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Disruption mechanism in the helix of SPF peptide by interchanging E5 and K10 residues: inference from molecular

P N Sunilkumar1, Divya G Nair, C Sadasivan

  • 1Department of Biotechnology and Microbiology, School of Life Sciences, Kannur University, Thalassery Campus, Kerala-670 661, India.

Journal of Biomolecular Structure & Dynamics
|December 26, 2008
PubMed

Insights

The helical structure of the SPF peptide, crucial for its antimicrobial activity, is disrupted by specific amino acid substitutions. Molecular simulations reveal that charged residue positions, particularly K10, are vital for maintaining SPF

Area of Science:

  • Biochemistry and Molecular Biology
  • Computational Biophysics

Background:

  • Seminalplasmin (SPLN) is a bovine seminal plasma peptide with broad-spectrum antimicrobial activity and no hemolytic effects.
  • The 28-40 segment, SPF, is hydrophobic, responsible for membrane perturbation, and possesses a helical structure.

Purpose of the Study:

  • To investigate the mechanism by which interchanging E5 and K10 residues disrupts the helical structure of the SPF peptide.
  • To understand the role of charged residues and hydrogen bonding in maintaining SPF's helical conformation.

Main Methods:

  • Simulated annealing and molecular dynamics simulations were performed on SPF and four analogues with specific amino acid substitutions (K10E, K10D, E5K, E5K & K10E).
  • Analysis focused on changes in helical content and hydrogen bond formation/rupture.

Main Results:

  • The K10 residue plays a critical role in maintaining the highest helical content in the SPF peptide.
  • Specific substitutions, particularly E5K and K10E, disrupt the helical structure.
  • Disruption involves the formation of new long-range hydrogen bonds and the rupture of short-range bonds involving the K10 residue.

Conclusions:

  • The positions of charged residues, especially K10, are crucial for the helical stability of the SPF peptide.
  • Understanding these structural dynamics provides insights into the mechanism of action for antimicrobial peptides.

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