Simple model for the simulation of peptide folding and aggregation with different sequences.
We present a coarse-grained interaction potential that, using just one single interaction bead per amino acid and only realistic interactions, can reproduce the most representative features of peptide folding. We combine a simple hydrogen bond potential, recently developed in our group, with a reduced alphabet for the amino acid sequence, which takes into account hydrophobic interactions. The sequence does not pose any additional influence in the torsional properties of the chain, as it often appears in previously published work. Our model is studied in equilibrium simulations at different temperatures and concentrations. At low concentrations the effect of hydrophobic interactions is determinant, as α-helices (isolated or in bundles) or β-sheets are the most populated conformations, depending on the simulated sequence. On the other hand, an increase in concentration translates into a higher influence of the hydrogen bond interactions, which mostly favor the formation of β-type aggregates, in agreement with experimental observations. These aggregates, however, still keep some distinct characteristics for different sequences.
Departamento de Química Física I, Facultad de Ciencias Químicas, Universidad Complutense, E-28040 Madrid, Spain.
Marta
M
Enciso
Antonio
A
Rey
D000595:Amino Acid Sequence; D006860:Hydrogen Bonding; D057927:Hydrophobic and Hydrophilic Interactions; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry*; D011487:Protein Conformation; D017510:Protein Folding; D055503:Protein Multimerization; D013696:Temperature
D010455:Peptides