Alessandro Laio: "Exploring the universe of protein structures by atomistic simulations: beyond the Protein Data Bank"
von 16:15 bis 17:00
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Open to University employees
SISSA, Trieste, Italy
Exploring the universe of protein structures by atomistic simulations: beyond the Protein Data Bank
It is currently believed that the atlas of existing protein structures is faithfully represented in the Protein Data Bank. However, whether this atlas covers the full universe of all possible protein structures is still a debated issue. By using a bias exchange metadynamics, we performed an exhaustive exploration of the conformational space of a 60 amino acid polypeptide chain described with an accurate all-atom interaction potential. We generated a database of around 30,000 compact folds that plausibly represents the universe of protein folds of similar length. However, we discover that the known folds form a rather small subset. Natural and possible folds differ by the contact order, on average significantly smaller in the former. This suggests the presence of an evolutionary bias, towards structures with shorter loops between contacting residues.