Conformational dynamics and internal friction in homopolymer globules: equilibrium vs. non-equilibrium simulations

Abstract

We study the conformational dynamics within homopolymer globules by solvent-implicit Brownian dynamics simulations. A strong dependence of the internal chain dynamics on the Lennard-Jones cohesion strength ε and the globule size N (G) is observed. We find two distinct dynamical regimes: a liquid-like regime (for ε < ε(s) with fast internal dynamics and a solid-like regime (for ε > ε(s) with slow internal dynamics. The cohesion strength ε(s) of this freezing transition depends on N (G) . Equilibrium simulations, where we investigate the diffusional chain dynamics within the globule, are compared with non-equilibrium simulations, where we unfold the globule by pulling the chain ends with prescribed velocity (encompassing low enough velocities so that the linear-response, viscous regime is reached). From both simulation protocols we derive the internal viscosity within the globule. In the liquid-like regime the internal friction increases continuously with ε and scales extensive in N (G) . This suggests an internal friction scenario where the entire chain (or an extensive fraction thereof) takes part in conformational reorganization of the globular structure.

Atypical effects of incorporated surfactants on stability and dissolution properties of amorphous polymeric dispersions

“…This goes in line with previous studies that showed that the solvent used to dissolve the polymer could have significant impact on properties of formed particles . The polymer takes up a globular conformation when dissolved in a poor solvent while exhibiting an extended conformation in a good solvent . Indeed, we have shown previously that replacing water with methanol to spray dry solid dispersions of GF can lead to dramatic changes into properties of the solid dispersion, although unexpected but changing the order of adding the polymers and drug seemed to result in particles with different properties.…”

How osmolytes influence hydrophobic polymer conformations: A unified view from experiment and theory

“…Investigations by several theoretical groups (40)(41)(42)(43) have suggested that a hydrophobic polymer in solution will collapse into a surface area-minimized globule (such as those seen by AFM scans; see Fig. 1A) and that forcing a part of the polymer into solution causes the polymer to assemble into coexisting chain and globule regions (Fig.…”

Confinement-Dependent Friction in Peptide Bundles

“…For a realistic protein system, the intricate coupling of solvent friction, dissipation within the peptidic backbone, and friction between residues that are distant in sequence space has not allowed formulation of a simple theoretical model thus far. The actual situation is even more complicated because the number of native contacts increases as the final folded state is approached and thus internal friction is expected to increase toward the native state (22)(23)(24)(25), as was also demonstrated in coarse-grained simulations of homopolymeric globules (26,27). In other words, a fast initial low-friction collapse is expected to be followed by a much slower high-friction search for the native configuration (28,29).…”