Sequence dependent self-assembly of beta-peptides: Insights from a coarse-grained model.
The sequence-directed self-assembly of amphiphilic beta-peptides is studied using Monte Carlo simulations. A phenomenological model is employed where each molecule is modeled as a rigid nanorod with side groups located at positions to mimic globally amphiphilic (GA) and nonglobally amphiphilic (non-GA) isomers of beta-peptides. The strength and the range of interactions between side groups are chosen based on the types of residues. The simulations show that the aggregation of beta-peptides is sensitive to the sequence and the residue types. For one type of beta-peptide the GA isomer has a greater tendency to aggregate while for the other the non-GA isomer has a greater tendency to aggregate. The trends observed in the simulations are consistent with recent experiments [Pomerantz et al., J. Am. Chem. Soc. 128, 8730 (2006); Pomerantz et al., Angew. Chem., Int. Ed. 47, 1 (2008)], although the molecules do not spontaneously form the hollow fibers seen in experiment. Simulations with initial configurations as hollow fibers show that the stability of the fibers follows the same trend as the tendency for aggregation. The simulations demonstrate that the details matter: the self-assembly of the molecules is sensitive to the strength of the short-ranged interactions and the size of the side groups, in addition to the global amphiphilicity of the molecules. This suggests the possibility of designing molecules for desired nanostructures.
Mondal
Jagannath
J
Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA.
Sung
Bong June
BJ
Yethiraj
Arun
A
D000595:Amino Acid Sequence; D003198:Computer Simulation; D007536:Isomerism; D008958:Models, Molecular; D009010:Monte Carlo Method; D010455:Peptides / Q000737:chemistry*; D055550:Protein Stability; D017433:Protein Structure, Secondary; D014867:Water / Q000737:chemistry
D010455:Peptides; D014867:Water