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Bacellar C, Kinschel D, Mancini GF, Ingle RA, Rouxel J, Cannelli O, Cirelli C, Knopp G, Szlachetko J, Lima FA, Menzi S, Pamfilidis G, Kubicek K, Khakhulin D, Gawelda W, Rodriguez-Fernandez A, Biednov M, Bressler C, Arrell CA, Johnson PJM, Milne CJ, Chergui M. Spin cascade and doming in ferric hemes: Femtosecond X-ray absorption and X-ray emission studies. Proc Natl Acad Sci U S A 2020; 117:21914-21920. [PMID: 32848065 PMCID: PMC7486745 DOI: 10.1073/pnas.2009490117] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The structure-function relationship is at the heart of biology, and major protein deformations are correlated to specific functions. For ferrous heme proteins, doming is associated with the respiratory function in hemoglobin and myoglobins. Cytochrome c (Cyt c) has evolved to become an important electron-transfer protein in humans. In its ferrous form, it undergoes ligand release and doming upon photoexcitation, but its ferric form does not release the distal ligand, while the return to the ground state has been attributed to thermal relaxation. Here, by combining femtosecond Fe Kα and Kβ X-ray emission spectroscopy (XES) with Fe K-edge X-ray absorption near-edge structure (XANES), we demonstrate that the photocycle of ferric Cyt c is entirely due to a cascade among excited spin states of the iron ion, causing the ferric heme to undergo doming, which we identify. We also argue that this pattern is common to a wide diversity of ferric heme proteins, raising the question of the biological relevance of doming in such proteins.
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Affiliation(s)
- Camila Bacellar
- Laboratoire de Spectroscopie Ultrarapide, Institut des Sciences et Ingéniéries Chimiques and Lausanne Centre for Ultrafast Science, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Dominik Kinschel
- Laboratoire de Spectroscopie Ultrarapide, Institut des Sciences et Ingéniéries Chimiques and Lausanne Centre for Ultrafast Science, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Giulia F Mancini
- Laboratoire de Spectroscopie Ultrarapide, Institut des Sciences et Ingéniéries Chimiques and Lausanne Centre for Ultrafast Science, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Rebecca A Ingle
- Laboratoire de Spectroscopie Ultrarapide, Institut des Sciences et Ingéniéries Chimiques and Lausanne Centre for Ultrafast Science, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Jérémy Rouxel
- Laboratoire de Spectroscopie Ultrarapide, Institut des Sciences et Ingéniéries Chimiques and Lausanne Centre for Ultrafast Science, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Oliviero Cannelli
- Laboratoire de Spectroscopie Ultrarapide, Institut des Sciences et Ingéniéries Chimiques and Lausanne Centre for Ultrafast Science, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Claudio Cirelli
- Swiss Free Electron Laser, Paul-Scherrer-Institut (PSI), 5232 Villigen PSI, Switzerland
| | - Gregor Knopp
- Swiss Free Electron Laser, Paul-Scherrer-Institut (PSI), 5232 Villigen PSI, Switzerland
| | - Jakub Szlachetko
- Institute of Nuclear Physics, Polish Academy of Sciences, 31-342 Kraków, Poland
| | | | - Samuel Menzi
- Swiss Free Electron Laser, Paul-Scherrer-Institut (PSI), 5232 Villigen PSI, Switzerland
| | - Georgios Pamfilidis
- Swiss Free Electron Laser, Paul-Scherrer-Institut (PSI), 5232 Villigen PSI, Switzerland
| | | | | | - Wojciech Gawelda
- European X-ray Free Electron Laser, D-22869 Schenefeld, Germany
- Faculty of Physics, Adam Mickiewicz University, 61-614 Poznan, Poland
| | | | - Mykola Biednov
- European X-ray Free Electron Laser, D-22869 Schenefeld, Germany
| | | | - Christopher A Arrell
- Swiss Free Electron Laser, Paul-Scherrer-Institut (PSI), 5232 Villigen PSI, Switzerland
| | - Philip J M Johnson
- Swiss Free Electron Laser, Paul-Scherrer-Institut (PSI), 5232 Villigen PSI, Switzerland
| | - Christopher J Milne
