All-Atom Level Computational Study of Peptide Aggregation

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All-atom level computational study of peptide
aggregation into protofibril structures
Soonmin Jang and Jungho Shin
Department of Chemistry, Sejong University, Gwangjin-Gu Gunja-Dong 98, Seoul 143-747,
Korea
Aggregation of peptides became intense research topics recently due to its importance
in biomedical, biotechnological, and material science. It is important to understand the
detailed rules governing the self assembly of peptides, which could be different from
that of single protein folding. In many cases, experimental techniques have difficulty
in identification of the detailed structure behind the resulting aggregates. Therefore,
computer simulations based on reasonable model could be alternative approach to
understand the peptide aggregation.
We have performed molecular dynamics simulation of peptide aggregation that is
known to form amyloid fibril-like structure. Using efficient sampling scheme coupled
with all-atom model, we observed direct aggregation of peptides into protofibril
structures. The resulting aggregates are investigated to elucidate the stability and the
detailed interaction features. Characteristics of those aggregates as well as its
temperature dependence will be presented.
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