvarez C, Yoo BK, Pietri R, Lamarre I, Martin JL, Lopez-Garriga J, Negrerie M. Reactivity and dynamics of H2S, NO, and O2 interacting with hemoglobins from Lucina pectinata. Biochemistry 2013; 52:7007-21. [PMID: 24040745 DOI: 10.1021/bi400745a] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Hemoglobin HbI from the clam Lucina pectinata is involved in H2S transport, whereas homologous heme protein HbII/III is involved in O2 metabolism. Despite similar tertiary structures, HbI and HbII/III exhibit very different reactivity toward heme ligands H2S, O2, and NO. To investigate this reactivity at the heme level, we measured the dynamics of ligand interaction by time-resolved absorption spectroscopy in the picosecond to nanosecond time range. We demonstrated that H2S can be photodissociated from both ferric and ferrous HbI. H2S geminately rebinds to ferric and ferrous out-of-plane iron with time constants (τgem) of 12 and 165 ps, respectively, with very different proportions of photodissociated H2S exiting the protein (24% in ferric and 80% in ferrous HbI). The Gln(E7)His mutation considerably changes H2S dynamics in ferric HbI, indicating the role of Gln(E7) in controling H2S reactivity. In ferric HbI, the rate of diffusion of H2S from the solvent into the heme pocket (kentry) is 0.30 μM(-1) s(-1). For the HbII/III-O2 complex, we observed mainly a six-coordinate vibrationally excited heme-O2 complex with O2 still bound to the iron. This explains the low yield of O2 photodissociation and low koff from HbII/III, compared with those of HbI and Mb. Both isoforms behave very differently with regard to NO and O2 dynamics. Whereas the amplitude of geminate rebinding of O2 to HbI (38.5%) is similar to that of myoglobin (34.5%) in spite of different distal heme sites, it appears to be much larger for HbII/III (77%). The distal Tyr(B10) side chain present in HbII/III increases the energy barrier for ligand escape and participates in the stabilization of bound O2 and NO.
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Affiliation(s)
- Cacimar Ramos-Alvarez
- Department of Chemistry, University of Puerto Rico , Mayagüez Campus, Mayagüez 00680, Puerto Rico
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6
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Zhang P, Ahn SW, Straub JE. “Strange Kinetics” in the Temperature Dependence of Methionine Ligand Rebinding Dynamics in Cytochrome c. J Phys Chem B 2013; 117:7190-202. [DOI: 10.1021/jp400481m] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Ping Zhang
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Steven Wooseok Ahn
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - John E. Straub
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
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7
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Yoo BK, Lamarre I, Martin JL, Andrew CR, Negrerie M. Picosecond binding of the His ligand to four-coordinate heme in cytochrome c': a one-way gate for releasing proximal NO. J Am Chem Soc 2013; 135:3248-54. [PMID: 23373628 DOI: 10.1021/ja312140f] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
We provide a direct demonstration of a "kinetic trap" mechanism in the proximal 5-coordinate heme-nitrosyl complex (5c-NO) of cytochrome c' from Alcaligenes xylosoxidans (AXCP) in which picosecond rebinding of the endogenous His ligand following heme-NO dissociation acts as a one-way gate for the release of proximal NO into solution. This demonstration is based upon picosecond transient absorption changes following NO photodissociation of the proximal 5c-NO AXCP complex. We have determined the absolute transient absorption spectrum of 4-coordinate ferrous heme to which NO rebinds with a time constant τ(NO) = 7 ps (k(NO) = 1.4 × 10(11) s(-1)) and shown that rebinding of the proximal histidine to the 4-coordinate heme takes place with a time constant τ(His) = 100 ± 10 ps (k(His) = 10(10) s(-1)) after the release of NO from the proximal heme pocket. This rapid His reattachment acts as a one-way gate for releasing proximal NO by precluding direct proximal NO rebinding once it has left the proximal heme pocket and requiring NO rebinding from solution to proceed via the distal heme face.
