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Sketching protein aggregation with a physics-based toy model

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Enciso, Marta and Rey Gayo, Antonio (2013) Sketching protein aggregation with a physics-based toy model. The Journal of Chemical Physics, 139 (11). 115101 1-115101 10. ISSN 0021-9606

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Official URL: http://dx.doi.org/10.1063/1.4820793




Abstract

We explore the applicability of a single-bead coarse-grained molecular model to describe the competition between protein folding and aggregation. We have designed very simple and regular sequences, based on our previous studies on peptide aggregation, that successfully fold into the three main protein structural families (all-α, all-β, and α + β). Thanks to equilibrium computer simulations, we evaluate how temperature and concentration promote aggregation. Aggregates have been obtained for all the amino acid sequences considered, showing that this process is common to all proteins, as previously stated. However, each structural family presents particular characteristics that can be related to its specific balance between hydrogen bond and hydrophobic interactions. The model is very simple and has limitations, yet it is able to reproduce both the cooperative folding of isolated polypeptide chains with regular sequences and the formation of different types of aggregates at high concentrations.


Item Type:Article
Uncontrolled Keywords:amino acid sequence; chemical phenomena; chemical structure; chemistry; molecular genetics; protein conformation; protein folding; article; chemistry
Subjects:Sciences > Computer science > Bioinformatics
Sciences > Chemistry > Biochemistry
Sciences > Chemistry > Chemistry, Physical and theoretical
ID Code:40937
Deposited On:25 Jan 2017 12:17
Last Modified:25 Jan 2017 12:24

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