Analysis of disordered regions of AIMR1/p43 protein from human multisynthetase complex with bioinformatics methods

TitleAnalysis of disordered regions of AIMR1/p43 protein from human multisynthetase complex with bioinformatics methods
Publication TypeJournal Article
Year of Publication2016
AuthorsLimanska, TS, Nyporko, AYu., Kornelyuk, AI
Abbreviated Key TitleDopov. Nac. akad. nauk Ukr.
DOI10.15407/dopovidi2016.06.103
Issue6
SectionBiology
Pagination103-111
Date Published6/2016
LanguageUkrainian
Abstract

Features of the secondary structure and locations of the disordered regions in the structure of AIMRI protein — component of the human multisynthetase complex are investigated with several in silico approaches. It is revealed that the longest part of the protein disclosed to fold into a disordered structure is located from 103 to 148 amino acid residue. Interestingly, within this region (from about 121 to residue 140), the presence of α-helix is also possible. This seeming contradiction is simply explained by the saturation of the appropriate region by both lysine residues (marker of disordered regions of proteins) and glutamate residues (typical marker of α-helical elements). With high probability, we can assume that this spiral is metastable, i. e., moving to a disordered state and back due to natural fluctuations of the protein molecule.

KeywordsAIMR1/p43, bioinformatics, disordered regions, secondary structure
References: 
  1. Oldfield C. J., Dunker A. K. Annu. Rev Biochem., 2014, 83: 553–584. https://doi.org/10.1146/annurev-biochem-072711-164947
  2. Odynets K. A., Kornelyuk A. I. Biopolym. Cell., 2005, 21: 446–453. https://doi.org/10.7124/bc.000709
  3. Kim J. H., Han J. M., Kim S. Top. Curr. Chem., 2014, 344: 119–144. https://doi.org/10.1007/128_2013_479
  4. Renault L., Kerjan P., Pasqualato S. et al. EMBO J., 2001, 20: 570–578. https://doi.org/10.1093/emboj/20.3.570
  5. Berman H. M., Westbrook J., Feng Z. et al. Nucleic Acids Res., 2000, 28: 235–242. https://doi.org/10.1093/nar/28.1.235
  6. Fu Y., Kim Y., Jin K. S. et al. Proc. Natl. Acad. Sci. USA, 2014, 111: 15 084–15 089.
  7. The UniProt Consortium. Nucleic Acids Res., 2014, 42: D191–D198. https://doi.org/10.1093/nar/gkt1140
  8. Buchan D. W. A., Minneci F., Nugent T. C. O. et al. Nucleic Acids Res., 2013, 41: W340–W348. https://doi.org/10.1093/nar/gkt381
  9. Yachdav G., Kloppmann E., Kajan L. et al. Nucleic Acids Res., 2014, 42, Web Server issue: W337–W343.
  10. Ishida T., Kinoshita K. Nucleic Acids Res., 2007, 35 (Web Server issue): W460–W464.
  11. Linding R., Russell R. B., Neduva V., Gibson T. J. Nucleic Acid Res., 2003, 31: 3701–3708. https://doi.org/10.1093/nar/gkg519
  12. Prilusky J., Felder C. E., Zeev-Ben-Mordehai T. et al. Bioinformatics, 2005, 21: 3435–3438. https://doi.org/10.1093/bioinformatics/bti537
  13. Linding R., Jensen L. J., Diella F. et al. Structure, 2003, 11: 1453–1459. https://doi.org/10.1016/j.str.2003.10.002
  14. Ward J. J., Sodhi J. S., McGuffin L. J. et al. J. Mol. Biol., 2004, 337: 635–645. https://doi.org/10.1016/j.jmb.2004.02.002
  15. Sickmeier M., Hamilton J. A., LeGall T. et al. Bioinformatics, 2005, 21: 137–140. https://doi.org/10.1093/bioinformatics/bth476