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Andrew CR, Petrova ON, Lamarre I, Lambry JC, Rappaport F, Negrerie M. The Dynamics Behind the Affinity: Controlling Heme-Gas Affinity via Geminate Recombination and Heme Propionate Conformation in the NO Carrier Cytochrome c'. ACS Chem Biol 2016; 11:3191-3201. [PMID: 27709886 DOI: 10.1021/acschembio.6b00599] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nitric oxide (NO) sensors are heme proteins which may also bind CO and O2. Control of heme-gas affinity and their discrimination are achieved by the structural properties and reactivity of the heme and its distal and proximal environments, leading to several energy barriers. In the bacterial NO sensor cytochrome c' from Alcaligenes xylosoxidans (AXCP), the single Leu16Ala distal mutation boosts the affinity for gas ligands by a remarkable 106-108-fold, transforming AXCP from one of the lowest affinity gas binding proteins to one of the highest. Here, we report the dynamics of diatomics after photodissociation from wild type and L16A-AXCP over 12 orders of magnitude in time. For the L16A variant, the picosecond geminate rebinding of both CO and NO appears with an unprecedented 100% yield, and no exit of these ligands from protein to solvent could be observed. Molecular dynamic simulations saliently demonstrate that dissociated CO stays within 4 Å from Fe2+, in contrast to wild-type AXCP. The L16A mutation confers a heme propionate conformation and docking site which traps the diatomics, maximizing the probability of recombination and directly explaining the ultrahigh affinities for CO, NO, and O2. Overall, our results point to a novel mechanism for modulating heme-gas affinities in proteins.
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Affiliation(s)
- Colin R. Andrew
- Department
of Chemistry and Biochemistry, Eastern Oregon University, La Grande, Oregon 97850, United States
| | - Olga N. Petrova
- Laboratoire
d’Optique et Biosciences, INSERM, Ecole Polytechnique, 91128 Palaiseau, France
| | - Isabelle Lamarre
- Laboratoire
d’Optique et Biosciences, INSERM, Ecole Polytechnique, 91128 Palaiseau, France
| | - Jean-Christophe Lambry
- Laboratoire
d’Optique et Biosciences, INSERM, Ecole Polytechnique, 91128 Palaiseau, France
| | - Fabrice Rappaport
- Laboratoire
de Physiologie Membranaire et Moléculaire du Chloroplaste, CNRS, Université Pierre et Marie Curie, 75005 Paris, France
| | - Michel Negrerie
- Laboratoire
d’Optique et Biosciences, INSERM, Ecole Polytechnique, 91128 Palaiseau, France
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2
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Nishimura R, Shibata T, Ishigami I, Ogura T, Tai H, Nagao S, Matsuo T, Hirota S, Shoji O, Watanabe Y, Imai K, Neya S, Suzuki A, Yamamoto Y. Electronic Control of Discrimination between O2 and CO in Myoglobin Lacking the Distal Histidine Residue. Inorg Chem 2013; 53:1091-9. [DOI: 10.1021/ic402625s] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ryu Nishimura
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Tomokazu Shibata
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Izumi Ishigami
- Department of Life Science, Graduate
School of Life Science, University of Hyogo, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
| | - Takashi Ogura
- Department of Life Science, Graduate
School of Life Science, University of Hyogo, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
| | - Hulin Tai
- Graduate School of Materials Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Satoshi Nagao
- Graduate School of Materials Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Takashi Matsuo
- Graduate School of Materials Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Shun Hirota
- Graduate School of Materials Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Osami Shoji
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Yoshihito Watanabe
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Kiyohiro Imai
- Department of Frontier Bioscience, Faculty
of Bioscience and Applied Chemistry, Hosei University, Koganei, Tokyo 184-8584, Japan
| | - Saburo Neya
- Department of Physical Chemistry, Graduate
School of Pharmaceutical Sciences, Chiba University, Chuoh-Inohana, Chiba 260-8675, Japan
| | - Akihiro Suzuki
- Department of Materials Engineering, Nagaoka National College of Technology, Nagaoka 940-8532, Japan
| | - Yasuhiko Yamamoto
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
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3
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Terazima M. Ligand Dissociation Process from Myoglobin Monitored by the Time-Resolved Volume Change. J CHIN CHEM SOC-TAIP 2013. [DOI: 10.1002/jccs.200600029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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4
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El-Mashtoly SF, Nakashima S, Tanaka A, Shimizu T, Kitagawa T. Roles of Arg-97 and Phe-113 in Regulation of Distal Ligand Binding to Heme in the Sensor Domain of Ec DOS Protein. J Biol Chem 2008; 283:19000-10. [DOI: 10.1074/jbc.m801262200] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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Yamashita T, Hoashi Y, Tomisugi Y, Ishikawa Y, Uno T. The C-helix in CooA Rolls upon CO Binding to Ferrous Heme. J Biol Chem 2004; 279:47320-5. [PMID: 15326178 DOI: 10.1074/jbc.m407766200] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
