4885
2013
eng
3363
3371
22-23
111
article
0
--
--
--
pH-dependent Response of Coiled Coils: A Coarse-Grained Molecular Simulation Study
Molecular Physics
10.1080/00268976.2013.827254
Yes
Marta Enciso
Erlinda Körnig
Christof Schütte
Luigi Delle Site
Numerical Mathematics
Schütte, Christof
5580
eng
reportzib
0
--
2015-08-24
--
Influence of pH and sequence in peptide aggregation via molecular simulation
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.
1438-0064
urn:nbn:de:0297-zib-55805
Appeared in: Journal of Chemical Physics 2015
Marta Enciso
Erlinda Koernig
Christof Schütte
Luigi Delle Site
ZIB-Report
15-42
eng
uncontrolled
coarse graining
eng
uncontrolled
peptide aggregation dynamics
eng
uncontrolled
Monte Carlo
Monte Carlo methods
Numerical methods (including Monte Carlo methods)
Numerical Mathematics
Schütte, Christof
SFB-1114-B3
https://opus4.kobv.de/opus4-zib/files/5580/ZIB-Report_15-42.pdf
5656
2015
eng
24
143
article
0
--
--
--
Influence of pH and sequence in peptide aggregation via molecular simulation
Journal of Chemical Physics
https://doi.org/10.1063/1.4935707
yes
urn:nbn:de:0297-zib-55805
Marta Enciso
Erlinda Körnig
Christof Schütte
Luigi Delle Site
Numerical Mathematics
Schütte, Christof
SFB-1114-B3
5215
2013
eng
6118
6127
26
9
article
0
--
--
--
A pH-dependent coarse-grained model for peptides
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.
Soft Matter
10.1039/C3SM27893J
yes
Marta Enciso
Erlinda Körnig
Christof Schütte
Luigi Delle Site
Numerical Mathematics
Schütte, Christof
2671
2012
2013
eng
6118
6127
26
9
article
0
--
--
--
A pH-dependent coarse-grained model of peptides
Soft Matter
http://publications.imp.fu-berlin.de/1192/
10.1039/C3SM27893J
Marta Enciso
Christof Schütte
Luigi Delle Site
Schütte, Christof