TY - JOUR A1 - Enciso, Marta A1 - Schütte, Christof A1 - Delle Site, Luigi T1 - pH-dependent Response of Coiled Coils: A Coarse-Grained Molecular Simulation Study JF - Molecular Physics Y1 - 2013 U6 - https://doi.org/10.1080/00268976.2013.827254 VL - 111 IS - 22-23 SP - 3363 EP - 3371 ER - TY - GEN A1 - Enciso, Marta A1 - Schütte, Christof A1 - Delle Site, Luigi T1 - Influence of pH and sequence in peptide aggregation via molecular simulation N2 - 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. T3 - ZIB-Report - 15-42 KW - coarse graining KW - peptide aggregation dynamics KW - Monte Carlo Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-55805 SN - 1438-0064 ER - TY - JOUR A1 - Enciso, Marta A1 - Schütte, Christof A1 - Delle Site, Luigi T1 - Influence of pH and sequence in peptide aggregation via molecular simulation JF - Journal of Chemical Physics Y1 - 2015 U6 - https://doi.org/https://doi.org/10.1063/1.4935707 VL - 143 IS - 24 ER - TY - JOUR A1 - Enciso, Marta A1 - Schütte, Christof A1 - Delle Site, Luigi T1 - A pH-dependent coarse-grained model for peptides JF - Soft Matter N2 - We propose the first, to our knowledge, coarse-grained modeling strategy for peptides where the effect of changes of the pH can be efficiently described. The idea is based on modeling the effects of the pH value on the main driving interactions. We use reference data from atomistic simulations and experimental databases and transfer their main physical features to the coarse-grained resolution according to the principle of “consistency across the scales”. The coarse-grained model is refined by finding a set of parameters that, when applied to peptides with different sequences and experimental properties, reproduces the experimental and atomistic data of reference. We use such a parameterized model for performing several numerical tests to check its transferability to other systems and to prove the universality of the related modeling strategy. We have tried systems with rather different responses to pH variations, showing a highly satisfactory performance of the model. Y1 - 2013 U6 - https://doi.org/10.1039/C3SM27893J VL - 9 IS - 26 SP - 6118 EP - 6127 ER - TY - JOUR A1 - Enciso, Marta A1 - Schütte, Christof A1 - Site, Luigi Delle T1 - A pH-dependent coarse-grained model of peptides JF - Soft Matter Y1 - 2012 UR - http://publications.imp.fu-berlin.de/1192/ U6 - https://doi.org/10.1039/C3SM27893J VL - 9 IS - 26 SP - 6118 EP - 6127 ER -