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PDBsum entry 3cln
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Calcium binding protein
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PDB id
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3cln
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Contents |
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* Residue conservation analysis
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J Mol Biol
204:191-204
(1988)
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PubMed id:
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Structure of calmodulin refined at 2.2 A resolution.
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Y.S.Babu,
C.E.Bugg,
W.J.Cook.
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ABSTRACT
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The crystal structure of mammalian calmodulin has been refined at 2.2 A (1 A =
0.1 nm) resolution using a restrained least-squares method. The final
crystallographic R-factor, based on 6685 reflections in the range 2.2 A less
than or equal to d less than or equal to 5.0 A with intensities exceeding 2.5
sigma, is 0.175. Bond lengths and bond angles in the molecule have
root-mean-square deviations from ideal values of 0.016 A and 1.7 degrees,
respectively. The refined model includes residues 5 to 147, four Ca2+ and 69
water molecules per molecule of calmodulin. The electron density for residues 1
to 4 and 148 is poorly defined, and they are not included in the model. The
molecule is shaped somewhat like a dumbbell, with an overall length of 65 A; the
two lobes are connected by a seven-turn alpha-helix. Prominent secondary
structural features include seven alpha-helices, four Ca2+-binding loops, and
two short, double-stranded antiparallel beta-sheets between pairs of adjacent
Ca2+-binding loops. The four Ca2+-binding domains in calmodulin have a typical
EF hand conformation (helix-loop-helix) and are similar to those described in
other Ca2+-binding proteins. The X-ray structure determination of calmodulin
shows a large hydrophobic cleft in each half of the molecule. These hydrophobic
regions probably represent the sites of interaction with many of the
pharmacological agents known to bind to calmodulin.
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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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J.Snijder,
R.J.Rose,
R.Raijmakers,
and
A.J.Heck
(2011).
Site-specific methionine oxidation in calmodulin affects structural integrity and interaction with Ca2+/calmodulin-dependent protein kinase II.
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J Struct Biol,
174,
187-195.
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G.L.Butterfoss,
E.F.DeRose,
S.A.Gabel,
L.Perera,
J.M.Krahn,
G.A.Mueller,
X.Zheng,
and
R.E.London
(2010).
Conformational dependence of 13C shielding and coupling constants for methionine methyl groups.
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J Biomol NMR,
48,
31-47.
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S.Pepke,
T.Kinzer-Ursem,
S.Mihalas,
and
M.B.Kennedy
(2010).
A dynamic model of interactions of Ca2+, calmodulin, and catalytic subunits of Ca2+/calmodulin-dependent protein kinase II.
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PLoS Comput Biol,
6,
e1000675.
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C.Li,
J.Chan,
F.Haeseleer,
K.Mikoshiba,
K.Palczewski,
M.Ikura,
and
J.B.Ames
(2009).
Structural Insights into Ca2+-dependent Regulation of Inositol 1,4,5-Trisphosphate Receptors by CaBP1.
|
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J Biol Chem,
284,
2472-2481.
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D.Yamamoto,
N.Nagura,
S.Omote,
M.Taniguchi,
and
T.Ando
(2009).
Streptavidin 2D crystal substrates for visualizing biomolecular processes by atomic force microscopy.
|
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Biophys J,
97,
2358-2367.
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J.L.Kitevski-LeBlanc,
F.Evanics,
and
R.S.Prosser
(2009).
Approaches for the measurement of solvent exposure in proteins by 19F NMR.
|
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J Biomol NMR,
45,
255-264.
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K.Teilum,
J.G.Olsen,
and
B.B.Kragelund
(2009).
Functional aspects of protein flexibility.
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Cell Mol Life Sci,
66,
2231-2247.
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M.Hemond,
T.L.Rothstein,
and
G.Wagner
(2009).
Fas apoptosis inhibitory molecule contains a novel beta-sandwich in contact with a partially ordered domain.
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J Mol Biol,
386,
1024-1037.
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PDB code:
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P.F.Chen,
and
K.K.Wu
(2009).
Two synthetic peptides corresponding to the proximal heme-binding domain and CD1 domain of human endothelial nitric-oxide synthase inhibit the oxygenase activity by interacting with CaM.
|
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Arch Biochem Biophys,
486,
132-140.
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S.Dobney,
D.Chiasson,
P.Lam,
S.P.Smith,
and
W.A.Snedden
(2009).
The calmodulin-related calcium sensor CML42 plays a role in trichome branching.
|
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J Biol Chem,
284,
31647-31657.
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T.I.Evans,
and
M.A.Shea
(2009).
Energetics of calmodulin domain interactions with the calmodulin binding domain of CaMKII.
