Dresden 2017 – scientific programme

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BP: Fachverband Biologische Physik

BP 61: Topological Problems in the Physics of Polymers, Biopolymers and Fibers II (Joint Focus Session CPP/BP)

BP 61.6: Invited Talk

Friday, March 24, 2017, 12:00–12:30, ZEU 222

All-atom simulations of folding of proteins with topologically complex native structures. — •Pietro Faccioli and Silvio a Beccara — Physics Department , Trento University, Trento, Italy

Investigating protein folding using MD remains a formidable task. Using the Anton supercomputer it is now possibile to perform folding simulations of small globular proteins, with folding times in the ms scale. On the other hand, proteins with topologically complex or even knotted native structures can take much longer to fold. Thus investigating these processes by plain MD is well beyond the reach of any present nor foreseen supercomputer.

Our group has developed an enhanced path sampling approach based on a rigorous variational approximation, which enables to simulate the folding of protein of virtually any size with folding time as long as tens of minutes using all atom force fields. This method has been first validated against the results of Anton and then applied to larger systems with increasingly complex topology. In this talk I will review our recent results concerning the folding of the smallest knotted protein and of a serpin, a large (~400 amino-acid) misfold-prone protein with a very complex native structure architecture.

In both cases we find that, in contrast to what happens to simpler globular proteins, sequence-dependent non-native interactions are playing an important role in guiding the folding process, in particular by ensuring that the native contacts are formed in the right order.