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Operational definition of intrinsically unstructured protein sequences based on susceptibility to the 20S proteasome
Author(s) -
Tsvetkov Peter,
Asher Gad,
Paz Aviv,
Reuven Nina,
Sussman Joel L.,
Silman Israel,
Shaul Yosef
Publication year - 2008
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.21614
Subject(s) - proteasome , false positive paradox , computational biology , in vitro , biology , chemistry , microbiology and biotechnology , biochemistry , computer science , machine learning
Intrinsically unstructured proteins (IUPs), also known as natively unfolded proteins, lack well‐defined secondary and tertiary structure under physiological conditions. In recent years, growing experimental and theoretical evidence has accumulated, indicating that many entire proteins and protein sequences are unstructured under physiological conditions, and that they play significant roles in diverse cellular processes. Bioinformatic algorithms have been developed to identify such sequences in proteins for which structural data are lacking, but still generate substantial numbers of false positives and negatives. We describe here a simple and reliable in vitro assay for identifying IUP sequences based on their susceptibility to 20S proteasomal degradation. We show that 20S proteasomes digest IUP sequences, under conditions in which native, and even molten globule states, are resistant. Furthermore, we show that protein–protein interactions can protect IUPs against 20S proteasomal action. Taken together, our results thus suggest that the 20S proteasome degradation assay provides a powerful system for operational definition of IUPs. Proteins 2008. © 2007 Wiley‐Liss, Inc.