2 research outputs found
Hydrodynamic Interactions in Protein Folding
We incorporate hydrodynamic interactions (HI) in a coarse-grained and
structure-based model of proteins by employing the Rotne-Prager hydrodynamic
tensor. We study several small proteins and demonstrate that HI facilitate
folding. We also study HIV-1 protease and show that HI make the flap closing
dynamics faster. The HI are found to affect time correlation functions in the
vicinity of the native state even though they have no impact on same time
characteristics of the structure fluctuations around the native state
Stretching and twisting of the DNA duplexes in coarse grained dynamical models
Three coarse-grained models of the double-stranded DNA are proposed and
compared in the context of mechanical manipulation such as twisting and various
schemes of stretching. The models differ in the number of effective beads
(between two and five) representing each nucleotide. They all show similar
behavior and, in particular, lead to a torque-force phase diagrams
qualitatively consistent with experiments and all-atom simulations