Comparison of van der Waals and semiempirical calculations of the molecular volumes of small molecules and proteins.

Molecular volumes for hydrocarbons, amino acids, peptides, and 14 globular proteins were calculated by techniques using van der Waals radii and by semiempirical molecular orbital methods. The resulting values were compared to experimentally determined volumes. The values obtained by methods employing van der Waals radii were found to be up to three times smaller than the experimentally determined values in the case of proteins, 25% smaller than the experimental values for peptides, and up to 50% greater than experimental values for simple hydrocarbons.

Structure and stability of histone HMf from the hyperthermophilic archaeon Methanothermus fervidus.

The secondary and quaternary structures and stabilities of recombinant (r) forms of the HMfA and HMfB histones from Methanothermus fervidus have been investigated by CD spectroscopy and formaldehyde-mediated protein-protein cross-linking. Both proteins were shown to be dimers in solutions containing 5-1300 mM KCl, at pH 6-10 and 25-83 degrees C, and specifically in 1 M KCl, at pH 7.5 and 83 degrees C, conditions which approximate those in vivo in M.

Osmolyte mediation of T7 DNA polymerase and plasmid DNA stability.

The thermal stability of T7 DNA polymerase and pGEM4Z plasmid DNA in the presence and absence of the osmolyte N-methylglycine (sarcosine) was determined by means of UV spectroscopy. The decrease in melting temperature observed upon addition of sarcosine to solutions containing the plasmid DNA is linear with the concentration of sarcosine present. The enthalpy of the transition is also linear in its relationship to the melting temperature, and the entropy of the transition is linear in the natural log of the melting temperature.

pH-induced conformational transitions of Cry IA(a), Cry IA(c), and Cry IIIA delta-endotoxins in Bacillus thuringiensis.

Three protoxins and corresponding delta-endotoxins from Bacillus thuringiensis (BT) were studied by means of circular dichroism spectroscopy and size-exclusion HPLC. At neutral pH, the Cry IIIA toxin exists only as a 65-kDa monomer. The toxins of Cry IA(a) and Cry IA(c) exist both as 66-kDa monomers and as oligomers with apparent molecular masses greater than 220 kDa.