The detection of membrane-bound proteins by standard proteomic methods, however, is challenging due to their relative low abundance in total cell lysates, their frequently large size and most notably their hydrophobic characteristics (Santoni et al. Thus, identification of new, differentially expressed membrane proteins reflecting certain disease properties has the potential of providing novel biomarkers and therapeutic targets. Furthermore, it is estimated that about two-thirds of all future drugs will target membrane proteins (Hopkins et al. The importance of membrane proteins for clinical application is underlined by the fact that they account for 70–80% of all drug targets. Alterations in protein patterns often lead to cell dysfunctions and disease phenotypes (Carter et al. Membrane proteins are critical for normal cellular differentiation and diverse functions (Sanders and Myers 2004). Based on purity of membranous fraction, protein yield, time and costs, we show superiority of two commercial extraction kits for downstream proteome analyses of membrane proteins. We also demonstrate by means of polyacrylamide gel electrophoresis (SDS–PAGE) and Western blot analysis that the majority of commercial membrane extraction kits harbor a substantial cytosolic contamination of their membranous fraction. We present a comparative study of different membrane protein extraction methods that vary in total protein yield between 0.02 and 4.8 mg using constant cell pellets of the colorectal carcinoma cell line SW620. We thus aimed to identify protocols that allow for highly efficient isolation and purification of membrane-bound proteins for subsequent protein profiling. Unfortunately, isolation and analysis of membrane-bound proteins is hampered by their relative low abundance in total cell lysates, their frequently large size and their hydrophobic properties. Identification of new, differentially expressed membrane proteins reflecting distinct disease properties is thus of high importance. Membrane proteins account for 70–80% of all pharmaceutical targets emphasizing their clinical relevance.
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