CooA is a homodimeric transcriptional activator from Rhodospirillum rubrum containing one heme in each subunit. CO binding to the heme in its sensor domain activates CooA, facilitating the binding to DNA by its DNA-binding domain. The C-helix links the two domains and shapes an interface between the subunits. To probe the nature of CO activation, residues at positions 112-121 on the C-helix were replaced by Asn or Gln and their effects were evaluated by resonance Raman spectroscopy and by the measurements of CO binding affinity. The nu(Fe-CO) stretching Raman line in CO-bound wild-type CooA was up-shifted by 6 cm(-1) in the L116Q, G117N, and L120Q mutants, indicating unequivocally that these residues are close to the bound CO. Residues Leu116 and Leu120 from each subunit form contacts with the corresponding residues in the opposite subunit, enabling hydrophobic interactions in the inactive ferrous form. Thus, in the CO-bound activated form, both C-helices appear to roll to direct these residues toward the heme, forming a hydrophobic pocket for the bound CO. The CO affinity is approximately one order of magnitude higher in the L112Q, I115Q, L116Q, G117N, L120Q, and T121N mutants but reduced in A114N mutant. The variation indicates that these residues are close to the heme in the ferrous and/or CO-bound forms and are responsible for CooA activation. A roll-and-slide mechanism is proposed for CO activation of CooA.
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Affiliation(s)
- Taku Yamashita
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Oehonmachi, Kumamoto 862-0973, Japan
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6
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Nishihara Y, Sakakura M, Kimura Y, Terazima M. The Escape Process of Carbon Monoxide from Myoglobin to Solution at Physiological Temperature. J Am Chem Soc 2004; 126:11877-88. [PMID: 15382923 DOI: 10.1021/ja038877w] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The carbon monoxide (CO) docking sites involved in the ligand escape process from the iron atom in hem of myoglobin (Mb) to solution at physiological temperature were studied on the basis of the effect of xenon (Xe) on the ligand escape rate by the transient grating (TG) technique. The TG method provides a direct measurement of the changes in molecular volume. The apparent CO escaping rate and the volume contraction increase with increasing Xe pressure. The pressure dependence of the rate is consistent with that of the Xe population at the Xe(1) site. This result clearly shows that CO is trapped at the Xe(1) site before escaping to solvent in a Xe-free solution at room temperature. It is shown that only CO but not the trapped Xe is released by the photoexcitation of the Xe-trapped MbCO. A dissociation scheme is proposed to explain the enhancement of the escaping rate by the presence of Xe(1). There are two branches for the CO escaping pathway. The dominant part of the dissociated CO escapes to the solvent through the Xe(1) trapping site under the Xe-free condition, and there are at least three intermediate states along this pathway. When a Xe atom blocks the Xe(1) site, the CO escapes through another route.
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Affiliation(s)
- Yasutaka Nishihara
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, 606-8502, Japan
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7
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Terazima M. Time-Resolved Thermodynamic Properties of Intermediate Species during Photochemical Reactions. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2004. [DOI: 10.1246/bcsj.77.23] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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8
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Takahashi T, Ogura T. Resonance Raman Spectra of CytochromecOxidase in Whole Mitochondria. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2002. [DOI: 10.1246/bcsj.75.1001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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9
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Hirota S, Kishi M, Yamauchi O, Wang YH, Huang ZX. Carbon monoxide complex of cytochrome b(5) at acidic pH. Biochem Biophys Res Commun 2001; 282:351-5. [PMID: 11264014 DOI: 10.1006/bbrc.2001.4544] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
CO complex of cyt b(5) generated at acidic pH is investigated by absorption, resonance Raman (RR), and far UV CD measurements. The Soret maximum wavelength blue-shifted to 420 nm with other absorption bands observed around 540 and 570 nm for reduced cyt b(5) upon interaction with CO at acidic pH (pH 3.1-3.5). Under this condition, the iron-carbon stretching RR band was observed at 529 cm(-1) (520 cm(-1) for C(18)O), which indicated formation of a heme&bond;CO adduct with a histidine as an axial ligand. Heme dissociated from the reduced cyt b(5) protein at pH approximately 3.5, whereas its rate decreased under CO atmosphere compared with N(2) atmosphere, due to formation of a heme&bond;CO adduct with a histidine as an axial ligand.
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Affiliation(s)
- S Hirota
- Department of Chemistry, Research Center for Materials Science, Nagoya University, Chikusa-ku, Nagoya, 464-8602, Japan.
