Significance of Knotted Structures for Function of Proteins and Nucleic Acids
Thursday Abstracts
Multiscale Modeling of Protein Flexibility
Sebastian Kmiecik
, Michal Jamroz, Maciej Blaszczyk, Andrzej Kolinski.
University of Warsaw, Warsaw, Poland.
Conformational flexibility plays an important role in protein function. Structural characterization
of protein flexibility is a challenge for both, experimental and simulation techniques.
Recently, we have developed a multiscale modeling procedure for the efficient simulation of
flexibility of globular proteins. The method have been made available as CABS-flex server
(
) [1]. The CABS-flex method was shown to be a
computationally efficient alternative to all-atom molecular dynamics - a classical simulation
approach [2]. We also demonstrated that the relative fluctuations of protein residues obtained
from CABS-flex are well correlated to those of NMR ensembles [3].
Since CABS-flex requires an input in the form of a complete (without breaks) protein chain, the
CABS-flex input for the proteins with missing structure data needs to be additionally prepared.
In such cases, the modeling can be supported with our other tool for the prediction of protein
structure: the CABS-fold server (
) [4].
References
[1] Michal Jamroz, Andrzej Kolinski and Sebastian Kmiecik. CABS-flex: server for fast
simulation of protein structure fluctuations. Nucleic Acids Research, 41: W427-W431, 2013.
[2] Michał Jamroz, Modesto Orozco, Andrzej Kolinski and Sebastian Kmiecik. Consistent View
of Protein Fluctuations from All-Atom Molecular Dynamics and Coarse-Grained Dynamics with
Knowledge-Based Force-Field. Journal of Chemical Theory and Computation, 9: 119-125, 2013.
[3] Michal Jamroz, Andrzej Kolinski and Sebastian Kmiecik. CABS-flex predictions of protein
flexibility compared with NMR ensembles. Bioinformatics, doi: 10.1093/bioinformatics/btu184,
2014.
[4] Maciej Blaszczyk, Michal Jamroz, Sebastian Kmiecik, Andrzej Kolinski. CABS-fold: server
for the de novo and consensus-based prediction of protein structure. Nucleic Acids Research,
41:W406-W411, 2013.
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