- Swiss Free Electron Laser, Paul-Scherrer-Institut (PSI), 5232 Villigen PSI, Switzerland
| | - Majed Chergui
- Laboratoire de Spectroscopie Ultrarapide, Institut des Sciences et Ingéniéries Chimiques and Lausanne Centre for Ultrafast Science, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland;
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2
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Lima FA, Penfold TJ, van der Veen RM, Reinhard M, Abela R, Tavernelli I, Rothlisberger U, Benfatto M, Milne CJ, Chergui M. Probing the electronic and geometric structure of ferric and ferrous myoglobins in physiological solutions by Fe K-edge absorption spectroscopy. Phys Chem Chem Phys 2014; 16:1617-31. [PMID: 24317683 DOI: 10.1039/c3cp53683a] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present an iron K-edge X-ray absorption study of carboxymyoglobin (MbCO), nitrosylmyoglobin (MbNO), oxymyoglobin (MbO2), cyanomyoglobin (MbCN), aquomet myoglobin (metMb) and unligated myoglobin (deoxyMb) in physiological media. The analysis of the XANES region is performed using the full-multiple scattering formalism, implemented within the MXAN package. This reveals trends within the heme structure, absent from previous crystallographic and X-ray absorption analysis. In particular, the iron-nitrogen bond lengths in the porphyrin ring converge to a common value of about 2 Å, except for deoxyMb whose bigger value is due to the doming of the heme. The trends of the Fe-Nε (His93) bond length is found to be consistent with the effect of ligand binding to the iron, with the exception of MbNO, which is explained in terms of the repulsive trans effect. We derive a high resolution description of the relative geometry of the ligands with respect to the heme and quantify the magnitude of the heme doming in the deoxyMb form. Finally, time-dependent density functional theory is used to simulate the pre-edge spectra and is found to be in good agreement with the experiment. The XAS spectra typically exhibit one pre-edge feature which arises from transitions into the unoccupied dσ and dπ - πligand* orbitals. 1s → dπ transitions contribute weakly for MbO2, metMb and deoxyMb. However, despite this strong Fe d contribution these transitions are found to be dominated by the dipole (1s → 4p) moment due to the low symmetry of the heme environment.
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Affiliation(s)
- Frederico A Lima
- École Polytechnique Fédérale de Lausanne, Laboratoire de Spectroscopie Ultrarapide, ISIC, FSB-BSP, CH-1015 Lausanne, CH, Switzerland.
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3
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Borfecchia E, Garino C, Salassa L, Lamberti C. Synchrotron ultrafast techniques for photoactive transition metal complexes. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2013; 371:20120132. [PMID: 23776294 DOI: 10.1098/rsta.2012.0132] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
In the last decade, the use of time-resolved X-ray techniques has revealed the structure of light-generated transient species for a wide range of samples, from small organic molecules to proteins. Time resolutions of the order of 100 ps are typically reached, allowing one to monitor thermally equilibrated excited states and capture their structure as a function of time. This review aims at providing a general overview of the application of time-resolved X-ray solution scattering (TR-XSS) and time-resolved X-ray absorption spectroscopy (TR-XAS), the two techniques prevalently employed in the investigation of light-triggered structural changes of transition metal complexes. In particular, we herein describe the fundamental physical principles for static XSS and XAS and illustrate the theory of time-resolved XSS and XAS together with data acquisition and analysis strategies. Selected pioneering examples of photoactive transition metal complexes studied by TR-XSS and TR-XAS are discussed in depth.
