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PDBsum entry 1akk
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Electron transport
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PDB id
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1akk
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* Residue conservation analysis
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PDB id:
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| Name: |
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Electron transport
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Title:
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Solution structure of oxidized horse heart cytochromE C, nmr, minimized average structure
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Structure:
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CytochromE C. Chain: a
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Source:
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Equus caballus. Horse. Organism_taxid: 9796. Organ: heart
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NMR struc:
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1 models
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Authors:
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L.Banci,I.Bertini,H.B.Gray,C.Luchinat,T.Reddig,A.Rosato,P.Turano
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Key ref:
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L.Banci
et al.
(1997).
Solution structure of oxidized horse heart cytochrome c.
Biochemistry,
36,
9867-9877.
PubMed id:
DOI:
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Date:
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22-May-97
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Release date:
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17-Sep-97
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PROCHECK
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Headers
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References
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P00004
(CYC_HORSE) -
Cytochrome c from Equus caballus
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Seq:
Struc:
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105 a.a.
104 a.a.
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Key: |
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PfamA domain |
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Secondary structure |
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CATH domain |
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DOI no:
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Biochemistry
36:9867-9877
(1997)
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PubMed id:
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Solution structure of oxidized horse heart cytochrome c.
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L.Banci,
I.Bertini,
H.B.Gray,
C.Luchinat,
T.Reddig,
A.Rosato,
P.Turano.
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ABSTRACT
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The solution structure of oxidized horse heart cytochrome c was obtained at pH
7.0 in 100 mM phosphate buffer from 2278 NOEs and 241 pseudocontact shift
constraints. The final structure was refined through restrained energy
minimization. A 35-member family, with RMSD values with respect to the average
structure of 0.70 +/- 0.11 A and 1.21 +/- 0.14 A for the backbone and all heavy
atoms, respectively, and with an average penalty function of 130 +/- 4.0 kJ/mol
and 84 +/- 3.7 kJ/mol for NOE and pseudocontact shift constraints, respectively
(corresponding to a target function of 0.9 A2 and 0.2 A2), was obtained. The
solution structure is somewhat different from that recently reported (Qi et al.,
1996) and appears to be similar to the X-ray structure of the same oxidation
state (Bushnell et al., 1990). A noticeable difference is a rotation of 17 +/- 8
degrees of the imidazole plane between solid and solution structure. Detailed
and accurate structural determinations are important within the frame of the
current debate of the structural rearrangements occurring upon oxidation or
reduction. From the obtained magnetic susceptibility tensor a separation of the
hyperfine shifts into their contact and pseudocontact contributions is derived
and compared to that of the analogous isoenzyme from S. cerevisiae and to
previous results.
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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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S.M.Singh,
R.L.Hutchings,
and
K.M.Mallela
(2011).
Mechanisms of m-cresol-induced protein aggregation studied using a model protein cytochrome c.
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J Pharm Sci,
100,
1679-1689.
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T.Suemoto,
H.Ebihara,
H.Nakao,
and
M.Nakajima
(2011).
Observation of ultrafast Q-band fluorescence in horse heart cytochrome c in reduced and oxidized forms.
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J Chem Phys,
134,
034502.
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R.Santucci,
F.Sinibaldi,
A.Patriarca,
D.Santucci,
and
L.Fiorucci
(2010).
Misfolded proteins and neurodegeneration: role of non-native cytochrome c in cell death.
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Expert Rev Proteomics,
7,
507-517.
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|
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S.Hirota,
Y.Hattori,
S.Nagao,
M.Taketa,
H.Komori,
H.Kamikubo,
Z.Wang,
I.Takahashi,
S.Negi,
Y.Sugiura,
M.Kataoka,
and
Y.Higuchi
(2010).
Cytochrome c polymerization by successive domain swapping at the C-terminal helix.
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Proc Natl Acad Sci U S A,
107,
12854-12859.
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PDB codes:
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S.Monari,
D.Millo,
A.Ranieri,
G.Di Rocco,
G.van der Zwan,
C.Gooijer,
S.Peressini,
C.Tavagnacco,
P.Hildebrandt,
and
M.Borsari
(2010).
The impact of urea-induced unfolding on the redox process of immobilised cytochrome c.
|
| |
J Biol Inorg Chem,
15,
1233-1242.
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L.A.Abriata,
A.Cassina,
V.Tórtora,
M.Marín,
J.M.Souza,
L.Castro,
A.J.Vila,
and
R.Radi
(2009).
Nitration of solvent-exposed tyrosine 74 on cytochrome c triggers heme iron-methionine 80 bond disruption. Nuclear magnetic resonance and optical spectroscopy studies.
