PubMed · 14066513
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C MATHIS, G OURISSON. 1963. [FUNCTIONAL ANALYSIS BY THIN LAYER CHROMATOGRAPHY].. https://doi.org/10.1016/s0021-9673(01)83651-7
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Human tumor necrosis factor-alpha (TNF-alpha) is a trimeric protein consisting primarily of beta-sheet. GdnHCl-induced unfolding of TNF-alpha was investigated at room temperature by circular dichroism (CD) and size exclusion chromatography. The secondary and tertiary structure of TNF-alpha persisted up to 0.9N GdnHCl regardless of incubation time, but, in the range of 1.2 N to 2.1 N GdnHCl, there was loss of tertiary structure accompanied by the formation of an alpha-helix, as revealed by far- and near-UV CD spectra. The structural changes occurred gradually in 1.2 and 2.1 N GdnHCl, but were rapid in 1.5 and 1.8 N GdnHCl. The GdnHCl-induced state of TNF-alpha is an unfolded, alpha-helical aggregate of about 130 monomers, as shown by size exclusion chromatography. We suggest the most likely pathway for the transition from beta-sheet to alpha-helix.
Both spatial and temporal peaks that are produced by the discrete parcel model can be mathematically approximated by Gaussian functions, but the transformation from a spatial pattern to a temporal image requires a convolution treatment. A first-order convolution is given for temporal peaks under a linear isotherm, whereas a second-order convolution is proposed for those under non-linear isotherms. Numerical tests show that the peak shapes generated by the proposed temporally convoluted Gaussian equations (TCG) match perfectly with those obtained by the discrete parcel model. Although the full TCG equation may be quite complicated, it can be made easier by a recursion calculation technique, and a group of peak curves can be plotted simultaneously on computer worksheet. The results also suggest that the temporal distortion effect should be predominately considered, in addition to those known-to-exist spatial effects, for explaining the peak asymmetry.
UNLABELLED: Expressed sequence tags (ESTs) offer a low-cost approach to gene discovery and are being used by an increasing number of laboratories to obtain sequence information for a wide variety of organisms. The challenge lies in processing and organizing this data within a genomic context to facilitate large scale analyses. Here we present PartiGene, an integrated sequence analysis suite that uses freely available public domain software to (1) process raw trace chromatograms into sequence objects suitable for submission to dbEST; (2) place these sequences within a genomic context; (3) perform customizable first-pass annotation of the data; and (4) present the data as HTML tables and an SQL database resource. PartiGene has been used to create a number of non-model organism database resources including NEMBASE (http://www.nematodes.org) and LumbriBase (http://www.earthworms.org/). The packages are readily portable, freely available and can be run on simple Linux-based workstations. AVAILABILITY: PartiGene is available from http://www.nematodes.org/PartiGene and also forms part of the EST analysis software, associated with the Natural Environmental Research Council (UK) Bio-Linux project (http://envgen.nox.ac.uk/biolinux.html).