Table of Contents
Computational Biology Journal
Volume 2014 (2014), Article ID 909268, 14 pages
http://dx.doi.org/10.1155/2014/909268
Research Article

Identification of Plant Homologues of Dual Specificity Yak1-Related Kinases

1Department of Genomics and Molecular Biotechnology, Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Osipovskogo Street 2a, Kyiv 04123, Ukraine
2Department of General and Molecular Genetics, Taras Shevchenko National University of Kyiv (KNU), Glushkova Street 2, Kyiv 02090, Ukraine

Received 28 April 2014; Revised 16 September 2014; Accepted 25 September 2014; Published 8 December 2014

Academic Editor: Mihaly Mezei

Copyright © 2014 Pavel Karpov et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Supplementary Material

S1 - Complete FASTA sequences of all proteins used in the study (for details please see Table 1, Figure 1):

(A) 18 "Reviewed" UniProtKB sequences of animal DYRKs from Homo sapiens (DYR1A (Q13627), DYR1B (Q9Y463), DYRK2 (Q92630), DYRK3 (O43781), DYRK4 (Q9NR20)), Macaca fascicularis (DYRK3 (Q4R6S5)), Mus musculus (DYR1A (Q61214), DYR1B (Q9Z188), DYRK2 (Q5U4C9), DYRK3 (Q922Y0), DYRK4 (Q8BI55)), Rattus norvegicus (DYR1A (Q63470), DYRK3 (Q4V8A3)), Xenopus laevis (DYR1A (Q2TAE3)), X. tropicalis (DYR1A (Q0IJ08)), Gallus gallus (DYRK2 (Q5ZIU3)), Drosophila melanogaster (DYRK2 (Q9V3D5, smi35A), DYRK3 (P83102)), and 2 (DYRK1 (Q76NV1), DYRK2 (Q54BC9)) from Dictyostelium discoideum (Mycetozoa).

(B) 14 plant DYRK-like kinases selected based on the Blastp results of UniProt knowledgebase scanning: A9U0E5-Physcomitrella patens subsp. patens, A9RDR5-Physcomitrella patens subsp. patens, A9TA59-Physcomitrella patens subsp. patens, C0PR87-Picea sitchensis, D7MHY5-Arabidopsis lyratalyrata, Q8RWH3-Arabidopsis thaliana, B9SDF7-Ricinus communis, C1MRI0- Micromonas pusilla, Q00ZG2-Ostreococcus tauri, A4RXI5-Ostreococcus lucimarinus, Q019C0-Ostreococcus tauri, D8RDP5-Selaginella moellendorffii, A9TKQ3-Physcomitrella patens subsp. patens, D8RRY9-Selaginella moellendorffii.

S2 - Kinase domain sequences (*.fasta) of all protein kinases used in the study (for details please see Table 1, Figure 1, S1).

S3 - ClustalW2 (http://www.clustal.org/clustal2/) multiple sequence alignment of kinase domains of all protein kinases used in the study (for details please see Table 1, Figure 1, S1).

S4 - Supplement for Figure 1. *.dnd file of Neighbour-Joining tree built based on catalytic domain sequences clustering (S1). (For visualization please use MEGA5: http://www.megasoftware.net/)

S5 - Supplement for Figure 3. PyMOL session file (*.psf): Models of spatial structure of DYRK1A homologues (green) catalytic domain from P. patens (a) and A. thaliana (b) and their structural superimposition with 2VX3 (chain A) Protein Data Bank structure of human DYRKA1 (pink). YxY site - YxYxxS motif in the activation loop, also known as T-loop. (For visualization please use PyMOL: http://www.pymol.org/)

S6 - 3D-model of catalytic domain from Arabidopsis thaliana (UniProtKB: ARATH_Q8RWH3). Please use any program for *.pdb file visualization.

S7 - 3D-model of catalytic domain from Physcomitrella patens (UniProtKB: PHYPA_A9U0E5). Please use any program for *.pdb file visualization.

S8 - Supplement for Figure 7. Structural alignment of DYRK1A inhibitors (EHB, d15, IRB) and ADP. (For visualization please use PyMOL: http://www.pymol.org/)

S9 - (a, b, c). PyMOL session file (*.psf) demonstrating final frames from molecular dynamics simulations for human and plant d15-protein complexes displaying final position of ligand in the ATP-binding site: (a) human DYRKA1; (b) Q8RWH3 from Arabidopsis thaliana; (c) A9U0E5 from Physcomitrella patens. (For visualization please use PyMOL: http://www.pymol.org/)

S10 - Supplement for Figure 9 (d). PyMOL session file (*.psf) demonstrating superimposition of d15 in binding site in human DYRK1A (red) and the similar regions in plant homologues from Arabidopsis thaliana (green) and Physcomitrella patens (light green). (For visualization please use PyMOL: http://www.pymol.org/)

S11 - Supplement for Figures 2 and 10. Microsoft Excel file (*.xls) with results of molecular dynamic simulations carried out during the study: Sheet 1 (Figure 2) - The RMSD of DYRK1A proteins for 26 ns MD simulation: human DYRK1A (1), Q8RWH3 from Arabidopsis thaliana (2), A9U0E5 from Physcomitrella patens (3); Sheet 2 (Figure 10(a)) / Sheet 3 (Figure 10(a)) - The RMSD (Sheet 2) of a ligand and short range columbic interaction energy (Sheet 3) of DYRK1A proteins in complex with d15 during 26 ns MD simulation: human DYRK1A (1), Q8RWH3 from Arabidopsis thaliana (2), and A9U0E5 from Physcomitrella patens (3).

  1. Supplementary Material