title: Rare-event trajectory ensemble analysis reveals metastable dynamical phases in lattice proteins.
abstract: We explore the dynamical large deviations of a lattice heteropolymer model of a protein by means of path sampling of trajectories. We uncover the existence of nonequilibrium dynamical phase transitions in ensembles of trajectories between active and inactive dynamical phases, whose nature depends on the properties of the interaction potential. We consider three potentials: two heterogeneous interaction potentials and a homogeneous Gō potential. When preserving the full heterogeneity of interactions due to a given amino acid sequence, either in a fully interacting model or in a native contacts interacting model (heterogeneous Gō model), the observed dynamic transitions occur between equilibrium highly native states and highly native but kinetically trapped states. A native activity is defined that allows us to distinguish these dynamic phases. In contrast, for the homogeneous Gō model, where all native interaction energies are uniform and the amino acid sequence plays no role, the dynamical transition is a direct consequence of the static bistability between the unfolded and the native state. In the two heterogeneous interaction models the native-active and native-inactive states, despite their thermodynamic similarity, have widely varying dynamical properties, and the transition between them occurs even in lattice proteins whose sequences are designed to make them optimal folders.
authors.affiliation: School of Physics & Astronomy, University of Nottingham, Nottingham NG7 2RD, United Kingdom.
authors.forename: Antonia S J S
authors.initials: AS
authors.lastname: Mey
authors.affiliation: Department of Chemistry, University of California at Berkeley, Berkeley, California 94720, USA and Chemical Sciences and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.
authors.forename: Phillip L
authors.initials: PL
authors.lastname: Geissler
authors.affiliation: School of Physics & Astronomy, University of Nottingham, Nottingham NG7 2RD, United Kingdom.
authors.forename: Juan P
authors.initials: JP
authors.lastname: Garrahan
mesh_terms: D000595:Amino Acid Sequence; D003198:Computer Simulation; D008956:Models, Chemical; D008958:Models, Molecular; D015233:Models, Statistical; D011487:Protein Conformation; D011489:Protein Denaturation; D011506:Proteins / Q000737:chemistry* / Q000648:ultrastructure*
chemical_list: D011506:Proteins