Mapping the Pathways for O2 Entry Into and Exit from Myoglobin

Scott, Emily E.; Gibson, Quentin H.; Olson, John S.

doi:10.1074/jbc.m008282200

Cited by 356 publications

(630 citation statements)

References 55 publications

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“…A specific example of an important yet small conformational change controlling ligand access to the heme is that involving the distal histidine residue (72) and termed the His-gate in Mb (73). It has recently been estimated that for Mb essentially all CO exits via the His-gate following photodissociation from the heme iron (74,75). Our analysis of bimolecular CO binding suggests that a qualitatively similar (but far less efficient) mechanism may determine the CO escape yield from the distal pocket in cyt.…”

Section: Bimolecular Combination Of Gaseous Ligands With M80xmentioning

confidence: 99%

Ligand Dynamics in an Electron Transfer Protein

Silkstone

Jasaitis

Wilson

et al. 2007

Journal of Biological Chemistry

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Substitution of the heme coordination residue Met-80 of the electron transport protein yeast iso-1-cytochrome c allows external ligands like CO to bind and thus increase the effective redox potential. This mutation, in principle, turns the protein into a quasi-native photoactivable electron donor. We have studied the kinetic and spectral characteristics of geminate recombination of heme and CO in a series of single M80X (X ‫؍‬ Ala, Ser, Asp, Arg) mutants, using femtosecond transient absorption spectroscopy. In these proteins, all geminate recombination occurs on the picosecond and early nanosecond time scale, in a multiphasic manner, in which heme relaxation takes place on the same time scale. The extent of geminate recombination varies from >99% (Ala, Ser) to ϳ70% (Arg), the latter value being in principle low enough for electron injection studies. The rates and extent of the CO geminate recombination phases are much higher than in functional ligand-binding proteins like myoglobin, presumably reflecting the rigid and hydrophobic properties of the heme environment, which are optimized for electron transfer. Thus, the dynamics of CO recombination in cytochrome c are a tool for studying the heme pocket, in a similar way as NO in myoglobin. We discuss the differences in the CO kinetics between the mutants in terms of the properties of the heme environment and strategies to enhance the CO escape yield. Experiments on double mutants in which Phe-82 is replaced by Asp or Gly as well as the M80D substitution indicate that such steric changes substantially increase the motional freedom-dissociated CO.

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Section: Bimolecular Combination Of Gaseous Ligands With M80xmentioning

confidence: 99%

Ligand Dynamics in an Electron Transfer Protein

Silkstone

Jasaitis

Wilson

et al. 2007

Journal of Biological Chemistry

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“…b The ferric form of Ngb (1Q1F [43]) is shown as a white stick model. CO-ligated Ngb (1W92 [44]) is shown in gray, with the CO in van der Waals representation incoming ligands at the primary docking site B [23]. The Mb mutant Leu(B10)Phe demonstrates how structural variations of the distal pocket can have large functional effects (Fig.…”

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confidence: 99%

“…Detailed ligand-binding studies on Mb with both spectroscopic [19][20][21][22][23] and crystallographic [24][25][26][27][28][29][30] techniques have disclosed that the amino acids at positions E7 and B10 play important roles in regulating ligand access to the heme iron. No permanent channel exists in the molecular structure of Mb that connects the active site to the outside, but an outward movement of the HisE7 imidazole side chain may transiently open a pathway through which ligands may enter or exit the distal heme cavity [31,32].…”

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confidence: 99%

Influence of Distal Residue B10 on CO Dynamics in Myoglobin and Neuroglobin

Nienhaus

2007

J Biol Phys

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For many years, myoglobin has served as a paradigm for structure-function studies in proteins. Ligand binding and migration within myoglobin has been studied in great detail by crystallography and spectroscopy, showing that gaseous ligands such as O 2 , CO, and NO not only bind to the heme iron but may also reside transiently in three internal ligand docking sites, the primary docking site B and secondary sites C and D. These sites affect ligand association and dissociation in specific ways. Neuroglobin is another vertebrate heme protein that also binds small ligands. Ligand migration pathways in neuroglobin have not yet been elucidated. Here, we have used Fourier transform infrared temperature derivative spectroscopy at cryogenic temperatures to compare the influence of the side chain volume of amino acid residue B10 on ligand migration to and rebinding from docking sites in myoglobin and neuroglobin.