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10
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Das TK, Couture M, Guertin M, Rousseau DL. Distal Interactions in the Cyanide Complex of Ferric Chlamydomonas Hemoglobin. J Phys Chem B 2000. [DOI: 10.1021/jp000452y] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tapan Kanti Das
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, and Department of Biochemistry and Microbiology, Faculty of Sciences and Engineering, Laval University, Quebec, G1K 7P4, Canada
| | - Manon Couture
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, and Department of Biochemistry and Microbiology, Faculty of Sciences and Engineering, Laval University, Quebec, G1K 7P4, Canada
| | - Michel Guertin
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, and Department of Biochemistry and Microbiology, Faculty of Sciences and Engineering, Laval University, Quebec, G1K 7P4, Canada
| | - Denis L. Rousseau
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, and Department of Biochemistry and Microbiology, Faculty of Sciences and Engineering, Laval University, Quebec, G1K 7P4, Canada
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11
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Tomita T, Hirota S, Ogura T, Olson JS, Kitagawa T. Resonance Raman Investigation of Fe−N−O Structure of Nitrosylheme in Myoglobin and Its Mutants. J Phys Chem B 1999. [DOI: 10.1021/jp991106n] [Citation(s) in RCA: 73] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Takeshi Tomita
- The Graduate University for Advanced Studies and Institute for Molecular Science, Okazaki National Research Institutes, Myodaiji, Okazaki, 444-8585 Japan, and Department of Biochemistry and Cell Biology, Rice University, Houston, Texas 77005-1892
| | - Shun Hirota
- The Graduate University for Advanced Studies and Institute for Molecular Science, Okazaki National Research Institutes, Myodaiji, Okazaki, 444-8585 Japan, and Department of Biochemistry and Cell Biology, Rice University, Houston, Texas 77005-1892
| | - Takashi Ogura
- The Graduate University for Advanced Studies and Institute for Molecular Science, Okazaki National Research Institutes, Myodaiji, Okazaki, 444-8585 Japan, and Department of Biochemistry and Cell Biology, Rice University, Houston, Texas 77005-1892
| | - John S. Olson
- The Graduate University for Advanced Studies and Institute for Molecular Science, Okazaki National Research Institutes, Myodaiji, Okazaki, 444-8585 Japan, and Department of Biochemistry and Cell Biology, Rice University, Houston, Texas 77005-1892
| | - Teizo Kitagawa
- The Graduate University for Advanced Studies and Institute for Molecular Science, Okazaki National Research Institutes, Myodaiji, Okazaki, 444-8585 Japan, and Department of Biochemistry and Cell Biology, Rice University, Houston, Texas 77005-1892
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12
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The temperature dependence of the kinetics of cyanide dissociation from the cyanide complex of myoglobin studied by cyclic voltammetry. J Electroanal Chem (Lausanne) 1999. [DOI: 10.1016/s0022-0728(99)00142-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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13
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Mukai M, Nakashima S, Olson JS, Kitagawa T. Time-Resolved UV Resonance Raman Detection of a Transient Open Form of the Ligand Pathway in Tyr64(E7) Myoglobin. J Phys Chem B 1998. [DOI: 10.1021/jp980070g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Masahiro Mukai
- Institute for Molecular Science, Okazaki National Research Institutes, Myodaiji, Okazaki, 444 Japan, and Department of Biochemistry and Cell Biology, Rice University, Houston, Texas 77251, U.S.A
| | - Satoru Nakashima
- Institute for Molecular Science, Okazaki National Research Institutes, Myodaiji, Okazaki, 444 Japan, and Department of Biochemistry and Cell Biology, Rice University, Houston, Texas 77251, U.S.A
| | - John S. Olson
- Institute for Molecular Science, Okazaki National Research Institutes, Myodaiji, Okazaki, 444 Japan, and Department of Biochemistry and Cell Biology, Rice University, Houston, Texas 77251, U.S.A
| | - Teizo Kitagawa
- Institute for Molecular Science, Okazaki National Research Institutes, Myodaiji, Okazaki, 444 Japan, and Department of Biochemistry and Cell Biology, Rice University, Houston, Texas 77251, U.S.A
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14
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Cohen DJ, King BC, Hawkridge FM. Spectroelectrochemical and electrochemical determination of ligand binding and electron transfer properties of myoglobin, cyanomyoglobin, and imidazolemyoglobin. J Electroanal Chem (Lausanne) 1998. [DOI: 10.1016/s0022-0728(98)00020-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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15