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Affiliation(s)
- Elisa Borfecchia
- Department of Chemistry, NIS Centre of Excellence, University of Turin, via P. Giuria 7, 10125 Turin, Italy
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4
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Dickson CF, Rich AM, D'Avigdor WMH, Collins DAT, Lowry JA, Mollan TL, Khandros E, Olson JS, Weiss MJ, Mackay JP, Lay PA, Gell DA. α-Hemoglobin-stabilizing protein (AHSP) perturbs the proximal heme pocket of oxy-α-hemoglobin and weakens the iron-oxygen bond. J Biol Chem 2013; 288:19986-20001. [PMID: 23696640 DOI: 10.1074/jbc.m112.437509] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
α-Hemoglobin (αHb)-stabilizing protein (AHSP) is a molecular chaperone that assists hemoglobin assembly. AHSP induces changes in αHb heme coordination, but how these changes are facilitated by interactions at the αHb·AHSP interface is not well understood. To address this question we have used NMR, x-ray absorption spectroscopy, and ligand binding measurements to probe αHb conformational changes induced by AHSP binding. NMR chemical shift analyses of free CO-αHb and CO-αHb·AHSP indicated that the seven helical elements of the native αHb structure are retained and that the heme Fe(II) remains coordinated to the proximal His-87 side chain. However, chemical shift differences revealed alterations of the F, G, and H helices and the heme pocket of CO-αHb bound to AHSP. Comparisons of iron-ligand geometry using extended x-ray absorption fine structure spectroscopy showed that AHSP binding induces a small 0.03 Å lengthening of the Fe-O2 bond, explaining previous reports that AHSP decreases αHb O2 affinity roughly 4-fold and promotes autooxidation due primarily to a 3-4-fold increase in the rate of O2 dissociation. Pro-30 mutations diminished NMR chemical shift changes in the proximal heme pocket, restored normal O2 dissociation rate and equilibrium constants, and reduced O2-αHb autooxidation rates. Thus, the contacts mediated by Pro-30 in wild-type AHSP promote αHb autooxidation by introducing strain into the proximal heme pocket. As a chaperone, AHSP facilitates rapid assembly of αHb into Hb when βHb is abundant but diverts αHb to a redox resistant holding state when βHb is limiting.
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Affiliation(s)
- Claire F Dickson
- Menzies Research Institute Tasmania, University of Tasmania, Hobart, TAS 7000, Australia
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5
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Lima FA, Milne CJ, Amarasinghe DCV, Rittmann-Frank MH, van der Veen RM, Reinhard M, Pham VT, Karlsson S, Johnson SL, Grolimund D, Borca C, Huthwelker T, Janousch M, van Mourik F, Abela R, Chergui M. A high-repetition rate scheme for synchrotron-based picosecond laser pump/x-ray probe experiments on chemical and biological systems in solution. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2011; 82:063111. [PMID: 21721678 DOI: 10.1063/1.3600616] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
We present the extension of time-resolved optical pump/x-ray absorption spectroscopy (XAS) probe experiments towards data collection at MHz repetition rates. The use of a high-power picosecond laser operating at an integer fraction of the repetition rate of the storage ring allows exploitation of up to two orders of magnitude more x-ray photons than in previous schemes based on the use of kHz lasers. Consequently, we demonstrate an order of magnitude increase in the signal-to-noise of time-resolved XAS of molecular systems in solution. This makes it possible to investigate highly dilute samples at concentrations approaching physiological conditions for biological systems. The simplicity and compactness of the scheme allows for straightforward implementation at any synchrotron beamline and for a wide range of x-ray probe techniques, such as time-resolved diffraction or x-ray emission studies.
