Fast and accurate protein substructure searching with simulated annealing and GPUs

Background  

Searching a database of protein structures for matches to a query structure, or occurrences of a structural motif, is an important task in structural biology and bioinformatics. While there are many existing methods for structural similarity searching, faster and more accurate approaches are still required, and few current methods are capable of substructure (motif) searching.     

Protein precipitation using an anionic surfactant

The precipitation of lysozyme from aqueous solution by direct addition of the anionic surfactant sodium bis-(2-ethylhexyl) sulfosuccinate (AOT) was investigated as a function of the AOT and lysozyme molar ratio between 5 and 35, and a pH ranging from 2 to 12. An optimum stoichiometric molar ratio of 16:1 (AOT:lysozyme) achieved 100% removal efficiency of lysozyme at pH 6.2. The effect of pH on protein removal indicated that electrostatic interactions between oppositely charged protein and surfactant molecules drives the precipitation process. This ionic interaction induces the formation of an uncharged lysozyme–AOT complex which is not soluble and hence precipitates. The change of lysozyme structure in the aqueous phase after precipitation was measured using circular dichroism spectroscopy and liquid chromatography, and considerable insight has been gained into surfactant initiated protein precipitation.     

ENVIRONMENTAL FACTORS AND THE GROWTH OF NATIVE ORCHIDS

The environments in which native orchids grow were examined in terms of factors which might determine the survival and reproduction of the various species. Soil tests were made for 34 species now known to be growing in Rhode Island. Soil reaction appears to be related to growth of orchids, but other factors in the environment were found to be of equal if not greater importance. These include light, moisture, temperature and destruction by animals. Fertility was not found to be limiting under the conditions observed.