title: Computational design of model scaffold for anion recognition based on the 'CαNN' motif.
abstract: The 'novel phosphate binding 'CαNN' motif', consisting of three consecutive amino acid residues, usually occurs in the protein loop regions preceding a helix. Recent computational and complementary biophysical experiments on a series of chimeric peptides containing the naturally occurring 'CαNN' motif at the N-terminus of a designed helix establishes that the motif segment recognizes the anion (sulfate and phosphate ions) through local interaction along with extension of the helical conformation which is thermodynamically favored even in a context-free, nonproteinaceous isolated system. However, the strength of the interaction depends on the amino acid sequence/conformation of the motif. Such a locally-mediated recognition of anions validates its intrinsic affinity towards anions and confirms that the affinity for recognition of anions is embedded within the 'local sequence' of the motif. Based on the knowledge gathered on the sequence/structural aspects of the naturally occurring 'CαNN' segment, which provides the guideline for rationally engineering model scaffolds, we have modeled a series of templates and investigated their interactions with anions using computational approach. Two of these designed scaffolds show more efficient anion recognition than those of the naturally occurring 'CαNN' motif which have been studied. This may provide an avenue in designing better anion receptors suitable for various biochemical applications.
authors.affiliation: Maulana Abul Kalam Azad University of Technology, West Bengal (Formerly Known as West Bengal University of Technology), BF-142, Sector-1, Salt Lake, Kolkata, 700064, India.
authors.forename: Tridip
authors.initials: T
authors.lastname: Sheet
authors.affiliation: Maulana Abul Kalam Azad University of Technology, West Bengal (Formerly Known as West Bengal University of Technology), BF-142, Sector-1, Salt Lake, Kolkata, 700064, India.
authors.forename: Suvankar
authors.initials: S
authors.lastname: Ghosh
authors.affiliation: Indian Institute of Science, Bangalore, 560012, India.
authors.forename: Debnath
authors.initials: D
authors.lastname: Pal
authors.affiliation: Maulana Abul Kalam Azad University of Technology, West Bengal (Formerly Known as West Bengal University of Technology), BF-142, Sector-1, Salt Lake, Kolkata, 700064, India.
authors.forename: Raja
authors.initials: R
authors.lastname: Banerjee
mesh_terms: D020816:Amino Acid Motifs; D000838:Anions / Q000737:chemistry; D001665:Binding Sites; D006860:Hydrogen Bonding; D062105:Molecular Docking Simulation; D010455:Peptides / Q000138:chemical synthesis / Q000737:chemistry*; D010710:Phosphates / Q000737:chemistry; D011789:Quantum Theory; D013431:Sulfates / Q000737:chemistry; D013816:Thermodynamics
chemical_list: D000838:Anions; D010455:Peptides; D010710:Phosphates; D013431:Sulfates
keywords: anion affinity; designed peptidic scaffold; molecular docking; molecular dynamics; ‘CαNN' motif