Free energies and forces in helix―coil transition of homopolypeptides under stretching

We show here that constant velocity steered molecular dynamics (SMD) simulations of alpha-helices in a vacuum present a well defined plateau in the force-extension relationship for homopolypeptides having more than (approximately) twenty residues. With the processes being far away from equilibrium,...

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Bibliographic Details
Published in:Physical chemistry chemical physics : PCCP 2009-01, Vol.11 (20), p.4019-4024
Main Authors: ZEGARRA, Fabio C, PERALTA, Gian N, CORONADO, Alberto M, YI QIN GAO
Format: Article
Language:English
Subjects:
Alanine - chemistry
Amino Acid Sequence
Biomechanical Phenomena
Chemistry
Exact sciences and technology
General and physical chemistry
Models, Molecular
Molecular Sequence Data
Peptides - chemistry
Protein Denaturation
Protein Structure, Secondary
Thermodynamics
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Summary:We show here that constant velocity steered molecular dynamics (SMD) simulations of alpha-helices in a vacuum present a well defined plateau in the force-extension relationship for homopolypeptides having more than (approximately) twenty residues. With the processes being far away from equilibrium, the energies strongly depend on the stretching velocity. Importantly, for a given velocity variation, the energy variation depends also on the helix sequence. Additionally, our observations show that homopolypeptides made of ten different amino acids (Ala, Cys, Gln, Ile, Leu, Met, Phe, Ser, Thr and Val) present a linear helix-coil transition.
ISSN:1463-9076
1463-9084
DOI:10.1039/b820021a