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Affiliation(s)
- Byung-Kuk Yoo
- Laboratoire d'Optique et Biosciences, INSERM, Ecole Polytechnique, 91128 Palaiseau Cedex, France
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8
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Yoo BK, Lamarre I, Rappaport F, Nioche P, Raman CS, Martin JL, Negrerie M. Picosecond to second dynamics reveals a structural transition in Clostridium botulinum NO-sensor triggered by the activator BAY-41-2272. ACS Chem Biol 2012; 7:2046-54. [PMID: 23009307 DOI: 10.1021/cb3003539] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Soluble guanylate cyclase (sGC) is the mammalian endogenous nitric oxide (NO) receptor that synthesizes cGMP upon NO activation. In synergy with the artificial allosteric effector BAY 41-2272 (a lead compound for drug design in cardiovascular treatment), sGC can also be activated by carbon monoxide (CO), but the structural basis for this synergistic effect are unknown. We recorded in the unusually broad time range from 1 ps to 1 s the dynamics of the interaction of CO binding to full length sGC, to the isolated sGC heme domain β(1)(200) and to the homologous bacterial NO-sensor from Clostridium botulinum. By identifying all phases of CO binding in this full time range and characterizing how these phases are modified by BAY 41-2272, we show that this activator induces the same structural changes in both proteins. This result demonstrates that the BAY 41-2272 binding site resides in the β(1)(200) sGC heme domain and is the same in sGC and in the NO-sensor from Clostridium botulinum.
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Affiliation(s)
- Byung-Kuk Yoo
- Laboratoire d’Optique et Biosciences,
INSERM U696, CNRS UMR 7645, Ecole Polytechnique, 91128 Palaiseau Cedex, France
| | - Isabelle Lamarre
- Laboratoire d’Optique et Biosciences,
INSERM U696, CNRS UMR 7645, Ecole Polytechnique, 91128 Palaiseau Cedex, France
| | - Fabrice Rappaport
- Institut de Biologie Physico-Chimie, UMR
7141 CNRS-UPMC, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Pierre Nioche
- Laboratoire de Toxicologie et
Pharmacologie, UMR S747, Centre Universitaire des Saints-Pères, 75006 Paris, France
| | - C. S. Raman
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201,
United States
| | - Jean-Louis Martin
- Laboratoire d’Optique et Biosciences,
INSERM U696, CNRS UMR 7645, Ecole Polytechnique, 91128 Palaiseau Cedex, France
| | - Michel Negrerie
- Laboratoire d’Optique et Biosciences,
INSERM U696, CNRS UMR 7645, Ecole Polytechnique, 91128 Palaiseau Cedex, France
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9
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Zhang P, Małolepsza E, Straub JE. Dynamics of Methionine Ligand Rebinding in Cytochrome c. J Phys Chem B 2012; 116:6980-90. [DOI: 10.1021/jp300783j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ping Zhang
- Department
of Chemistry, Boston University, Boston,
Massachusetts 02215, United States
| | - Edyta Małolepsza
- Department
of Chemistry, Boston University, Boston,
Massachusetts 02215, United States
| | - John E. Straub
- Department
of Chemistry, Boston University, Boston,
Massachusetts 02215, United States
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10
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Cazade PA, Huang J, Yosa J, Szymczak JJ, Meuwly M. Atomistic simulations of reactive processes in the gas- and condensed-phase. INT REV PHYS CHEM 2012. [DOI: 10.1080/0144235x.2012.694694] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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11
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Jasaitis A, Ouellet H, Lambry JC, Martin JL, Friedman JM, Guertin M, Vos MH. Ultrafast heme–ligand recombination in truncated hemoglobin HbO from Mycobacterium tuberculosis: A ligand cage. Chem Phys 2012. [DOI: 10.1016/j.chemphys.2011.04.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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12
