MA16 Has an Intrinsically Disordered Domain

Disorder predictor

Prediction of unstructured regions in the MA16 protein was using the Disopred2 method

(http://bioinf.cs.ucl.ac.uk/disopred) that considers the whole sequence rather than amino acid composition or sequence complexity. The algorithm is based on a support vector machine trained on a set of around

750 non-redundant sequences, with high resolution X-ray structures but with coordinates missing from the electron density map (Ward et al. 2004).

MA16 has an intrinsically disordered domain

Considering that many proteins involved in RNA chaperone activities contain intrinsically disordered regions (Rajkowitsch et al. 2007), the MA16 protein was analysed with the Disopred2 predictor program

(Ward et al. 2004).

Disopred2 predicts a long disordered region at the carboxy-terminal region of MA16 (Fig S1). This predicted unstructured region consists of the repeating sequence motif RR(E/D)(G)nY(G)n with a net positive charge, and low hydrophobicity quite similar to proteins containing RGG boxes, such as nucleolin (Lapeyre et al. 1987) and fibrillarin (Ochs et al. 1985). This region could adopt an extended conformation that may be crucial to provide a folding platform for interactions with many different RNA partners. Figure S1 MA16 has a long unstructured region at the carboxy-terminal. MA16 RNA-binding protein was analysed by the Disopred2 program. The disordered profile plot predicts a long unstructured region with a high disorder probability in the second-half of the protein that corresponds to the glycine-rich domain.

References

Lapeyre B, Bourbon H, Amalric F (1987) Nucleolin, the major nucleolar protein of growing eukaryotic cells: an unusual protein structure revealed by the nucleotide sequence. Proc Natl Acad Sci USA 84:1472-1476

Ochs RL, Lischwe MA, Spohn WH, Busch H (1985) Fibrillarin: a new protein of the nucleolus identified by autoimmune sera. Biol Cell 54:123-133

Rajkowitsch L, Chen D, Stampfl S, Semrad K, Waldsich C, Mayer O, Jantsch MF, Konrat R, Blasi U,

Schroeder R (2007) RNA chaperones, RNA annealers and RNA helicases. RNA Biol 4: 118-130

Ward JJ, Sodhi JS, McGuffin LJ, Buxton BF, Jones DT (2004) Predictions and functional analysis of native disorder in proteins from the three kingdoms of life. J Mol Biol 337:635-645