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Influence of pH and sequence in peptide aggregation via molecular simulation

Please always quote using this URN: urn:nbn:de:0297-zib-55805
  • We employ a recently developed coarse-grained model for peptides and proteins where the effect of pH is automatically included. We explore the effect of pH in the aggregation process of the amyloidogenic peptide KTVIIE and two related sequences, using three different pH environments. Simulations using large systems (24 peptides chains per box) allow us to correctly account for the formation of realistic peptide aggregates. We evaluate the thermodynamic and kinetic implications of changes in sequence and pH upon peptide aggregation, and we discuss how a minimalistic coarse- grained model can account for these details.

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Author:Marta Enciso, Christof Schütte, Luigi Delle Site
Document Type:ZIB-Report
Tag:Monte Carlo; coarse graining; peptide aggregation dynamics
MSC-Classification:78-XX OPTICS, ELECTROMAGNETIC THEORY (For quantum optics, see 81V80) / 78Mxx Basic methods / 78M31 Monte Carlo methods
91-XX GAME THEORY, ECONOMICS, SOCIAL AND BEHAVIORAL SCIENCES / 91Gxx Mathematical finance / 91G60 Numerical methods (including Monte Carlo methods)
Date of first Publication:2015/08/24
Series (Serial Number):ZIB-Report (15-42)
Published in:Appeared in: Journal of Chemical Physics 2015
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