Publication: Simple model for the simulation of peptide folding and aggregation with different sequences
Loading...
Official URL
Full text at PDC
Publication Date
2012
Authors
Advisors (or tutors)
Editors
Journal Title
Journal ISSN
Volume Title
Publisher
American Institute of Physics
Citations
Exportar
Abstract
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.