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J Biol Chem,
284,
17-26.
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L.Cubo,
A.Casini,
C.Gabbiani,
G.Mastrobuoni,
L.Messori,
J.Jiménez-Barbero,
C.Navarro-Ranninger,
and
A.G.Quiroga
(2009).
Solution behaviour and biomolecular interactions of two cytotoxic trans-platinum(II) complexes bearing aliphatic amine ligands.
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Chemistry,
15,
9139-9146.
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R.Kumar,
and
A.K.Bhuyan
(2009).
Entropic stabilization of myoglobin by subdenaturing concentrations of guanidine hydrochloride.
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J Biol Inorg Chem,
14,
11-21.
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B.M.Leu,
Y.Zhang,
L.Bu,
J.E.Straub,
J.Zhao,
W.Sturhahn,
E.E.Alp,
and
J.T.Sage
(2008).
Resilience of the iron environment in heme proteins.
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Biophys J,
95,
5874-5889.
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D.Deriu,
S.E.Pagnotta,
R.Santucci,
and
N.Rosato
(2008).
Spectroscopic and electrochemical characterization of cytochrome c encapsulated in a bio sol-gel matrix.
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Biometals,
21,
417-423.
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K.Breuker,
and
F.W.McLafferty
(2008).
Stepwise evolution of protein native structure with electrospray into the gas phase, 10(-12) to 10(2) s.
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Proc Natl Acad Sci U S A,
105,
18145-18152.
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M.Z.Steinberg,
R.Elber,
F.W.McLafferty,
R.B.Gerber,
and
K.Breuker
(2008).
Early structural evolution of native cytochrome c after solvent removal.
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Chembiochem,
9,
2417-2423.
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P.Weinkam,
J.Zimmermann,
L.B.Sagle,
S.Matsuda,
P.E.Dawson,
P.G.Wolynes,
and
F.E.Romesberg
(2008).
Characterization of alkaline transitions in ferricytochrome c using carbon-deuterium infrared probes.
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Biochemistry,
47,
13470-13480.
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A.Casini,
G.Mastrobuoni,
M.Terenghi,
C.Gabbiani,
E.Monzani,
G.Moneti,
L.Casella,
and
L.Messori
(2007).
Ruthenium anticancer drugs and proteins: a study of the interactions of the ruthenium(III) complex imidazolium trans-[tetrachloro(dimethyl sulfoxide)(imidazole)ruthenate(III)] with hen egg white lysozyme and horse heart cytochrome c.
|
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J Biol Inorg Chem,
12,
1107-1117.
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A.S.Domazou,
and
W.H.Koppenol
(2007).
Oxidation-state-dependent reactions of cytochrome c with the trioxidocarbonate(*1-) radical: a pulse radiolysis study.
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J Biol Inorg Chem,
12,
118-125.
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C.D.Putnam,
M.Hammel,
G.L.Hura,
and
J.A.Tainer
(2007).
X-ray solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in solution.
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Q Rev Biophys,
40,
191-285.
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L.Andolfi,
P.Caroppi,
A.R.Bizzarri,
M.C.Piro,
F.Sinibaldi,
T.Ferri,
F.Polticelli,
S.Cannistraro,
and
R.Santucci
(2007).
Nanoscopic and redox characterization of engineered horse cytochrome C chemisorbed on a bare gold electrode.
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Protein J,
26,
271-279.
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M.V.Williams,
J.S.Wishnok,
and
S.R.Tannenbaum
(2007).
Covalent adducts arising from the decomposition products of lipid hydroperoxides in the presence of cytochrome c.
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Chem Res Toxicol,
20,
767-775.
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M.Ye,
Q.L.Zhang,
H.Li,
Y.X.Weng,
W.C.Wang,
and
X.G.Qiu
(2007).
Infrared spectroscopic discrimination between the loop and alpha-helices and determination of the loop diffusion kinetics by temperature-jump time-resolved infrared spectroscopy for cytochrome c.
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Biophys J,
93,
2756-2766.
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M.Z.Steinberg,
K.Breuker,
R.Elber,
and
R.B.Gerber
(2007).
The dynamics of water evaporation from partially solvated cytochrome c in the gas phase.
|
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Phys Chem Chem Phys,
9,
4690-4697.
|
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P.T.Kasper,
J.W.Back,
M.Vitale,
A.F.Hartog,
W.Roseboom,
L.J.de Koning,
J.H.van Maarseveen,
A.O.Muijsers,
C.G.de Koster,
and
L.de Jong
(2007).
