Computational prediction of the optimal oligomeric state for membrane-inserted β-barrels of protegrin-1 and related mutants.

ABSTRACT: Protegrin-1 is a widely studied 18-residue β-hairpin antimicrobial peptide. Evidence suggests that it acts via a β-barrel pore formation mechanism, but the exact number of peptides comprising the pore state is unknown. In this study, we performed molecular dynamics simulations of β-barrels of protegrin and three related mutants (v14v16l, v14v16a, and r4n) in NCNC parallel topology in implicit membrane pores of varying radius and curvature for oligomeric numbers 6-14. We then identified the optimal pore radius and curvature values for all constructs and determined the total effective energy and the translational and rotational entropic losses. These, along with an estimate of membrane deformation free energy from experimental line tension values, provided an estimate of the overall energeti

SUBMITTER: Lipkin R 

PROVIDER: S-EPMC5689075 | biostudies-literature | 2017 Apr

REPOSITORIES: biostudies-literature