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Affiliation(s)
- Frederico A Lima
- Laboratoire de Spectroscopie Ultrarapide, Ecole Polytechnique Fédérale de Lausanne, ISIC, FSB, 1015 Lausanne, Switzerland
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6
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Leu BM, Ching TH, Zhao J, Sturhahn W, Alp EE, Sage JT. Vibrational dynamics of iron in cytochrome C. J Phys Chem B 2009; 113:2193-200. [PMID: 19173569 DOI: 10.1021/jp806574t] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Nuclear resonance vibrational spectroscopy (NRVS) and Raman spectroscopy on (54)Fe- and (57)Fe-enriched cytochrome c (cyt c) identify multiple bands involving vibrations of the heme Fe. Comparison with predictions from Fe isotope shifts reveals that 70% of the NRVS signal in the 300-450 cm(-1) frequency range corresponds to vibrations resolved in Soret-enhanced Raman spectra. This frequency range dominates the "stiffness", an effective force constant determined by the Fe vibrational density of states (VDOS), which measures the strength of nearest-neighbor interactions with Fe. The stiffness of the low-spin Fe environment in both oxidation states of cyt c significantly exceeds that for the high-spin Fe in deoxymyoglobin, where the 200-300 cm(-1) frequency range dominates the VDOS. This situation is reflected in the shorter Fe-ligand bond lengths in the former with respect to the latter. The longer Fe-S(Met80) in oxidized cyt c with respect to reduced cyt c leads to a decrease in the stiffness of the iron environment upon oxidation. Comparison with NRVS measurements allows us to assess assignments for vibrational modes resolved in this region of the heme Raman spectrum. We consider the possibility that the 372 cm(-1) band in reduced cyt c involves the Fe-S(Met80) bond.
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Affiliation(s)
- Bogdan M Leu
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115, USA
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7
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Shi W, Zhan C, Ignatov A, Manjasetty BA, Marinkovic N, Sullivan M, Huang R, Chance MR. Metalloproteomics: High-Throughput Structural and Functional Annotation of Proteins in Structural Genomics. Structure 2005; 13:1473-86. [PMID: 16216579 DOI: 10.1016/j.str.2005.07.014] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2005] [Revised: 07/06/2005] [Accepted: 07/07/2005] [Indexed: 11/21/2022]
Abstract
A high-throughput method for measuring transition metal content based on quantitation of X-ray fluorescence signals was used to analyze 654 proteins selected as targets by the New York Structural GenomiX Research Consortium. Over 10% showed the presence of transition metal atoms in stoichiometric amounts; these totals as well as the abundance distribution are similar to those of the Protein Data Bank. Bioinformatics analysis of the identified metalloproteins in most cases supported the metalloprotein annotation; identification of the conserved metal binding motif was also shown to be useful in verifying structural models of the proteins. Metalloproteomics provides a rapid structural and functional annotation for these sequences and is shown to be approximately 95% accurate in predicting the presence or absence of stoichiometric metal content. The project's goal is to assay at least 1 member from each Pfam family; approximately 500 Pfam families have been characterized with respect to transition metal content so far.
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Affiliation(s)
- Wuxian Shi
- New York Structural GenomiX Research Consortium, Bronx, New York 10461, USA
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8
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Chance MR, Fiser A, Sali A, Pieper U, Eswar N, Xu G, Fajardo JE, Radhakannan T, Marinkovic N. High-throughput computational and experimental techniques in structural genomics. Genome Res 2004; 14:2145-54. [PMID: 15489337 PMCID: PMC528931 DOI: 10.1101/gr.2537904] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Structural genomics has as its goal the provision of structural information for all possible ORF sequences through a combination of experimental and computational approaches. The access to genome sequences and cloning resources from an ever-widening array of organisms is driving high-throughput structural studies by the New York Structural Genomics Research Consortium. In this report, we outline the progress of the Consortium in establishing its pipeline for structural genomics, and some of the experimental and bioinformatics efforts leading to structural annotation of proteins. The Consortium has established a pipeline for structural biology studies, automated modeling of ORF sequences using solved (template) structures, and a novel high-throughput approach (metallomics) to examining the metal binding to purified protein targets. The Consortium has so far produced 493 purified proteins from >1077 expression vectors. A total of 95 have resulted in crystal structures, and 81 are deposited in the Protein Data Bank (PDB). Comparative modeling of these structures has generated >40,000 structural models. We also initiated a high-throughput metal analysis of the purified proteins; this has determined that 10%-15% of the targets contain a stoichiometric structural or catalytic transition metal atom. The progress of the structural genomics centers in the U.S. and around the world suggests that the goal of providing useful structural information on most all ORF domains will be realized. This projected resource will provide structural biology information important to understanding the function of most proteins of the cell.
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Affiliation(s)
- Mark R Chance
- New York Structural Genomics Research Consortium, Albert Einstein College of Medicine, Bronx, New York 10461, USA.
