Self-assembly of beta-sheet forming peptides into chiral fibrillar aggregates.
The authors introduce a novel mid-resolution off-lattice coarse-grained model to investigate the self-assembly of beta-sheet forming peptides. The model retains most of the peptide backbone degrees of freedom as well as one interaction center describing the side chains. The peptide consists of a core of alternating hydrophobic and hydrophilic residues, capped by two oppositely charged residues. Nonbonded interactions are described by Lennard-Jones and Coulombic terms. The influence of different levels of "hydrophobic" and "steric" forces between the side chains of the peptides on the thermodynamics and kinetics of aggregation was investigated using Langevin dynamics. The model is simple enough to allow the simulation of systems consisting of hundreds of peptides, while remaining realistic enough to successfully lead to the formation of chiral, ordered beta tapes, ribbons, as well as higher order fibrillar aggregates.
Bellesia
Giovanni
G
Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, USA. gbellesia@chem.ucsb.edu
Shea
Joan-Emma
JE
D001703:Biophysics / Q000379:methods*; D002627:Chemistry, Physical / Q000379:methods*; D003198:Computer Simulation; D007700:Kinetics; D008958:Models, Molecular; D015233:Models, Statistical; D008968:Molecular Conformation; D010455:Peptides / Q000737:chemistry*; D011336:Probability; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D055672:Static Electricity; D013696:Temperature; D013816:Thermodynamics; D013997:Time Factors
D010455:Peptides