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PDBsum entry 1cll
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Calcium-binding protein
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PDB id
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1cll
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Contents |
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* Residue conservation analysis
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DOI no:
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J Mol Biol
228:1177-1192
(1992)
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PubMed id:
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Calmodulin structure refined at 1.7 A resolution.
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R.Chattopadhyaya,
W.E.Meador,
A.R.Means,
F.A.Quiocho.
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ABSTRACT
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We have determined and refined the crystal structure of a recombinant calmodulin
at 1.7 A resolution. The structure was determined by molecular replacement,
using the 2.2 A published native bovine brain structure as the starting model.
The final crystallographic R-factor, using 14,469 reflections in the 10.0 to 1.7
A range with structure factors exceeding 0.5 sigma, is 0.216. Bond lengths and
bond angle distances have root-mean-square deviations from ideal values of 0.009
A and 0.032 A, respectively. The final model consists of 1279 non-hydrogen
atoms, including four calcium ions, 1130 protein atoms, including three Asp118
side-chain atoms in double conformation, 139 water molecules and one ethanol
molecule. The electron densities for residues 1 to 4 and 148 of calmodulin are
poorly defined, and not included in our model, except for main-chain atoms of
residue 4. The calmodulin structure from our crystals is very similar to the
earlier 2.2 A structure described by Babu and coworkers with a root-mean-square
deviation of 0.36 A. Calmodulin remains a dumb-bell-shaped molecule, with
similar lobes and connected by a central alpha-helix. Each lobe contains three
alpha-helices and two Ca2+ binding EF hand loops, with a short antiparallel
beta-sheet between adjacent EF hand loops and one non-EF hand loop. There are
some differences in the structure of the central helix. The crystal packing is
extensively studied, and facile crystal growth along the z-axis of the triclinic
crystals is explained. Herein, we describe hydrogen bonding in the various
secondary structure elements and hydration of calmodulin.
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Selected figure(s)
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Figure 2.
Figure 2. The K-termnal domain is shown including all sidechains and most of the water molecules (circle) in the
region i stereo. Polar side-chain interacting with water molecules are labeled. (Ball and stick.) Part of the cent~ral
a-helix can be seen close to the viewer, going left an down towards th c-domain, which is not shown in this ig.
Residues 8 to 72 are displayed in this Fig. The view is clse to that in Fig. 1, but not identicl. Calcium ions 1 and 2 ar
shown as triple concentric circles.
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Figure 3.
Figure 3. The central cl-helix is shown in stereo, and ts polar residues labeled. (Ball and stick.) The view is diRerent
from Figs 2 and 4. The view is chosen so that the helix is seen vertical in this Fig. Some of the main-chain-side-chain and
side-chain-side-chain bonds can also be seen for residues belonging to this helix (described in able 4, sections D and E).
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(1992,
228,
1177-1192)
copyright 1992.
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Figures were
selected
by an automated process.
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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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Z.Grabarek
(2011).
Insights into modulation of calcium signaling by magnesium in calmodulin, troponin C and related EF-hand proteins.
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Biochim Biophys Acta,
1813,
913-921.
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A.K.Wernimont,
J.D.Artz,
P.Finerty,
Y.H.Lin,
M.Amani,
A.Allali-Hassani,
G.Senisterra,
M.Vedadi,
W.Tempel,
F.Mackenzie,
I.Chau,
S.Lourido,
L.D.Sibley,
and
R.Hui
(2010).
Structures of apicomplexan calcium-dependent protein kinases reveal mechanism of activation by calcium.
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Nat Struct Mol Biol,
17,
596-601.
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PDB codes:
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E.Kovacs,
J.Tóth,
B.G.Vértessy,
and
K.Liliom
(2010).
Dissociation of calmodulin-target peptide complexes by the lipid mediator sphingosylphosphorylcholine: implications in calcium signaling.
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J Biol Chem,
285,
1799-1808.
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G.L.Butterfoss,
E.F.Derose,
S.A.Gabel,
L.Perera,
J.M.Krahn,
G.A.Mueller,
X.Zheng,
and
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(2010).
Conformational dependence of (13)C shielding and coupling constants for methionine methyl groups.
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J Biomol NMR,
48,
31-47.
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J.Jiang,
Y.Zhou,
J.Zou,
Y.Chen,
P.Patel,
J.J.Yang,
and
E.M.Balog
(2010).
