Posttranslational modifications predictions

ExPASy Proteomics tools (http //expasy.org/tools/), tools and online programs for protein identification and characterization, similarity searches, pattern and profile searches, posttranslational modification prediction, topology prediction, primary structure analysis, or secondary and tertiary structure prediction. 

Catalases have proven to be a treasure trove of unusual modifications. The first noted modification was the oxidation of Met53 of PMC to a methionine sulfone (77). Met53 is situated in the distal side active site adjacent to the essential His54 in a location where oxidation by a molecule of peroxide would not be unexpected. Among the catalases whose structures have been solved, PMC is unique in having the sulfone because valine is the more common replacement in other catalases. The sulfone does not seem to have a role in the catalytic mechanism and is clearly generated as a posttranslational modification. A small number of catalases from other sources, principally bacteria, have Met in the same location as PMC, and it is a reasonable prediction that the same oxidation occurs in those enzymes as well, although this has not been demonstrated. 

Bik inhibitory strength and selectivity for serine proteases vary greatly with peptide sequence and posttranslational modifications such as fragmentation and glycoconjugation [6, 14, 15]. Predicted Bik fragmentation sites via trypsin binding and/or hydrolysis are shown (Fig. 2). 

Eisenhaber F, Eisenhaber B, Kubina W, Maurer-Stroh S, Neu-berger G, et al. 2003. Prediction of lipid posttranslational modifications and localization signals from protein sequences Big n, NMT and PTS1. Nucleic Acids Res 31 3631-3634. 

Literally hundreds of bioinformatics tools can be applied to obtain additional supporting data for functional inference. Among others, those tools can be used to predict posttranslational modifications (e.g., phosphorylation, myristoylation, sulfation,... 

To ensure that proteins end up in a location appropriate to their function in a timely and predictable way, it is necessary to have a targeting mechanism. The signaling process begins with specific signal sequences, which determine where translation will be completed. Specific localization sequences and/or posttranslational modification of the product protein then ensures delivery of the protein to its target location. 

The functional microarray typically consists of a collection of full-length functional proteins or protein domains printed on glass slides that are then exposed to a protein preparation from a cell that represents the entire proteome of that cell. This method is useful in determining protein-protein interactions. In addition, this method is useful in predicting the interaction of proteins with DNA, RNA, phospholipids, and small molecules. RPA includes glass slides on which a cellular protein preparation is fixed and then probed with a known antibody. This method helps in identifying the proteins that are altered and cannot bind with a known antibody in the proteome of diseased cell types. This method also identifies the proteins that are altered as a result of phosphorylation or other posttranslational modifications in normal and disease conditions or under growth conditions. 

In cases where the predicted mass calculated from the amino acid sequence does not match the observed mass, top-down sequencing is used to determine sites of posttranslational modifications as seen in Fig. 5. 

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