An aptly positioned azido group in the spacer of a protein cross-linker for facile mapping of lysines in close proximity.
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| |
Chembiochem,
8,
1281-1292.
|
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|
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F.Sinibaldi,
B.D.Howes,
M.C.Piro,
P.Caroppi,
G.Mei,
F.Ascoli,
G.Smulevich,
and
R.Santucci
(2006).
Insights into the role of the histidines in the structure and stability of cytochrome c.
|
| |
J Biol Inorg Chem,
11,
52-62.
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|
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F.Sinibaldi,
M.C.Piro,
M.Coletta,
and
R.Santucci
(2006).
Salt-induced formation of the A-state of ferricytochrome c--effect of the anion charge on protein structure.
|
| |
FEBS J,
273,
5347-5357.
|
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A.N.Khan,
and
P.N.Lewis
(2005).
Unstructured conformations are a substrate requirement for the Sir2 family of NAD-dependent protein deacetylases.
|
| |
J Biol Chem,
280,
36073-36078.
|
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|
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C.Kawai,
F.M.Prado,
G.L.Nunes,
P.Di Mascio,
A.M.Carmona-Ribeiro,
and
I.L.Nantes
(2005).
pH-Dependent interaction of cytochrome c with mitochondrial mimetic membranes: the role of an array of positively charged amino acids.
|
| |
J Biol Chem,
280,
34709-34717.
|
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|
|
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|
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F.Sinibaldi,
G.Mei,
F.Polticelli,
M.C.Piro,
B.D.Howes,
G.Smulevich,
R.Santucci,
F.Ascoli,
and
L.Fiorucci
(2005).
ATP specifically drives refolding of non-native conformations of cytochrome c.
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Protein Sci,
14,
1049-1058.
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G.Battistuzzi,
M.Bellei,
M.Borsari,
G.Di Rocco,
A.Ranieri,
and
M.Sola
(2005).
Axial ligation and polypeptide matrix effects on the reduction potential of heme proteins probed on their cyanide adducts.
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J Biol Inorg Chem,
10,
643-651.
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K.Breuker,
and
F.W.McLafferty
(2005).
The thermal unfolding of native cytochrome c in the transition from solution to gas phase probed by native electron capture dissociation.
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Angew Chem Int Ed Engl,
44,
4911-4914.
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S.Hirota,
H.Okumura,
S.Kuroiwa,
N.Funasaki,
and
Y.Watanabe
(2005).
Reduction of ferricytochrome c by tyrosyltyrosylphenylalanine.
|
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J Biol Inorg Chem,
10,
355-363.
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T.A.Rinaldi,
I.L.Tersariol,
F.H.Dyszy,
F.M.Prado,
O.R.Nascimento,
P.Di Mascio,
and
I.L.Nantes
(2004).
Protonation of two adjacent tyrosine residues influences the reduction of cytochrome c by diphenylacetaldehyde: a possible mechanism to select the reducer agent of heme iron.
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Free Radic Biol Med,
36,
802-810.
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F.E.Romesberg
(2003).
Multidisciplinary experimental approaches to characterizing biomolecular dynamics.
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Chembiochem,
4,
563-571.
|
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M.Assfalg,
I.Bertini,
P.Turano,
A.Grant Mauk,
J.R.Winkler,
and
H.B.Gray
(2003).
15N-1H Residual dipolar coupling analysis of native and alkaline-K79A Saccharomyces cerevisiae cytochrome c.
|
| |
Biophys J,
84,
3917-3923.
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S.Chevance,
E.Le Rumeur,
J.D.de Certaines,
G.Simonneaux,
and
A.Bondon
(2003).
1H NMR structural characterization of the cytochrome c modifications in a micellar environment.
|
| |
Biochemistry,
42,
15342-15351.
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U.H.Verkerk,
M.Peschke,
and
P.Kebarle
(2003).
Effect of buffer cations and of H3O+ on the charge states of native proteins. Significance to determinations of stability constants of protein complexes.
|
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J Mass Spectrom,
38,
618-631.
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D.M.Tiede,
R.Zhang,
and
S.Seifert
(2002).
Protein conformations explored by difference high-angle solution X-ray scattering: oxidation state and temperature dependent changes in cytochrome C.
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Biochemistry,
41,
6605-6614.
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K.M.Pearson,
L.K.Pannell,
and
H.M.Fales
(2002).
Intramolecular cross-linking experiments on cytochrome c and ribonuclease A using an isotope multiplet method.
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Rapid Commun Mass Spectrom,
16,
149-159.