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Proteins,
76,
47-61.
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V.Borsi,
C.Luchinat,
and
G.Parigi
(2009).
Global and local mobility of apocalmodulin monitored through fast-field cycling relaxometry.
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Biophys J,
97,
1765-1771.
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W.W.Streicher,
M.M.Lopez,
and
G.I.Makhatadze
(2009).
Annexin I and annexin II N-terminal peptides binding to S100 protein family members: specificity and thermodynamic characterization.
|
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Biochemistry,
48,
2788-2798.
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Y.Huang,
Y.Zhou,
A.Castiblanco,
W.Yang,
E.M.Brown,
and
J.J.Yang
(2009).
Multiple Ca(2+)-binding sites in the extracellular domain of the Ca(2+)-sensing receptor corresponding to cooperative Ca(2+) response.
|
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Biochemistry,
48,
388-398.
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Y.Timsit,
Z.Acosta,
F.Allemand,
C.Chiaruttini,
and
M.Springer
(2009).
The role of disordered ribosomal protein extensions in the early steps of eubacterial 50 s ribosomal subunit assembly.
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Int J Mol Sci,
10,
817-834.
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A.C.Rintala-Dempsey,
A.Rezvanpour,
and
G.S.Shaw
(2008).
S100-annexin complexes--structural insights.
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FEBS J,
275,
4956-4966.
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B.Kim,
and
A.Chilkoti
(2008).
Allosteric actuation of inverse phase transition of a stimulus-responsive fusion polypeptide by ligand binding.
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J Am Chem Soc,
130,
17867-17873.
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E.Laine,
J.D.Yoneda,
A.Blondel,
and
T.E.Malliavin
(2008).
The conformational plasticity of calmodulin upon calcium complexation gives a model of its interaction with the oedema factor of Bacillus anthracis.
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Proteins,
71,
1813-1829.
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E.M.Jones,
T.C.Squier,
and
C.A.Sacksteder
(2008).
An altered mode of calcium coordination in methionine-oxidized calmodulin.
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Biophys J,
95,
5268-5280.
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M.I.Stefan,
S.J.Edelstein,
and
N.Le Novère
(2008).
An allosteric model of calmodulin explains differential activation of PP2B and CaMKII.
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Proc Natl Acad Sci U S A,
105,
10768-10773.
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Q.Wang,
B.Shui,
M.I.Kotlikoff,
and
H.Sondermann
(2008).
Structural basis for calcium sensing by GCaMP2.
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Structure,
16,
1817-1827.
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PDB codes:
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Q.Ye,
H.Wang,
J.Zheng,
Q.Wei,
and
Z.Jia
(2008).
The complex structure of calmodulin bound to a calcineurin peptide.
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Proteins,
73,
19-27.
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PDB code:
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S.L.Reichow,
and
T.Gonen
(2008).
Noncanonical binding of calmodulin to aquaporin-0: implications for channel regulation.
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Structure,
16,
1389-1398.
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T.Ly,
and
R.R.Julian
(2008).
Protein-metal interactions of calmodulin and alpha-synuclein monitored by selective noncovalent adduct protein probing mass spectrometry.
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J Am Soc Mass Spectrom,
19,
1663-1672.
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X.Zhao,
S.Wang,
H.Pang,
K.Yang,
and
M.Bartlam
(2008).
Crystallization and preliminary X-ray diffraction studies of the calcium-binding protein CalD from Streptomyces coelicolor.
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Acta Crystallogr Sect F Struct Biol Cryst Commun,
64,
816-818.
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J.S.Sharp,
and
K.B.Tomer
(2007).
Analysis of the oxidative damage-induced conformational changes of apo- and holocalmodulin by dose-dependent protein oxidative surface mapping.
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Biophys J,
92,
1682-1692.
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J.T.Warren,
Q.Guo,
and
W.J.Tang
(2007).
A 1.3-A structure of zinc-bound N-terminal domain of calmodulin elucidates potential early ion-binding step.
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J Mol Biol,
374,
517-527.
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PDB code:
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K.Dunlap
(2007).
Calcium channels are models of self-control.
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J Gen Physiol,
129,
379-383.
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L.Jiang,
D.Fernandes,
N.Mehta,
J.L.Bean,
M.L.Michaelis,
and
A.Zaidi
(2007).
Partitioning of the plasma membrane Ca2+-ATPase into lipid rafts in primary neurons: effects of cholesterol depletion.
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J Neurochem,
102,
378-388.
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M.A.Zhukovsky,
I.Markovic,
and
A.L.Bailey
(2007).
Influence of calcium on lipid mixing mediated by influenza hemagglutinin.
|
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Arch Biochem Biophys,
465,
101-108.
