Conservation of closed loops

Boon K. Yew, Sree V. Chintapalli, Graham G.C. Upton, Christopher A. Reynolds

Research output: Contribution to journalArticlepeer-review

9 Citations (Scopus)


The closed loop hypothesis of Berezovsky and Trifonov implicates the closure of loops of length 25-35 through hydrophobic interactions at the 'locks' as a key event in protein folding. The hypothesis is supported by published analyses of nine major superfolds. Here, we have generated multiple sequence alignments for the nine superfolds with PDB codes lthb, 1ilb, 256b, 2rhe, 1aps, 2stv, 4fxn (2fox), lubq and 7tim and have analysed the degree of conservation at the loop ends. Seventy percent of these loop ends are found to be well conserved and the peak in the distribution of distances between these well conserved regions lies at around 25 residues; both observations are consistent with the Berezovsky and Trifonov's hypothesis.

Original languageEnglish
Pages (from-to)652-655
Number of pages4
JournalJournal of Molecular Graphics and Modelling
Issue number3
Early online date27 Mar 2007
Publication statusPublished - 1 Oct 2007
Externally publishedYes


  • Closed loops
  • Conservation
  • Entropy
  • Hydrophobicity
  • Leventhal paradox
  • Protein folding

ASJC Scopus subject areas

  • Spectroscopy
  • Physical and Theoretical Chemistry
  • Computer Graphics and Computer-Aided Design
  • Materials Chemistry


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