Structural characterization of β-catenin and RX-5902 binding to phospho-p68 RNA helicase by molecular dynamics simulation

Progress in Biophysics and Molecular Biology - Tập 140 - Trang 79-89 - 2018
Waqar Ali1, Shagufta Shafique1, Sajid Rashid1
1National Centre for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan

Tài liệu tham khảo

Abraham, 2011, Optimization of parameters for molecular dynamics simulation using smooth particle-mesh Ewald in GROMACS 4.5, J. Comput. Chem., 32, 2031, 10.1002/jcc.21773 Andrusier, 2007, FireDock: fast interaction refinement in molecular docking, Proteins: Struct. Funct. Bioinfo., 69, 139, 10.1002/prot.21495 Beier, 2006, Overexpression of p68 mRNA in head and neck squamous cell carcinoma cells, Anticancer Res., 26, 1941 Berman, 2000, The Protein Data Bank and the challenge of structural genomics, Nat. Struct. Mol. Biol., 7, 957, 10.1038/80734 Biovia, 2017 Campo, 2010, Structural and dynamic properties of SPC/E water, Pap. Phys., 2 Carter, 2010, Phosphorylated p68 RNA helicase activates Snail1 transcription by promoting HDAC1 dissociation from the Snail1 promoter, Oncogene, 29, 5427, 10.1038/onc.2010.276 Causevic, 2001, Overexpression and poly-ubiquitylation of the DEAD-box RNA helicase p68 in colorectal tumours, Oncogene, 20, 7734, 10.1038/sj.onc.1204976 Chen, 2010, MolProbity: all-atom structure validation for macromolecular crystallography, Acta Crystallogr. Sect. D Biol. Crystallogr., 66, 12, 10.1107/S0907444909042073 Clark, 2008, The RNA helicase p68 is a novel androgen receptor coactivator involved in splicing and is overexpressed in prostate cancer, Canc. Res., 68, 7938, 10.1158/0008-5472.CAN-08-0932 Colovos, 1993, Verification of protein structures: patterns of nonbonded atomic interactions, Protein Sci., 2, 1511, 10.1002/pro.5560020916 Dai, 2014, P68 RNA helicase as a molecular target for cancer therapy, J. Exp. Clin. Canc. Res., 33, 64, 10.1186/s13046-014-0064-y de Vries, 2011, CPORT: a consensus interface predictor and its performance in prediction-driven docking with HADDOCK, PLoS One, 6, e17695, 10.1371/journal.pone.0017695 Dey, 2012, Phosphorylation of p68 RNA helicase by p38 MAP kinase contributes to colon cancer cells apoptosis induced by oxaliplatin, BMC Cell Biol., 13, 27, 10.1186/1471-2121-13-27 Dominguez, 2003, HADDOCK: a protein− protein docking approach based on biochemical or biophysical information, J. Am. Chem. Soc., 125, 1731, 10.1021/ja026939x Duan, 2003, A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations, J. Comput. Chem., 24, 1999, 10.1002/jcc.10349 Emsley, 2010, Features and development of coot, Acta Crystallogr. Sect. D Biol. Crystallogr., 66, 486, 10.1107/S0907444910007493 Fuller-Pace, 2013, DEAD box RNA helicase functions in cancer, RNA Biol., 10, 121, 10.4161/rna.23312 Gutierrez, 2016 Haines, 1996, Expression of the double-stranded RNA-dependent protein kinase (p68) in human breast tissues, Tumor Biol., 17, 5, 10.1159/000217961 Hanwell, 2012, Avogadro: an advanced semantic chemical editor, visualization, and analysis platform, J. Cheminf., 4, 17, 10.1186/1758-2946-4-17 Jeong, 2017, A validated HPLC—MS/MS method for the quantification of supinoxin in rat plasma and its application to pharmacokinetic study, Acta Chromatogr., 1 Kim, 2015, PubChem substance and compound databases, Nucleic Acids Res., 44, D1202, 10.1093/nar/gkv951 Kitagawa, 2013, Downregulation of the microRNA biogenesis components and its association with poor prognosis in hepatocellular carcinoma, Canc. Sci., 104, 543, 10.1111/cas.12126 Kost, 2015, A novel anti-cancer agent, 1-(3,5-Dimethoxyphenyl)-4-[(6-Fluoro-2-Methoxyquinoxalin-3-yl) aminocarbonyl] piperazine (RX-5902), interferes with β-catenin function through Y593 phospho-p68 RNA helicase, J. Cell. Biochem., 116, 1595, 10.1002/jcb.25113 Labík, 1994, Scaled particle theory and the efficient calculation of the chemical potential of hard spheres in the NVT ensemble, Mol. Simulat., 12, 23, 10.1080/08927029408022533 Liithy, 1992, Assessment of protein models with three-dimensional profiles, Nature, 356, 83, 10.1038/356083a0 Linder, 2013, Looking back on the birth of DEAD-box RNA helicases, Biochimica