posted on 2013-03-01, 00:00authored byRichard
S. L. Stein, Nan Li, Wei He, Elizabeth Komives, Wei Wang
Lysine methylation is one of the important post-translational
modifications
(PTMs) that regulate protein functions. Up to now, proteomic identification
of this PTM remains a challenge due to the lack of effective enrichment
methods in mass spectrometry experiments. To address this challenge,
we present here a systematic approach to predicting peptides in which
lysine residues may be methylated to mediate protein–protein
interactions. We used the chromodomain of the polycomb protein in Drosophila melanogaster as a model system to illustrate
the success of this approach. We started with molecular dynamics simulations
and free energy analyses on the histone peptides complexed with the
polycomb chromodomain to understand how the binding specificity is
achieved. We next conducted virtual mutagenesis to quantify each domain
and peptide residue’s contribution to the domain-peptide recognition,
based on which scoring scheme was developed to evaluate the possibility
of any lysine-containing peptides to be methylated and recognized
by the chromodomain. A peptide microarray experiment on a panel of
conserved histone peptides showed a satisfactory prediction accuracy
of the scoring scheme. Next, we implemented a bioinformatics pipeline
that integrates multiple lines of evidence including conservation,
subcellular localization, and mass spectrometry data to scan the fly
proteome for a systematic identification of possible methyllysine-containing
peptides. These putative chromodomain-binding peptides suggest unknown
functions of the important regulator protein polycomb and provide
a list of candidate methylation events for follow-up investigations.