dc.description.sponsorship | www.nature.com/scientificreports/
11
Scientific
Repo
R
ts
| 5:11687 | DO
i
: 10.1038/srep11687
25.
Bahia, D., Andrade, L. F., Ludolf, F., Mortara, R. A. & Oliveira, G. Protein tyrosine kinases in Schistosoma mansoni.
Mem Inst
Oswaldo Cruz
101
Suppl 1, 137–143 (2006).
26.
Costa, M. P.
et al.
In silico analysis and developmental expression of ubiquitin-conjugating enzymes in Schistosoma mansoni.
Parasitol Res
114,
1769–77 (2015).
27.
Pereira, R. V.
et al.
Molecular characterization of SUMO E2 conjugation enzyme: differential expression profile in Schistosoma
mansoni.
Parasitol Res
109,
1537–1546 (2011).
28.
Santos, D. N.
et al.
Schistosoma mansoni: Heterologous complementation of a yeast null mutant by SmRbx, a protein similar to
a RING box protein involved in ubiquitination.
Exp Parasitol
116,
440–449 (2007).
29.
Franceschini, A.
et al.
STRING v9.1: protein-protein interaction networks, with increased coverage and integration.
Nucleic Acids
Res
41,
D808–815 (2013).
30.
Xiao, H.
et al.
Pellino 3b negatively regulates interleukin-1-induced TAK1-dependent NF kappaB activation.
J Biol Chem
283,
14654–14664 (2008).
31.
Consortium, S. j. G. S. a. F. A. The Schistosoma japonicum genome reveals features of host-parasite interplay.
Nature
460,
345–351 (2009).
32.
Bennett, J. A.
et al.
Pellino-1 selectively regulates epithelial cell responses to rhinovirus.
J Virol
86,
6595–6604 (2012).
33.
Butler, M. P., Hanly, J. A. & Moynagh, P. N. Pellino3 is a novel upstream regulator of p38 MAPK and activates CREB in a p38-
dependent manner.
J Biol Chem
280,
27759–27768 (2005).
34.
Andrade, L. F.
et al.
Regulation of Schistosoma mansoni development and reproduction by the mitogen-activated protein kinase
signaling pathway.
PLoS Negl Trop Dis
8,
e2949 (2014).
35.
Osman, A., Niles, E. G. & LoVerde, P. T. Expression of functional Schistosoma mansoni Smad4: role in Erk-mediated transforming
growth factor beta (TGF-beta) down-regulation.
J Biol Chem
279,
6474–6486 (2004).
36.
Da’dara, A. A. & Skelly, P. J. Gene suppression in schistosomes using RNAi.
Methods in molecular biology
1201,
143–164 (2015).
37.
Sali, A. & Blundell, T. Comparative protein modelling by satisfaction of spatial restraints.
J Mol Biol
234,
779–815 (1993).
38.
Sali, A. & Overington, J. Derivation of rules for comparative protein modeling from a database of protein structure alignments.
Protein Sci
3,
1582–1596 (1994).
39.
Bowie, J. U., Lüthy, R. & Eisenberg, D. A method to identify protein sequences that fold into a known three-dimensional
structure.
Science
253,
164–170 (1991).
40.
Laskowski, R., Rullmannn, J., MacArthur, M., Kaptein, R. & Thornton, J. AQUA and PROCHECK-NMR: programs for checking
the quality of protein structures solved by NMR.
J Biomol NMR
8,
477–486 (1996).
41.
Colovos, C. & Yeates, T. Verification of protein structures: patterns of nonbonded atomic interactions.
Protein Sci
2,
1511–1519
(1993).
42.
Phillips, J. C.
et al.
Scalable molecular dynamics with NAMD.
J Comput Chem
26,
1781–1802 (2005).
43.
MacKerell, A. D.
et al.
All-atom empirical potential for molecular modeling and dynamics studies of proteins.
J Phys Chem B
102,
3586–3616 (1998).
44.
Mackerell, A. D. Empirical force fields for biological macromolecules: overview and issues.
J Comput Chem
25,
1584–1604
(2004).
45.
Jorgensen, W. L., Chandrasekhar, J., Buckner, J. K. & Madura, J. D. Computer simulations of organic reactions in solution.
Ann
N Y Acad Sci
482,
198–209 (1986).
46.
Humphrey, W., Dalke, A. & Schulten, K. VMD: visual molecular dynamics.
J Mol Graph
14,
33–38, 27–38 (1996).
47.
Darriba, D., Taboada, G. L., Doallo, R. & Posada, D. ProtTest 3: fast selection of best-fit models of protein evolution.
Bioinformatics
27,
1164–1165 (2011).
48.
Stamatakis, A., Ludwig, T. & Meier, H. RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic
trees.
Bioinformatics
21,
456–463 (2005).
Acknowledgements
We are grateful to Matt Berriman for input and comments on the manuscript. This work was supported
by the Health Research Board PhD in Molecular Medicine research programme, Science Foundation
Ireland, and the National Children’s Research Centre. We thank N. Delagic for assistance with
in vitro
signaling assays. The authors wish to acknowledge the DJEI/DES/SFI/HEA Irish Centre for High-End
Computing (ICHEC) for the provision of computational facilities and support. NAMD was developed
by the Theoretical and Computational Biophysics Group in the Beckman Institute for Advanced Science
and Technology at the University of Illinois at Urbana-Champaign | en |