title: Conformational preference of 'CαNN' short peptide motif towards recognition of anions.
abstract: Among several 'anion binding motifs', the recently described 'C(α)NN' motif occurring in the loop regions preceding a helix, is conserved through evolution both in sequence and its conformation. To establish the significance of the conserved sequence and their intrinsic affinity for anions, a series of peptides containing the naturally occurring 'C(α)NN' motif at the N-terminus of a designed helix, have been modeled and studied in a context free system using computational techniques. Appearance of a single interacting site with negative binding free-energy for both the sulfate and phosphate ions, as evidenced in docking experiments, establishes that the 'C(α)NN' segment has an intrinsic affinity for anions. Molecular Dynamics (MD) simulation studies reveal that interaction with anion triggers a conformational switch from non-helical to helical state at the 'C(α)NN' segment, which extends the length of the anchoring-helix by one turn at the N-terminus. Computational experiments substantiate the significance of sequence/structural context and justify the conserved nature of the 'C(α)NN' sequence for anion recognition through "local" interaction.
authors.affiliation: Department of Bioinformatics, West Bengal University of Technology, Salt Lake, Kolkata, India.
authors.forename: Tridip
authors.initials: T
authors.lastname: Sheet
authors.forename: Subhrangshu
authors.initials: S
authors.lastname: Supakar
authors.forename: Raja
authors.initials: R
authors.lastname: Banerjee
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D000838:Anions / Q000737:chemistry* / Q000378:metabolism; D006860:Hydrogen Bonding; D009682:Magnetic Resonance Spectroscopy; D062105:Molecular Docking Simulation; D056004:Molecular Dynamics Simulation; D010455:Peptides / Q000737:chemistry* / Q000378:metabolism; D011485:Protein Binding; D011487:Protein Conformation; D013431:Sulfates / Q000737:chemistry
chemical_list: D000838:Anions; D010455:Peptides; D013431:Sulfates