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PDBsum entry 1mob
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Oxygen storage
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PDB id
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1mob
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Contents |
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* Residue conservation analysis
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J Mol Biol
234:140-155
(1993)
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PubMed id:
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High-resolution crystal structures of distal histidine mutants of sperm whale myoglobin.
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M.L.Quillin,
R.M.Arduini,
J.S.Olson,
G.N.Phillips.
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ABSTRACT
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The highly conserved distal histidine residue (His64) of sperm whale myoglobin
modulates the affinity of ligands. In an effort to fully characterize the
effects of mutating residue 64, we have determined the high-resolution crystal
structures of the Gly64, Val64, Leu64, Thr64 and Gln64 mutants in several
liganded forms. Metmyoglobins with hydrophobic substitutions at residue 64
(Val64 and Leu64) lack a water molecule at the sixth coordination position,
while those with polar amino acid residues at this position (wild-type and
Gln64) retain a covalently bound water molecule. In the Thr64 mutant, the bound
water position is only partially occupied. In contrast, mutating the distal
histidine residue to glycine does not cause loss of the coordinated water
molecule, because the hydrogen bond from the imidazole side-chain is replaced by
one from a well-ordered solvent water molecule. Differences in water structure
around the distal pocket are apparent also in the structures of deoxymyoglobin
mutants. The water molecule that is hydrogen-bonded to the N epsilon atom of
histidine 64 in wild-type deoxymyoglobin is not found in any of the position 64
mutant structures that were determined. Comparison of the carbonmonoxy
structures of wild-type, Gly64, Leu64 and Gln64 myoglobins in the P6 crystal
form shows that the conformation of the Fe-C-O complex is nearly linear and is
independent of the identity of the amino acid residue at position 64. However,
the effect of CO binding on the conformation of residue 64 is striking.
Superposition of deoxy and carbonmonoxy structures reveals significant
displacements of the residue 64 side-chain in the wild-type and Gln64
myoglobins, but no displacement in the Leu64 mutant. These detailed structural
studies provide key insights into the mechanisms of ligand binding and
discrimination in myoglobin.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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A.Benabbas,
X.Ye,
M.Kubo,
Z.Zhang,
E.M.Maes,
W.R.Montfort,
and
P.M.Champion
(2010).
Ultrafast dynamics of diatomic ligand binding to nitrophorin 4.
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J Am Chem Soc,
132,
2811-2820.
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R.M.Esquerra,
I.López-Peña,
P.Tipgunlakant,
I.Birukou,
R.L.Nguyen,
J.Soman,
J.S.Olson,
D.S.Kliger,
and
R.A.Goldbeck
(2010).
Kinetic spectroscopy of heme hydration and ligand binding in myoglobin and isolated hemoglobin chains: an optical window into heme pocket water dynamics.
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Phys Chem Chem Phys,
12,
10270-10278.
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A.Ioanoviciu,
Y.T.Meharenna,
T.L.Poulos,
and
P.R.Ortiz de Montellano
(2009).
DevS oxy complex stability identifies this heme protein as a gas sensor in Mycobacterium tuberculosis dormancy.
|
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Biochemistry,
48,
5839-5848.
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A.Vergara,
M.Franzese,
A.Merlino,
G.Bonomi,
C.Verde,
D.Giordano,
G.di Prisco,
H.C.Lee,
J.Peisach,
and
L.Mazzarella
(2009).
Correlation between hemichrome stability and the root effect in tetrameric hemoglobins.
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Biophys J,
97,
866-874.
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PDB code:
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J.P.Collman,
R.A.Decréau,
A.Dey,
and
Y.Yang
(2009).
Water may inhibit oxygen binding in hemoprotein models.
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Proc Natl Acad Sci U S A,
106,
4101-4105.
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J.P.Collman,
R.A.Decréau,
H.Lin,
A.Hosseini,
Y.Yang,
A.Dey,
and
T.A.Eberspacher
(2009).
Role of a distal pocket in the catalytic O2 reduction by cytochrome c oxidase models immobilized on interdigitated array electrodes.
|
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Proc Natl Acad Sci U S A,
106,
7320-7323.