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Development of a new class of aromatase inhibitors: design, synthesis and inhibitory activity of 3-phenylchroman-4-one (isoflavanone) derivatives. Bioorg Med Chem 2012; 20:2603-13. [PMID: 22444875 DOI: 10.1016/j.bmc.2012.02.042] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2011] [Revised: 02/11/2012] [Accepted: 02/17/2012] [Indexed: 01/23/2023]
Abstract
Aromatase (CYP19) catalyzes the aromatization reaction of androgen substrates to estrogens, the last and rate-limiting step in estrogen biosynthesis. Inhibition of aromatase is a new and promising approach to treat hormone-dependent breast cancer. We present here the design and development of isoflavanone derivatives as potential aromatase inhibitors. Structural modifications were performed on the A and B rings of isoflavanones via microwave-assisted, gold-catalyzed annulation reactions of hydroxyaldehydes and alkynes. The in vitro aromatase inhibition of these compounds was determined by fluorescence-based assays utilizing recombinant human aromatase (baculovirus/insect cell-expressed). The compounds 3-(4-phenoxyphenyl)chroman-4-one (1h), 6-methoxy-3-phenylchroman-4-one (2a) and 3-(pyridin-3-yl)chroman-4-one (3b) exhibited potent inhibitory effects against aromatase with IC(50) values of 2.4 μM, 0.26 μM and 5.8 μM, respectively. Docking simulations were employed to investigate crucial enzyme/inhibitor interactions such as hydrophobic interactions, hydrogen bonding and heme iron coordination. This report provides useful information on aromatase inhibition and serves as a starting point for the development of new flavonoid aromatase inhibitors.
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13
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Peng Q, Pavlik JW, Scheidt WR, Wiest O. Predicting Nuclear Resonance Vibrational Spectra of [Fe(OEP)(NO)]. J Chem Theory Comput 2012; 8:214-223. [PMID: 23204948 PMCID: PMC3507453 DOI: 10.1021/ct2006456] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nuclear Resonance Vibrational Spectroscopy (NRVS) is a sensitive vibrational probe for biologically important heme complexes. The exquisite sensitivity of the NRVS data to the electronic structure provides detailed insights into the nature of these interesting compounds, but requires highly accurate computational methods for the mode assignments. To determine the best combinations of density functionals and basis sets, a series of benchmark DFT calculations on the previously characterized complex [Fe(OEP)NO] (OEP(2-)=octaethylporphyrinatio dianion) were performed. A test set of 21 methodology combinations including 8 functionals (BP86, mPWPW91, B3LYP, PBE1PBE, M062X, M06L, LC-BP86 and ωB97X-D) and 5 basis set (VTZ, TZVP, Lanl2DZ for iron and 6-31G*, 6-31+G* for other atoms) was carried out to calculate electronic structures and vibrational frequencies. We also implemented the conversion of frequency calculations into orientation-selective mode composition factors (e(2)), which can used to simulate the Vibrational Density Of States (VDOS) using Gaussian normal distribution functions. These use a series of user-friendly scripts for their application to NRVS. The structures as well as the isotropic and anisotropic NRVS of [Fe(OEP)NO] obtained with the M06L functional with a variety of basis sets are found to best reproduce the available experimental data, followed by B3LYP/LanL2DZ calculations. Other density functionals and basis sets do not produce the same level of accuracy. The noticeably worse agreement between theory and experiment for the out-plane NRVS compared with the excellent performance of the M06L functional for the in-plane prediction is attributed to deficiencies of the physical model rather than the computational methodology.