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“…For example, an exceptionally large internal volume of ∼300 Å 3 exists in neuroglobin, which allows the entire heme prosthetic group to slide deeper into the protein so as to resolve steric conflicts between the exogenous ligand and the distal histidine (97). In the (18,20,28,30,69,93,98). Covalent bond formation to the heme iron can only occur from the primary docking site, and these additional docking sites lower the rebinding probability until the dissociated ligand can finally leave the protein with the aid of a rare protein fluctuation that opens an escape pathway.…”

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confidence: 99%

Ligand Migration and Binding in the Dimeric Hemoglobin ofScapharca inaequivalvis^,

et al. 2007

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Using Fourier transform infrared (FTIR) spectroscopy combined with temperature derivative spectroscopy (TDS) at cryogenic temperatures, we have studied CO binding to the heme and CO migration among cavities in the interior of the dimeric hemoglobin of Scapharca inaequivalvis (HbI) after photodissociation. By combining these studies with x-ray crystallography, three transient ligand docking sites were identified: a primary docking site B in close vicinity to the heme iron, and two secondary docking sites C and D corresponding to the Xe4 and Xe2 cavities of myoglobin. To assess the relevance of these findings for physiological binding, we also performed flash photolysis experiments on HbICO at room temperature and equilibrium binding studies with dioxygen. Our results show that the Xe4 and Xe2 cavities serve as transient docking sites for unbound ligands in the protein, but not as way stations on the entry/exit pathway. For HbI, the so-called histidine gate mechanism proposed for other globins appears as a plausible entry/exit route as well.The globin superfamily of proteins includes vertebrate hemoglobins (Hb), vertebrate myoglobins (Mb), invertebrate globins, plant globins, and bacterial and fungal flavohemoproteins (1). These proteins all bind oxygen and a variety of other small molecules at the central iron of a heme group enwrapped by the polypeptide chain in its characteristic 'globin' fold. Yet they are structurally highly diverse, ranging in size from the small monomeric mini-hemoglobin of the nemertean worm Cerebratulus lacteus with only 109 amino acid residues (2) to the giant erythrocruorin protein found in the annelid Lumbricus terrestris that consists of 144 hemoglobin subunits held together by 36 linker proteins (3). Globins perform a multitude of tasks in biological systems, including oxygen storage and transport, NO scavenging, enzyme action and small-molecule sensor function (4,5).The monomeric Mb is arguably the best studied member of the globin family. For many years, Mb has served as a model system for protein structural dynamics (6-13). A surprising complexity was discovered in its seemingly simple ligand binding reaction, which involves Address correspondence to G. Ulrich Nienhaus, Institute of Biophysics, University of Ulm, 89069 Ulm, Germany, Tel.: +49 731 5023050, Fax.: +49 731 5023059, Email: uli@uiuc.edu. ∥ Current Address: Department of Biochemistry and Molecular Biology, University of Texas, Medical Branch at Galveston, 301 University Blvd, Galveston, TX 77551-1055, USA * The first two authors contributed equally. † G.U.N. was supported by the Deutsche Forschungsgemeinschaft (grant Ni 291/3) and the Fonds der Chemischen Industrie. W.E.R. was supported by the National Institutes of Health (grants DK43323 and GM66756). NIH Public Access Author ManuscriptBiochemistry. Author manuscript; available in PMC 2008 December 11. Published in final edited form as:Biochemistry. (FTIR) cryospectroscopy to study the migration of carbon monoxide (CO) among cavities within the protein interio...

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Mapping the Pathways for O2 Entry Into and Exit from Myoglobin

Abstract: The effects of mutagenesis on geminate and bimolecular O 2 rebinding to 90 mutants at 27 different positions were used to map pathways for ligand movement into and out of sperm whale myoglobin. By analogy to a baseball glove, the protein "catches" and then "holds"

Cited by 356 publications

References 55 publications

Ligand Dynamics in an Electron Transfer Protein

Ligand Dynamics in an Electron Transfer Protein

Influence of Distal Residue B10 on CO Dynamics in Myoglobin and Neuroglobin

Ligand Migration and Binding in the Dimeric Hemoglobin ofScapharca inaequivalvis^,

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Mapping the Pathways for O2 Entry Into and Exit from Myoglobin

Abstract: The effects of mutagenesis on geminate and bimolecular O 2 rebinding to 90 mutants at 27 different positions were used to map pathways for ligand movement into and out of sperm whale myoglobin. By analogy to a baseball glove, the protein "catches" and then "holds"

Cited by 356 publications

References 55 publications

Ligand Dynamics in an Electron Transfer Protein

Ligand Dynamics in an Electron Transfer Protein

Influence of Distal Residue B10 on CO Dynamics in Myoglobin and Neuroglobin

Ligand Migration and Binding in the Dimeric Hemoglobin ofScapharca inaequivalvis,

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Product

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Ligand Migration and Binding in the Dimeric Hemoglobin ofScapharca inaequivalvis^,