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S.C.Flores,
and
M.B.Gerstein
(2007).
FlexOracle: predicting flexible hinges by identification of stable domains.
|
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BMC Bioinformatics,
8,
215.
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S.L.Russell,
N.V.McFerran,
E.M.Hoey,
A.Trudgett,
and
D.J.Timson
(2007).
Characterisation of two calmodulin-like proteins from the liver fluke, Fasciola hepatica.
|
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Biol Chem,
388,
593-599.
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S.Mathur,
M.Badertscher,
M.Scott,
and
R.Zenobi
(2007).
Critical evaluation of mass spectrometric measurement of dissociation constants: accuracy and cross-validation against surface plasmon resonance and circular dichroism for the calmodulin-melittin system.
|
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Phys Chem Chem Phys,
9,
6187-6198.
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T.M.Lakowski,
G.M.Lee,
M.Okon,
R.E.Reid,
and
L.P.McIntosh
(2007).
Calcium-induced folding of a fragment of calmodulin composed of EF-hands 2 and 3.
|
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Protein Sci,
16,
1119-1132.
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PDB code:
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T.S.Priddy,
E.S.Price,
C.K.Johnson,
and
G.M.Carlson
(2007).
Single molecule analyses of the conformational substates of calmodulin bound to the phosphorylase kinase complex.
|
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Protein Sci,
16,
1017-1023.
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T.Strahl,
I.G.Huttner,
J.D.Lusin,
M.Osawa,
D.King,
J.Thorner,
and
J.B.Ames
(2007).
Structural insights into activation of phosphatidylinositol 4-kinase (Pik1) by yeast frequenin (Frq1).
|
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J Biol Chem,
282,
30949-30959.
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PDB code:
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Z.Han,
and
R.N.Harty
(2007).
Influence of calcium/calmodulin on budding of Ebola VLPs: implications for the involvement of the Ras/Raf/MEK/ERK pathway.
|
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Virus Genes,
35,
511-520.
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C.K.Johnson
(2006).
Calmodulin, conformational states, and calcium signaling. A single-molecule perspective.
|
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Biochemistry,
45,
14233-14246.
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E.Meirovitch,
Y.E.Shapiro,
A.Polimeno,
and
J.H.Freed
(2006).
Protein dynamics from NMR: the slowly relaxing local structure analysis compared with model-free analysis.
|
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J Phys Chem A,
110,
8366-8396.
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E.Project,
R.Friedman,
E.Nachliel,
and
M.Gutman
(2006).
A molecular dynamics study of the effect of Ca2+ removal on calmodulin structure.
|
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Biophys J,
90,
3842-3850.
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F.Capozzi,
F.Casadei,
and
C.Luchinat
(2006).
EF-hand protein dynamics and evolution of calcium signal transduction: an NMR view.
|
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J Biol Inorg Chem,
11,
949-962.
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H.Deng,
G.Chen,
W.Yang,
and
J.J.Yang
(2006).
Predicting calcium-binding sites in proteins - a graph theory and geometry approach.
|
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Proteins,
64,
34-42.
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J.B.Ames,
K.Levay,
J.N.Wingard,
J.D.Lusin,
and
V.Z.Slepak
(2006).
Structural basis for calcium-induced inhibition of rhodopsin kinase by recoverin.
|
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J Biol Chem,
281,
37237-37245.
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PDB code:
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J.M.Shifman,
M.H.Choi,
S.Mihalas,
S.L.Mayo,
and
M.B.Kennedy
(2006).
Ca2+/calmodulin-dependent protein kinase II (CaMKII) is activated by calmodulin with two bound calciums.
|
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Proc Natl Acad Sci U S A,
103,
13968-13973.
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K.Chen,
J.Ruan,
and
L.A.Kurgan
(2006).
Prediction of three dimensional structure of calmodulin.
|
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Protein J,
25,
57-70.
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K.Sharp,
and
J.J.Skinner
(2006).
Pump-probe molecular dynamics as a tool for studying protein motion and long range coupling.
|
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Proteins,
65,
347-361.
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L.L.Clainche,
M.Figuet,
V.Montjardet-Bas,
S.Blanchard,
and
C.Vita
(2006).
Modulating the affinity and the selectivity of engineered calmodulin EF-Hand peptides for lanthanides.
|
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Biotechnol Bioeng,
95,
29-36.
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M.Ikura,
and
J.B.Ames
(2006).
Genetic polymorphism and protein conformational plasticity in the calmodulin superfamily: two ways to promote multifunctionality.
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Proc Natl Acad Sci U S A,
103,
1159-1164.
