JOINT ICTP/SISSA COLLOQUIUM ON CONDENSED MATTER PHYSICS: "Exploring the universe of protein structures beyond the Protein Data Bank"
Starts 11 May 2011 17:30
Ends 11 May 2011 20:00
Central European Time
Leonardo da Vinci Building Luigi Stasi Seminar Room
Strada Costiera, 11
I - 34151 Trieste (Italy)
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 highly debated issue.
By using a sophisticated numerical approach, 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 with at least 30 % of secondary structure and corresponding to local minima of the potential energy.
This ensemble plausibly represents the universe of protein folds of similar length; indeed, all the known folds are represented in the set with good accuracy, despite of the fact the simulation is performed for a homopeptide. However, we discover that the known folds form a rather small subset, which cannot be reproduced by choosing random structures in the database. Rather, natural and possible folds differ by the contact order, on average significantly smaller in the former. This suggests the presence of an evolutionary bias, possibly related to kinetic accessibility, towards structures with shorter loops between contacting residues.