High levels of structural disorder in scaffold proteins as exemplified by a novel neuronal protein, CASK‐interactive protein1
Authors: Balázs Annamária , Csizmok Veronika , Buday László , Rakács Marianna , Kiss Robert , Bokor Mónika , Udupa Roopesh , Tompa Kálmán , Tompa Peter 
Published: June 2009

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 1H‐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)