et Biophysica Acta (BBA)-Gene Regul. Mech., 1829, 750, 10.1016/j.bbagrm.2013.03.007 McDonald, 1972, NpT-ensemble Monte Carlo calculations for binary liquid mixtures, Mol. Phys., 23, 41, 10.1080/00268977200100031 Mooney, 2009, Sumoylation of p68 and p72 RNA helicases affects protein stability and transactivation potential, Biochemistry, 49, 1, 10.1021/bi901263m Mooney, 2010, Pleiotropic effects of p300-mediated acetylation on p68 and p72 RNA helicase, J. Biol. Chem., 285, 30443, 10.1074/jbc.M110.143792 Pettersen, 2004, UCSF Chimera—a visualization system for exploratory research and analysis, J. Comput. Chem., 25, 1605, 10.1002/jcc.20084 Pronk, 2013, GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit, Bioinformatics, 29, 845, 10.1093/bioinformatics/btt055 Rozen, 1990, Bidirectional RNA helicase activity of eucaryotic translation initiation factors 4A and 4F, Mol. Cell Biol., 10, 1134, 10.1128/MCB.10.3.1134 Schneidman-Duhovny, 2005, PatchDock and SymmDock: servers for rigid and symmetric docking, Nucleic Acids Res., 33, W363367, 10.1093/nar/gki481 SchuÈttelkopf, 2004, PRODRG: a tool for high-throughput crystallography of protein–ligand complexes, Acta Crystallogr. Sect. D Biol. Crystallogr., 60, 1355, 10.1107/S0907444904011679 Schütz, 2010, Comparative structural analysis of human DEAD-box RNA helicases, PLoS One, 5, e12791, 10.1371/journal.pone.0012791 Shafique, 2016, Elucidation, functional clustering and structural characterization of βTrCP1 substrates through a molecular dynamics study, Mol. Biosyst., 12, 2233, 10.1039/C6MB00189K Shafique, 2018, Structural basis for Cullins and RING component inhibition: targeting E3 ubiquitin pathway conductors for cancer therapeutics, Int. J. Biol. Macromol., 106, 532, 10.1016/j.ijbiomac.2017.08.047 Shin, 2007, Involvement of RNA helicases p68 and p72 in colon cancer, Canc. Res., 67, 7572, 10.1158/0008-5472.CAN-06-4652 Singh, 1995, Expression of p68 in human colon cancer, Tumor Biol., 16, 281, 10.1159/000217945 Trott, 2010, AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading, J. Comput. Chem., 31, 455 Wallace, 1995, LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions, Protein Eng. Des. Sel., 8, 127, 10.1093/protein/8.2.127 Wang, 2012, Overexpression of RNA helicase p68 protein in cutaneous squamous cell carcinoma, Clin. Exp. Dermatol., 37, 882, 10.1111/j.1365-2230.2012.04365.x Wang, 2012, p68 RNA helicase promotes glioma cell proliferation in vitro and in vivo via direct regulation of NF-κB transcription factor p50, Neuro Oncol., 14, 1116, 10.1093/neuonc/nos131 Wang, 2015, DDX5 promotes proliferation and tumorigenesis of non-small-cell lung cancer cells by activating β-catenin signaling pathway, Canc. Sci., 106, 1303, 10.1111/cas.12755 Wang, 2016, Data set for phylogenetic tree and RAMPAGE Ramachandran plot analysis of SODs in Gossypium raimondii and G. arboreum, Data Brief, 9, 345, 10.1016/j.dib.2016.05.025 Webb, 2014, Protein structure modeling with MODELLER, Protein Struct. Predict., 1 Wiederstein, 2007, ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins, Nucleic Acids Res., 35, W407, 10.1093/nar/gkm290 Xing, 2003, Crystal structure of a β-catenin/axin complex suggests a mechanism for the β-catenin destruction complex, Genes Dev., 17, 2753, 10.1101/gad.1142603 Yang, 2005, Phosphorylations of DEAD box p68 RNA helicase are associated with cancer development and cell proliferation, Mol. Canc. Res., 3, 355, 10.1158/1541-7786.MCR-05-0022 Yang, 2006, P68 RNA helicase mediates PDGF-induced epithelial mesenchymal transition by displacing Axin from β-catenin, Cell, 127, 139, 10.1016/j.cell.2006.08.036 Yang, 2007, Phosphorylation of p68 RNA helicase plays a role in platelet-derived growth factor-induced cell proliferation by up-regulating cyclin D1 and c-Myc expression, J. Biol. Chem., 282, 16811, 10.1074/jbc.M610488200 Zhang, 1997, Determination of atomic desolvation energies from the structures of crystallized proteins, J. Mol. Biol., 267, 707, 10.1006/jmbi.1996.0859 Zhang, 2009, Alterations in miRNA processing and expression in pleomorphic adenomas of the salivary gland, Int. J. Canc., 124, 2855, 10.1002/ijc.24298