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Phys Rev E Stat Nonlin Soft Matter Phys. 2013 Jan;87(1):012706. Epub 2013 Jan 11.

Generic folding and transition hierarchies for surface adsorption of hydrophobic-polar lattice model proteins.

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1
Center for Simulational Physics, University of Georgia, Athens, Georgia 30602, USA. ywli@physast.uga.edu

Abstract

The thermodynamic behavior and structural properties of hydrophobic-polar (HP) lattice proteins interacting with attractive surfaces are studied by means of Wang-Landau sampling. Three benchmark HP sequences (48mer, 67mer, and 103mer) are considered with different types of surfaces, each of which attract either all monomers, only hydrophobic (H) monomers, or only polar (P) monomers, respectively. The diversity of folding behavior in dependence of surface strength is discussed. Analyzing the combined patterns of various structural observables, such as, e.g., the derivatives of the numbers of surface contacts, together with the specific heat, we are able to identify generic categories of folding and transition hierarchies. We also infer a connection between these transition categories and the relative surface strengths, i.e., the ratio of the surface attractive strength to the interchain attraction among H monomers. The validity of our proposed classification scheme is reinforced by the analysis of additional benchmark sequences. We thus believe that the folding hierarchies and identification scheme are generic for HP proteins interacting with attractive surfaces, regardless of chain length, sequence, or surface attraction.

PMID:
23410358
DOI:
10.1103/PhysRevE.87.012706
[Indexed for MEDLINE]
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