Agarose isoelectric focusing can improve resolution of membrane proteins in the two-dimensional electrophoresis of bacterial proteins

Challenges and solutions for the identification of membrane proteins in non-model plants

The workhorse for proteomics in non-model plants is classical two-dimensional electrophoresis, a combination of iso-electric focusing and SDS-PAGE. However, membrane proteins with multiple membrane spanning domains are hardly detected on classical 2-DE gels because of their low abundance and poor solubility in aqueous media. In the current review, solutions that have been proposed to handle these two problems in non-model plants are discussed. An overview of alternative techniques developed for membrane proteomics is provided together with a comparison of their strong and weak points. Subsequently, strengths and weaknesses of the different techniques and methods to evaluate the identification of membrane proteins are discussed. Finally, an overview of recent plant membrane proteome studies is provided with the used separation technique and the number of identified membrane proteins listed.

Exploring the membrane proteome--challenges and analytical strategies

The analysis of proteins in biological membranes forms a major challenge in proteomics. Despite continuous improvements and the development of more sensitive analytical methods, the analysis of membrane proteins has always been hampered by their hydrophobic properties and relatively low abundance. In this review, we describe recent successful strategies that have led to in-depth analyses of the membrane proteome. To facilitate membrane proteome analysis, it is essential that biochemical enrichment procedures are combined with special analytical workflows that are all optimized to cope with hydrophobic polypeptides. These include techniques for protein solubilization, and also well-matched developments in protein separation and protein digestion procedures. Finally, we discuss approaches to target membrane-protein complexes and lipid-protein interactions, as such approaches offer unique insights into function and architecture of cellular membranes.

Performance of agarose IEF gels as the first dimension support for non-denaturing micro-2-DE in the separation of high-molecular-mass plasma proteins and protein complexes

Agarose micro-column gels (1% w/v agarose, diameter 1.4 mm and length 35 mm) were prepared as the first-dimension IEF support for non-denaturing 2-DE and the performance was compared with that of polyacrylamide gels (4.2% T and 4.8% C, the same gel size) using a human plasma sample. Sorbitol was not added in the agarose IEF gels, since its presence not only delayed the focusing of the proteins but also deteriorated the protein resolution. The optimum IEF time of the agarose gels for separation of 2 microL plasma sample (ca. 120 microg proteins) was decided to be 46 min, which is much shorter than that of the polyacrylamide gels (75 min). MALDI-MS and PMF assignment of the spots on the micro-2-DE gels at apparent molecular mass above ca. 5x10(2) kDa and pI from 4 to 8 revealed that when polyacrylamide IEF gels were used, many of the high-molecular-mass proteins resided at the sample loading edge or in basic pI regions as smear bands. When agarose IEF gels were used, most of the high-molecular-mass proteins moved to more acidic pI positions and were better focused, and their apparent pI values matched well with those previously reported for purified proteins. These results demonstrated the advantages of agarose-IEF/2-DE for the separation of high-molecular-mass proteins and protein complexes under non-denaturing conditions.