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Navigation and analysis of the energy landscape of small proteins using the activation–relaxation technique

Normand Mousseau1, P Derreumaux2 and G Gilbert1

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The resolution of the protein folding problem has been tied to the development of a detailed understanding of the configurational energy or of the free energy landscape associated with these molecules. Using the activation–relaxation technique and a simplified energy model, we present here a detailed analysis of the energy landscape of 16-residue peptide that folds into a β-hairpin. Our results support the concept of an energy landscape with an effective topology consistent with a scale-free network.


PACS

87.15.Cc Folding: thermodynamics, statistical mechanics, models, and pathways

87.15.H- Dynamics of biomolecules

36.20.Hb Configuration (bonds, dimensions)

87.14.E- Proteins

87.15.B- Structure of biomolecules

Subjects

Soft matter, liquids and polymers

Atomic and molecular physics

Biological physics

Dates

Issue 4 (December 2005)

Received 15 May 2005, accepted for publication 28 July 2005

Published 9 November 2005

 
Superimposed conformation present in the folding trajectories using both the standard and barrier accept/reject criteria.


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