Thu, 21 Aug 2008 09:32:55 BST CiteULike: twentas gravy http://www.citeulike.org/user/twenta/tag/gravy CiteULike.org en-gb Copyright © 2004-2008 citeulike.org http://www.citeulike.org/user/twenta/article/2231757 <i>J. Biol. Chem., Vol. 279, No. 49. (3 December 2004), pp. 50915-50922.</i><br /><br />Proteomics of membrane proteins is essential for the understanding of cellular function. However, mass spectrometric analysis of membrane proteomes has been less successful than the proteomic determination of soluble proteins. To elucidate the mystery of transmembrane proteins in mass spectrometry, we present a detailed statistical analysis of experimental data derived from chloroplast membranes. This approach was further accomplished by the analysis of the Arabidopsis thaliana proteome after in silico digestion. We demonstrate that both the length and the hydrophobicity of the proteolytic fragments containing transmembrane segments are major determinants for detection by mass spectrometry. Based on a comparative analysis, we discuss possibilities to overcome the problem and provide possible protocols to shift the hydrophobicity of transmembrane segment-containing peptides to facilitate their detection. 10.1074/jbc.M405875200 Hiding behind Hydrophobicity: TRANSMEMBRANE SEGMENTS IN MASS SPECTROMETRY Lutz Eichacker Bernhard Granvogl Oliver Mirus Bernd Muller Christian Miess Enrico Schleiff doi:10.1074/jbc.M405875200 J. Biol. Chem., Vol. 279, No. 49. (3 December 2004), pp. 50915-50922. 2008-01-14T20:01:34-00:00 2004 J. Biol. Chem. 279 49 50915 50922 gauss gravy http://www.citeulike.org/user/twenta/article/927188 <i>Journal of Molecular Biology, Vol. 157, No. 1. (5 May 1982), pp. 105-132.</i><br /><br />A computer program that progressively evaluates the hydrophilicity and hydrophobicity of a protein along its amino acid sequence has been devised. For this purpose, a hydropathy scale has been composed wherein the hydrophilic and hydrophobic properties of each of the 20 amino acid side-chains is taken into consideration. The scale is based on an amalgam of experimental observations derived from the literature. The program uses a moving-segment approach that continuously determines the average hydropathy within a segment of predetermined length as it advances through the sequence. The consecutive scores are plotted from the amino to the carboxy terminus. At the same time, a midpoint line is printed that corresponds to the grand average of the hydropathy of the amino acid compositions found in most of the sequenced proteins. In the case of soluble, globular proteins there is a remarkable correspondence between the interior portions of their sequence and the regions appearing on the hydrophobic side of the midpoint line, as well as the exterior portions and the regions on the hydrophilic side. The correlation was demonstrated by comparisons between the plotted values and known structures determined by crystallography. In the case of membrane-bound proteins, the portions of their sequences that are located within the lipid bilayer are also clearly delineated by large uninterrupted areas on the hydrophobic side of the midpoint line. As such, the membrane-spanning segments of these proteins can be identified by this procedure. Although the method is not unique and embodies principles that have long been appreciated, its simplicity and its graphic nature make it a very useful tool for the evaluation of protein structures. A simple method for displaying the hydropathic character of a protein Jack Kyte Russell Doolittle doi:10.1016/0022-2836(82)90515-0 Journal of Molecular Biology, Vol. 157, No. 1. (5 May 1982), pp. 105-132. 2006-11-03T14:37:44-00:00 1982 Journal of Molecular Biology 157 1 105 132 gravy hydrophobicity