Mey Antonia S J S, Geissler Phillip L, Garrahan Juan P
School of Physics & Astronomy, University of Nottingham, Nottingham NG7 2RD, United Kingdom.
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.
Phys Rev E Stat Nonlin Soft Matter Phys. 2014 Mar;89(3):032109. doi: 10.1103/PhysRevE.89.032109. Epub 2014 Mar 11.
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.
我们通过轨迹的路径采样来探索蛋白质晶格杂聚物模型的动力学大偏差。我们揭示了在活跃和非活跃动力学相之间的轨迹系综中存在非平衡动力学相变，其性质取决于相互作用势的性质。我们考虑三种势：两种非均匀相互作用势和一种均匀的戈势。当在完全相互作用模型或天然接触相互作用模型（非均匀戈模型）中由于给定氨基酸序列而保持相互作用的完全非均匀性时，观察到的动态转变发生在平衡的高度天然态和高度天然但动力学上被困的状态之间。定义了一种天然活性，使我们能够区分这些动态相。相比之下，对于均匀戈模型，其中所有天然相互作用能都是均匀的且氨基酸序列不起作用，动力学转变是未折叠态和天然态之间静态双稳性的直接结果。在这两种非均匀相互作用模型中，天然活性态和天然非活性态尽管在热力学上相似，但具有广泛不同的动力学性质，并且即使在其序列被设计为使其成为最优折叠体的晶格蛋白质中，它们之间的转变也会发生。