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9
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Lim M, Jackson TA, Anfinrud PA. Orientational distribution of CO before and after photolysis of MbCO and HbCO: a determination using time-resolved polarized Mid-IR spectroscopy. J Am Chem Soc 2004; 126:7946-57. [PMID: 15212544 DOI: 10.1021/ja035475f] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The technique of time-resolved polarized mid-IR spectroscopy was used to probe the orientational distribution of carbon monoxide (CO) bound to and docked within horse myoglobin, sperm whale myoglobin, and human hemoglobin A in neutral pH solution at 283 K. An accurate determination of the orientation required that the experimentally measured polarization anisotropy be corrected for the effects of fractional photolysis in an optically thick sample. The experimental method measures the direction of the transition dipole, which is parallel to the CO bond axis when docked and nearly parallel when bound to the heme. The polarization anisotropy of bound CO is virtually the same for all protein systems investigated and is unchanging across its inhomogeneously broadened mid-IR absorption spectrum. From these results, it was concluded that the transition dipole moment of bound CO is oriented </=7 degrees from the heme plane normal. The polarized absorbance spectra of docked CO are similar for all protein systems investigated, but in stark contrast to bound CO, the polarization anisotropy is strongly correlated with vibrational frequency. The frequency-dependent anisotropy imposes severe constraints on the orientational probability distribution function of the transition dipole, which is well described as a dipole bathed in a Stark field whose out-of-plane motion is constrained by a simple double-well potential. The orientational and spatial constraints imposed on docked CO by the surrounding highly conserved amino acids serve to mediate ligand transport to and from the binding site and thereby control the rates and pathways for geminate ligand rebinding and ligand escape.
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Affiliation(s)
- Manho Lim
- Department of Chemistry, Pusan National University, Busan, 609-735, Korea
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10
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Affiliation(s)
- Christian Bressler
- Laboratoire de Spectroscopie Ultrarapide, ISIC-FSB-BSP, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
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11
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Frenkel AI, Kleifeld O, Wasserman SR, Sagi I. Phase speciation by extended x-ray absorption fine structure spectroscopy. J Chem Phys 2002. [DOI: 10.1063/1.1473193] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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12
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Metzler DE, Metzler CM, Sauke DJ. How Macromolecules Associate. Biochemistry 2001. [DOI: 10.1016/b978-012492543-4/50010-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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13
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Edwards AM, Zhang K, Nordgren CE, Blasie JK. Heme structure and orientation in single monolayers of cytochrome c on polar and nonpolar soft surfaces. Biophys J 2000; 79:3105-17. [PMID: 11106616 PMCID: PMC1301187 DOI: 10.1016/s0006-3495(00)76545-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Polarized x-ray absorption fine structure (XAFS) spectroscopy has been performed in fluorescence mode under total external reflection conditions on frozen hydrated single monolayers of yeast cytochrome c (YCC). The protein molecules were vectorially oriented within the monolayer by tethering their naturally occurring and unique surface cysteine residues to the sulfhydryl-endgroups at the surface of a mixed organic self-assembled monolayer, itself covalently attached to an ultrapure silicon wafer. The sulfhydryl-endgroups were isolated by dilution with either methyl- or hydroxyl-endgroups, producing macroscopically nonpolar or uncharged-polar soft surfaces, respectively. Independent information on the heme-plane orientation relative to the monolayer plane was obtained experimentally via optical linear dichroism. The polarized XAFS data have been analyzed both qualitatively and by a global mapping approach limited to systematically altering the various iron-ligand distances within a model for the local atomic environment of the heme prosthetic group, and comparing the theoretically generated XAFS spectra with those obtained experimentally. A similar analysis of unpolarized XAFS data from a frozen solution of YCC was performed using either the heme environment from the NMR solution or the x-ray crystallographic data for YCC as the model structure. All resulting iron-ligand distances were then used in molecular dynamics (MD) computer simulations of YCC in these three systems to investigate the possible effects of anisotropic ligand motions on the fits of the calculated to the experimental XAFS spectra.
