The The Structural, Functional Identification of Natural Resistance-Associated Macrophage Protein as Transporter Elements in Oryza Sativa
Structural, Functional of NRAMP Family in rice
Keywords:Oryza sativa, interaction analysis, structure prediction, OsNRAMP transporter proteins, physiochemical properties
The NRAMP (natural resistance-associated macrophage protein) family of transporter proteins has four members in Oryza sativa. OsNRAMP1, OsNRAMP2, OsNRAMP3, and OsNRAMP4 have been reported and considered for this study. These NRAMP transporter proteins have been studied in rice plants to transport a variety of metal ions such as Mn_2+, Cd_2+, Zn_2+, Fe_2+, and others. As a result, it's critical to predicting and properties of the OsNRAMP family of transporters computationally to study and understand them. In future research, it will be important to understand their biological insights. In this research, different in-silico methodologies, and strategies were used for the investigation of NRAMP-transporter proteins. The protein sequences' physiochemical parameters were evaluated, putative transmembrane domains and helices, localization and hydrophobicity, phylogenetic analysis, correlated motif patterns of the transporter proteins were identified, and proteins-interaction associates were predicted. The online structure prediction method was used to obtain 3D models of all OsNRAMP transporter participants, which were then analysed. Since there is currently limited information about the functional and structural dimensions of these transporters, this research will anticipate the theoretical details regarding us.
Atashgahi, S. (2019). Discovered by genomics: putative reductive dehalogenases with N-terminus transmembrane helixes. FEMS microbiology ecology, 95(5), fiz048.
Bailey, T. L., Boden, M., Buske, F. A., Frith, M., Grant, C. E., Clementi, L., . . . Noble, W. S. (2009). MEME SUITE: tools for motif discovery and searching. Nucleic acids research, 37(suppl_2), W202-W208.
Bateman, A., Birney, E., Cerruti, L., Durbin, R., Etwiller, L., Eddy, S. R., . . . Sonnhammer, E. L. (2002). The Pfam protein families database. Nucleic acids research, 30(1), 276-280.
Cellier, M., Prive, G., Belouchi, A., Kwan, T., Rodrigues, V., Chia, W., & Gros, P. (1995). Nramp defines a family of membrane proteins. Proceedings of the National Academy of Sciences, 92(22), 10089-10093.
Ehrnstorfer, I. A., Manatschal, C., Arnold, F. M., Laederach, J., & Dutzler, R. (2017). Structural and mechanistic basis of proton-coupled metal ion transport in the SLC11/NRAMP family. Nature Communications, 8(1), 1-11.
Gasteiger, E., Hoogland, C., Gattiker, A., Wilkins, M. R., Appel, R. D., & Bairoch, A. (2005). Protein identification and analysis tools on the ExPASy server. The proteomics protocols handbook, 571-607.
Lear, S., & Cobb, S. L. (2016). Pep-Calc. com: a set of web utilities for the calculation of peptide and peptoid properties and automatic mass spectral peak assignment. Journal of computer-aided molecular design, 30(3), 271-277.
Lovell, S. C., Davis, I. W., Arendall III, W. B., De Bakker, P. I., Word, J. M., Prisant, M. G., . . . Richardson, D. C. (2003). Structure validation by Cα geometry: ϕ, ψ and Cβ deviation. Proteins: Structure, Function, and Bioinformatics, 50(3), 437-450.
Migeon, A., Blaudez, D., Wilkins, O., Montanini, B., Campbell, M. M., Richaud, P., . . . Chalot, M. (2010). Genome-wide analysis of plant metal transporters, with an emphasis on poplar. Cellular and Molecular Life Sciences, 67(22), 3763-3784.
Narayanan, N. N., Vasconcelos, M. W., & Grusak, M. A. (2007). Expression profiling of Oryza sativa metal homeostasis genes in different rice cultivars using a cDNA macroarray. Plant physiology and Biochemistry, 45(5), 277-286.
Nelson, N. (1999). Metal ion transporters and homeostasis. The EMBO Journal, 18(16), 4361-4371.
Ouvry‐Patat, S. A., Torres, M. P., Quek, H. H., Gelfand, C. A., O'Mullan, P., Nissum, M., . . . Dryhurst, D. (2008). Free‐flow electrophoresis for top‐down proteomics by Fourier transform ion cyclotron resonance mass spectrometry. Proteomics, 8(14), 2798-2808.
Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004). UCSF Chimera—a visualization system for exploratory research and analysis. Journal of computational chemistry, 25(13), 1605-1612.
Pottier, M., Oomen, R., Picco, C., Giraudat, J., Scholz‐Starke, J., Richaud, P., . . . Thomine, S. (2015). Identification of mutations allowing Natural Resistance Associated Macrophage Proteins (NRAMP) to discriminate against cadmium. The Plant Journal, 83(4), 625-637.
Rizvi, S. M. D., Shakil, S., & Haneef, M. (2013). A simple click by click protocol to perform docking: AutoDock 4.2 made easy for non-bioinformaticians. EXCLI journal, 12, 831.
Sakai, H., Lee, S. S., Tanaka, T., Numa, H., Kim, J., Kawahara, Y., . . . Abe, T. (2013). Rice Annotation Project Database (RAP-DB): an integrative and interactive database for rice genomics. Plant and Cell Physiology, 54(2), e6-e6.
Schwede, T., Kopp, J., Guex, N., & Peitsch, M. C. (2003). SWISS-MODEL: an automated protein homology-modeling server. Nucleic acids research, 31(13), 3381-3385.
Sievers, F., & Higgins, D. G. (2014). Clustal Omega, accurate alignment of very large numbers of sequences Multiple sequence alignment methods (pp. 105-116): Springer.
Szklarczyk, D., Morris, J. H., Cook, H., Kuhn, M., Wyder, S., Simonovic, M., . . . Bork, P. (2016). The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible. Nucleic acids research, gkw937.
Thomine, S., Wang, R., Ward, J. M., Crawford, N. M., & Schroeder, J. I. (2000). Cadmium and iron transport by members of a plant metal transporter family in Arabidopsis with homology to Nramp genes. Proceedings of the National Academy of Sciences, 97(9), 4991-4996.
Von Mering, C., Jensen, L. J., Snel, B., Hooper, S. D., Krupp, M., Foglierini, M., . . . Bork, P. (2005). STRING: known and predicted protein–protein associations, integrated and transferred across organisms. Nucleic acids research, 33(suppl_1), D433-D437.
Xia, J., Yamaji, N., Kasai, T., & Ma, J. F. (2010). Plasma membrane-localized transporter for aluminum in rice. Proceedings of the National Academy of Sciences, 107(43), 18381-18385.
Xia, J., Yamaji, N., & Ma, J. F. (2011). Further characterization of an aluminum influx transporter in rice. Plant signaling & behavior, 6(1), 160-163.
Yu, C.-S., Cheng, C.-W., Su, W.-C., Chang, K.-C., Huang, S.-W., Hwang, J.-K., & Lu, C.-H. (2014). CELLO2GO: a web server for protein subCELlular LOcalization prediction with functional gene ontology annotation. PloS one, 9(6), e99368.
How to Cite
Copyright (c) 2021 European journal of volunteering and community-based projects
This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.