From coarse-grain to all-atom: Toward multiscale analysis of protein landscapes

Publication Type:

Journal Article

Authors:

Heath, A.P.; Kavraki, L.E.; Clementi, C.

Source:

Proteins: Structure, Function and Bioinformatics, Volume 68, Number 3, p.646-661 (2007)

Keywords:

bioinformatics; multiscale representation of proteins

Abstract:

Multiscale methods are becoming increasingly promising as a way to characterize the dynamics of large protein systems on biologically relevant time-scales. The underlying assumption in multiscale simulations is that it is possible to move reliably between different resolutions. We present a method that efficiently generates realistic all-atom protein structures starting from the C(alpha) atom positions, as obtained for instance from extensive coarse-grain simulations. The method, a reconstruction algorithm for coarse-grain structures (RACOGS), is validated by reconstructing ensembles of coarse-grain structures obtained during folding simulations of the proteins src-SH3 and S6. The results show that RACOGS consistently produces low energy, all-atom structures. A comparison of the free energy landscapes calculated using the coarse-grain structures versus the all-atom structures shows good correspondence and little distortion in the protein folding landscape.