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Affiliation(s)
- Qian Peng
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556 (USA)
| | - Jeffrey W. Pavlik
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556 (USA)
| | - W. Robert Scheidt
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556 (USA)
| | - Olaf Wiest
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556 (USA)
- School of Chemical Biology and Biotechnology, Peking University, Shenzhen Graduate School, Shenzhen 518055, China
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Pavlik JW, Barabanschikov A, Oliver AG, Alp EE, Sturhahn W, Zhao J, Sage JT, Scheidt WR. Probing vibrational anisotropy with nuclear resonance vibrational spectroscopy. Angew Chem Int Ed Engl 2010; 49:4400-4. [PMID: 20422668 DOI: 10.1002/anie.201000928] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jeffrey W Pavlik
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
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15
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Picosecond primary structural transition of the heme is retarded after nitric oxide binding to heme proteins. Proc Natl Acad Sci U S A 2010; 107:13678-83. [PMID: 20643970 DOI: 10.1073/pnas.0912938107] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
We investigated the ultrafast structural transitions of the heme induced by nitric oxide (NO) binding for several heme proteins by subpicosecond time-resolved resonance Raman and femtosecond transient absorption spectroscopy. We probed the heme iron motion by the evolution of the iron-histidine Raman band intensity after NO photolysis. Unexpectedly, we found that the heme response and iron motion do not follow the kinetics of NO rebinding. Whereas NO dissociation induces quasi-instantaneous iron motion and heme doming (<0.6 ps), the reverse process results in a much slower picosecond movement of the iron toward the planar heme configuration after NO binding. The time constant for this primary domed-to-planar heme transition varies among proteins (approximately 30 ps for myoglobin and its H64V mutant, approximately 15 ps for hemoglobin, approximately 7 ps for dehaloperoxidase, and approximately 6 ps for cytochrome c) and depends upon constraints exerted by the protein structure on the heme cofactor. This observed phenomenon constitutes the primary structural transition in heme proteins induced by NO binding.
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16
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Pavlik J, Barabanschikov A, Oliver A, Alp E, Sturhahn W, Zhao J, Sage J, Scheidt W. Probing Vibrational Anisotropy with Nuclear Resonance Vibrational Spectroscopy. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201000928] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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17
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Silkstone G, Kapetanaki SM, Husu I, Vos MH, Wilson MT. Nitric oxide binds to the proximal heme coordination site of the ferrocytochrome c/cardiolipin complex: formation mechanism and dynamics. J Biol Chem 2010; 285:19785-92. [PMID: 20395293 DOI: 10.1074/jbc.m109.067736] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mammalian mitochondrial cytochrome c interacts with cardiolipin to form a complex (cyt. c/CL) important in apoptosis. Here we show that this interaction leads to structural changes in ferrocytochrome c that leads to an open coordinate site on the central iron, resulting from the dissociation of the intrinsic methionine residue, where NO can rapidly bind (k = 1.2 x 10(7) m(-1) s(-1)). Accompanying NO binding, the proximal histidine dissociates leaving the heme pentacoordinate, in contrast to the hexacoordinate nitrosyl adducts of native ferrocytochrome c or of the protein in which the coordinating methionine is removed by chemical modification or mutation. We present the results of stopped-flow and photolysis experiments that show that following initial NO binding to the heme, there ensues an unusually complex set of kinetic steps. The spectral changes associated with these kinetic transitions, together with their dependence on NO concentration, have been determined and lead us to conclude that NO binding to cyt. c/CL takes place via an overall scheme comparable to that described for cytochrome c' and guanylate cyclase, the final product being one in which NO resides on the proximal side of the heme. In addition, novel features not observed before in other heme proteins forming pentacoordinate nitrosyl species, include a high yield of NO escape after dissociation, rapid (<1 ms) dissociation of proximal histidine upon NO binding and its very fast binding (60 ps) after NO dissociation, and the formation of a hexacoordinate intermediate. These features all point at a remarkable mobility of the proximal heme environment induced by cardiolipin.
