Journal
JOURNAL OF CHEMICAL PHYSICS
Volume 132, Issue 23, Pages -Publisher
AMER INST PHYSICS
DOI: 10.1063/1.3436723
Keywords
biochemistry; hydrogen bonds; molecular biophysics; proteins
Funding
- Spanish Ministerio de Ciencia e Innovacion [FIS2009-13364-C02-02, CSD2007-00010]
- Comunidad Autonoma de Madrid [S2009/PPQ-1551]
- Universidad Complutense de Madrid/Banco Santander Central Hispano [GR58/08-910068]
- Spanish Ministerio de Educacion
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One of the major disadvantages of coarse-grained hydrogen bond potentials, for their use in protein folding simulations, is the appearance of abnormal structures when these potentials are used in flexible chain models, and no other geometrical restrictions or energetic contributions are defined into the system. We have efficiently overcome this problem, for chains of adequate size in a relevant temperature range, with a refined coarse-grained hydrogen bond potential. With it, we have been able to obtain nativelike alpha-helices and beta-sheets in peptidic systems, and successfully reproduced the competition between the populations of these secondary structure elements by the effect of temperature and concentration changes. In this manuscript we detail the design of the interaction potential and thoroughly examine its applicability in energetic and structural terms, considering factors such as chain length, concentration, and temperature. (c) 2010 American Institute of Physics. [doi: 10.1063/1.3436723]
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