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L.Banci,
I.Bertini,
S.Ciurli,
A.Dikiy,
J.Dittmer,
A.Rosato,
G.Sciara,
and
A.R.Thompsett
(2002).
NMR solution structure, backbone mobility, and homology modeling of c-type cytochromes from gram-positive bacteria.
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Chembiochem,
3,
299-310.
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PDB codes:
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Y.Furukawa,
K.Ishimori,
and
I.Morishima
(2002).
Oxidation-state-dependent protein docking between cytochrome c and cytochrome b(5): high-pressure laser flash photolysis study.
|
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Biochemistry,
41,
9824-9832.
|
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G.Battistuzzi,
M.Borsari,
and
M.Sola
(2001).
Redox properties of cytochrome c.
|
| |
Antioxid Redox Signal,
3,
279-291.
|
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|
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I.Bertini,
D.A.Bryant,
S.Ciurli,
A.Dikiy,
C.O.Fernández,
C.Luchinat,
N.Safarov,
A.J.Vila,
and
J.Zhao
(2001).
Backbone dynamics of plastocyanin in both oxidation states. Solution structure of the reduced form and comparison with the oxidized state.
|
| |
J Biol Chem,
276,
47217-47226.
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PDB codes:
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P.D.Barker,
I.Bertini,
R.Del Conte,
S.J.Ferguson,
P.Hajieva,
E.Tomlinson,
P.Turano,
and
M.S.Viezzoli
(2001).
A further clue to understanding the mobility of mitochondrial yeast cytochrome c: a (15)N T1rho investigation of the oxidized and reduced species.
|
| |
Eur J Biochem,
268,
4468-4476.
|
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|
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S.G.Sivakolundu,
and
P.A.Mabrouk
(2001).
Insights into the alkaline transformation of ferricytochrome c from (1)H NMR studies in 30% acetonitrile-water.
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| |
Protein Sci,
10,
2291-2300.
|
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A.Kostrzewa,
T.Páli,
W.Froncisz,
and
D.Marsh
(2000).
Membrane location of spin-labeled cytochrome c determined by paramagnetic relaxation agents.
|
| |
Biochemistry,
39,
6066-6074.
|
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D.Zhao,
H.M.Hutton,
P.R.Gooley,
N.E.MacKenzie,
and
M.A.Cusanovich
(2000).
Redox-related conformational changes in Rhodobacter capsulatus cytochrome c2.
|
| |
Protein Sci,
9,
1828-1837.
|
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|
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|
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D.Zhao,
H.M.Hutton,
T.E.Meyer,
F.A.Walker,
N.E.MacKenzie,
and
M.A.Cusanovich
(2000).
Structure and stability effects of the mutation of glycine 34 to serine in Rhodobacter capsulatus cytochrome c(2).
|
| |
Biochemistry,
39,
4053-4061.
|
|
|
|
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|
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F.Arnesano,
L.Banci,
I.Bertini,
S.Ciofi-Baffoni,
T.L.Woodyear,
C.M.Johnson,
and
P.D.Barker
(2000).
Structural consequences of b- to c-type heme conversion in oxidized Escherichia coli cytochrome b562.
|
| |
Biochemistry,
39,
1499-1514.
|
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PDB code:
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I.Bertini,
H.J.Hartmann,
T.Klein,
G.Liu,
C.Luchinat,
and
U.Weser
(2000).
High resolution solution structure of the protein part of Cu7 metallothionein.
|
| |
Eur J Biochem,
267,
1008-1018.
|
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PDB code:
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L.Banci,
I.Bertini,
A.Rosato,
and
S.Scacchieri
(2000).
Solution structure of oxidized microsomal rabbit cytochrome b5. Factors determining the heterogeneous binding of the heme.
|
| |
Eur J Biochem,
267,
755-766.
|
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PDB code:
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|
|
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M.Borsari,
E.Dikaya,
A.Dikiy,
M.V.Gonchar,
M.M.Maidan,
R.Pierattelli,
and
A.A.Sibirny
(2000).
Isolation and physico-chemical characterization of a cytochrome c from the methylotrophic yeast Hansenula polymorpha.
|
| |
Biochim Biophys Acta,
1543,
174-188.
|
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|
|
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|
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P.Pristovsek,
C.Lücke,
B.Reincke,
B.Ludwig,
and
H.Rüterjans
(2000).
Solution structure of the functional domain of Paracoccus denitrificans cytochrome c552 in the reduced state.
|
| |
Eur J Biochem,
267,
4205-4212.
|
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PDB code:
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T.Okuno,
S.Hirota,
and
O.Yamauchi
(2000).
