A Coarse-Grained Model for Protein Backbone Dynamics

Allostery in a coarse-grained model of protein dynamics.

We propose a criterion for optimal parameter selection in coarse-grained models of proteins and develop a refined elastic network model (ENM) of bovine trypsinogen. The unimodal density-of-states distribution of the trypsinogen ENM disagrees with the bimodal distribution obtained from an all-atom model; however, the bimodal distribution is recovered by strengthening interactions between atoms t...

Coarse-grained protein molecular dynamics simulations.

A limiting factor in biological science is the time-scale gap between experimental and computational trajectories. At this point, all-atom explicit solvent molecular dynamics (MD) are clearly too expensive to explore long-range protein motions and extract accurate thermodynamics of proteins in isolated or multimeric forms. To reach the appropriate time scale, we must then resort to coarse grain...

Coarse-Grained Modeling of Protein Unfolding Dynamics

We present a new dynamic elastic network model (DENM) that describes the unfolding process of a force-loaded protein. The protein interaction network and its potentials are constructed based on information of its native-state structure obtained from the Protein Data Bank, with network nodes positioned at the Cα coordinates of the protein backbone. Specifically, to mimic the unfolding process, i...

A Coarse-Grained DNA Model for Bubble Formation and Dynamics

A coarse-grained molecular dynamics model for crystalline solids

A general mathematical framework for coarse-graining molecular dynamics (MD) model for solid system is presented. The formulation is based directly on the full MD model. The reduction of the atomic degrees of freedom is accomplished using the Mori–Zwanzig projection method. We also demonstrate how to simplify the model under this framework to make the numerical implementation much easier. Copyr...