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Nakashima S, Kitagawa T, Olson JS. Time-resolved resonance Raman study of intermediates generated after photodissociation of wild-type and mutant co-myoglobins. Chem Phys 1998. [DOI: 10.1016/s0301-0104(97)00353-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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16
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Ma J, Huo S, Straub JE. Molecular Dynamics Simulation Study of the B-States of Solvated Carbon Monoxymyoglobin. J Am Chem Soc 1997. [DOI: 10.1021/ja9608252] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jianpeng Ma
- Contribution from the Department of Chemistry, Boston University, Boston, Massachusetts 02215
| | - Shuanghong Huo
- Contribution from the Department of Chemistry, Boston University, Boston, Massachusetts 02215
| | - John E. Straub
- Contribution from the Department of Chemistry, Boston University, Boston, Massachusetts 02215
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17
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Anderton CL, Hester RE, Moore JN. A chemometric analysis of the resonance Raman spectra of mutant carbonmonoxy-myoglobins reveals the effects of polarity. BIOCHIMICA ET BIOPHYSICA ACTA 1997; 1338:107-20. [PMID: 9074621 DOI: 10.1016/s0167-4838(96)00194-x] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Resonance Raman spectra of 10 carbonmonoxy-myoglobins have been obtained, including sperm whale native, pig wild-type, and the mutants H64L, H64A, V68T, V68N, H64V/V68T, F43W, F46V, and L29F. This series was chosen in order to study the effect of ligand binding pocket polarity on the positions of the v(Fe-CO) and delta (Fe-C-O) bands. Spectra of both 12CO and 13CO isotopic forms have been obtained and a detailed analysis has facilitated the identification of both the ligand-specific bands and six underlying porphyrin bands which are insensitive to this isotopic substitution. Along with a band-fitting analysis of infrared spectra, these resonance Raman data provide a comprehensive evaluation of the vibrations of the FeCO unit. The band positions of the ligand-specific modes are found to depend on the structure of the ligand binding pocket, arising from the strength of back-bonding within the FeCO unit, and clear correlations exist between the v(Fe-CO), delta (Fe-C-O), and v(C-O) band positions which characterize this synergic bonding. The results are consistent with the proposal that the vibration band positions are determined primarily by the electrostatic potential at the ligand. Five discrete band sets are observed for this set of mutants, suggesting that 5 discrete conformations occur.
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18
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Kushkuley B, Stavrov SS. Theoretical study of the electrostatic and steric effects on the spectroscopic characteristics of the metal-ligand unit of heme proteins. 2. C-O vibrational frequencies, 17O isotropic chemical shifts, and nuclear quadrupole coupling constants. Biophys J 1997; 72:899-912. [PMID: 9017215 PMCID: PMC1185613 DOI: 10.1016/s0006-3495(97)78724-1] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The quantum chemical calculations, vibronic theory of activation, and London-Pople approach are used to study the dependence of the C-O vibrational frequency, 17O isotropic chemical shift, and nuclear quadrupole coupling constant on the distortion of the porphyrin ring and geometry of the CO coordination, changes in the iron-carbon and iron-imidazole distances, magnitude of the iron displacement out of the porphyrin plane, and presence of the charged groups in the heme environment. It is shown that only the electrostatic interactions can cause the variation of all these parameters experimentally observed in different heme proteins, and the heme distortions could modulate this variation. The correlations between the theoretically calculated parameters are shown to be close to the experimentally observed ones. The study of the effect of the electric field of the distal histidine shows that the presence of the four C-O vibrational bands in the infrared absorption spectra of the carbon monoxide complexes of different myoglobins and hemoglobins can be caused by the different orientations of the different tautomeric forms of the distal histidine. The dependence of the 17O isotropic chemical shift and nuclear quadrupole coupling constant on pH and the distal histidine substitution can be also explained from the same point of view.
