Proteomics From Sequences to Functions

Before the era of proteomics, structure and function were characterized, often in 

As we begin to appreciate that there is much information about drug targets that genomics cannot provide, the focus has shifted from genomics to proteomics. The shift in focus parallels the appreciation of the complexity of proteins, which exceeds the complexity of DNA sequences. While a DNA sequence may allow one to predict the amino-acid sequence of a protein—in cases where an open reading frame sequence (with a start and stop codon) is apparent—it can neither assure expression nor provide information about protein function. 

Stop protein translation sites. Furthermore, protein synthesis and stability may also be regulated by constantly changing cellular processes and extracellular signals such as heat shock proteins, growth factors, and toxins. The end result of these processes could lead to changes in protein localization and interactions, generation of protein fragments, and alteration in protein function and turnover rates. 

Protein fragmentation, on the other hand, may be needed for functional activity of some proteins, such as chymotrypsin and insulin, which assume active forms after removal of amino-acid sequences in chy-motrypsinogen and proinsuhn. Additional complexity in analytical methodologies to deduce protein function in situ could also arise from a single protein exhibiting more than one function. Conversely, a given function may require integration of multiple proteins, or that many other proteins can perform the same function. 

Other examples of basic binding blocks include (1) ATP binding cassette transporter with a characteristic nucleotidebinding domain signature, (2) cyclic AMP or cyclic GMP receptor proteins, and (3) BH domain signature found in Bcl-fami-lies. A more complete description of these proteins with common structural and functional domains is listed in Table 16.5. The 

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