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Folding of Polyalanine into Helical Hairpins
Author(s) -
Palenčár Peter,
Bleha Tomáš
Publication year - 2010
Publication title -
macromolecular theory and simulations
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.37
H-Index - 56
eISSN - 1521-3919
pISSN - 1022-1344
DOI - 10.1002/mats.201000034
Subject(s) - folding (dsp implementation) , chemistry , biophysics , biology , electrical engineering , engineering
The variation of the secondary structure and dimensions of long PA peptides was examined by means of all‐atom MD simulations. It was found that on cooling, instead of straight helices, hairpin‐like structures with two and three parallel helical legs were formed. The exclusive population of hairpins in PA at room temperature was proved by the bimodality of the distribution functions of the end‐to‐end distance and the radius of gyration. The helix‐turn‐helix motif revealed in PA simulations is pertinent for the structure of transmembrane proteins. The potential energy analysis showed a crucial role of the van der Waals forces in stabilization of the hairpins. It was underlined that this is a feature shared with folding of hydrocarbon chains, such as PE, into the crystal lamellae.