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Conformational subspace in simulation of early-stage protein folding
JURKOWSKI, Wiktor; Brylinski, Michal; Konieczny, Leszek et al.
2004In Proteins, 55 (1), p. 115-27
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Abstract :
[en] A probability calculus was used to simulate the early stages of protein folding in ab initio structure prediction. The probabilities of particular phi and psi angles for each of 20 amino acids as they occur in crystal forms of proteins were used to calculate the amount of information necessary for the occurrence of given phi and psi angles to be predicted. It was found that the amount of information needed to predict phi and psi angles with 5 degrees precision is much higher than the amount of information actually carried by individual amino acids in the polypeptide chain. To handle this problem, a limited conformational space for the preliminary search for optimal polypeptide structure is proposed based on a simplified geometrical model of the polypeptide chain and on the probability calculus. These two models, geometric and probabilistic, based on different sources, yield a common conclusion concerning how a limited conformational space can represent an early stage of polypeptide chain-folding simulation. The ribonuclease molecule was used to test the limited conformational space as a tool for modeling early-stage folding.
Disciplines :
Biochemistry, biophysics & molecular biology
Identifiers :
UNILU:UL-ARTICLE-2012-588
Author, co-author :
JURKOWSKI, Wiktor ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)
Brylinski, Michal
Konieczny, Leszek
Wiiniowski, Zdzislaw
Roterman, Irena
External co-authors :
yes
Language :
English
Title :
Conformational subspace in simulation of early-stage protein folding
Publication date :
2004
Journal title :
Proteins
ISSN :
0887-3585
eISSN :
1097-0134
Publisher :
Wiley Liss, Inc., New York, United States - New York
Volume :
55
Issue :
1
Pages :
115-27
Peer reviewed :
Peer Reviewed verified by ORBi
Available on ORBilu :
since 08 April 2016

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