Molecular characterization of EhAK6, an endonuclease V domain-containing aurora kinase protein from Entamoeba histolytica: Protein-protein interaction, docking and functional aspect

Current Research in Biotechnology - Tập 3 - Trang 225-234 - 2021
Pinaki Biswas1, Raktim Ghosh1, Moubonny Das1, Suchetana Pal1, Somasri Dam1
1Department of Microbiology, The University of Burdwan, Burdwan 713104, West Bengal, India

Tài liệu tham khảo

Afonso, 2017, Late mitotic functions of Aurora kinases, Chromosoma, 126, 93, 10.1007/s00412-016-0594-5 Azuara-Liceaga, 2018, The Sole DNA Ligase in Entamoeba histolytica Is a High-Fidelity DNA Ligase Involved in DNA Damage Repair, Front. Cell. Infect. Microbiol., 8, 10.3389/fcimb.2018.00214 Benkert, 2011, Toward the estimation of the absolute quality of individual protein structure models, Bioinformatics, 27, 343, 10.1093/bioinformatics/btq662 Bercu, 2007, Amebic colitis: new insights into pathogenesis and treatment, Curr Gastroenterol Rep, 9, 429, 10.1007/s11894-007-0054-8 Berjanskii, 2012, Resolution-by-proxy: a simple measure for assessing and comparing the overall quality of NMR protein structures, J. Biomol. NMR, 53, 167, 10.1007/s10858-012-9637-2 Biswas, 2020, In Silico Analysis of Molecular Interaction of EhSir2a with its Interacting Proteins from Human Pathogen Entamoeba histolytica. Haya: The Saudi Journal of, Life Sci., 5, 140 Bradford, 1976, A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding, Anal Biochem, 72, 248, 10.1016/0003-2697(76)90527-3 Brown, 2004, Evolutionary relationships of Aurora kinases: implications for model organism studies and the development of anti-cancer drugs, BMC Evol. Biol., 4, 39, 10.1186/1471-2148-4-39 Cao, 2013, Endonuclease V: an unusual enzyme for repair of DNA deamination, Cellular and molecular life sciences : CMLS, 70, 3145, 10.1007/s00018-012-1222-z Carmena, 2003, The cellular geography of aurora kinases, Nat. Rev. Mol. Cell Biol., 4, 842, 10.1038/nrm1245 Castro, 2002, The D-Box-activating domain (DAD) is a new proteolysis signal that stimulates the silent D-Box sequence of Aurora-A, EMBO Rep., 3, 1209, 10.1093/embo-reports/kvf241 Dam, 2019, Oxidative Stress in Entamoeba histolytica, 257 Dam, 2010, Entamoeba histolytica sirtuin EhSir2a deacetylates tubulin and regulates the number of microtubular assemblies during the cell cycle, Cell. Microbiol., 12, 1002, 10.1111/j.1462-5822.2010.01449.x Diamond, 1978, A new medium for the axenic cultivation of Entamoeba histolytica and other Entamoeba, Trans R Soc Trop Med Hyg, 72, 431, 10.1016/0035-9203(78)90144-X Geourjon, 1995, SOPMA: significant improvements in protein secondary structure prediction by consensus prediction from multiple alignments, Computer applications in the biosciences : CABIOS, 11, 681 Grewal, 2013, The calcium binding protein EhCaBP6 is a microtubular-end binding protein in Entamoeba histolytica, Cell. Microbiol., 15, 2020, 10.1111/cmi.12167 Hamann, 1995, Transfection and continuous expression of heterologous genes in the protozoan parasite Entamoeba histolytica, Proc. Nat. Acad. Sci. USA, 92, 8975, 10.1073/pnas.92.19.8975 Kelso, 2015, Entamoeba histolytica Dmc1 Catalyzes Homologous DNA Pairing and Strand Exchange That Is Stimulated by Calcium and Hop2-Mnd1, PLoS ONE, 10, 10.1371/journal.pone.0139399 Ko, 2012, GalaxyWEB server for protein structure prediction and refinement, Nucleic Acids Res., 40, W294, 10.1093/nar/gks493 Kozakov, 2017, The ClusPro web server for protein-protein docking, Nat. Protoc., 12, 255, 10.1038/nprot.2016.169 Kuraoka, 2015, Diversity of Endonuclease V: From DNA Repair to RNA Editing, Biomolecules, 5, 2194, 10.3390/biom5042194 la Cour, 2004, Analysis and prediction of leucine-rich nuclear export signals, Protein