A virtual library of constrained cyclic tetrapeptides that mimics all four side-chain orientations for over half the reverse turns in the protein data bank

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Abstract

Reverse turns are often recognition sites for protein/protein interactions and, therefore, valuable potential targets for determining recognition motifs in development of potential therapeutics. A virtual combinatorial library of cyclic tetrapeptides (CTPs) was generated and the bonds in the low-energy structures were overlapped with canonical reverse-turn Cα-Cβ bonds (Tran et al., J Comput Aided Mol Des 19(8):551-566, 2005) to determine the utility of CTPs as reverse-turn peptidomimetics. All reverse turns in the Protein Data Bank (PDB) with a crystal structures resolution ≤3.0 Å were classified into the same known canonical reverse-turn Cα-Cβ bond clusters (Tran et al., J Comput Aided Mol Des 19(8):551-566, 2005). CTP reverse-turn mimics were compiled that mimicked both the relative orientations of three of the four as well as all four Cα-Cβ bonds in the reverse turns of the PDB. 54% of reverse turns represented in the PDB had eight or more CTPs structures that mimicked the orientation of all four of the Cα-Cβ bonds in the reverse turn.

Original languageEnglish
Pages (from-to)87-95
Number of pages9
JournalJournal of Computer-Aided Molecular Design
Volume23
Issue number2
DOIs
StatePublished - 2009

Keywords

  • Conformational search
  • Cyclic tetrapeptide
  • Mimic
  • Reverse turn

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