Functional site residues mapping

From a map at low resolution (5 A or higher) one can obtain the shape of the molecule and sometimes identify a-helical regions as rods of electron density. At medium resolution (around 3 A) it is usually possible to trace the path of the polypeptide chain and to fit a known amino acid sequence into the map. At this resolution it should be possible to distinguish the density of an alanine side chain from that of a leucine, whereas at 4 A resolution there is little side chain detail. Gross features of functionally important aspects of a structure usually can be deduced at 3 A resolution, including the identification of active-site residues. At 2 A resolution details are sufficiently well resolved in the map to decide between a leucine and an isoleucine side chain, and at 1 A resolution one sees atoms as discrete balls of density. However, the structures of only a few small proteins have been determined to such high resolution. 

The availability of ALAS site-directed mutants of other functionally important residues permitted Tan et al. [113] to map the ALAS active site and assess whether these residues are contributed to the active site from the same subunit or from the two subunits K313, D279 and R439 are contributed to the ALAS active site from the same subrmit but different from that of R149 (Figure 2-6). 

Each of these pathways involves a kinase cascade resulting in the phosphorylation and activation of the MAP kinase family member. Each contains a dual phosphorylation site (TEY, TPY, or TGY) and the central residue in the motif characteristic of the class, as shown in Table 8.1. It is evident that cells are endowed with parallel signal-transduction pathways and that they may operate individually or in combination to initiate specific patterns of gene expression. Additionally, crosstalk between the pathways undoubtedly occurs. None of these pathways has a unique function it is more likely that the combination of pathways that are activated (or silenced) together with the... 

Phosphorylation on serine, threonine, and tyrosine residues is an extremely important modulator of protein function. Phosphorylation can be analyzed by mass spectrometry with enrichment of compounds of interest using immobilized metal affinity chromatography and chemical tagging techniques, detection of phosphopep-tides using mass mapping and precursor ion scans, localization of phosphorylation sites by peptide sequencing, and quantitation of phosphorylation by the introduction of mass tags (McLachlin and Chait 2001). 

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