Protein local sequence patterns

On the Correlation of Protein Structure with Local Sequence Patterns... 

The aim of the fust dimension breadth is to reveal sequence-function relationships by comparing protein sequences by sequence similarity. Simple bioinformatic algorithms can be used to compare a pair of related proteins or for sequence similarity searches e.g., BLAST (Basic Local Alignment Search Tool). Improved algorithms allow multiple alignments of larger number of proteins and extraction of consensus sequence pattern and sequence profiles or structural templates, which can be related to some functions, see e.g., under http //www. expasy.ch/tools/ similarity. 

Drawid, A., and M. Gerstein. 2000. A Bayesian system integrating expression data with sequence patterns for localizing proteins Comprehensive application to the yeast genome. J Mol Biol 301 1059-75. 

BLAST Basic Local Alignment Search Tool is the most popular nucleotide and protein similarity searching tool in bioinformatics. It is web-accessible, free, fast, and can search many databases at the same time. It can detect isolated sequence patterns, especially if used with the more recent position-specific iterative method PSI-BLAST. Similarity of residues can be defined via mutation or physicochemical substitution matrices. 

Definition of Ej and E2 eonformations of the a subunit of Na,K-ATPase involves identification of cleavage points in the protein as well as association of cleavage with different rates of inactivation of Na,K-ATPase and K-phosphatase activities [104,105]. In the Ei form of Na,K-ATPase the cleavage patterns of the two serine proteases are clearly distinct. Chymotrypsin cleaves at Leu (C3), Fig. 3A, and both Na,K-ATPase and K-phosphatase are inactivated in a monoexponential pattern [33,106]. Trypsin cleaves the E form rapidly at Lys ° (T2) and more slowly at Arg (T3) to produce the characteristie biphasic pattern of inactivation. Localization of these splits was determined by sequencing N-termini of fragments after isolation on high resolution gel filtration columns [107]. 

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