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Simple model for the simulation of peptide folding and aggregation with different sequences

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Enciso, Marta and Rey Gayo, Antonio (2012) Simple model for the simulation of peptide folding and aggregation with different sequences. The Journal of Chemical Physics, 136 . 215103 1-215103 9. ISSN 0021-9606

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Official URL: http://dx.doi.org/10.1063/1.4725883




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.


Item Type:Article
Uncontrolled Keywords:amino acid sequence; article; chemical phenomena; chemical structure; chemistry; hydrogen bond; protein conformation; protein folding; protein multimerization; temperature
Subjects:Sciences > Chemistry > Biochemistry
Sciences > Chemistry > Chemistry, Physical and theoretical
ID Code:40936
Deposited On:25 Jan 2017 12:21
Last Modified:25 Jan 2017 12:28

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