Exploring the energy landscape of model proteins: a metric criterion for the determination of dynamical connectivity

A method to reconstruct the energy landscape of small peptides is presented with reference to a two-dimensional off-lattice model. The starting point is a statistical analysis of the configurational distances between generic minima and directly connected pairs (DCP). As the mutual distance of DCP is...

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Bibliographic Details
Published in:Physical review. E, Statistical, nonlinear, and soft matter physics Statistical, nonlinear, and soft matter physics, 2005-11, Vol.72 (5 Pt 1), p.051929-051929, Article 051929
Main Authors: Bongini, Lorenzo, Livi, Roberto, Politi, Antonio, Torcini, Alessandro
Format: Article
Language:English
Subjects:
Amino Acid Sequence
Computer Simulation
Energy Transfer
Models, Chemical
Models, Molecular
Molecular Sequence Data
Protein Conformation
Protein Denaturation
Protein Folding
Proteins - chemistry
Sequence Analysis, Protein - methods
Thermodynamics
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Summary:A method to reconstruct the energy landscape of small peptides is presented with reference to a two-dimensional off-lattice model. The starting point is a statistical analysis of the configurational distances between generic minima and directly connected pairs (DCP). As the mutual distance of DCP is typically much smaller than that of generic pairs, a metric criterion can be established to identify the great majority of DCP. Advantages and limits of this approach are thoroughly analyzed for three different heteropolymeric chains. A funnel-like structure of the energy landscape is found in all of the three cases, but the escape rates clearly reveal that the native configuration is more easily accessible (and is significantly more stable) for the sequence that is expected to behave as a real protein.
ISSN:1539-3755
1550-2376
DOI:10.1103/PhysRevE.72.051929