The proper location and timing of Dnmt1 activation are essential for DNA methylation
maintenance. We demonstrate here that Dnmt1 utilizes two-mono-ubiquitylated histone H3 as a …

Mode coupling in a protein molecule was studied by a molecular dynamics simulation of the
intramolecular vibrational energy transfer in myoglobin at near zero temperature. It was …

Large-scale conformational changes in proteins involve barrier-crossing transitions on the
complex free energy surfaces of high-dimensional space. Such rare events cannot be …

The major cytoskeleton protein actin undergoes cyclic transitions between the monomeric G-form
and the filamentous F-form, which drive organelle transport and cell motility. This …

A multiscale simulation method,“multiscale essential sampling (MSES),” is proposed for
calculating free energy surface of proteins in a sizable dimensional space with good scalability. …

Molecular functions of intrinsically disordered proteins (IDPs) or intrinsically disordered
regions (IDRs), such as molecular recognition and cellular signaling, are ascribed to dynamic …

Coarse-graining of protein interactions provides a means of simulating large biological
systems. Here, a coarse-graining method, REACH, is introduced, in which the force constants of …

10.7554/eLife.31715.001 The multidrug transporter AcrB transports a broad range of drugs
out of the cell by means of the proton-motive force. The asymmetric crystal structure of …

The anharmonic dynamics of a protein molecule was studied by molecular dynamics
simulations of the intramolecular vibrational energy transfer in myoglobin. A small excess kinetic …

A molecular level understanding of the structure, dynamics and mechanics of cellulose fibers
can aid in understanding the recalcitrance of biomass to hydrolysis in cellulosic biofuel …