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Title:From polymers to proteins: the effect of side chains and broken symmetry on the formation of secondary structures within a Wang–Landau approach
Authors:Giacometti, Achille (Authorship owner)
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Language:English
Work type:Not categorized (r6)
Tipology:1.01 - Original Scientific Article
Organization:UNG - University of Nova Gorica
Abstract:We use a micro-canonical Wang–Landau technique to study the equilibrium properties of a single flexible homopolymer where consecutive monomers are represented by impenetrable hard spherical beads tangential to each other, and non-consecutive monomers interact via a square-well potential. To mimic the characteristics of a protein-like system, the model is then refined in two different directions. Firstly, by allowing partial overlap between consecutive beads, we break the spherical symmetry and thus provide a severe constraint on the possible conformations of the chain. Alternatively, we introduce additional spherical beads at specific positions in the direction normal to the backbone, to represent the steric hindrance of the side chains in real proteins. Finally, we consider also a combination of these two ingredients. In all three systems, we obtain the full phase diagram in the temperature-interaction range plane and find the presence of helicoidal structures at low temperatures in the intermediate range of interactions. The effect of the range of the square-well attraction is highlighted, and shown to play a role similar to that found in simple liquids and polymers. Perspectives in terms of protein folding are finally discussed.
Keywords:Wang-Landau approach, Monte-Carlo simulations, proteins, secondary structures
Year of publishing:2016
Number of pages:13
Numbering:0
COBISS_ID:2954852  Link is opened in a new window
URN:URN:SI:UNG:REP:X5Z2MTSO
DOI:10.1039/C6SM00542J Link is opened in a new window
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Record is a part of a journal

Title:Soft Matter
Publisher:Royal Society of Chemistry
ISSN:1744-683X
Year of publishing:2016

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