The harmonic analysis of cylindrically symmetric proteins: a comparison of Dronpa and a DNA sliding clamp.

The harmonic analysis of two types of proteins with cylindrical symmetry is performed by the Standard Force Field Normal Mode Analysis and by the elastic network model. For both proteins the global elastic modes are assigned to their characteristic topologies. Dronpa is a rigid β-barrel structure, presenting the twisting, bending and breathing motion of a cylindrical rod.

Normal mode analysis of Trp RNA binding attenuation protein: structure and collective motions.

The Trp RNA-binding protein (TRAP) has a toroidal topology and a perfect 11-fold symmetry, which makes it an excellent candidate for a vibrational study of elastic properties. Normal mode analysis in combination with correlation matrix calculations was used to detect collective low-frequency motions in TRAP. The results reveal the presence of highly correlated modes at the lower end of the spectrum, which directly reflect the annular and toroidal topology.

The leapfrog principle for boron fullerenes: a theoretical study of structure and stability of B112.

Two leapfrog isomers of a B(112) boron fullerene are constructed from small C(28) fullerenes (T(d) and D(2) symmetries) by the leapfrog transformation combined with omnicapping of the new hexagons. Their electronic structure is analyzed using the density functional theory at the B3LYP/SVP and BHLYP/SVP levels. Both isomers are characterized as minima on the potential energy hypersurface with a HOMO-LUMO gap at B3LYP/SVP of 1.

Growth mechanism and chemical bonding in scandium-doped copper clusters: experimental and theoretical study in concert.

Size matters! The electronic structure and size-dependent stability of neutral and cationic scandium-doped copper clusters have been investigated by mass spectrometric studies (for the cations) and also quantum chemical computations. The proposed reaction paths ultimately lead to the most stable Frank-Kasper-shaped Cu(16)Sc(+) cluster (shown here), which could be the germ of a new crystallization process.Electronic structure and size-dependent stability of scandium-doped copper cluster cations, Cu(n)Sc(+), were investigated by using a dual-target dual-laser vaporization production scheme followed by mass spectrometric studies and also quantum chemical computations in the density functional theory framework.

How Is cis-trans Isomerization Controlled in Dronpa Mutants? A Replica Exchange Molecular Dynamics Study.

The reversibly photoactivatable green fluorescent protein analog Dronpa holds great promise as a marker for various new cellular imaging applications. Using a replica exchange method which combines both Hamiltonian and temperature exchanges, the ground-state dynamics of Dronpa and two mutants with increased switching kinetics, Val157Gly and Met159Thr, were compared. The dominant chromophore state was found to be the cis isomer in all three proteins.