Wednesday 12 Sepember 2012 at 9:00
DTU, meeting room S7 in building 101
All-atom molecular dynamics simulations provide a vehicle for capturing the structures, motions, and interactions of biological macromolecules in full atomic detail. Such simulations have, however, been limited both in the timescales they could access and in the accuracy of computational models used in the simulations. I will begin by presenting briefly how progress has been made in both of these areas so that it is now possible to access the millisecond timescale, and how we have been able to parameterize relatively accurate energy functions. I will then present recent results that highlight how such long-timescale simulations have been used to provide insight in to protein dynamics.
In the area of protein folding, we have used simulations to describe the general principles of how fast-folding proteins fold. In simulations of 12 structurally diverse proteins, representing all three major structural classes, we observe the proteins to spontaneously and repeatedly folded to their experimentally determined native structures. I will present the results of the analyses we performed to identify the common principles that underlie the folding of these proteins. I will also describe how simulations can be used to describe slow motions present in proteins, in both folded and unfolded states.
Everybody is welcome. Registration is not necessary.