Folding character of cytochrome c studied by o-nitrobenzyl modification of methionine 65 and subsequent ultraviolet light irradiation.
|
| |
Biochemistry,
39,
7538-7545.
|
|
|
|
|
|
|
A.E.García,
and
G.Hummer
(1999).
Conformational dynamics of cytochrome c: correlation to hydrogen exchange.
|
| |
Proteins,
36,
175-191.
|
|
|
|
|
|
|
F.Arnesano,
L.Banci,
I.Bertini,
I.C.Felli,
and
D.Koulougliotis
(1999).
Solution structure of the B form of oxidized rat microsomal cytochrome b5 and backbone dynamics via 15N rotating-frame NMR-relaxation measurements. Biological implications.
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| |
Eur J Biochem,
260,
347-354.
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PDB code:
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F.Arnesano,
L.Banci,
I.Bertini,
J.Faraone-Mennella,
A.Rosato,
P.D.Barker,
and
A.R.Fersht
(1999).
The solution structure of oxidized Escherichia coli cytochrome b562.
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| |
Biochemistry,
38,
8657-8670.
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PDB code:
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G.Battistuzzi,
M.Borsari,
J.A.Cowan,
C.Eicken,
L.Loschi,
and
M.Sola
(1999).
Redox chemistry and acid-base equilibria of mitochondrial plant cytochromes c.
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| |
Biochemistry,
38,
5553-5562.
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G.Battistuzzi,
M.Borsari,
L.Loschi,
A.Martinelli,
and
M.Sola
(1999).
Thermodynamics of the alkaline transition of cytochrome c.
|
| |
Biochemistry,
38,
7900-7907.
|
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I.Bertini,
and
C.Luchinat
(1999).
New applications of paramagnetic NMR in chemical biology.
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| |
Curr Opin Chem Biol,
3,
145-151.
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J.Read,
R.Gill,
S.L.Dales,
J.B.Cooper,
S.P.Wood,
and
C.Anthony
(1999).
The molecular structure of an unusual cytochrome c2 determined at 2.0 A; the cytochrome cH from Methylobacterium extorquens.
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| |
Protein Sci,
8,
1232-1240.
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PDB code:
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S.M.Baxter,
and
J.S.Fetrow
(1999).
Hydrogen exchange behavior of [U-15N]-labeled oxidized and reduced iso-1-cytochrome c.
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| |
Biochemistry,
38,
4493-4503.
|
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F.Arnesano,
L.Banci,
I.Bertini,
and
D.Koulougliotis
(1998).
Solution structure of oxidized rat microsomal cytochrome b5 in the presence of 2 M guanidinium chloride: monitoring the early steps in protein unfolding.
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| |
Biochemistry,
37,
17082-17092.
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PDB code:
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J.S.Fetrow,
J.S.Spitzer,
B.M.Gilden,
S.J.Mellender,
T.J.Begley,
B.J.Haas,
and
T.L.Boose
(1998).
Structure, function, and temperature sensitivity of directed, random mutants at proline 76 and glycine 77 in omega-loop D of yeast iso-1-cytochrome c.
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| |
Biochemistry,
37,
2477-2487.
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L.Banci,
I.Bertini,
M.A.De la Rosa,
D.Koulougliotis,
J.A.Navarro,
and
O.Walter
(1998).
Solution structure of oxidized cytochrome c6 from the green alga Monoraphidium braunii.
|
| |
Biochemistry,
37,
4831-4843.
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PDB codes:
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M.Ubbink,
M.Ejdebäck,
B.G.Karlsson,
and
D.S.Bendall
(1998).
The structure of the complex of plastocyanin and cytochrome f, determined by paramagnetic NMR and restrained rigid-body molecular dynamics.
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| |
Structure,
6,
323-335.
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PDB code:
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T.Haruyama,
S.Shiino,
Y.Yanagida,
E.Kobatake,
and
M.Aizawa
(1998).
Two types of electrochemical nitric oxide (NO) sensing systems with heat-denatured Cyt C and radical scavenger PTIO.
|
| |
Biosens Bioelectron,
13,
763-769.
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Y.Xu,
L.Mayne,
and
S.W.Englander
(1998).
Evidence for an unfolding and refolding pathway in cytochrome c.
|
| |
Nat Struct Biol,
5,
774-778.
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L.Banci,
G.Gori-Savellini,
and
P.Turano
(1997).
A molecular dynamics study in explicit water of the reduced and oxidized forms of yeast iso-1-cytochrome c--solvation and dynamic properties of the two oxidation states.
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| |
Eur J Biochem,
249,
716-723.
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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
codes are
shown on the right.
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Links
