RT Journal Article
T1 Simple model for the simulation of peptide folding and aggregation with different sequences
A1 Enciso, Marta
A1 Rey Gayo, Antonio
AB 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.
PB American Institute of Physics
SN 0021-9606
YR 2012
FD 2012
LK https://hdl.handle.net/20.500.14352/42592
UL https://hdl.handle.net/20.500.14352/42592
LA eng
NO Ministerio de Ciencia e Innovación (MICINN)
NO Comunidad de Madrid
NO Universidad Complutense de Madrid/Banco Santander
DS Docta Complutense
RD 26 ene 2026