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J.Yi,
J.Heinecke,
H.Tan,
P.C.Ford,
and
G.B.Richter-Addo
(2009).
The distal pocket histidine residue in horse heart myoglobin directs the O-binding mode of nitrite to the heme iron.
|
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J Am Chem Soc,
131,
18119-18128.
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PDB codes:
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L.Guo,
J.Park,
T.Lee,
P.Chowdhury,
M.Lim,
and
F.Gai
(2009).
Probing the role of hydration in the unfolding transitions of carbonmonoxy myoglobin and apomyoglobin.
|
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J Phys Chem B,
113,
6158-6163.
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R.A.Goldbeck,
M.L.Pillsbury,
R.A.Jensen,
J.L.Mendoza,
R.L.Nguyen,
J.S.Olson,
J.Soman,
D.S.Kliger,
and
R.M.Esquerra
(2009).
Optical detection of disordered water within a protein cavity.
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J Am Chem Soc,
131,
12265-12272.
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PDB codes:
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W.K.Erbil,
M.S.Price,
D.E.Wemmer,
and
M.A.Marletta
(2009).
A structural basis for H-NOX signaling in Shewanella oneidensis by trapping a histidine kinase inhibitory conformation.
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Proc Natl Acad Sci U S A,
106,
19753-19760.
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PDB codes:
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F.Gruia,
M.Kubo,
X.Ye,
D.Ionascu,
C.Lu,
R.K.Poole,
S.R.Yeh,
and
P.M.Champion
(2008).
Coherence spectroscopy investigations of the low-frequency vibrations of heme: effects of protein-specific perturbations.
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J Am Chem Soc,
130,
5231-5244.
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F.Gruia,
M.Kubo,
X.Ye,
and
P.M.Champion
(2008).
Investigations of vibrational coherence in the low-frequency region of ferric heme proteins.
|
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Biophys J,
94,
2252-2268.
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L.M.Moreira,
A.L.Poli,
A.J.Costa-Filho,
and
H.Imasato
(2008).
Ferric species equilibrium of the giant extracellular hemoglobin of Glossoscolex paulistus in alkaline medium: HALS hemichrome as a precursor of pentacoordinate species.
|
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Int J Biol Macromol,
42,
103-110.
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R.J.Debus
(2008).
Protein Ligation of the Photosynthetic Oxygen-Evolving Center.
|
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Coord Chem Rev,
252,
244-258.
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R.M.Esquerra,
R.A.Jensen,
S.Bhaskaran,
M.L.Pillsbury,
J.L.Mendoza,
B.W.Lintner,
D.S.Kliger,
and
R.A.Goldbeck
(2008).
The pH dependence of heme pocket hydration and ligand rebinding kinetics in photodissociated carbonmonoxymyoglobin.
|
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J Biol Chem,
283,
14165-14175.
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Y.H.Ouellet,
R.Daigle,
P.Lagüe,
D.Dantsker,
M.Milani,
M.Bolognesi,
J.M.Friedman,
and
M.Guertin
(2008).
Ligand Binding to Truncated Hemoglobin N from Mycobacterium tuberculosis Is Strongly Modulated by the Interplay between the Distal Heme Pocket Residues and Internal Water.
|
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J Biol Chem,
283,
27270-27278.
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Z.N.Zahran,
L.Chooback,
D.M.Copeland,
A.H.West,
and
G.B.Richter-Addo
(2008).
Crystal structures of manganese- and cobalt-substituted myoglobin in complex with NO and nitrite reveal unusual ligand conformations.
|
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J Inorg Biochem,
102,
216-233.
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PDB codes:
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A.Vergara,
M.Franzese,
A.Merlino,
L.Vitagliano,
C.Verde,
G.di Prisco,
H.C.Lee,
J.Peisach,
and
L.Mazzarella
(2007).
Structural characterization of ferric hemoglobins from three antarctic fish species of the suborder notothenioidei.
|
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Biophys J,
93,
2822-2829.
