Aggregation kinetics of short peptides: All-atom and coarse-grained molecular dynamics study
1Adam Mickiewicz University in Poznań, Faculty of Chemistry, Umultowska 89b, 61-614 Poznań, Poland.
Biophysical Chemistry
|July 14, 2019
Summary
Peptide aggregation kinetics were similar across different sequences using molecular dynamics. Sequence-specific differences emerge during the later stages of aggregate reorganization into ordered structures.
Area of Science:
- Biophysics
- Computational Chemistry
- Materials Science
Background:
- Peptide aggregation into ordered structures is a key area of research.
- Understanding aggregation mechanisms and evolving structures is crucial for various applications.
Purpose of the Study:
- To investigate the sequence-dependence of peptide aggregation kinetics using molecular dynamics simulations.
- To compare aggregation behavior of octaalanine (Ala8), octaasparagine (Asn8), and GNNQQNY (GNN) peptides.
Main Methods:
- Utilized molecular dynamics simulations with both coarse-grained (MARTINI) and atomistic (OPLS-AA) force fields.
- Analyzed early-stage aggregation kinetics for systems of 20 and 72 peptides.
- Quantified aggregation kinetics using rate equations.
Main Results:
- Aggregation kinetics showed similarities between MARTINI and OPLS-AA force fields for Ala8, Asn8, and GNN.
- Initial aggregation stages involve monomer addition, followed by cluster-cluster coalescence.
- Initial aggregation kinetics were similar for all tested peptides, but molecular details differed.
Conclusions:
- Peptide aggregation likely proceeds in two steps: amorphous aggregate formation followed by reorganization into ordered structures.
- Sequence-specific differences in aggregation become apparent in the second reorganization step.
- Molecular dynamics simulations provide insights into the complex process of peptide self-assembly.
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