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Affiliation(s)
- B Kushkuley
- Sackler Institute of Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Ramat Aviv, Israel
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19
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Kiger L, Baudin V, Desbois A, Pagnier J, Kister J, Griffon N, Henry Y, Poyart C, Marden MC. Recombinant [Phe(beta)63]hemoglobin shows rapid oxidation of the beta chains and low-affinity, non-cooperative oxygen binding to the alpha subunits. EUROPEAN JOURNAL OF BIOCHEMISTRY 1997; 243:365-73. [PMID: 9030761 DOI: 10.1111/j.1432-1033.1997.0365a.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
We have engineered alpha2beta2 [Phe63]hemoglobin by changing the highly conserved distal histidine of the beta chains to a phenylalanine. The mutant tetramer binds four high-affinity ligands, such as CO or NO, to the ferrous form, or CN to the oxidized iron; however, it binds only two low-affinity ligands, oxygen and azide. The absorption spectrum of the ferrous deoxy or ferric forms are not normal, displaying an enhanced absorption of the visible band near 560 nm. Half of the autooxidation process, attributed to the mutated beta subunits, is over 1000-fold faster than for Hb A. The mutant Hb exhibits non-cooperative binding of two oxygens with an affinity about fivefold lower than those of HbA valency hybrids (alpha met beta)2. Functional properties of this mutant Hb resemble those of Hb Saskatoon ([Tyr63]Hb) [Suzuki, T., Hayashi, A., Shimizu, A. & Yamamura, Y. (1966) Biochim. Biophys. Acta 127, 280-282]. Flash-photolysis experiments also indicate non-cooperative behaviour: the CO-recombination kinetics were independent of the fraction dissociated. Furthermore, the amplitude of the CO bimolecular phase was the same for the (alpha(CO)metbeta)2 valency hybrid or the (alphaCO betaCO)2 form, suggesting mainly geminate CO-recombination kinetics to the beta chains. EPR and Resonance Raman spectra did not show evidence for a hemichrome, normally considered as a six-coordinated iron with low-spin character. The EPR and resonance Raman spectra for the mutated beta subunits demonstrate the presence of a high-spin compound in the ferric and deoxy ferrous forms. In particular, the ferrous mutated beta subunits are penta-coordinated. The abnormal absorption spectra are possibly due to an interaction between the porphyrin and the phenyl ring in the distal position rather than to direct binding to the iron.
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Affiliation(s)
- L Kiger
- INSERM U299, Hôpital de Bicêtre, Le Kremlin-Bicêtre, France
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20
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Chen E, Goldbeck RA, Kliger DS. Nanosecond time-resolved spectroscopy of biomolecular processes. ANNUAL REVIEW OF BIOPHYSICS AND BIOMOLECULAR STRUCTURE 1997; 26:327-55. [PMID: 9241422 DOI: 10.1146/annurev.biophys.26.1.327] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Over the past two decades, nanosecond absorption and vibrational spectroscopies have developed into powerful tools for monitoring the secondary, tertiary, and quaternary structural relaxations of biological macromolecules under near-physiological conditions of solvent and temperature. Observed through such methods, the dynamic response of a biomolecule to photoinitiated excursions from equilibrium can reveal valuable information about the structure-function relationship, information beyond that obtained from the static structures provided by X-ray crystallography, nuclear magnetic resonance spectroscopy, and other steady-state methods. Most recently, the development of ultra-sensitive polarization techniques for absorption spectroscopy has greatly enhanced the amount of time-resolved structural information that can be obtained from the broadened electronic spectra of biomolecules. This review examines nanosecond absorption, vibrational, and polarized absorption methods, and their applications to protein function and folding, emphasizing the complementary nature of information obtained from electronic and vibrational spectra measured on the nanosecond time scale.
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Affiliation(s)
- E Chen
- Department of Chemistry and Biochemistry, University of California, Santa Cruz 95064, USA
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21
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Hirota S, Li T, Phillips, GN, Olson JS, Mukai M, Kitagawa T. Perturbation of the Fe−O2 Bond by Nearby Residues in Heme Pocket: Observation of νFe-O2 Raman Bands for Oxymyoglobin Mutants. J Am Chem Soc 1996. [DOI: 10.1021/ja9608297] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shun Hirota
- Institute for Molecular Science Okazaki National Research Institutes Myodaiji, Okazaki, 444 Japan Department of Biochemistry and Cell Biology and The W. M. Keck Center for Computational Biology Rice University, Houston, Texas 77005-1892
| | - Tiansheng Li
- Institute for Molecular Science Okazaki National Research Institutes Myodaiji, Okazaki, 444 Japan Department of Biochemistry and Cell Biology and The W. M. Keck Center for Computational Biology Rice University, Houston, Texas 77005-1892
| | - George N. Phillips,
- Institute for Molecular Science Okazaki National Research Institutes Myodaiji, Okazaki, 444 Japan Department of Biochemistry and Cell Biology and The W. M. Keck Center for Computational Biology Rice University, Houston, Texas 77005-1892
| | - John S. Olson
- Institute for Molecular Science Okazaki National Research Institutes Myodaiji, Okazaki, 444 Japan Department of Biochemistry and Cell Biology and The W. M. Keck Center for Computational Biology Rice University, Houston, Texas 77005-1892
| | - Masahiro Mukai
- Institute for Molecular Science Okazaki National Research Institutes Myodaiji, Okazaki, 444 Japan Department of Biochemistry and Cell Biology and The W. M. Keck Center for Computational Biology Rice University, Houston, Texas 77005-1892
| | - Teizo Kitagawa
- Institute for Molecular Science Okazaki National Research Institutes Myodaiji, Okazaki, 444 Japan Department of Biochemistry and Cell Biology and The W. M. Keck Center for Computational Biology Rice University, Houston, Texas 77005-1892
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Leclerc-L'Hostis E, Franzen S, Lambry JC, Martin JL, Leclerc L, Poyart C, Marden MC. Picosecond geminate recombination of CO to the complexes calmodulin*heme-CO and calmodulin*heme-CO*melittin. BIOCHIMICA ET BIOPHYSICA ACTA 1996; 1293:140-6. [PMID: 8652619 DOI: 10.1016/0167-4838(95)00237-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Picosecond CO recombination kinetics have been measured after photodissociation of the artificial complexes calmodulin*heme-CO and calmodulin*heme-CO*melittin. These systems show an enhancement of the geminate fraction of kinetics relative to unbound heme-CO, due in part to fast geminate kinetics (tau=50ps for the initial phase), as well as a decrease in the rate of migration of CO away from the binding site. This indicates that calmodulin provides a complete pocket around the heme group. Rather than competing with the hemes for binding to calmodulin, the melittin seems to act as a cap to further enclose the hemes; melittin increases the affinity of calmodulin for heme-CO, but only weakly affects the CO recombination kinetics.
