Local interactions and protein folding: A three-dimensional off-lattice approach

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Abstract

The thermodynamic behavior of a three-dimensional off-lattice model for protein folding is probed. The model has only two types of residues, hydrophobia and hydrophilic. In absence of local interactions, native structure formation does not occur for the temperatures considered. By including sequence independent local interactions, which qualitatively reproduce local properties of functional proteins, the dominance of a native state for many sequences is observed. As in lattice model approaches, folding takes place by gradual compactification, followed by a sequence dependent folding transition. Our results differ from lattice approaches in that bimodal energy distributions are not observed and that high folding temperatures are accompanied by relatively low temperatures for the peak of the specific heat. Also, in contrast to earlier studies using lattice models, our results convincingly demonstrate that one does not need more than two types of residues to generate sequences with good thermodynamic folding properties in three dimensions.

Detaljer

Författare
Enheter & grupper
Originalspråkengelska
Sidor (från-till)273-282
Antal sidor10
TidskriftJournal of Chemical Physics
Volym107
Utgivningsnummer1
StatusPublished - 1997 jul 1
PublikationskategoriForskning
Peer review utfördJa