Scaffolding of an Antimicrobial Peptide (KSL) by a Scale-Down Coarse-Grained Approach
Document Type
Article
Publication Date
2011
Department
Physics and Astronomy
School
Mathematics and Natural Sciences
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 = 2 π/λ (λ is the wavelength), S(q) proportional to q-1/v provides an insight into its multi-scale mass (N) distribution. The effective dimension De = 1/v of the peptide assembly over the spatial distribution (R) can be estimated using N ∝ RDe. On scales larger than the size (i.e. the radius of gyration Rg) of the peptide, De ≈ 1.303 ± 0.070 to De ≈ to 1.430 ± 0.096, a rather fibrous morphology appears perhaps due to directed pinning while the morphology appears like an ideal chain, De ≈ to 1.809 ± 0.017 to De approximate to 1.978 ± 0.017, at a smaller scale R ≤ Rg.
Publication Title
Physical Chemistry Chemical Physics
Volume
13
Issue
48
First Page
21262
Last Page
21272
Recommended Citation
Hissam, R.,
Farmer, B. L.,
Pandey, R. B.
(2011). Scaffolding of an Antimicrobial Peptide (KSL) by a Scale-Down Coarse-Grained Approach. Physical Chemistry Chemical Physics, 13(48), 21262-21272.
Available at: https://aquila.usm.edu/fac_pubs/545