Structural characteristics of novel protein folds

Narcis Fernandez-Fuentes, Joseph M. Dybas, Andras Fiser

Research output: Contribution to journalArticle

37 Citations (Scopus)

Abstract

Folds are the basic building blocks of protein structures. Understanding the emergence of novel protein folds is an important step towards understanding the rules governing the evolution of protein structure and function and for developing tools for protein structure modeling and design. We explored the frequency of occurrences of an exhaustively classified library of supersecondary structural elements (Smotifs), in protein structures, in order to identify features that would define a fold as novel compared to previously known structures. We found that a surprisingly small set of Smotifs is sufficient to describe all known folds. Furthermore, novel folds do not require novel Smotifs, but rather are a new combination of existing ones. Novel folds can be typified by the inclusion of a relatively higher number of rarely occurring Smotifs in their structures and, to a lesser extent, by a novel topological combination of commonly occurring Smotifs. When investigating the structural features of Smotifs, we found that the top 10% of most frequent ones have a higher fraction of internal contacts, while some of the most rare motifs are larger, and contain a longer loop region

Original languageEnglish (US)
JournalPLoS Computational Biology
Volume6
Issue number4
DOIs
StatePublished - Apr 2010

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protein structure
Fold
Protein Structure
fold
Proteins
Protein
protein
proteins
new combination
Libraries
Building Blocks
Inclusion
Contact
Sufficient
Internal
Modeling
modeling

ASJC Scopus subject areas

  • Cellular and Molecular Neuroscience
  • Ecology
  • Molecular Biology
  • Genetics
  • Ecology, Evolution, Behavior and Systematics
  • Modeling and Simulation
  • Computational Theory and Mathematics

Cite this

Structural characteristics of novel protein folds. / Fernandez-Fuentes, Narcis; Dybas, Joseph M.; Fiser, Andras.

In: PLoS Computational Biology, Vol. 6, No. 4, 04.2010.

Research output: Contribution to journalArticle

Fernandez-Fuentes, Narcis ; Dybas, Joseph M. ; Fiser, Andras. / Structural characteristics of novel protein folds. In: PLoS Computational Biology. 2010 ; Vol. 6, No. 4.
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