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PDB code:
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E.H.Sousa,
J.R.Tuckerman,
G.Gonzalez,
and
M.A.Gilles-Gonzalez
(2007).
DosT and DevS are oxygen-switched kinases in Mycobacterium tuberculosis.
|
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Protein Sci,
16,
1708-1719.
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G.Battistuzzi,
M.Bellei,
L.Casella,
C.A.Bortolotti,
R.Roncone,
E.Monzani,
and
M.Sola
(2007).
Redox reactivity of the heme Fe3+/Fe 2+ couple in native myoglobins and mutants with peroxidase-like activity.
|
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J Biol Inorg Chem,
12,
951-958.
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K.Nienhaus,
J.E.Knapp,
P.Palladino,
W.E.Royer,
and
G.U.Nienhaus
(2007).
Ligand migration and binding in the dimeric hemoglobin of Scapharca inaequivalvis.
|
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Biochemistry,
46,
14018-14031.
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PDB codes:
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M.A.Martí,
L.Capece,
D.E.Bikiel,
B.Falcone,
and
D.A.Estrin
(2007).
Oxygen affinity controlled by dynamical distal conformations: the soybean leghemoglobin and the Paramecium caudatum hemoglobin cases.
|
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Proteins,
68,
480-487.
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O.V.Moskvin,
S.Kaplan,
M.A.Gilles-Gonzalez,
and
M.Gomelsky
(2007).
Novel heme-based oxygen sensor with a revealing evolutionary history.
|
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J Biol Chem,
282,
28740-28748.
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U.Samuni,
D.Dantsker,
C.J.Roche,
and
J.M.Friedman
(2007).
Ligand recombination and a hierarchy of solvent slaved dynamics: the origin of kinetic phases in hemeproteins.
|
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Gene,
398,
234-248.
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Y.Ran,
H.Zhu,
M.Liu,
M.Fabian,
J.S.Olson,
R.Aranda,
G.N.Phillips,
D.M.Dooley,
and
B.Lei
(2007).
Bis-methionine ligation to heme iron in the streptococcal cell surface protein Shp facilitates rapid hemin transfer to HtsA of the HtsABC transporter.
|
| |
J Biol Chem,
282,
31380-31388.
|
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|
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R.A.Goldbeck,
S.Bhaskaran,
C.Ortega,
J.L.Mendoza,
J.S.Olson,
J.Soman,
D.S.Kliger,
and
R.M.Esquerra
(2006).
Water and ligand entry in myoglobin: assessing the speed and extent of heme pocket hydration after CO photodissociation.
|
| |
Proc Natl Acad Sci U S A,
103,
1254-1259.
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D.Dantsker,
C.Roche,
U.Samuni,
G.Blouin,
J.S.Olson,
and
J.M.Friedman
(2005).
The position 68(E11) side chain in myoglobin regulates ligand capture, bond formation with heme iron, and internal movement into the xenon cavities.
|
| |
J Biol Chem,
280,
38740-38755.
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D.Ionascu,
F.Gruia,
X.Ye,
A.Yu,
F.Rosca,
C.Beck,
A.Demidov,
J.S.Olson,
and
P.M.Champion
(2005).
Temperature-dependent studies of NO recombination to heme and heme proteins.
|
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J Am Chem Soc,
127,
16921-16934.
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S.Park,
and
J.G.Saven
(2005).
Statistical and molecular dynamics studies of buried waters in globular proteins.
|
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Proteins,
60,
450-463.
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W.Zhang,
J.S.Olson,
and
G.N.Phillips
(2005).
Biophysical and kinetic characterization of HemAT, an aerotaxis receptor from Bacillus subtilis.
|
| |
Biophys J,
88,
2801-2814.
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D.Li,
D.J.Stuehr,
S.R.Yeh,
and
D.L.Rousseau
(2004).
Heme distortion modulated by ligand-protein interactions in inducible nitric-oxide synthase.
|
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J Biol Chem,
279,
26489-26499.
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G.Hummer,
F.Schotte,
and
P.A.Anfinrud
(2004).
