Identifying proteins of high designability via surface-exposure patterns

Eldon G. Emberly, Jonathan Miller, Chen Zeng, Ned S. Wingreen, Chao Tang

Research output: Contribution to journalArticlepeer-review

9 Scopus citations

Abstract

Using an off-lattice model, we fully enumerate folded conformations of polypeptide chains of up to N = 19 monomers. Structures are found to differ markedly in designability, defined as the number of sequences with that structure as a unique lowest-energy conformation. We find that designability is closely correlated with the pattern of surface exposure of the folded structure. For longer chains, complete enumeration of structures is impractical. Instead, structures can be randomly sampled, and relative designability estimated either from designability within the random sample, or directly from surface-exposure pattern. We compare the surface-exposure patterns of those structures identified as highly designable to the patterns of naturally occurring proteins.

Original languageEnglish (US)
Pages (from-to)295-304
Number of pages10
JournalProteins: Structure, Function and Genetics
Volume47
Issue number3
DOIs
StatePublished - May 15 2002

All Science Journal Classification (ASJC) codes

  • Structural Biology
  • Biochemistry
  • Molecular Biology

Keywords

  • Hydrophobicity
  • Off-lattice model
  • Protein design
  • Protein structure prediction

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