Mean-Field HP Model, Designability and Alpha-Helices in Protein Structures

Abstract

Analysis of the geometric properties of a mean-field HP model on a square lattice for protein structure shows that structures with large number of switch backs between surface and core sites are chosen favorably by peptides as unique ground states. Global comparison of model (binary) peptide sequences with concatenated (binary) protein sequences listed in the Protein Data Bank and the Dali Domain Dictionary indicates that the highest correlation occurs between model peptides choosing the favored structures and those portions of protein sequences containing alpha-helices.

4 pages, 2 figures

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Cited by in corpus (8)

• Symmetry and designability for lattice protein models
• Simple Models of the Protein Folding Problem
• Fast Tree Search for Enumeration of a Lattice Model of Protein Folding
• Geometry Selects Highly Designable Structures
• Geometric and Statistical Properties of the Mean-Field HP Model, the LS Model and Real Protein Sequences
• Characteristic Length Scale of Electric Transport Properties of Genomes
• Structure Space of Model Proteins --A Principle Component Analysis
• Unfolding designable structures