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23
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Kushkuley B, Stavrov SS. Theoretical study of the distal-side steric and electrostatic effects on the vibrational characteristics of the FeCO unit of the carbonylheme proteins and their models. Biophys J 1996; 70:1214-29. [PMID: 8785279 PMCID: PMC1225049 DOI: 10.1016/s0006-3495(96)79680-7] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The vibronic theory of activation and quantum chemical intermediate neglect of differential overlap (INDO) calculations are used to study the activation of carbon monoxide (change of the C-O bond index and force field constant) by the imidazole complex with heme in dependence on the distortion of the porphyrin ring, geometry of the CO coordination, iron-carbon and iron-imidazole distances, iron displacement out of the porphyrin plane, and presence of the charged groups in the heme environment. It is shown that the main contribution to the CO activation stems from the change in the sigma donation from the 5 sigma CO orbital to iron, and back-bonding from the iron to the 2 pi orbital of CO. It follows from the results that none of the studied distortions can explain, by itself, the wide variation of the C-O vibrational frequency in the experimentally studied model compounds and heme proteins. To study the dependence of the properties of the FeCO unit on the presence of charged groups in the heme environment, the latter are simulated by the homogeneous electric field and point charges of different magnitude and location. The results show that charged groups can strongly affect the strength of the C-O bond and its vibrational frequency. It is found that the charges located on the distal side of the heme plane can affect the Fe-C and C-O bond indexes (and, consequently, the Fe-C and C-O vibrational frequencies), both in the same and in opposite directions, depending on their position. The theoretical results allow us to understand the peculiarities of the effect of charged groups on the properties of the FeCO unit both in heme proteins and in their model compounds.
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Affiliation(s)
- B Kushkuley
- Sackler Institute of Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Israel
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24
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Deinum G, Stone JR, Babcock GT, Marletta MA. Binding of nitric oxide and carbon monoxide to soluble guanylate cyclase as observed with Resonance raman spectroscopy. Biochemistry 1996; 35:1540-7. [PMID: 8634285 DOI: 10.1021/bi952440m] [Citation(s) in RCA: 126] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Resonance Raman spectra have been recorded for the ferrous heme of soluble guanylate cyclase (sGC), the only receptor known thus far for .NO. On the basis of the frequencies of porphyrin core sensitive vibrations in the high frequency region of the Raman spectrum, we conclude that the ferrous heme is five-coordinate, high spin, when no exogenous ligands are present. We assign a prominent vibration that occurs at 204 cm-1 in the reduced enzyme to the heme Fe(2+)-proximal histidine stretching vibration. In the .NO bound form of the enzyme, the heme Fe2+ retains a five-coordinate geometry. Assuming that .NO binds to the distal side of the heme, this observation indicates that the weak Fe-His bond breaks when .NO binds. Two isotope-sensitive vibrations are observed in the .NO bound enzyme, one at 1677 cm-1, attributed to the N-O stretching vibration, and one at 525 cm-1, attributed to the Fe-NO stretching vibration. When CO is bound to the ferrous heme, the heme ligation is six-coordinate. From this, we conclude that the Fe-His bond is still intact and that, if cleavage of the Fe-proximal ligand bond is necessary for complete activation of sGC, then CO should only weakly activate the enzyme, which has been shown to be the case. In the carbonmonoxy enzyme, the Fe-CO stretching vibration is observed at 472 cm-1 and the Fe-C-O bending vibration is detected at 562 cm-1. These frequencies are the lowest yet observed for the Fe-CO stretching and Fe-C-O bending modes in heme proteins or model systems with imidazole as the proximal ligand and suggest that there is significant negative polarity in the distal pocket. The negative polarity and the low frequency of the Fe-His stretching vibration may account for the very low O2 affinity of sGC.
