In:
The Journal of Chemical Physics, AIP Publishing, Vol. 129, No. 1 ( 2008-07-07)
Abstract:
In this work, the interactions between β-peptides are investigated for helix-forming peptides using molecular simulation. The role of electrostatic interactions in the self-assembly of these peptides is studied by calculating the dipole moment of various 14-helical β-peptides using molecular dynamics simulations. The stability of a β-peptide that is known to form a liquid crystalline phase is determined by calculating the potential of mean force using the expanded ensemble density of states method. This peptide is found to form a mechanically stable 14-helix in an implicit solvent model. The interaction between two of these peptides is examined by calculating the potential of mean force between the two peptides in implicit solvent. The peptides are shown to favorably associate in an end-to-end manner, driven largely by dipolar interactions. In order to understand the possible structures that form when many peptides interact in solution, a coarse-grained model is developed. Brownian dynamics simulations of the coarse-grained model at intermediate concentrations (1–50mM) are performed, and the aggregation behavior is understood by calculating the diffusivity and the radial distribution function. An analysis of the resultant structures reveals that the coarse-grained model of the peptide leads to the formation of spherical clusters.
Type of Medium:
Online Resource
ISSN:
0021-9606
,
1089-7690
Language:
English
Publisher:
AIP Publishing
Publication Date:
2008
detail.hit.zdb_id:
3113-6
detail.hit.zdb_id:
1473050-9
