ABSTRACT
WW domains are protein modules that mediate protein-protein interactions through recognition of proline-rich peptide motifs and phosphorylated serine/threonine-proline sites. To pursue the functional properties of WW domains, we employed mass spectrometry to identify 148 proteins that associate with 10 human WW domains. Many of these proteins represent novel WW domain-binding partners and are components of multiprotein complexes involved in molecular processes, such as transcription, RNA processing, and cytoskeletal regulation. We validated one complex in detail, showing that WW domains of the AIP4 E3 protein-ubiquitin ligase bind directly to a PPXY motif in the p68 subunit of pre-mRNA cleavage and polyadenylation factor Im in a manner that promotes p68 ubiquitylation. The tested WW domains fall into three broad groups on the basis of hierarchical clustering with respect to their associated proteins; each such cluster of bound proteins displayed a distinct set of WW domain-binding motifs. We also found that separate WW domains from the same protein or closely related proteins can have different specificities for protein ligands and also demonstrated that a single polypeptide can bind multiple classes of WW domains through separate proline-rich motifs. These data suggest that WW domains provide a versatile platform to link individual proteins into physiologically important networks.
Subject(s)
Multiprotein Complexes/chemistry , Amino Acid Motifs , Amino Acid Sequence , Cell Line , Chromatin/chemistry , Chromatography, Liquid , Cluster Analysis , DNA, Complementary/metabolism , Databases, Protein , Electrophoresis, Polyacrylamide Gel , Glutathione Transferase/metabolism , Humans , Jurkat Cells , Ligands , Mass Spectrometry , Models, Biological , Molecular Sequence Data , Peptides/chemistry , Phosphorylation , Phylogeny , Proline/chemistry , Protein Binding , Protein Structure, Tertiary , RNA Splicing , RNA, Messenger/metabolism , Recombinant Fusion Proteins/chemistry , Transcription, Genetic , Trypsin/pharmacology , Ubiquitin/chemistry , Ubiquitin-Protein Ligases/chemistryABSTRACT
The development of robotic sample preparation systems has allowed the throughput of protein analysis to be accelerated. However, one of the rate-limiting steps in preparing protein samples for analysis by mass spectrometry is their proteolytic cleavage. Robots have been successfully used for the in-gel tryptic digestion of proteins as well as the desalting, concentration, and loading of protein digests onto matrix-assisted laser desorption/ionization (MALDI) targets. The advantages of these instruments are fast and stable sample processing and precise spotting. It seems reasonable to use these advantages for the entire protein sample preparation in a single instrument. In this paper,we describe a method to achieve this goal by performing protein sample concentration, all the digestion chemistry steps, and MALDI target loading on Zip-Tips using a rapid and fully automated method.