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Affiliation(s)
- Gary Silkstone
- Department of Biological Sciences, Wivenhoe Park, University of Essex, Colchester CO4 3SQ, United Kingdom
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18
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Salazar-Salinas K, Jauregui LA, Kubli-Garfias C, Seminario JM. Molecular biosensor based on a coordinated iron complex. J Chem Phys 2009; 130:105101. [DOI: 10.1063/1.3070235] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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19
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Kubo M, Uchida T, Nakashima S, Kitagawa T. Construction of a subnanosecond time-resolved, high-resolution ultraviolet resonance Raman measurement system and its application to reveal the dynamic structures of proteins. APPLIED SPECTROSCOPY 2008; 62:30-37. [PMID: 18230205 DOI: 10.1366/000370208783412573] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
A subnanosecond time-resolved ultraviolet (UV) resonance Raman system has been developed to study protein structural dynamics. The system is based on a 1 kHz Nd:YLF-pumped Ti:Sapphire regenerative amplifier with harmonic generation that can deliver visible (412, 440, 458, and 488 nm) and UV (206, 220, 229, and 244 nm) pulses. A subnanosecond (0.2 ns) tunable near-infrared pulse from a custom-made Ti:Sapphire oscillator is used to seed the regenerative amplifier. A narrow linewidth of the subnanosecond pulse offers the advantage of high resolution of UV resonance Raman spectra, which is critical to obtain site-specific information on protein structures. By combination with a 1 m single spectrograph equipped with a 3600 grooves/mm holographic grating and a custom-made prism prefilter, the present system achieves excellent spectral (<10 cm(-1)) and frequency (approximately 1 cm(-1)) resolutions with a relatively high temporal resolution (<0.5 ns). We also report the application of this system to two heme proteins, hemoglobin A and CooA, with the 440 nm pump and 220 nm probe wavelengths. For hemoglobin A, a structural change during the transition to the earliest intermediate upon CO photodissociation is successfully observed, specifically, nanosecond cleavage of the A-E interhelical hydrogen bonds within each subunit at Trpalpha14 and Trpbeta15 residues. For CooA, on the other hand, rapid structural distortion (<0.5 ns) by CO photodissociation and nanosecond structural relaxation following CO geminate recombination are observed through the Raman bands of Phe and Trp residues located near the heme. These results demonstrate the high potential of this instrument to detect local protein motions subsequent to photoreactions in their active sites.
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Affiliation(s)
- Minoru Kubo
- Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, Okazaki 444-8787, Japan
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Ultrafast dynamics of ligands within heme proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2007; 1777:15-31. [PMID: 17996720 DOI: 10.1016/j.bbabio.2007.10.004] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2007] [Revised: 10/10/2007] [Accepted: 10/15/2007] [Indexed: 11/21/2022]
Abstract
Physiological bond formation and bond breaking events between proteins and ligands and their immediate consequences are difficult to synchronize and study in general. However, diatomic ligands can be photodissociated from heme, and thus in heme proteins ligand release and rebinding dynamics and trajectories have been studied on timescales of the internal vibrations of the protein that drive many biochemical reactions, and longer. The rapidly expanding number of characterized heme proteins involved in a large variety of functions allows comparative dynamics-structure-function studies. In this review, an overview is given of recent progress in this field, and in particular on initial sensing processes in signaling proteins, and on ligand and electron transfer dynamics in oxidases and cytochromes.
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Kruglik SG, Jasaitis A, Hola K, Yamashita T, Liebl U, Martin JL, Vos MH. Subpicosecond oxygen trapping in the heme pocket of the oxygen sensor FixL observed by time-resolved resonance Raman spectroscopy. Proc Natl Acad Sci U S A 2007; 104:7408-13. [PMID: 17446273 PMCID: PMC1863486 DOI: 10.1073/pnas.0700445104] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Dissociation of oxygen from the heme domain of the bacterial oxygen sensor protein FixL constitutes the first step in hypoxia-induced signaling. In the present study, the photodissociation of the heme-O2 bond was used to synchronize this event, and time-resolved resonance Raman (TR(3)) spectroscopy with subpicosecond time resolution was implemented to characterize the heme configuration of the primary photoproduct. TR(3) measurements on heme-oxycomplexes are highly challenging and have not yet been reported. Whereas in all other known six-coordinated heme protein complexes with diatomic ligands, including the oxymyoglobin reported here, heme iron out-of-plane motion (doming) occurs faster than 1 ps after iron-ligand bond breaking; surprisingly, no sizeable doming is observed in the oxycomplex of the Bradyrhizobium japonicum FixL sensor domain (FixLH). This assessment is deduced from the absence of the iron-histidine band around 217 cm(-1) as early as 0.5 ps. We suggest that efficient ultrafast oxygen rebinding to the heme occurs on the femtosecond time scale, thus hindering heme doming. Comparing WT oxy-FixLH, mutant proteins FixLH-R220H and FixLH-R220Q, the respective carbonmonoxy-complexes, and oxymyoglobin, we show that a hydrogen bond of the terminal oxygen atom with the residue in position 220 is responsible for the observed behavior; in WT FixL this residue is arginine, crucially implicated in signal transmission. We propose that the rigid O2 configuration imposed by this residue, in combination with the hydrophobic and constrained properties of the distal cavity, keep dissociated oxygen in place. These results uncover the origin of the "oxygen cage" properties of this oxygen sensor protein.