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Affiliation(s)
- G Deinum
- Department of Chemistry, Michigan State University, East Lansing 48824-1322, USA
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25
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Navarro AM, Maldonado M, González-Lagoa J, López-Mejía R, López-Garriga J, Colón JL. Control of carbon monoxide binding states and dynamics in hemoglobin I of Lucina pectinata by nearby aromatic residues. Inorganica Chim Acta 1996. [DOI: 10.1016/0020-1693(95)04903-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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26
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Chen E, Kliger DS. Time-resolved near UV circular dichroism and absorption studies of carbonmonoxymyoglobin photolysis intermediates. Inorganica Chim Acta 1996. [DOI: 10.1016/0020-1693(95)04860-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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27
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Nakashima S, Kitagawa T, Olson JS. Time-resolved resonance raman study of the recombination dynamics photodissociated carbon monoxide to sperm whale myoglobin and its mutants. J Mol Liq 1995. [DOI: 10.1016/0167-7322(95)00822-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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28
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Bogumil R, Maurus R, Hildebrand DP, Brayer GD, Mauk AG. Origin of the pH-dependent spectroscopic properties of pentacoordinate metmyoglobin variants. Biochemistry 1995; 34:10483-90. [PMID: 7654702 DOI: 10.1021/bi00033a021] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The pH dependence of the electronic and EPR spectra of two variants of horse heart myoglobin (Mb) in which the distal His64 ligand has been replaced by either Thr or Ile has been studied. Both of these variants exhibit spectroscopic changes with pH that are indicative of a transition between two ferric high-spin forms that occurs with a pKa of 9.49 for the His64Thr variant and 9.26 for the His64Ile variant and that is distinctly different from the pH-dependent spectroscopic changes related to titration of the distal aquo ligand of wild-type Mb. The electronic and EPR spectra of both variants at all values of pH studied are consistent with the presence of a pentacoordinate heme iron center. For the His64Thr variant, a high-resolution (1.9 A) structure determination establishes the lack of the distal aquo ligand and demonstrates an out-of-plane movement of the ferric iron toward the proximal histidine together with a decrease of the Fe-His bond length. Investigation of this pH-linked equilibrium by EPR spectroscopy reveals rhombically split high-spin signals at both pH 7 and 11 with a greater degree of rhombicity exhibited by the alkaline species. We propose that the pH-linked spectroscopic transition exhibited by these distal histidine variants results from the deprotonation of the proximal His93 residue to produce imidazolate ligation at alkaline pH.
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Affiliation(s)
- R Bogumil
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada
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29
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Dou Y, Admiraal SJ, Ikeda-Saito M, Krzywda S, Wilkinson AJ, Li T, Olson JS, Prince RC, Pickering IJ, George GN. Alteration of axial coordination by protein engineering in myoglobin. Bisimidazole ligation in the His64-->Val/Val68-->His double mutant. J Biol Chem 1995; 270:15993-6001. [PMID: 7608158 DOI: 10.1074/jbc.270.27.15993] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Pig and human myoglobin have been engineered to reverse the positions of the distal histidine and valine (i.e. His64(E7)-->Val and Val68(E11)-->His). Spectroscopic and ligand binding properties have been measured for human and pig H64V/V68H myoglobin, and the structure of the pig H64V/V68H double mutant has been determined to 2.07-A resolution by x-ray crystallography. The crystal structure shows that the N epsilon of His68 is located 2.3 A away from the heme iron, resulting in the formation of a hexacoordinate species. The imidazole plane of His68 is tilted relative to the heme normal; moreover it is not parallel to that of His93, in agreement with our previous proposal (Qin, J., La Mar, G. N., Dou, Y., Admiraal, S. J., and Ikeda-Saito, M. (1994) J. Biol. Chem. 269, 1083-1090). At cryogenic temperatures, the heme iron is in a low spin state, which exhibits a highly anisotropic EPR spectrum (g1 = 3.34, g2 = 2.0, and g3 < 1), quite different from that of the imidazole complex of metmyoglobin. The mean iron-nitrogen distance is 2.01 A for the low spin ferric state as determined by x-ray spectroscopy. The ferrous form of H64V/V68H myoglobin shows an optical spectrum that is similar to that of b-type cytochromes and consistent with the hexacoordinate bisimidazole hemin structure determined by the x-ray crystallography. The double mutation lowers the ferric/ferrous couple midpoint potential from +54 mV of the wild-type protein to -128 mV. Ferrous H64V/V68H myoglobin binds CO and NO to form stable complexes, but its reaction with O2 results in a rapid autooxidation to the ferric species. All of these results demonstrate that the three-dimensional positions of His64 and Val68 in the wild-type myoglobin are as important as the chemical nature of the side chains in facilitating reversible O2 binding and inhibiting autooxidation.
