Protein sequencing rationale

The previous section established one rationale for comparing two similar DNA (or protein) sequences. In fact, however, the utility of sequence comparison is extensive and rests on the observation that sufficiently similar sequences often share a consistent biological function. A relevant example is the DNA sequence from rhesus monkey with accession number XR 011473 computational methods predict XR 011473 to be a protein-coding gene, while similarity to NM 000773 suggests that the encoded protein may be the rhesus monkey equivalent of the enzyme CYP2E1. This section aims to elucidate the details of a comparison between two sequences such as XR 011473 and NM 000773. Our discussion begins at the source of sequence similarity. 

This Chapter focuses on analyses that can be performed based solely on the primary sequence of a protein. Several rationales can be applied. Physico-chemical characteristics of individual amino acids are one basis for predictions of gross structural features. For example, particular repetitive patterns may suggest a coiled-coil structure while in general secondary structure can be predicted based on an a statistical analysis of the primary sequence. The definition of signals recognized by the cellular transport machinery allow the prediction of subcellular location. Although somewhat unsystematic such observations can provide valuable hints as to the structure and/or function of a protein. 

Sequence inversion and racemization have been associated with uncatalyzed formation of the cyclic dipeptides and has been shown to greatly complicate the kinetics of formation. Cyclic dipeptide formation, by uncatalyzed processes, is rapid enough to pose an apparent threat to the stability of proteins and a possible rationale for the posttranslational N-acetylation of proteins that have been observed in higher organisms. The rate of DKP formation will also depend on the carbonyl ester protecting groups or the structures of the peptide-resin linkage in the solid-phase mode. Furthermore, cyclization is a concentration-independent reaction and demands the use of dilute solutions. ... 

Genome mapping of sites implicated in DNA-protein interaction. Specific DNA-protein interactions play a key role in gene expression and DNA replication. Methylation provides an important approach to the identification and characterization of the DNA sequences involved in such interactions. The rationale is that endogenous or artificially introduced MTases methylate all genomic targets except... 

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