Internal Dynamics of an Analytically Coarse-Grained Protein

Abstract

An analytical coarse-grained model (ACG) is introduced to represent individual macromolecules for simulation of dynamic processes in cells. In the ACG model, a macromolecular structure is treated as a fully coarse-grained entity with a uniform mass density without the explicit atomic details. The excluded volume and surface of the ACG macromolecular species are explicitly treated by a spherical harmonic representation in the present study (although ellipsoidal, solid, and radial augmented functions can be used), which can provide any desired accuracy and detail depending on the problem of interest. The present paper focuses on the description of the internal fluctuations of a single ACG macromolecule, modeled by the superposition of low frequency quasiharmonic modes from explicit molecular dynamics simulation. A procedure for estimating the amplitudes, time scales of the quasiharmonic motions and the corresponding phases is presented and used to synthesize the complex motion. The analytical description and numerical algorithm can provide an adequate representation of the internal protein fluctuations revealed from the corresponding atomistic simulations, although the internal motions of ACG macromolecules do not explore motions not exhibited in the dynamic simulations.

Hierarchical Order Parameters for Macromolecular Assembly Simulations. 1. Construction and Dynamical Properties of Order Parameters

“…The masses primarily decrease with an increase in the order of polynomial basis functions. Considering systems with spatially uniform mass distribution, this suggests that the higher-order OPs with smaller effective masses probe relatively smaller regions in space. However, these OP masses vary over similar ranges of magnitude for both the hierarchical and nonhierarchical cases.…”

“…This idea has been demonstrated on the dynamics of a dimeric enzyme orotidine 5–monophosphate decarboxylase. 28 However, this model, as well as several others (reviewed in Ref. 18), does not provide all-atom details.…”

“…One of the suggested ways to incorporate internal dynamics in coarse-grained models is via superposition of low frequency quasiharmonic modes. This idea has been demonstrated on the dynamics of a dimeric enzyme orotidine 5-monophosphate decarboxylase . However, this model, as well as several others (reviewed in ref ), does not provide all-atom details.…”

Modelling spray coating using a combined CFD–DEM and spherical harmonic formulation

“…Current computational chemistry research into proteinprotein and protein-ligand binding makes use of spherical harmonics to represent molecular surfaces in dynamic docking simulations (Richie and Kemp, 1999;Cai et al, 2002;Mavridis et al, 2007). A recently developed model by Mazack et al (2010) uses spherical harmonic functions to represent interacting macromolecules. The application of spherical harmonics to represent surface distributions in DEM is, however, entirely novel.…”