We present a new method for protein secondary structure prediction, based on the recognition of well-defined pentapeptides, in a large databank. Using a databank of 635 protein chains, we obtained a success rate of 68.6%. We show that progress is achieved when the databank is enlarged, when the 20 amino acids are adequately grouped in 10 sets and when more pentapeptides are attributed one of the defined conformations, alpha-helices or beta-strands. The analysis of the model indicates that the essential variable is the number of pentapeptides of well-defined structure in the database. Our model is simple, does not rely on arbitrary parameters and allows the analysis in detail of the results of each chosen hypothesis.

The APS Journal Legacy Content is the corpus of 100 years of historical scientific research from the American Physiological Society research journals. This package goes back to the first issue of each of the APS journals including the American Journal of Physiology, first published in 1898. The full text scanned images of the printed pages are easily searchable. Downloads quickly in PDF format.

No abstract

No abstract

The interaction of L-aromatic aminoacids with bases and nucleosides is described. Of these, L-tryptophan interacts more strongly with bases and nucleosides as indicated by nuclear magnetic resonance, circular dichroism and solubility measurements.A possible ring-ring type interaction between the aminoacid and bases or nucleosides is proposed; this interaction being such that the hydrodinamic behaviour of the DNA molecule is unchanged.Ultra violet irradiated DNA is protected by L-tryptophan. A mechanism of energy transfer from the DNA to tryptophan trough triplet-triplet states is discussed.In previous communications 2 we described the interaction of L-tryptophan with ribonucleosides and DNA, as studied by NMR and ultraviolet spectroscopy.In this paper, the interaction of L-tryptophan with ribonucleosides and DNA as shown by solubility, circular dichroism and viscosity measurements are reported. Also some preliminary results of the interaction of this aminoacid with DNA at excited levels, are included. Materials and MethodsNitrogen bases, DNA (salmon sperm) were obtained from Calbiochem and nucleosides from Sigma.For the solubility experiments, saturated solutions of bases or nucleosides at 60° were prepared. These solutions, and those containing besides the aminoacid were incubated at 30 °C in a shaking water bath. The incubation flaks had two compartments separated by a sintered glass disk. The sample was placed in one of those compartments. After four days of incubation the flasks were inverted and filtered through the disk in the bath, avoiding temperature changes. These experiments were run in triplicate; the standard deviation of the mean value of solubility being less than 6 percent.The circular dichroism measurements were performed on a Shimatzu Seisakusho QU50 instrument with a DC attachment model CD1. For the ultraviolet spectroscopy, a Beckman DU instrument was used.Viscosity determinations were performed with a Beckman rotatory viscosimeter. Nuclear Magnetic Resonance measurementsAll of the proton spectra were recorded on a Hitachi temperature of 30 °C. The chemical shifts were measured with respect to DSS as an internal standard and were calibrated by the usual side band modulation technique to within ± 0.3 cps. The samples were dissolved in D20 (99.7%) and acidified to pD2 with concentrated HCl. The pD of the solutions were checked before and after recording the spectra. Ultraviolet irradiation was done at room temperature with a General Electric 30 Watt-lamp (G30T8) at a distance of 25 cm from the surface of the solutions. The energy out put of the lamp was approximatively 90 ergs/sec mm 2 *. ResultsAs we have shown previously the interaction at pH 2 of L-tryptophan with ribonucleosides, was evaluated through the magnetic up-field shifts of the ribonucleosides protons as a function of tryptophan concentration.By using NMR techniques we also investigated other possible interactions between L-aminoacids and ribonucleosides.Of those which could be studied (i. e. those which had enough solubility in wa...