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Conservation of closed loops.

Authors
  • Yew, Boon K1
  • Chintapalli, Sree V
  • Upton, Graham G C
  • Reynolds, Christopher A
  • 1 Department of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, United Kingdom.
Type
Published Article
Journal
Journal of Molecular Graphics and Modelling
Publisher
Elsevier
Publication Date
October 2007
Volume
26
Issue
3
Pages
652–655
Identifiers
PMID: 17459747
Source
Medline
License
Unknown

Abstract

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.

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