Unveiling functional protein motions with picosecond x-ray crystallography and molecular dynamics simulations.
|
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Proc Natl Acad Sci U S A,
101,
15330-15334.
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H.Nasri,
M.K.Ellison,
M.Shang,
C.E.Schulz,
and
W.R.Scheidt
(2004).
Variable pi-bonding in iron(II) porphyrinates with nitrite, CO, and tert-butyl isocyanide: characterization of [Fe(TpivPP)(NO2)(CO)]-.
|
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Inorg Chem,
43,
2932-2942.
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K.Nienhaus,
E.M.Maes,
A.Weichsel,
W.R.Montfort,
and
G.U.Nienhaus
(2004).
Structural dynamics controls nitric oxide affinity in nitrophorin 4.
|
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J Biol Chem,
279,
39401-39407.
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PDB code:
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K.Nienhaus,
J.M.Kriegl,
and
G.U.Nienhaus
(2004).
Structural dynamics in the active site of murine neuroglobin and its effects on ligand binding.
|
| |
J Biol Chem,
279,
22944-22952.
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P.K.Chowdhury,
M.Halder,
L.Sanders,
R.A.Arnold,
Y.Liu,
D.W.Armstrong,
S.Kundu,
M.S.Hargrove,
X.Song,
and
J.W.Petrich
(2004).
The complex of apomyoglobin with the fluorescent dye coumarin 153.
|
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Photochem Photobiol,
79,
440-446.
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T.Uno,
D.Ryu,
H.Tsutsumi,
Y.Tomisugi,
Y.Ishikawa,
A.J.Wilkinson,
H.Sato,
and
T.Hayashi
(2004).
Residues in the distal heme pocket of neuroglobin. Implications for the multiple ligand binding steps.
|
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J Biol Chem,
279,
5886-5893.
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C.M.Dunham,
E.M.Dioum,
J.R.Tuckerman,
G.Gonzalez,
W.G.Scott,
and
M.A.Gilles-Gonzalez
(2003).
A distal arginine in oxygen-sensing heme-PAS domains is essential to ligand binding, signal transduction, and structure.
|
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Biochemistry,
42,
7701-7708.
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PDB code:
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J.Miksovská,
J.H.Day,
and
R.W.Larsen
(2003).
Volume and enthalpy profiles of CO rebinding to horse heart myoglobin.
|
| |
J Biol Inorg Chem,
8,
621-625.
|
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K.Nienhaus,
P.Deng,
J.S.Olson,
J.J.Warren,
and
G.U.Nienhaus
(2003).
Structural dynamics of myoglobin: ligand migration and binding in valine 68 mutants.
|
| |
J Biol Chem,
278,
42532-42544.
|
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K.Shikama,
and
A.Matsuoka
(2003).
Human haemoglobin: a new paradigm for oxygen binding involving two types of alphabeta contacts.
|
| |
Eur J Biochem,
270,
4041-4051.
|
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S.Kundu,
and
M.S.Hargrove
(2003).
Distal heme pocket regulation of ligand binding and stability in soybean leghemoglobin.
|
| |
Proteins,
50,
239-248.
|
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W.Zhang,
and
G.N.Phillips
(2003).
Structure of the oxygen sensor in Bacillus subtilis: signal transduction of chemotaxis by control of symmetry.
|
| |
Structure,
11,
1097-1110.
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PDB codes:
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M.Sakakura,
I.Morishima,
and
M.Terazima
(2002).
Structural dynamics of distal histidine replaced mutants of myoglobin accompanied with the photodissociation reaction of the ligand.
|
| |
Biochemistry,
41,
4837-4846.
|
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S.Kundu,
B.Snyder,
K.Das,
P.Chowdhury,
J.Park,
J.W.Petrich,
and
M.S.Hargrove
(2002).
The leghemoglobin proximal heme pocket directs oxygen dissociation and stabilizes bound heme.
|
| |
Proteins,
46,
268-277.
|
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|
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T.Tomita,
G.Gonzalez,
A.L.Chang,
M.Ikeda-Saito,
and
M.A.Gilles-Gonzalez
(2002).