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N.Wu,
S.M.Hanson,
D.J.Francis,
S.A.Vishnivetskiy,
M.Thibonnier,
C.S.Klug,
M.Shoham,
and
V.V.Gurevich
(2006).
Arrestin binding to calmodulin: a direct interaction between two ubiquitous signaling proteins.
|
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J Mol Biol,
364,
955-963.
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P.Radivojac,
S.Vucetic,
T.R.O'Connor,
V.N.Uversky,
Z.Obradovic,
and
A.K.Dunker
(2006).
Calmodulin signaling: analysis and prediction of a disorder-dependent molecular recognition.
|
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Proteins,
63,
398-410.
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S.Lim,
and
S.J.Franklin
(2006).
Engineered lanthanide-binding metallohomeodomains: designing folded chimeras by modular turn substitution.
|
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Protein Sci,
15,
2159-2165.
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T.Ikeya,
T.Terauchi,
P.Güntert,
and
M.Kainosho
(2006).
Evaluation of stereo-array isotope labeling (SAIL) patterns for automated structural analysis of proteins with CYANA.
|
| |
Magn Reson Chem,
44,
S152-S157.
|
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Y.Timsit,
F.Allemand,
C.Chiaruttini,
and
M.Springer
(2006).
Coexistence of two protein folding states in the crystal structure of ribosomal protein L20.
|
| |
EMBO Rep,
7,
1013-1018.
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PDB code:
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A.A.Pandyra,
A.P.Yamniuk,
V.V.Andrushchenko,
H.Wieser,
and
H.J.Vogel
(2005).
Isotope-labeled vibrational circular dichroism studies of calmodulin and its interactions with ligands.
|
| |
Biopolymers,
79,
231-237.
|
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A.K.Dunker,
M.S.Cortese,
P.Romero,
L.M.Iakoucheva,
and
V.N.Uversky
(2005).
Flexible nets. The roles of intrinsic disorder in protein interaction networks.
|
| |
FEBS J,
272,
5129-5148.
|
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A.Sinz,
S.Kalkhof,
and
C.Ihling
(2005).
Mapping protein interfaces by a trifunctional cross-linker combined with MALDI-TOF and ESI-FTICR mass spectrometry.
|
| |
J Am Soc Mass Spectrom,
16,
1921-1931.
|
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C.L.Chyan,
P.C.Huang,
T.H.Lin,
J.W.Huang,
S.S.Lin,
H.B.Huang,
and
Y.C.Chen
(2005).
Purification, crystallization and preliminary crystallographic studies of a calmodulin-OLFp hybrid molecule.
|
| |
Acta Crystallogr Sect F Struct Biol Cryst Commun,
61,
785-787.
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G.Fiorin,
R.R.Biekofsky,
A.Pastore,
and
P.Carloni
(2005).
Unwinding the helical linker of calcium-loaded calmodulin: a molecular dynamics study.
|
| |
Proteins,
61,
829-839.
|
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G.Larsson,
J.Schleucher,
J.Onions,
S.Hermann,
T.Grundström,
and
S.S.Wijmenga
(2005).
Backbone dynamics of a symmetric calmodulin dimer in complex with the calmodulin-binding domain of the basic-helix-loop-helix transcription factor SEF2-1/E2-2: a highly dynamic complex.
|
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Biophys J,
89,
1214-1226.
|
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G.M.Contessa,
M.Orsale,
S.Melino,
V.Torre,
M.Paci,
A.Desideri,
and
D.O.Cicero
(2005).
Structure of calmodulin complexed with an olfactory CNG channel fragment and role of the central linker: residual dipolar couplings to evaluate calmodulin binding modes outside the kinase family.
|
| |
J Biomol NMR,
31,
185-199.
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PDB code:
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J.E.Debreczeni,
L.Farkas,
V.Harmat,
C.Hetényi,
I.Hajdú,
P.Závodszky,
K.Kohama,
and
L.Nyitray
(2005).
Structural evidence for non-canonical binding of Ca2+ to a canonical EF-hand of a conventional myosin.
|
| |
J Biol Chem,
280,
41458-41464.
|
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PDB code:
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J.N.Wingard,
J.Chan,
I.Bosanac,
F.Haeseleer,
K.Palczewski,
M.Ikura,
and
J.B.Ames
(2005).
Structural analysis of Mg2+ and Ca2+ binding to CaBP1, a neuron-specific regulator of calcium channels.
|
| |
J Biol Chem,
280,
37461-37470.
|
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M.Bartoli,
and
I.Richard
(2005).
Calpains in muscle wasting.
|
| |
Int J Biochem Cell Biol,
37,
2115-2133.
|
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