Incorporating dipolar solvents with variable density in Poisson-Boltzmann electrostatics.

We describe a new way to calculate the electrostatic properties of macromolecules that goes beyond the classical Poisson-Boltzmann treatment with only a small extra CPU cost. The solvent region is no longer modeled as a homogeneous dielectric media but rather as an assembly of self-orienting interacting dipoles of variable density. The method effectively unifies both the Poisson-centric view and the Langevin Dipole model.

NOMAD-Ref: visualization, deformation and refinement of macromolecular structures based on all-atom normal mode analysis.

Normal mode analysis (NMA) is an efficient way to study collective motions in biomolecules that bypasses the computational costs and many limitations associated with full dynamics simulations. The NOMAD-Ref web server presented here provides tools for online calculation of the normal modes of large molecules (up to 100,000 atoms) maintaining a full all-atom representation of their structures, as well as access to a number of programs that utilize these collective motions for deformation and refinement of biomolecular structures. Applications include the generation of sets of decoys with correct stereochemistry but arbitrary large amplitude movements, the quantification of the overlap between alternative conformations of a molecule, refinement of structures against experimental data, such as X-ray diffraction structure factors or Cryo-EM maps and optimization of docked complexes by modeling receptor/ligand flexibility through normal mode motions.

PDB_Hydro: incorporating dipolar solvents with variable density in the Poisson-Boltzmann treatment of macromolecule electrostatics.

We describe a new way to calculate the electrostatic properties of macromolecules which eliminates the assumption of a constant dielectric value in the solvent region, resulting in a Generalized Poisson-Boltzmann-Langevin equation (GPBLE). We have implemented a web server (http://lorentz.immstr.

Developmental studies of the first step of the initiation of brain protein synthesis, role for initiation factor 2.

Developmental changes at the level of initiation step of translation in the rat brain were studied. The level of deacylated tRNAimet in rat brain was measured at two stages of postnatal development. Although the amount of tRNA was slightly lower in adult than in young (4 day old) rats, the charging capacity of initiator tRNAimet in vitro was similar at both ages.

Protein kinase activities associated with ribosomes of developing rat brain. Identification of eukaryotic initiation factor 2 kinases.

Protein kinases associated with ribosomes in the brains of suckling (4-10 days) and adult (2 months) rats were extracted from ribosomal fraction with 0.5 M KCl. The different protein kinase activities were characterized by their ability to phosphorylate three exogenous substrates: casein, histone IIs and histone IIIs in the presence of different modulators.