A comparative resonance Raman analysis of heme-binding PAS domains: heme iron coordination structures of the BjFixL, AxPDEA1, EcDos, and MtDos proteins.
|
| |
Biochemistry,
41,
4819-4826.
|
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A.L.Chang,
J.R.Tuckerman,
G.Gonzalez,
R.Mayer,
H.Weinhouse,
G.Volman,
D.Amikam,
M.Benziman,
and
M.A.Gilles-Gonzalez
(2001).
Phosphodiesterase A1, a regulator of cellulose synthesis in Acetobacter xylinum, is a heme-based sensor.
|
| |
Biochemistry,
40,
3420-3426.
|
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|
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B.Stec,
and
G.N.Phillips
(2001).
How the CO in myoglobin acquired its bend: lessons in interpretation of crystallographic data.
|
| |
Acta Crystallogr D Biol Crystallogr,
57,
751-754.
|
|
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|
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J.Xu,
W.A.Baase,
M.L.Quillin,
E.P.Baldwin,
and
B.W.Matthews
(2001).
Structural and thermodynamic analysis of the binding of solvent at internal sites in T4 lysozyme.
|
| |
Protein Sci,
10,
1067-1078.
|
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PDB codes:
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M.D.Fayer
(2001).
Fast protein dynamics probed with infrared vibrational echo experiments.
|
| |
Annu Rev Phys Chem,
52,
315-356.
|
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N.Haruta,
M.Aki,
S.Ozaki,
Y.Watanabe,
and
T.Kitagawa
(2001).
Protein conformation change of myoglobin upon ligand binding probed by ultraviolet resonance Raman spectroscopy.
|
| |
Biochemistry,
40,
6956-6963.
|
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|
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R.J.Debus,
K.A.Campbell,
W.Gregor,
Z.L.Li,
R.L.Burnap,
and
R.D.Britt
(2001).
Does histidine 332 of the D1 polypeptide ligate the manganese cluster in photosystem II? An electron spin echo envelope modulation study.
|
| |
Biochemistry,
40,
3690-3699.
|
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S.Ozaki,
I.Hara,
T.Matsui,
and
Y.Watanabe
(2001).
Molecular engineering of myoglobin: the improvement of oxidation activity by replacing Phe-43 with tryptophan.
|
| |
Biochemistry,
40,
1044-1052.
|
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Y.Shibata,
H.Ishikawa,
S.Takahashi,
and
I.Morishima
(2001).
Time-resolved hole-burning study on myoglobin: fluctuation of restricted water within distal pocket.
|
| |
Biophys J,
80,
1013-1023.
|
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C.Garcia,
C.Nishimura,
S.Cavagnero,
H.J.Dyson,
and
P.E.Wright
(2000).
Changes in the apomyoglobin folding pathway caused by mutation of the distal histidine residue.
|
| |
Biochemistry,
39,
11227-11237.
|
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C.Tetreau,
M.Tourbez,
and
D.Lavalette
(2000).
Conformational relaxation in hemoproteins: the cytochrome P-450cam case.
|
| |
Biochemistry,
39,
14219-14231.
|
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J.A.Lukin,
V.Simplaceanu,
M.Zou,
N.T.Ho,
and
C.Ho
(2000).
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PDB code:
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H.Schulze,
O.Ristau,
and
C.Jung
(1994).
The carbon monoxide stretching modes in camphor-bound cytochrome P-450cam. The effect of solvent conditions, temperature, and pressure.
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Eur J Biochem,
224,
1047-1055.
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I.De Baere,
M.F.Perutz,
L.Kiger,
M.C.Marden,
and
C.Poyart
(1994).
Formation of two hydrogen bonds from the globin to the heme-linked oxygen molecule in Ascaris hemoglobin.
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Proc Natl Acad Sci U S A,
91,
1594-1597.
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P.Jewsbury,
and
T.Kitagawa
(1994).
The distal residue-CO interaction in carbonmonoxy myoglobins: a molecular dynamics study of two distal histidine tautomers.
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Biophys J,
67,
2236-2250.
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
code is
shown on the right.
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Links