engineering, design & selection : PEDS, 17, 527, 10.1093/protein/gzh062 Laskowski, 2005, ProFunc: a server for predicting protein function from 3D structure, Nucleic Acids Res., 33, W89, 10.1093/nar/gki414 Lee, 2011, New family of deamination repair enzymes in uracil-DNA glycosylase superfamily, The Journal of biological chemistry, 286, 31282, 10.1074/jbc.M111.249524 Lindon, 2015, Ubiquitin-Mediated Degradation of Aurora Kinases, Front. Oncol., 5, 307 Livak, 2001, Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method, Methods, 25, 402, 10.1006/meth.2001.1262 Lohia, 2007, Genome re-duplication and irregular segregation occur during the cell cycle of Entamoeba histolytica, Biosci. Rep., 27, 373, 10.1007/s10540-007-9058-8 Lovell, 2003, Structure validation by Calpha geometry: phi, psi and Cbeta deviation, Proteins, 50, 437, 10.1002/prot.10286 Lu, 2020, CDD/SPARCLE: the conserved domain database in 2020, Nucleic Acids Res., 48, D265, 10.1093/nar/gkz991 Maton, 2003, Cdc2-cyclin B triggers H3 kinase activation of Aurora-A in Xenopus oocytes, J. Biol. Chem., 278, 21439, 10.1074/jbc.M300811200 Morgado, 2016, Recent advances in Entamoeba biology: RNA interference, drug discovery, and gut microbiome, F1000Res, 5, 2578, 10.12688/f1000research.9241.1 Parikh, 2000, Lessons learned from structural results on uracil-DNA glycosylase, Mutat. Res., 460, 183, 10.1016/S0921-8777(00)00026-4 Pearl, 2000, Structure and function in the uracil-DNA glycosylase superfamily, Mutat. Res., 460, 165, 10.1016/S0921-8777(00)00025-2 Pineda, 2017, Entamoeba histolytica under Oxidative Stress: What Countermeasure Mechanisms Are in Place?, Cells, 6, 44, 10.3390/cells6040044 Shen, 2006, Ensemble classifier for protein fold pattern recognition, Bioinformatics, 22, 1717, 10.1093/bioinformatics/btl170 Sievers, 2011, Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega, Mol. Syst. Biol., 7, 539, 10.1038/msb.2011.75 Szklarczyk, 2019, STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets, Nucleic Acids Res., 47, D607, 10.1093/nar/gky1131 Trasvina-Arenas, 2019, Evolution of Base Excision Repair in Entamoeba histolytica is shaped by gene loss, gene duplication, and lateral gene transfer, DNA Repair (Amst), 76, 76, 10.1016/j.dnarep.2019.02.009 Wallace, 1995, LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions, Protein Eng., 8, 127, 10.1093/protein/8.2.127 Wallner, 2003, Can correct protein models be identified?, Protein science : a publication of the Protein Society, 12, 1073, 10.1110/ps.0236803 Wang, 2014, Aurora-A: a potential DNA repair modulator, Tumour biology : the journal of the International Society for Oncodevelopmental Biology and Medicine, 35, 2831, 10.1007/s13277-013-1393-8 Weber, 2009, Effects of DNA damage induced by UV irradiation on gene expression in the protozoan parasite Entamoeba histolytica, Mol. Biochem. Parasitol., 164, 165, 10.1016/j.molbiopara.2008.12.005 Weng, 2019, HawkDock: a web server to predict and analyze the protein-protein complex based on computational docking and MM/GBSA, Nucleic Acids Res., 47, W322, 10.1093/nar/gkz397 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 Wilkins, 1999, Protein identification and analysis tools in the ExPASy server, Methods Mol Biol, 112, 531 Willems, 2018, The functional diversity of Aurora kinases: a comprehensive review, Cell division, 13, 7, 10.1186/s13008-018-0040-6 Ximénez, 2010, Human amebiasis: breaking the paradigm?, Int J Environ Res Public Health, 7, 1105, 10.3390/ijerph7031105 Ye, 2016, Aurora A Kinase Amplifies a Midzone Phosphorylation Gradient to Promote High-Fidelity Cytokinesis, The Biological bulletin, 231, 61, 10.1086/689591 Yu, 2006, Prediction of protein subcellular localization, Proteins, 64, 643, 10.1002/prot.21018