Site-specific modification of calmodulin Ca²(+) affinity tunes the skeletal muscle ryanodine receptor activation profile.
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Biochem J,
432,
89-99.
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J.Orans,
M.D.Johnson,
K.A.Coggan,
J.R.Sperlazza,
R.W.Heiniger,
M.C.Wolfgang,
and
M.R.Redinbo
(2010).
Crystal structure analysis reveals Pseudomonas PilY1 as an essential calcium-dependent regulator of bacterial surface motility.
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Proc Natl Acad Sci U S A,
107,
1065-1070.
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PDB code:
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K.Shiba,
T.Niidome,
E.Katoh,
H.Xiang,
L.Han,
T.Mori,
and
Y.Katayama
(2010).
Polydispersity as a parameter for indicating the thermal stability of proteins by dynamic light scattering.
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Anal Sci,
26,
659-663.
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M.D.Feldkamp,
S.E.O'Donnell,
L.Yu,
and
M.A.Shea
(2010).
Allosteric effects of the antipsychotic drug trifluoperazine on the energetics of calcium binding by calmodulin.
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Proteins,
78,
2265-2282.
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R.C.Cheng,
and
B.S.Zhorov
(2010).
Docking of calcium ions in proteins with flexible side chains and deformable backbones.
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Eur Biophys J,
39,
825-838.
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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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D.Homouz,
H.Sanabria,
M.N.Waxham,
and
M.S.Cheung
(2009).
Modulation of calmodulin plasticity by the effect of macromolecular crowding.
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J Mol Biol,
391,
933-943.
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E.Bitto,
C.A.Bingman,
L.Bittova,
R.O.Frederick,
B.G.Fox,
and
G.N.Phillips
(2009).
X-ray structure of Danio rerio secretagogin: A hexa-EF-hand calcium sensor.
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Proteins,
76,
477-483.
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PDB code:
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F.Guo,
and
J.M.Friedman
(2009).
Charge density-dependent modifications of hydration shell waters by Hofmeister ions.
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J Am Chem Soc,
131,
11010-11018.
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K.S.Keating,
S.C.Flores,
M.B.Gerstein,
and
L.A.Kuhn
(2009).
StoneHinge: hinge prediction by network analysis of individual protein structures.
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Protein Sci,
18,
359-371.
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S.J.Abraham,
R.P.Nolet,
R.J.Calvert,
L.M.Anderson,
and
V.Gaponenko
(2009).
The hypervariable region of K-Ras4B is responsible for its specific interactions with calmodulin.
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Biochemistry,
48,
7575-7583.
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S.Tripathi,
and
J.J.Portman
(2009).
Inherent flexibility determines the transition mechanisms of the EF-hands of calmodulin.
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Proc Natl Acad Sci U S A,
106,
2104-2109.
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S.Yang,
S.Park,
L.Makowski,
and
B.Roux
(2009).
A rapid coarse residue-based computational method for x-ray solution scattering characterization of protein folds and multiple conformational states of large protein complexes.
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Biophys J,
96,
4449-4463.
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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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E.Project,
E.Nachliel,
and
M.Gutman
(2008).
Parameterization of Ca+2-protein interactions for molecular dynamics simulations.
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J Comput Chem,
29,
1163-1169.
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J.Liu,
T.Vaithianathan,
K.Manivannan,
A.Parrill,
and
A.M.Dopico
(2008).
Ethanol modulates BKCa channels by acting as an adjuvant of calcium.
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Mol Pharmacol,
74,
628-640.
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J.O.Schulze,
C.Quedenau,
Y.Roske,
T.Adam,
H.Schüler,
J.Behlke,
A.P.Turnbull,
V.Sievert,
C.Scheich,
U.Mueller,
U.Heinemann,
and
K.Büssow
(2008).
Structural and functional characterization of human Iba proteins.
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FEBS J,
275,
4627-4640.
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PDB codes:
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K.Ruan,
K.B.Briggman,
and
J.R.Tolman
(2008).
De novo determination of internuclear vector orientations from residual dipolar couplings measured in three independent alignment media.
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J Biomol NMR,
41,
61-76.
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N.Juranić,
J.J.Dannenberg,
G.Cornilescu,
P.Salvador,
E.Atanasova,
H.C.Ahn,
S.Macura,
J.L.Markley,
and
F.G.Prendergast
(2008).
