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High levels of structural disorder in scaffold proteins as exemplified by a novel neuronal protein, CASK‐interactive protein1
Author(s) -
Balázs Annamária,
Csizmok Veronika,
Buday László,
Rakács Marianna,
Kiss Robert,
Bokor Mónika,
Udupa Roopesh,
Tompa Kálmán,
Tompa Peter
Publication year - 2009
Publication title -
the febs journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.981
H-Index - 204
eISSN - 1742-4658
pISSN - 1742-464X
DOI - 10.1111/j.1742-4658.2009.07090.x
Subject(s) - scaffold protein , amino acid , scaffold , cask , linker , intrinsically disordered proteins , protein structure , docking (animal) , chemistry , computational biology , biochemistry , biophysics , biology , genetics , computer science , database , medicine , signal transduction , nursing , operating system
CASK‐interactive protein1 is a newly recognized post‐synaptic density protein in mammalian neurons. Although its N‐terminal region contains several well‐known functional domains, its entire C‐terminal proline‐rich region of 800 amino acids lacks detectable sequence homology to any previously characterized protein. We used multiple techniques for the structural characterization of this region and its three fragments. By bioinformatics predictions, CD spectroscopy, wide‐line and 1 H‐NMR spectroscopy, limited proteolysis and gel filtration chromatography, we provided evidence that the entire proline‐rich region of CASK‐interactive protein1 is intrinsically disordered. We also showed that the proline‐rich region is biochemically functional, as it interacts with the adaptor protein Abl‐interactor‐2. To extend the finding of a high level of disorder in this scaffold protein, we collected 74 scaffold proteins (also including proteins denoted as anchor and docking), and predicted their disorder by three different algorithms. We found that a very high fraction (53.6% on average) of the residues fall into local disorder and their ordered domains are connected by linker regions which are mostly disordered (64.5% on average). Because of this high frequency of disorder, the usual design of scaffold proteins of short globular domains (86 amino acids on average) connected by longer linker regions (140 amino acids on average) and the noted binding functions of these regions in both CASK‐interactive protein1 and the other proteins studied, we suggest that structurally disordered regions prevail and play key recognition roles in scaffold proteins. Structured digital abstract• MINT‐7034649 : Caskin1 (uniprotkb: Q8VHK2 ) physically interacts ( MI:0915 ) with L1CAM (uniprotkb: P32004 ) by two hybrid ( MI:0018 ) • MINT‐7034677 : Caskin1 (uniprotkb: Q8VHK2 ) physically interacts ( MI:0915 ) with NCK1 (uniprotkb: P16333 ) by two hybrid ( MI:0018 ) • MINT‐7034706 : Caskin1 (uniprotkb: Q8VHK2 ) physically interacts ( MI:0915 ) with Stathmin‐3 (uniprotkb: Q9NZ72 ) by two hybrid ( MI:0018 ) • MINT‐7034579 : Caskin1 (uniprotkb: Q8VHK2 ) physically interacts ( MI:0915 ) with ABI2 (uniprotkb: Q9NYB9 ) by two hybrid ( MI:0018 ) • MINT‐7034720 : Caskin1 (uniprotkb: Q8VHK2 ) physically interacts ( MI:0915 ) with Synaptotagmin (uniprotkb: P21579 ) by two hybrid ( MI:0018 ) • MINT‐7034691 : Caskin1 (uniprotkb: Q8VHK2 ) physically interacts ( MI:0915 ) with Neurexin‐2 (uniprotkb: Q9P2S2 ) by two hybrid ( MI:0018 ) • MINT‐7034617 : Caskin1 (uniprotkb: Q8VHK2 ) physically interacts ( MI:0915 ) with CASK (uniprotkb: P07498 ) by two hybrid ( MI:0018 ) • MINT‐7034748 : Caskin1 (uniprotkb: Q8VHK2 ) physically interacts ( MI:0915 ) with SIAH1 (uniprotkb: Q8IUQ4 ) by two hybrid ( MI:0018 ) • MINT‐7034663 : Caskin1 (uniprotkb: Q8VHK2 ) physically interacts ( MI:0915 ) with Myosin‐Ib (uniprotkb: O43795 ) by two hybrid ( MI:0018 ) • MINT‐7034734 : Caskin1 (uniprotkb: Q8VHK2 ) physically interacts ( MI:0915 ) with Septin‐4 (uniprotkb: O43236 ) by two hybrid ( MI:0018 ) • MINT‐7034634 : Caskin1 (uniprotkb: Q8VHK2 ) physically interacts ( MI:0915 ) with EPHA2 (uniprotkb: P29317 ) by two hybrid ( MI:0018 ) • MINT‐7034765 , MINT‐7034783 : Caskin1 (uniprotkb: Q8VHK2 ) physically interacts ( MI:0915 ) with ABI2 (uniprotkb: Q9NYB9 ) by pull down ( MI:0096 )