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PDBsum entry 2nr2
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Signaling protein
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PDB id
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2nr2
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Contents |
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* Residue conservation analysis
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J Biomol Nmr
37:117-135
(2007)
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PubMed id:
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The MUMO (minimal under-restraining minimal over-restraining) method for the determination of native state ensembles of proteins.
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B.Richter,
J.Gsponer,
P.Várnai,
X.Salvatella,
M.Vendruscolo.
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ABSTRACT
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While reliable procedures for determining the conformations of proteins are
available, methods for generating ensembles of structures that also reflect
their flexibility are much less well established. Here we present a systematic
assessment of the ability of ensemble-averaged molecular dynamics simulations
with ensemble-averaged NMR restraints to simultaneously reproduce the average
structure of proteins and their associated dynamics. We discuss the effects that
under-restraining (overfitting) and over-restraining (underfitting) have on the
structures generated in ensemble-averaged molecular simulations. We then
introduce the MUMO (minimal under-restraining minimal over-restraining) method,
a procedure in which different observables are averaged over a different number
of molecules. As both over-restraining and under-restraining are significantly
reduced in the MUMO method, it is possible to generate ensembles of
conformations that accurately characterize both the structure and the dynamics
of native states of proteins. The application of the MUMO method to the protein
ubiquitin yields a high-resolution structural ensemble with an RDC Q-factor of
0.19.
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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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L.Mollica,
G.Morra,
G.Colombo,
and
G.Musco
(2011).
HMGB1-Carbenoxolone Interactions: Dynamics Insights from Combined Nuclear Magnetic Resonance and Molecular Dynamics.
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Chem Asian J,
6,
1171-1180.
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M.Lin,
J.Zhang,
H.M.Lu,
R.Chen,
and
J.Liang
(2011).
Constrained proper sampling of conformations of transition state ensemble of protein folding.
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J Chem Phys,
134,
075103.
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A.F.Angyán,
B.Szappanos,
A.Perczel,
and
Z.Gáspári
(2010).
CoNSEnsX: an ensemble view of protein structures and NMR-derived experimental data.
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BMC Struct Biol,
10,
39.
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T.R.Lezon,
and
I.Bahar
(2010).
Using entropy maximization to understand the determinants of structural dynamics beyond native contact topology.
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PLoS Comput Biol,
6,
e1000816.
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C.A.Laughton,
M.Orozco,
and
W.Vranken
(2009).
COCO: a simple tool to enrich the representation of conformational variability in NMR structures.
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Proteins,
75,
206-216.
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C.Farès,
N.A.Lakomek,
K.F.Walter,
B.T.Frank,
J.Meiler,
S.Becker,
and
C.Griesinger
(2009).
Accessing ns-micros side chain dynamics in ubiquitin with methyl RDCs.
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J Biomol NMR,
45,
23-44.
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D.M.LeMaster,
J.S.Anderson,
and
G.Hernández
(2009).
Peptide conformer acidity analysis of protein flexibility monitored by hydrogen exchange.
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Biochemistry,
48,
9256-9265.
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G.Batta,
T.Barna,
Z.Gáspári,
S.Sándor,
K.E.Kövér,
U.Binder,
B.Sarg,
L.Kaiserer,
A.K.Chhillar,
A.Eigentler,
E.Leiter,
N.Hegedüs,
I.Pócsi,
H.Lindner,
and
F.Marx
(2009).
Functional aspects of the solution structure and dynamics of PAF--a highly-stable antifungal protein from Penicillium chrysogenum.
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FEBS J,
276,
2875-2890.
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PDB code:
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G.D.Friedland,
N.A.Lakomek,
C.Griesinger,
J.Meiler,
and
T.Kortemme
(2009).
A correspondence between solution-state dynamics of an individual protein and the sequence and conformational diversity of its family.
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PLoS Comput Biol,
5,
e1000393.
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PDB code:
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K.Lindorff-Larsen,
and
J.Ferkinghoff-Borg
(2009).
Similarity measures for protein ensembles.
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PLoS ONE,
4,
e4203.
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A.F.Angyán,
A.Perczel,
S.Pongor,
and
Z.Gáspári
(2008).
Fast protein fold estimation from NMR-derived distance restraints.
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Bioinformatics,
24,
272-275.
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D.L.Theobald,
and
D.S.Wuttke
(2008).
Accurate structural correlations from maximum likelihood superpositions.
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PLoS Comput Biol,
4,
e43.
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J.Gsponer,
J.Christodoulou,
A.Cavalli,
J.M.Bui,
B.Richter,
C.M.Dobson,
and
M.Vendruscolo
(2008).
A coupled equilibrium shift mechanism in calmodulin-mediated signal transduction.
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Structure,
16,
736-746.
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PDB codes:
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O.F.Lange,
N.A.Lakomek,
C.Farès,
G.F.Schröder,
K.F.Walter,
S.Becker,
J.Meiler,
H.Grubmüller,
C.Griesinger,
and
B.L.de Groot
(2008).
Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution.
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Science,
320,
1471-1475.
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PDB code:
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X.Salvatella,
B.Richter,
and
M.Vendruscolo
(2008).
Influence of the fluctuations of the alignment tensor on the analysis of the structure and dynamics of proteins using residual dipolar couplings.
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J Biomol NMR,
40,
71-81.
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G.Bouvignies,
P.R.Markwick,
and
M.Blackledge
(2007).
Simultaneous definition of high resolution protein structure and backbone conformational dynamics using NMR residual dipolar couplings.
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Chemphyschem,
8,
1901-1909.
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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
