title: Conformational dynamics of a short antigenic peptide in its free and antibody bound forms gives insight into the role of β-turns in peptide immunogenicity.
abstract: Earlier immunological experiments with a synthetic 36-residue peptide (75-110) from Influenza hemagglutinin have been shown to elicit anti-peptide antibodies (Ab) which could cross-react with the parent protein. In this article, we have studied the conformational features of a short antigenic (Ag) peptide ((98)YPYDVPDYASLRS(110)) from Influenza hemagglutinin in its free and antibody (Ab) bound forms with molecular dynamics simulations using GROMACS package and OPLS-AA/L all-atom force field at two different temperatures (293 K and 310 K). Multiple simulations for the free Ag peptide show sampling of ordered conformations and suggest different conformational preferences of the peptide at the two temperatures. The free Ag samples a conformation crucial for Ab binding (β-turn formed by "DYAS" sequence) with greater preference at 310 K while, it samples a native-like conformation with relatively greater propensity at 293 K. The sequence "DYAS" samples β-turn conformation with greater propensity at 310 K as part of the hemagglutinin protein also. The bound Ag too samples the β-turn involving "DYAS" sequence and in addition it also samples a β-turn formed by the sequence "YPYD" at its N-terminus, which seems to be induced upon binding to the Ab. Further, the bound Ag displays conformational flexibility at both 293 K and 310 K, particularly at terminal residues. The implications of these results for peptide immunogenicity and Ag-Ab recognition are discussed.
authors.affiliation: Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India.
authors.forename: Rashmi Tambe
authors.initials: RT
authors.lastname: Shukla
authors.affiliation: Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India.
authors.forename: Yellamraju U
authors.initials: YU
authors.lastname: Sasidhar
mesh_terms: D020816:Amino Acid Motifs; D000914:Antibodies, Viral / Q000737:chemistry* / Q000276:immunology; D000936:Antigen-Antibody Complex / Q000737:chemistry*; D000956:Antigens, Viral / Q000737:chemistry* / Q000276:immunology; D001665:Binding Sites; D006389:Hemagglutinins, Viral / Q000737:chemistry* / Q000276:immunology; D006801:Humans; D006860:Hydrogen Bonding; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D009975:Orthomyxoviridae / Q000737:chemistry / Q000276:immunology; D010455:Peptides / Q000737:chemistry* / Q000276:immunology; D011485:Protein Binding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D055672:Static Electricity; D013816:Thermodynamics
chemical_list: D000914:Antibodies, Viral; D000936:Antigen-Antibody Complex; D000956:Antigens, Viral; D006389:Hemagglutinins, Viral; D010455:Peptides
keywords: antibody; antigen; molecular dynamics simulations; peptide immunogenicity; β-turn