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Affiliation(s)
- Sergei G. Kruglik
- Laboratoire d'Optique et Biosciences, Centre National de la Recherche, Ecole Polytechnique, 91128 Palaiseau Cedex, France
- Institut National de la Santé et de la Recherche Médicale, Unité Mixte de Recherche 696, 91128 Palaiseau, France; and
- Laboratoire de Biophysique Moléculaire, Cellulaire, et Tissulaire, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7033, University Pierre & Marie Curie, Genopole Campus 1, Batiment Genavenir 8, 5 Rue Henri Desbrueres, 91030 Evry, France
| | - Audrius Jasaitis
- Laboratoire d'Optique et Biosciences, Centre National de la Recherche, Ecole Polytechnique, 91128 Palaiseau Cedex, France
- Institut National de la Santé et de la Recherche Médicale, Unité Mixte de Recherche 696, 91128 Palaiseau, France; and
| | - Klara Hola
- Laboratoire d'Optique et Biosciences, Centre National de la Recherche, Ecole Polytechnique, 91128 Palaiseau Cedex, France
- Institut National de la Santé et de la Recherche Médicale, Unité Mixte de Recherche 696, 91128 Palaiseau, France; and
| | - Taku Yamashita
- Laboratoire d'Optique et Biosciences, Centre National de la Recherche, Ecole Polytechnique, 91128 Palaiseau Cedex, France
- Institut National de la Santé et de la Recherche Médicale, Unité Mixte de Recherche 696, 91128 Palaiseau, France; and
| | - Ursula Liebl
- Laboratoire d'Optique et Biosciences, Centre National de la Recherche, Ecole Polytechnique, 91128 Palaiseau Cedex, France
- Institut National de la Santé et de la Recherche Médicale, Unité Mixte de Recherche 696, 91128 Palaiseau, France; and
| | - Jean-Louis Martin
- Laboratoire d'Optique et Biosciences, Centre National de la Recherche, Ecole Polytechnique, 91128 Palaiseau Cedex, France
- Institut National de la Santé et de la Recherche Médicale, Unité Mixte de Recherche 696, 91128 Palaiseau, France; and
| | - Marten H. Vos
- Laboratoire d'Optique et Biosciences, Centre National de la Recherche, Ecole Polytechnique, 91128 Palaiseau Cedex, France
- Institut National de la Santé et de la Recherche Médicale, Unité Mixte de Recherche 696, 91128 Palaiseau, France; and
- To whom correspondence should be addressed at the † address. E-mail:
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Ibrahim M, Xu C, Spiro TG. Differential sensing of protein influences by NO and CO vibrations in heme adducts. J Am Chem Soc 2006; 128:16834-45. [PMID: 17177434 PMCID: PMC2530899 DOI: 10.1021/ja064859d] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Heme proteins bind the gaseous ligands XO (X = C, N, O) via backbonding from Fe d(pi) electrons. Backbonding is modulated by distal interactions of the bound ligand with the surrounding protein and by variations in the strength of the trans proximal ligand. Vibrational modes associated with FeX and XO bond stretching coordinates report on these interactions, but the interpretive framework developed for CO adducts, involving anticorrelations of nuFeC and nuCO, has seemed not to apply to NO adducts. We have now obtained an excellent anticorrelation of nuFeN and nuNO, via resonance Raman spectroscopy on (N-methylimidazole)Fe(II)TPP-Y(NO), where TPP-Y is tetraphenylporphine with electron-donating or -withdrawing substituents, Y, that modulate the backbonding; the problem of laser-induced dissociation of the axial base was circumvented by using frozen solutions. New data are also reported for CO adducts. The anticorrelations are supported by DFT calculations of structures and spectra. When protein data are examined, the NO adducts show large deviations from the modeled anticorrelation when there are distal H-bonds or positive charges. These deviations are proposed to result from closing of the FeNO angle due to a shift in the valence isomer equilibrium toward the Fe(III)(NO-) form, an effect that is absent in CO adducts. The differing vibrational patterns of CO and NO adducts provide complementary information with respect to protein interactions, which may help to elucidate the mechanisms of ligand discrimination and signaling in heme sensor proteins.
