During ribosomal translocation, a process central to the elongation phase of protein synthesis, movement of mRNA and tRNAs requires large-scale rotation of the head domain of the small (30S) subunit of the ribosome. It has generally been accepted that the head rotates by pivoting around the neck helix (h28) of 16S rRNA, its sole covalent connection to the body domain. Surprisingly, we observe t...

Outer hair cell electromotility is crucial for the amplification, sharp frequency selectivity, and nonlinearities of the mammalian cochlea. Current modeling efforts based on morphological, physiological, and biophysical observations reveal transmembrane potential gradients and membrane tension as key independent variables controlling the passive and active mechanics of the cell. The cell's mech...

We present a molecular mechanics force field in AMBER format for the mixed-valence manganese vanadium oxide cluster [Mn4V4O17(OAc)3]3−—a synthetic analogue of oxygen-evolving complex that catalyzes water oxidation reaction photosystem II—with parameter sets two different states. Most parameters involving metal atoms have been newly parametrized and harmonic terms refined using hybrid quantum me...

Contact mechanics is related to the deformation study of solids that meet each other at one or more points. The physical and mathematical formulation of the problem is established upon the mechanics of materials and continuum mechanics and focuses on computations involving bodies with different characteristics in static or dynamic contact. Contact mechanics gives essential information for the s...

Tetracyclines (Tcs) are an important family of antibiotics that bind to the ribosome and several proteins. To model Tc interactions with protein and RNA, we have developed a molecular mechanics force field for 12 tetracyclines, consistent with the CHARMM force field. We considered each Tc variant in its zwitterionic tautomer, with and without a bound Mg(2+). We used structures from the Cambridg...

The hybrid quantum mechanics (QM) and molecular mechanics (MM) method is employed to simulate the His-tagged peptide adsorption to ionized region of nickel surface. Based on the previous experiments, the peptide interaction with one Ni ion is considered. In the QM/MM calculation, the imidazoles on the side chain of the peptide and the metal ion with several neighboring water molecules are treat...