title: From coarse-grain to all-atom: toward multiscale analysis of protein landscapes.
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.
authors.affiliation: Department of Computer Science, Rice University, Houston, Texas 77005, USA.
authors.forename: Allison P
authors.initials: AP
authors.lastname: Heath
authors.forename: Lydia E
authors.initials: LE
authors.lastname: Kavraki
authors.forename: Cecilia
authors.initials: C
authors.lastname: Clementi
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D009010:Monte Carlo Method; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*
chemical_list: D011506:Proteins