Protein features

Multiple myeloma is a malignancy of plasma cells that is characterized by an abnormal production of a monoclonal protein. Features of the disease include bone lesions, anemia, and... 

ExPASy (Expert Protein Analysis System, www.expasy.ch) or the National Centre for Biotechnology Information (NCBI, www.ncbi.nlm.gov) websites. Both websites provide bioinformatics tools, links to sequence databases and extensive bibliographic resources. As an example of the wealth of information available on individual enzymes, at the time of writing a search based on nitrilase in the Entrez protein section of NCBI will recover more than 10000 references to nitrilase enzyme amino acid sequences. These can be rapidly screened online by organism, and the individual entries will have links to amino acid and gene sequence, relevant literature and information on protein features (such as conserved domains). 

Protein Features of protein structure Effect on transcription Other properties In vivo expression and localization... 

Dyson, M. R., Shadbolt, S. R, Vincent, K. J., Perera, R. L. and McCafferty, J. (2004). Production of soluble mammalian proteins in Escherichia coli identification of protein features that correlate with successful expression. BMC Biotechnol. 4,32. 

HPRD is unique in that it assimilates diverse protein features such as PPIs, PTMs, subcellular localization, tissue expression, biological motifs, and domains derived from a variety of experimental platforms (Fig. 1). Thus HPRD can be used to perform complex queries involving multiple features of proteins. 

Total number of annotations added Total number of annotations contributed Protein feature type to HPRD (From 2003 to 2008) by Human Proteinpedia (in 2008)... 

MR, an a/f-barrel protein, features a high degree of similarity with muconate-lactonizing enzyme (MLE) of the /3-ketoadipate metabolism 26% sequence identity, the same symmetry and organization of subunits (octamer), a divalent metal ion requirement (Mn2+ for MLE, Mg + for MR). As MLE is almost ubiquitous among Pseudomonas, compared to 5% frequency of MR, it can be concluded that MLE is the older enzyme and probably the precedessor of MR. 

The amino acid and protein features can be represented in different ways to maximize information extraction. They may be represented as real-numbered measurements in a continuous scale (such as mass or hydrophobicity scales in Table 6.1), or as vectors of distances or frequencies (such as PAM matrix and sequence profile in Figures 6.2 and 6.3). But they can also be conveniently categorized into classes based on these properties. This effectively reduces the original 20-letter amino acid alphabet set to an alternative alphabet set of smaller sizes and emphasizes the various properties of the molecular residues and maximizes feature extraction. 

The rest of the known sequences of all four classes of BCB domain-containing proteins feature signal peptides in their precursors, indicating that they are translocated across the bacterial cytoplasmic membrane or are translated on the endoplasmic reticulum-bound ribosomes and sent to the secretory pathway in eukaryotes. Thus they are located in the bacterial periplasm, secreted into the extracellular milieu, or anchored to the cell surface. 

Blawas AS, Oliver TF, Pirrung MC et al (1998) Step-and-repeat photopatteming of protein features using caged/biotin-BSA characterization and resolution. Langmuir 14 4243 250 Conrad DW, Golightley SK, Bart JC (1998) Photoactivatable o-nitrobenzyl polyethylene glycol-silane for the production of patterned biomolecular arrays. US Patent 5,773,308... 

Peretz D, Williamson RA, Matsunaga Y, Serban H, Pinilla C, Bastidas RB, Rozenshteyn R, James TL, Houghten RA, Cohen FE, Prusiner SB, Burton DR (1997) A conformational transition at the N terminus of the prion protein features in formation of the scrapie isoform. J Mol Biol 273 614... 

Key Words Motif discovery sequence motif sequence pattern protein domain multiple alignment position-specific scoring matrix PSSM position-specific weight matrix PWM transcription factor-binding site transcription factor promoter protein features. 

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