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Affiliation(s)
- A M Edwards
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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14
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Franzen S, Boxer SG, Dyer RB, Woodruff WH. Resonance Raman Studies of Heme Axial Ligation in H93G Myoglobin. J Phys Chem B 2000. [DOI: 10.1021/jp001231v] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Stefan Franzen
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695-8420, Department of Chemistry, Stanford University, Stanford, California 94305, and Bioscience and Biotechnology Group, Los Alamos National Laboratory, Los Alamos, New Mexico 87545
| | - Steven G. Boxer
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695-8420, Department of Chemistry, Stanford University, Stanford, California 94305, and Bioscience and Biotechnology Group, Los Alamos National Laboratory, Los Alamos, New Mexico 87545
| | - R. Brian Dyer
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695-8420, Department of Chemistry, Stanford University, Stanford, California 94305, and Bioscience and Biotechnology Group, Los Alamos National Laboratory, Los Alamos, New Mexico 87545
| | - William H. Woodruff
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695-8420, Department of Chemistry, Stanford University, Stanford, California 94305, and Bioscience and Biotechnology Group, Los Alamos National Laboratory, Los Alamos, New Mexico 87545
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15
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Cheng MC, Rich AM, Armstrong RS, Ellis PJ, Lay PA. Determination of Iron−Ligand Bond Lengths in Ferric and Ferrous Horse Heart Cytochrome c Using Multiple-Scattering Analyses of XAFS Data. Inorg Chem 1999. [DOI: 10.1021/ic990395r] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ming-Chu Cheng
- School of Chemistry, University of Sydney, Sydney, NSW 2006, Australia
| | - Anne M. Rich
- School of Chemistry, University of Sydney, Sydney, NSW 2006, Australia
| | | | - Paul J. Ellis
- School of Chemistry, University of Sydney, Sydney, NSW 2006, Australia
| | - Peter A. Lay
- School of Chemistry, University of Sydney, Sydney, NSW 2006, Australia
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16
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Abstract
X-ray absorption near-edge structure (XANES) spectra of ferric myoglobin from horse heart have been acquired as a function of pH (between 5.3 and 11.3). At pH = 11.3 temperature-dependent spectra (between 20 and 293 K) have been collected as well. Experimental data solve three main conformations of the Fe-heme: the first, at low pH, is related to high-spin aquomet-myoglobin (Mb+OH2). The other two, at pH 11.3, are related to hydroxymet-myoglobin (Mb+OH-), and are in thermal equilibrium, corresponding to high- and low-spin Mb+OH-. The structure of the three Fe-heme conformations has been assigned according to spin-resolved multiple scattering simulations and fitting of the XANES data. The chemical transition between Mb+OH2 and high-spin Mb+OH-, and the spin transition of Mb+OH-, are accompanied by changes of the Fe coordination sphere due to its movement toward the heme plane, coupled to an increase of the axial asymmetry.
