title: Disruption mechanism in the helix of SPF peptide by interchanging E5 and K10 residues: inference from molecular dynamics study.
abstract: Seminalplasmin (SPLN) is a 47-residue peptide (SDEKASPDKHHRFSLSRYAKLANRLANPKLLETFLSKWIGDRGNRSV) from bovine seminal plasma. It has broad spectrum antimicrobial activity, without any hemolytic activity. The 28-40 segment of SPLN with the sequence PKLLETFLSKWIG, designated as SPF, is the most hydrophobic stretch of SPLN and primarily responsible for the membrane-perturbing activity of SPLN. It was reported that SPF has a helical structure and the interchange of E5 and K10 residues disrupted the helical structure. The present paper reports a possible mechanism of disruption of the helical structure of SPF peptide during the interchange of E5 and K10 residues. The result is based on simulated annealing and molecular dynamics simulation studies on SPF and its four analogues with K10E, K10D, E5K, and E5K & K10E substitutions. It showed that K10 residue has a critical role in maintaining the highest helical content and the positions of charged residues are also very important for maintaining the helical structure of the SPF peptide. Formation of some new long-range hydrogen bonds and the rupture of some short-range hydrogen bonds involving the tenth residue led to the disruption of helical structure of SPF peptide when E5 and K10 residues are interchanged.
authors.affiliation: Department of Biotechnology and Microbiology, School of Life Sciences, Kannur University, Thalassery Campus, Kerala-670 661, India.
authors.forename: P N
authors.initials: PN
authors.lastname: Sunilkumar
authors.forename: Divya G
authors.initials: DG
authors.lastname: Nair
authors.forename: C
authors.initials: C
authors.lastname: Sadasivan
authors.forename: M
authors.initials: M
authors.lastname: Haridas
mesh_terms: D000595:Amino Acid Sequence; D019943:Amino Acid Substitution; D000818:Animals; D002417:Cattle; D006860:Hydrogen Bonding; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D010446:Peptide Fragments / Q000737:chemistry*; D011485:Protein Binding; D017433:Protein Structure, Secondary; D029607:Seminal Vesicle Secretory Proteins / Q000737:chemistry* / Q000235:genetics
chemical_list: D010446:Peptide Fragments; D029607:Seminal Vesicle Secretory Proteins