title: 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.
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 Calpha-Cbeta 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 < or = 3.0 A were classified into the same known canonical reverse-turn Calpha-Cbeta 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 Calpha-Cbeta 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 Calpha-Cbeta bonds in the reverse turn.
authors.affiliation: Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA. sagearbor@gmail.com
authors.forename: Sage
authors.initials: S
authors.lastname: Arbor
authors.forename: Garland R
authors.initials: GR
authors.lastname: Marshall
mesh_terms: D003198:Computer Simulation; D030562:Databases, Protein; D008956:Models, Chemical; D009842:Oligopeptides / Q000737:chemistry*; D019151:Peptide Library; D010456:Peptides, Cyclic / Q000737:chemistry*; D011487:Protein Conformation; D013816:Thermodynamics
chemical_list: D009842:Oligopeptides; D019151:Peptide Library; D010456:Peptides, Cyclic
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