Structural dependencies of protein backbone 2JNC' couplings.
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Protein Sci,
17,
768-776.
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N.V.Valeyev,
D.G.Bates,
P.Heslop-Harrison,
I.Postlethwaite,
and
N.V.Kotov
(2008).
Elucidating the mechanisms of cooperative calcium-calmodulin interactions: a structural systems biology approach.
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BMC Syst Biol,
2,
48.
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N.V.Valeyev,
P.Heslop-Harrison,
I.Postlethwaite,
N.V.Kotov,
and
D.G.Bates
(2008).
Multiple calcium binding sites make calmodulin multifunctional.
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Mol Biosyst,
4,
66-73.
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Q.Guo,
J.E.Jureller,
J.T.Warren,
E.Solomaha,
J.Florián,
and
W.J.Tang
(2008).
Protein-protein docking and analysis reveal that two homologous bacterial adenylyl cyclase toxins interact with calmodulin differently.
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J Biol Chem,
283,
23836-23845.
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Q.Xiao,
A.Prussia,
K.Yu,
Y.Y.Cui,
and
H.C.Hartzell
(2008).
Regulation of bestrophin Cl channels by calcium: role of the C terminus.
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J Gen Physiol,
132,
681-692.
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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.W.Ho,
D.Jung,
J.R.Calhoun,
J.D.Lear,
M.Okon,
W.R.Scott,
R.E.Hancock,
and
S.K.Straus
(2008).
Effect of divalent cations on the structure of the antibiotic daptomycin.
|
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Eur Biophys J,
37,
421-433.
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T.L.Pukala,
T.Urathamakul,
S.J.Watt,
J.L.Beck,
R.J.Jackway,
and
J.H.Bowie
(2008).
Binding studies of nNOS-active amphibian peptides and Ca(2+) calmodulin, using negative ion electrospray ionisation mass spectrometry.
|
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Rapid Commun Mass Spectrom,
22,
3501-3509.
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Y.Zhang,
H.Tan,
Z.Jia,
and
G.Chen
(2008).
Ligand-induced dimer formation of calmodulin.
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J Mol Recognit,
21,
267-274.
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A.Isvoran,
C.T.Craescu,
and
E.Alexov
(2007).
Electrostatic control of the overall shape of calmodulin: numerical calculations.
|
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Eur Biophys J,
36,
225-237.
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C.Gourlaouen,
and
O.Parisel
(2007).
Is an electronic shield at the molecular origin of lead poisoning? A computational modeling experiment.
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Angew Chem Int Ed Engl,
46,
553-556.
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E.Lyman,
and
D.M.Zuckerman
(2007).
On the structural convergence of biomolecular simulations by determination of the effective sample size.
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J Phys Chem B,
111,
12876-12882.
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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.Henzler-Wildman,
and
D.Kern
(2007).
Dynamic personalities of proteins.
|
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Nature,
450,
964-972.
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L.Settimo,
S.Donnini,
A.H.Juffer,
R.W.Woody,
and
O.Marin
(2007).
Conformational changes upon calcium binding and phosphorylation in a synthetic fragment of calmodulin.
|
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Biopolymers,
88,
373-385.
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N.Juranić,
E.Atanasova,
J.H.Streiff,
S.Macura,
and
F.G.Prendergast
(2007).
Solvent-induced differentiation of protein backbone hydrogen bonds in calmodulin.
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Protein Sci,
16,
1329-1337.
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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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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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W.S.Jong,
C.M.ten Hagen-Jongman,
T.den Blaauwen,
D.J.Slotboom,
J.R.Tame,
D.Wickström,
J.W.de Gier,
B.R.Otto,
and
J.Luirink
(2007).
Limited tolerance towards folded elements during secretion of the autotransporter Hbp.
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Mol Microbiol,
63,
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A.A.Maximciuc,
J.A.Putkey,
Y.Shamoo,
and
K.R.Mackenzie
(2006).
Complex of calmodulin with a ryanodine receptor target reveals a novel, flexible binding mode.
|
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Structure,
14,
1547-1556.
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PDB code:
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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.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
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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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G.Fiorin,
A.Pastore,
P.Carloni,
and
M.Parrinello
(2006).
Using metadynamics to understand the mechanism of calmodulin/target recognition at atomic detail.
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Biophys J,
91,
2768-2777.
