Sequence alignment reveals possible MAPK docking motifs on HIV proteins.

PloS One
Perry EvansAydin Tozeren

Abstract

Over the course of HIV infection, virus replication is facilitated by the phosphorylation of HIV proteins by human ERK1 and ERK2 mitogen-activated protein kinases (MAPKs). MAPKs are known to phosphorylate their substrates by first binding with them at a docking site. Docking site interactions could be viable drug targets because the sequences guiding them are more specific than phosphorylation consensus sites. In this study we use multiple bioinformatics tools to discover candidate MAPK docking site motifs on HIV proteins known to be phosphorylated by MAPKs, and we discuss the possibility of targeting docking sites with drugs. Using sequence alignments of HIV proteins of different subtypes, we show that MAPK docking patterns previously described for human proteins appear on the HIV matrix, Tat, and Vif proteins in a strain dependent manner, but are absent from HIV Rev and appear on all HIV Nef strains. We revise the regular expressions of previously annotated MAPK docking patterns in order to provide a subtype independent motif that annotates all HIV proteins. One revision is based on a documented human variant of one of the substrate docking motifs, and the other reduces the number of required basic amino acids in the standard...Continue Reading

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Citations

Jun 8, 2011·PloS One·David SargeantMartin R Schiller
Aug 23, 2011·PloS One·Mahdi SarmadyAydin Tozeren
Jul 13, 2011·Biochimica Et Biophysica Acta·Slava RomFrancesca Peruzzi
Apr 13, 2015·Current Opinion in Structural Biology·Lucía Beatriz ChemesIgnacio Enrique Sánchez

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Software Mentioned

ZDOCK
UPGMA
Vorometric
YASARA
ELM
Eukaryotic Linear Motif ( ELM )
BLAST

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