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Affiliation(s)
- S Della Longa
- Dept. Medicina Sperimentale and INFM, Università dell'Aquila, I-67100 L'Aquila and Ist. Naz. Fisica Materia (INFM), Italy. dellalongo@vaxaq
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17
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Lee HC, Scheuring E, Peisach J, Chance MR. Electron Spin Echo Envelope Modulation and Extended X-ray Absorption Fine Structure Studies of Active Site Models of Oxygenated Cobalt-Substituted Hemoproteins: Correlating Electron-Nuclear Couplings and Metal−Ligand Bond Lengths. J Am Chem Soc 1997. [DOI: 10.1021/ja9717166] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- H. Caroline Lee
- Contribution from the Department of Physiology and Biophysics, Center for Synchrotron Biosciences, and Biotechnology Resource in Pulsed EPR Spectroscopy, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York 10461
| | - Eva Scheuring
- Contribution from the Department of Physiology and Biophysics, Center for Synchrotron Biosciences, and Biotechnology Resource in Pulsed EPR Spectroscopy, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York 10461
| | - Jack Peisach
- Contribution from the Department of Physiology and Biophysics, Center for Synchrotron Biosciences, and Biotechnology Resource in Pulsed EPR Spectroscopy, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York 10461
| | - Mark R. Chance
- Contribution from the Department of Physiology and Biophysics, Center for Synchrotron Biosciences, and Biotechnology Resource in Pulsed EPR Spectroscopy, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York 10461
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18
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Scheuring E, Padmakumar R, Banerjee R, Chance MR. Extended X-ray Absorption Fine Structure Analysis of Coenzyme B12 Bound to Methylmalonyl-Coenzyme A Mutase Using Global Mapping Techniques. J Am Chem Soc 1997. [DOI: 10.1021/ja9635239] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Eva Scheuring
- Center for Synchrotron Biosciences, Department of Physiology and Biophysics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, and Department of Biochemistry, University of Nebraska, Lincoln, Nebraska 68588-0664
| | - Rugmini Padmakumar
- Center for Synchrotron Biosciences, Department of Physiology and Biophysics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, and Department of Biochemistry, University of Nebraska, Lincoln, Nebraska 68588-0664
| | - Ruma Banerjee
- Center for Synchrotron Biosciences, Department of Physiology and Biophysics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, and Department of Biochemistry, University of Nebraska, Lincoln, Nebraska 68588-0664
| | - Mark R. Chance
- Center for Synchrotron Biosciences, Department of Physiology and Biophysics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, and Department of Biochemistry, University of Nebraska, Lincoln, Nebraska 68588-0664
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Wang H, Peng G, Miller LM, Scheuring EM, George SJ, Chance MR, Cramer SP. Iron L-Edge X-ray Absorption Spectroscopy of Myoglobin Complexes and Photolysis Products. J Am Chem Soc 1997. [DOI: 10.1021/ja961446b] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hongxin Wang
- Contribution from the Energy and Environment Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, Department of Applied Science, University of California, Davis, California 95616, and Department of Physiology and Biophysics, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York 10461
| | - Gang Peng
- Contribution from the Energy and Environment Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, Department of Applied Science, University of California, Davis, California 95616, and Department of Physiology and Biophysics, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York 10461
| | - Lisa M. Miller
- Contribution from the Energy and Environment Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, Department of Applied Science, University of California, Davis, California 95616, and Department of Physiology and Biophysics, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York 10461
| | - Eva M. Scheuring
- Contribution from the Energy and Environment Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, Department of Applied Science, University of California, Davis, California 95616, and Department of Physiology and Biophysics, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York 10461
| | - S. J. George
- Contribution from the Energy and Environment Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, Department of Applied Science, University of California, Davis, California 95616, and Department of Physiology and Biophysics, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York 10461
| | - Mark R. Chance
- Contribution from the Energy and Environment Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, Department of Applied Science, University of California, Davis, California 95616, and Department of Physiology and Biophysics, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York 10461
| | - Stephen P. Cramer
- Contribution from the Energy and Environment Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, Department of Applied Science, University of California, Davis, California 95616, and Department of Physiology and Biophysics, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York 10461
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Lim M, Jackson TA, Anfinrud PA. Ultrafast rotation and trapping of carbon monoxide dissociated from myoglobin. NATURE STRUCTURAL BIOLOGY 1997; 4:209-14. [PMID: 9164462 DOI: 10.1038/nsb0397-209] [Citation(s) in RCA: 170] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The nature of ligand motion within proteins has been investigated by measuring femtosecond time-resolved infrared (IR) spectra of CO photodissociated from the haem of myoglobin. Upon dissociation, the CO rotates approximately 90 degrees and becomes trapped within a ligand docking site located near the binding site. Two trajectories, distinguished spectroscopically and kinetically with time constants of 0.20 +/- 0.05 ps and 0.52 +/- 0.10 ps, lead to CO located within the docking site with opposite orientations. The protein reorganizes about the "docked' CO with a time constant of 1.6 +/- 0.3 ps and quickly establishes an energetic barrier that inhibits the reverse rebinding process.
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Affiliation(s)
- M Lim
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
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