Scaffolding of an antimicrobial peptide (KSL) by a scale-down coarse-grained approach

Abstract

A coarse-grained approach with enhanced representation of amino acid (involving four components, i.e. a central alpha carbon and its side group along with C and N terminals) is used to study the multi-scale assembly of an antimicrobial peptide (KSL) in an explicit solvent (in a scale-down hierarchy of Eby et al. [Phys. Chem. Chem. Phys., 2011, 13, 1123–1130]). Both local (mobility, solvent-surrounding, energy profiles) and global (variation of the root mean square displacement of peptides and its gyration radius with time steps, radial distribution function, and structure factors) physical quantities are analyzed as a function of the solvent quality (i.e. the solvent–residue interaction strength). We find that the mobility of the interacting side group (lysine) decays as the number of its surrounding solvent constituents grows systematically on increasing the interaction strength. Pinning of lysine directs the underlying segmental conformation that propagates to larger scale scaffolding. The radial distribution function (a measure of the correlated peptide assembly) decays with the distance (faster with stronger solvent interaction). Scaling of the structure factor (S(q)) of peptide assembly with the wave vector q = 2π/λ (λ is the wavelength), S(q) ∝ q^−1/ν provides an insight into its multi-scale mass (N) distribution. The effective dimension D_e = 1/ν of the peptide assembly over the spatial distribution (R) can be estimated using N ∝ R^D_e. On scales larger than the size (i.e. the radius of gyration R_g) of the peptide, D_e ≈ 1.303 ± 0.070 to D_e ≈ 1.430 ± 0.096, a rather fibrous morphology appears perhaps due to directed pinning while the morphology appears like an ideal chain, D_e ≈ 1.809 ± 0.017 to D_e ≈ 1.978 ± 0.017, at a smaller scale R ≤ R_g.