Nuclear envelope proteomics: Novel integral membrane proteins of the innernuclear membrane

The nuclear envelope (NE) is one of the least characterized structures of e ukaryotic cells. The study of its functional roles is hampered by the small number of proteins known to be specifically located to it. Here, we presen t a comprehensive characterization of the NE proteome. We applied different fractionation procedures and isolated protein subsets derived from distinc t NE compartments. We identified 148 different proteins by 16-benzyl dimeth yl hexadecyl ammonium chloride (16-BAC) gel electrophoresis and matrix-assi sted laser desorption ionization (MALDI) mass spectrometry; among them were 19 previously unknown or noncharacterized. The identification of known pro teins in particular NE fractions enabled us to assign novel proteins to NE substructures. Thus, our subcellular proteomics approach retains the screen ing character of classical proteomic studies, but also allows a number of p redictions about subcellular localization and interactions of previously no ncharacterized proteins. We demonstrate this result by showing that two nov el transmembrane proteins, a 100-kDa protein with similarity to Caenorhabdi tis elegans Unc-84A and an unrelated 45-kDa protein we named LUMA, reside i n the inner nuclear membrane and likely interact with the nuclear lamina. T he utility of our approach is not restricted to the investigation of the NE . Our approach should be applicable to the analysis of other complex membra ne structures of the cell as well.