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Affiliation(s)
- Y Dou
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106-4970, USA
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30
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Jewsbury P, Kitagawa T. Distal residue-CO interaction in carbonmonoxy myoglobins: a molecular dynamics study of three distal mutants. Biophys J 1995; 68:1283-94. [PMID: 7787018 PMCID: PMC1282024 DOI: 10.1016/s0006-3495(95)80302-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Six 90-ps molecular dynamics trajectories, two for each of three distal mutants of sperm whale carbonmonoxy myoglobin, are reported; solvent waters within 16 A of the active site have been included. In both His64GIn trajectories, the distal side chain remains part of the heme pocket, forming a "closed" conformation similar to that of the wild type 64N delta H tautomer. Despite a connectivity more closely resembling the N epsilon H histidine tautomer, close interactions with the carbonyl ligand similar to those observed for the wild type 64N epsilon H tautomer are prevented in this mutant by repulsive interactions between the carbonyl O and the 64O epsilon. The aliphatic distal side chain of the His64Leu mutant shows little interaction with the carbonyl ligand in either His64Leu trajectory. Solvent water molecules move into and out of the active site in the His64Gly mutant trajectories; during all the other carbonmonoxy myoglobin trajectories, including the wild type distal tautomers considered in an earlier work, solvent molecules rarely encroach closer than 6 A of the active site. These results are consistent with a recent structural interpretation of the wild type infrared spectrum, and the current reinterpretation that the distal-ligand interaction in carbonmonoxy myoglobin is largely electrostatic, not steric, in nature.
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Affiliation(s)
- P Jewsbury
- Institute for Molecular Science, Okazaki, Japan
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31
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Ling J, Li T, Olson JS, Bocian DF. Identification of the iron-carbonyl stretch in distal histidine mutants of carbonmonoxymyoglobin. BIOCHIMICA ET BIOPHYSICA ACTA 1994; 1188:417-21. [PMID: 7803455 DOI: 10.1016/0005-2728(94)90063-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Soret-excitation resonance Raman (RR) spectra are reported for six distal histidine mutants of carbonmonoxymyoglobin including H64A, H64V, H64L, H64I, H64W, and H64W/L29F. Based on 13CO isotope shifts, the iron-carbonyl stretching vibrations are unambiguously identified. The correct assignment of these modes eliminates the differences in the conformational substate occupations predicted by the RR versus IR data.
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Affiliation(s)
- J Ling
- Department of Chemistry, University of California, Riverside 92521-0403
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32
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Jewsbury P, Kitagawa T. The distal residue-CO interaction in carbonmonoxy myoglobins: a molecular dynamics study of two distal histidine tautomers. Biophys J 1994; 67:2236-50. [PMID: 7696465 PMCID: PMC1225607 DOI: 10.1016/s0006-3495(94)80708-8] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Four independent 90 ps molecular dynamics simulations of sperm-whale wild-type carbonmonoxy myoglobin (MbCO) have been calculated using a new AMBER force field for the haem prosthetic group. Two trajectories have the distal 64N delta nitrogen protonated, and two have the 64N epsilon nitrogen protonated; all water molecules within 16 A of the carbonyl O are included. In three trajectories, the distal residue remains part of the haem pocket, with the protonated distal nitrogen pointing into the active site. This is in contrast with the neutron diffraction crystal structure, but is consistent with the solution phase CO stretching frequencies (upsilon CO) of MbCO and various of its mutants. There are significant differences in the "closed" pocket structures found for each tautomer: the 64N epsilon H trajectories both show stable distal-CO interactions, whereas the 64N delta H tautomer) has a weaker interaction resulting in a more mobile distal side chain. One trajectory (a 64N delta H tautomer) has the distal histidine moving out into the "solvent", leaving the pocket in an "open" structure, with a large unhindered entrance to the active site. These trajectories suggest that the three upsilon CO frequencies observed for wild-type MbCO in solution, rather than representing significantly different Fe-C-O geometries as such, arise from three different haem pocket structures, each with different electric fields at the ligand. Each pocket structure corresponds to a different distal histidine conformer: the A3 band to the 64N epsilon H tautomer, the A1,2 band to the 64N delta H tautomer, and the A0 band to the absence of any significant interaction with the distal side chain.
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Affiliation(s)
- P Jewsbury
- Institute for Molecular Science, Okazaki, Japan
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33
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1H NMR investigation of distal mutant deoxy myoglobins. Interpretation of proximal His contact shifts in terms of a localized distal water molecule. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(18)43927-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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