title: Alternatingly twisted β-hairpins and nonglycine residues in the disallowed II' region of the Ramachandran plot.
abstract: The structure of the SH3 domain of α-spectrin (PDB code 1SHG) features Asn47 in the II' area of the Ramachandran plot, which as a rule admits only glycine residues, and this phenomenon still awaits its explanation. Here, we undertook a computational study of this particular case by means of molecular dynamics and bioinformatics approaches. We found that the region of the SH3 domain in the vicinity of Asn47 remains relatively stable during denaturing molecular dynamics simulations of the entire domain and of its parts. This increased stability may be connected with the dynamic hydrogen bonding that is susceptible to targeted in silico mutations of Arg49. Bioinformatics analysis indicated that Asn47 is in the β-turn of a distinctive structural fragment we called 'alternatingly twisted β-hairpin.' Fragments of similar conformation are quite abundant in a nonredundant set of PDB chains and are distinguished from ordinary β-hairpins by some surplus of glycine in their β-turns, lack of certain interpeptide hydrogen bonds, and an increased chirality index. Thus, the disallowed conformation of residues other than glycine is realized in the β-turns of alternatingly twisted β-hairpins.
authors: a Department of Chemistry , M.V. Lomonosov State University , 1-73 Leninskie Gory, Moscow , 119991 , Russian Federation .
authors: Ivan Yu
authors: IY
authors: Torshin
authors: Natalya G
authors: NG
authors: Esipova
authors: Vladimir G
authors: VG
authors: Tumanyan
mesh_terms: D001216:Asparagine / Q000737:chemistry; D005998:Glycine / Q000737:chemistry; D006860:Hydrogen Bonding; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D011487:Protein Conformation; D011489:Protein Denaturation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D013049:Spectrin / Q000737:chemistry / Q000648:ultrastructure*; D018909:src Homology Domains
chemical_list: D013049:Spectrin; D001216:Asparagine; D005998:Glycine