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J.H.Streiff,
T.W.Allen,
E.Atanasova,
N.Juranic,
S.Macura,
A.R.Penheiter,
and
K.A.Jones
(2006).
Prediction of volatile anesthetic binding sites in proteins.
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Biophys J,
91,
3405-3414.
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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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M.Kainosho,
T.Torizawa,
Y.Iwashita,
T.Terauchi,
A.Mei Ono,
and
P.Güntert
(2006).
Optimal isotope labelling for NMR protein structure determinations.
|
| |
Nature,
440,
52-57.
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PDB codes:
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S.K.Gerega,
and
K.M.Downard
(2006).
PROXIMO--a new docking algorithm to model protein complexes using data from radical probe mass spectrometry (RP-MS).
|
| |
Bioinformatics,
22,
1702-1709.
|
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S.O.Yesylevskyy,
V.N.Kharkyanen,
and
A.P.Demchenko
(2006).
The change of protein intradomain mobility on ligand binding: is it a commonly observed phenomenon?
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| |
Biophys J,
91,
3002-3013.
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T.C.Squier
(2006).
Redox modulation of cellular metabolism through targeted degradation of signaling proteins by the proteasome.
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Antioxid Redox Signal,
8,
217-228.
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C.Schöneich
(2005).
Mass spectrometry in aging research.
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Mass Spectrom Rev,
24,
701-718.
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C.Silve,
C.Petrel,
C.Leroy,
H.Bruel,
E.Mallet,
D.Rognan,
and
M.Ruat
(2005).
Delineating a Ca2+ binding pocket within the venus flytrap module of the human calcium-sensing receptor.
|
| |
J Biol Chem,
280,
37917-37923.
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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.Rabah,
R.Popescu,
J.A.Cox,
Y.Engelborghs,
and
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PDB code:
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NMR studies of the E140Q mutant of the carboxy-terminal domain of calmodulin reveal global conformational exchange in the Ca2+-saturated state.
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Biochemistry,
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The structure of a calmodulin mutant with a deletion in the central helix: implications for molecular recognition and protein binding.
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Structure,
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PDB code:
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Calcium binding decreases the stokes radius of calmodulin and mutants R74A, R90A, and R90G.
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Biophys J,
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Complexes formed between calmodulin and the antagonists J-8 and TFP in solution.
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Biochemistry,
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J Biol Chem,
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Solution X-ray scattering data show structural differences between yeast and vertebrate calmodulin: implications for structure/function.
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Biochemistry,
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The fourth EF-hand of calmodulin and its helix-loop-helix components: impact on calcium binding and enzyme activation.
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Biochemistry,
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Kinetic tuning of the EF-hand calcium binding motif: the gateway residue independently adjusts (i) barrier height and (ii) equilibrium.
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Biochemistry,
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Tuning the equilibrium ion affinity and selectivity of the EF-hand calcium binding motif: substitutions at the gateway position.
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Biochemistry,
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Oxidative modification of a carboxyl-terminal vicinal methionine in calmodulin by hydrogen peroxide inhibits calmodulin-dependent activation of the plasma membrane Ca-ATPase.
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Biochemistry,
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Y.Yao,
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Dynamic structure of the calmodulin-binding domain of the plasma membrane Ca-ATPase in native erythrocyte ghost membranes.
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Biochemistry,
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Variable conformation and dynamics of calmodulin complexed with peptides derived from the autoinhibitory domains of target proteins.
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Biochemistry,
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Structure,
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Calmodulin binding of a peptide derived from the regulatory domain of Bordetella pertussis adenylate cyclase.
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Mol Cell Biochem,
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Targeted disruption of Ca(2+)-calmodulin signaling in Drosophila growth cones leads to stalls in axon extension and errors in axon guidance.
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Neuron,
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Ca2+ binding to calmodulin and its role in Schizosaccharomyces pombe as revealed by mutagenesis and NMR spectroscopy.
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J Biol Chem,
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The calmodulin-nitric oxide synthase interaction. Critical role of the calmodulin latch domain in enzyme activation.
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J Biol Chem,
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Eur J Biochem,
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Calmodulin and the regulation of smooth muscle contraction.
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Mol Cell Biochem,
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Protein Sci,
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PDB code:
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|
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|
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|
|
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Citation data come partly from CiteXplore and partly
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only a partial list as not all journals are covered by
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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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