title: Neighbor effect on PPII conformation in alanine peptides.
abstract: The polyproline II (PPII) conformation is dominant in short alanine oligomers. The noncooperativity of PPII structure in alanine peptides indicates that PPII in water is locally determined and that alanine neighbors are consistent with Flory's isolated pair hypothesis. However, neighbor effects from beta-branched or bulky aromatic residues tend to increase the Phi angle of the nearest neighbor as observed in coil library data. Here we demonstrate directly the neighbor effect using short alanine model peptides GGAAAGG, GGLnALnGG (Ln is norleucine), GGIAAGG, and GGIAIGG. The far-UV CD spectra, NMR 3JalphaN coupling constant, and H-D hydrogen exchange measurements reveal that Ile reduces the PPII content of the probe Ala side chain relative to Ala or norLeu. The free energy differences are consistent with predictions from electrostatic solvation free energy (ESF) calculations. The results indicate that prediction of PPII propensities or scales requires including the neighbor effect.
authors: Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, USA.
authors: Kang
authors: K
authors: Chen
authors: Zhigang
authors: Z
authors: Liu
authors: Chunhui
authors: C
authors: Zhou
authors: Zhengshuang
authors: Z
authors: Shi
authors: Neville R
authors: NR
authors: Kallenbach
mesh_terms: D000409:Alanine / Q000737:chemistry*; D002942:Circular Dichroism; D009646:Norleucine / Q000737:chemistry; D019906:Nuclear Magnetic Resonance, Biomolecular; D009842:Oligopeptides / Q000737:chemistry*; D010455:Peptides / Q000737:chemistry*; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D013696:Temperature; D013816:Thermodynamics
chemical_list: D009842:Oligopeptides; D010455:Peptides; C011083:polyproline; D009646:Norleucine; D000409:Alanine