Prokaryotes proteome

Krause, F, 2006. Detection and analysis of protein-protein interactions in organellar and prokaryotic proteomes by native gel electrophoresis (Membrane) protein complexes and supercomplexes. Electrophoresis 27, 2759-2781. 

Before we describe the chemistry of the compartments involved, note that like prokaryotes, a number of oxidative enzymes are found in the cytoplasm but they do not release damaging chemicals (see Section 6.10). We also observed that such kinds of kinetic compartments are not enclosed by physical limitations such as membranes. We have also mentioned that increased size itself makes for kinetic compartments if diffusion is restricted. In this section, we see many additional advantages of eukaryotes from those given in Section 7.4. How deceptive it can be to use just the DNA, the all-embracing proteome, metabolome or metallome in discussing evolution without the recognition of the thermodynamic importance of compartments and their concentrations These data could be useful both here and in simpler studies of single-compartment bacteria even in the analysis of species but not much information is available. 

Before we conclude the functions of the elements and the proteome, there is a second general feature of eukaryote cells, much of which evolved from that of the prokaryotes - the types of metal-binding protein. The general supposition is that the number of folds are limited and certainly the number of metal-binding sites for any one metal ion is closely limited (see Section 4.15). We find that there are some general rules for protein-binding centres of metal ions and their geometry, mentioned only in brief in Chapters 5 and 6. 

The approach recruited to chemical proteomics in Reference [17] is called SILAC (stable isotope labeling with amino acids in cell culture) and is important in comparative proteomics (Figure 1). SILAC works well with cultured mammalian cells, but prokaryotes defeat it by metabolizing the label (usually supplied in lysine and arginine) into other amino acids. For applications beyond cultured eukaryotic cells, the reductive methylation route to differential labeling [18] is among the alternatives [15]-... 

Advantages and Applications of Gel-Free Proteomic Approaches in the Study of Prokaryotes... 

The subsequent downstream processing section, which includes visualization of quantified proteins, statistical validation of differences in treatments or samples, and biological interpretation, is much less defined in terms of work-flow regimens and is discussed toward the end of this chapter. In the succeeding text, various relevant aspects of proteomic workflows that impinge on the data obtained from proteomic analysis of prokaryotes assuming that a gel-free approach is used are discussed. 

STATE OF AFFAIRS IN THE STUDY OF PROKARYOTES VIA GEL-FREE PROTEOMICS... 

As already explained, analysing a proteome first involves the isolation of the biological sample of interest. Then the contained proteins have to be separated in order to allow their individual identification, characterization and possibly quantification (Figure 4.1.). The number of proteins to analyse is very often large, ranging from a few hundreds in low prokaryotes to possibly 500000 to one million in human samples [2],... 

---