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Affiliation(s)
- Mohammed Ibrahim
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544
| | - Changliang Xu
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544
| | - Thomas G. Spiro
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544
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Kruglik SG, Lambry JC, Cianetti S, Martin JL, Eady RR, Andrew CR, Negrerie M. Molecular basis for nitric oxide dynamics and affinity with Alcaligenes xylosoxidans cytochrome c. J Biol Chem 2006; 282:5053-5062. [PMID: 17158883 DOI: 10.1074/jbc.m604327200] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The bacterial heme protein cytochrome ć from Alcaligenes xylosoxidans (AXCP) reacts with nitric oxide (NO) to form a 5-coordinate ferrous nitrosyl heme complex. The crystal structure of ferrous nitrosyl AXCP has previously revealed that NO is bound in an unprecedented manner on the proximal side of the heme. To understand how the protein structure of AXCP controls NO dynamics, we performed absorption and Raman time-resolved studies at the heme level as well as a molecular computational dynamics study at the entire protein structure level. We found that after NO dissociation from the heme iron, the structure of the proximal heme pocket of AXCP confines NO close to the iron so that an ultrafast (7 ps) and complete (99 +/- 1%) geminate rebinding occurs, whereas the proximal histidine does not rebind to the heme iron on the timescale of NO geminate rebinding. The distal side controls the initial NO binding, whereas the proximal heme pocket controls its release. These dynamic properties allow the trapping of NO within the protein core and represent an extreme behavior observed among heme proteins.
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Affiliation(s)
- Sergei G Kruglik
- Ecole Polytechnique, Laboratoire d'Optique et Biosciences, CNRS UMR 7645, 91128 Palaiseau Cedex, France; BioMoCeTi, CNRS UMR 7033, University Pierre and Marie Curie, Genopole Campus 1, 91030 Evry, France
| | - Jean-Christophe Lambry
- Ecole Polytechnique, Laboratoire d'Optique et Biosciences, CNRS UMR 7645, 91128 Palaiseau Cedex, France; INSERM, U696, 91128 Palaiseau Cedex, France
| | - Simona Cianetti
- Ecole Polytechnique, Laboratoire d'Optique et Biosciences, CNRS UMR 7645, 91128 Palaiseau Cedex, France
| | - Jean-Louis Martin
- Ecole Polytechnique, Laboratoire d'Optique et Biosciences, CNRS UMR 7645, 91128 Palaiseau Cedex, France; INSERM, U696, 91128 Palaiseau Cedex, France
| | - Robert R Eady
- Department of Biological Chemistry, John Innes Centre, Norwich NR4 7UH, United Kingdom, and
| | - Colin R Andrew
- Department of Chemistry and Biochemistry, Eastern Oregon University, La Grande, Oregon 97850
| | - Michel Negrerie
- Ecole Polytechnique, Laboratoire d'Optique et Biosciences, CNRS UMR 7645, 91128 Palaiseau Cedex, France; INSERM, U696, 91128 Palaiseau Cedex, France.
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