Ramachandran plot analysis: Conformational validation of NifA protein structure in nitrogen-fixing Azorhizobium caulinodans
Research Paper | Journal Paper
Vol.8 , Issue.6 , pp.116-121, Jun-2020
CrossRef-DOI: https://doi.org/10.26438/ijcse/v8i6.116121
Abstract
With the increasing numbers of known protein structures and greater accuracy of ultra-high resolution protein structures in structural biology, high fidelity conformational information is used to explore the validation of three-dimensional protein structures using Ramachandran plots. In proteins structural determination method, amino acid residues (as nodes) and the close contact between the residues (as edges) have been used to explore basic network properties to study protein folding, its structural stability and for prediction of catalytic sites. In this study, in silico analysis and Ramachandran plot analysis of NifA protein using nitrogen-fixing Azorhizobium caulinodans was carried out on the basis of 3Drefine results. The percentage distribution of amino acids in different regions was recorded in I-TASSER and Raptor X models using Ramachandran plot analysis. In I-TASSER model, 79.9% of amino acid residues resided in most favoured red region and only 15.7% amino acid residues were found in the allowed (yellow region), out of total 523 amino acids analyzed in this model. On the other hand, 90.5% amino acid residues resided in most favoured (red) region in Raptor X model out of total 433 amino acids analyzed in this model. Only 6.7% amino acid residues were found in additional allowed (yellow) region, whereas only 1.2% residues were observed in generously allowed region. Thus, the number of amino acid residues belonging to “outlier, allowed, and favored” regions in Ramachandran plot analysis represents best quality metrics of experimental structure models before structure deposition.
Key-Words / Index Term
Ramachandran plot, NifA protein, Nitrogen fixation, I-TASSER model, Raptor X model, Amino acids, Structural stability
References
[1] G. J. Kleywegt, “Validation of protein crystal structures”, Acta Crystallography, Sect. D. Biological Crystallography, Vol. 56, pp. 249–265, 2000.
[2] A. Wlodawer, W. Minor, Z. Dauter, Jaskolski, M., “Protein crystallography for non-crystallographers, or how to get the best (but not more) from published macromolecular structures’, FEBS Journal, Vol. 275, pp. 1–21, 2008.
[3] R.J. Read, P.D. Adams, W.B. Arendall, A.T. Brunger, P. Emsley, R.P. Joosten, G.J. Kleywegt, E.B. Krissinel, T. L€utteke, Z. Otwinowski, et al., “A new generation of crystallographic validation tools for the Protein Data Bank”, Structure, Vol. 19, pp. 1395–1412, 2011.
[4] R. Henderson, A. Sali, M.L. Baker, B. Carragher, B. Devkota, K.H. Downing, E.H. Egelman, Z. Feng, J. Frank, N. Grigorieff, et al., “Outcome of the first electron microscopy validation task force meeting”, Structure, Vol. 20, pp. 205–214, 2012.
[5] S.K. Burley, H.M. Berman, C. Bhikadiya, C. Bi, L. Chen, L. Di Costanzo, C. Christie, K. Dalenberg, J.M. Duarte, S. Dutta, et al., “RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy”, Nucleic Acids Research, Vol. 47, pp. D464–D474, 2019.
[6] G.N. Ramachandran, C. Ramakrishnan, V. Sasisekharan, “Stereochemistry of polypeptide chain configurations”, Journal of Molecular Biology, Vol. 7, pp. 95–99, 1963.
[7] S.A. Hollingsworth, P.A. Karplus, “A fresh look at the Ramachandran plot and the occurrence of standard structures in proteins”; Biomolecule Concepts, Vol. 1, Issue 3-4, PP. 271–283, 2010. doi:10.1515/BMC.2010.022
[8] R.W.W. Hooft, G. Vriend, C. Sander, E.E. Abola, “Errors in protein structures”, Nature, Vol. 381, pp. 272, 1996.
[9] P. Newbould, “Use of nitrogen fertilizer in agriculture: where do we go sustainablely and ecologically”? Plant and Soil Vol. 115, pp. 297–311, 1989.
[10] J.N. Galloway, A.R. Townsend, J.W. Erisman, M. Bekunda, Z. Cai, J.R. Freney, L.A. Martinelli, S.P. Seitzinger, M.A. Sutton, “Transformation of the nitrogen cycle: Recent trends, questions, and potential solutions”, Science Vol. 320, pp. 889–892, 2008.
[11] P.M. Vitousek, D.N.L. Menge, S.C. Reed, C.C. Cleveland, “Biological nitrogen fixation: rates, patterns and ecological controls in terrestrial ecosystems”, Philosophical Transactions Royal Society B: Biological Sciences Vol. 368, pp. 20130119, 2013.
[12] C. Franche, K. Lindström, C. Elmerich, “Nitrogen-fixing bacteria associated with leguminous and non-leguminous plants”; Plant and Soil Vol. 321, Issue 1-2, pp. 35–59, 2009.
[13] J.K. Ladha, R.P. Pareek, M. Becker, “Stem-nodulating legume- Rhizobium symbiosis and its agronomic use in low land rice”, Advances in Soil Science, Vol. 20, pp. 147–192, 1992.
[14] H.M. Fischer, “Genetic regulation of nitrogen fixation in rhizobia”, Microbiological Reviews, Vol. 58, pp. 352–386, 1994.
[15] M. Pellegrini, E.M. Marcotte, M.J. Thompson, D. Eisenberg, T.O. Yeates, “Assigning protein functions by comparative genome analysis: protein phylogenetic profiles”, Proceedings National Academy Sciences USA, Vol. 96, pp. 4285–4288, 1999.
[16] E.M. Marcotte, M. Pellegrini, H.L. Ng, D.W. Rice, T.O. Yeates, D. Eisenberg, “Detecting protein function and protein-protein interactions from genome sequences”, Science, Vol. 285, pp. 751–753, 1999.
[17] A. Fiser, “Template-based protein structure modeling”, Methods Molecular Biology, Vol. 673, pp. 73–94, 2010.
[18] C.L. Gupta, S. Akhtar, P. Bajpai, “In silico protein modeling: possibilities and limitations”, EXCLI Journal, Vol. 13, pp. 513–515, 2014.
[19] S.D.V. Satyanarayana, M.S.R. Krishna, P.P. Kumar, S. Jeereddy, “In silico structural homology modeling of NifA protein of rhizobial strains in selective legume plants. Journal of Genetic Engineering and Biotechnology, Vol. 16, pp. 731–737, 2018.
[20] M.A. Marti-Renom, A.C. Stuart, A. Fiser, R. Sanchez, F. Melo, A. Sali, “Comparative protein structure modeling of genes and genomes”, Annual Review of Biophysics and Biomolecule Structure, Vol. 29, pp. 291–298, 2000.
[21] S.F. Altschul, T.L. Madden, A.A. Schaffer, J. Zhang, Z. Zhang, W. Miller, D.J. Lipman, “Gapped BLAST and PSI-BLAST: new generation of protein database search programs”, Nucleic Acids Res., Vol. 25, pp. 3389, 1997.
[22] E.W. Sayers, T. Barrett, D.A. Benson, S.H. Bryant, K. Canese, V. Chetvernin, D.M. Church, M. Dicuccio, R. Edgar, S. Federhen, et al., “Database resources of National Center for Biotechnology Information”. Nucleic Acids Research, Vol. 38, pp. D5–D16, 2010.
[23] E. Huala, F.M. Ausubel, “Central domain of Rhizobium meliloti NifA is sufficient to activate transcription from R. meliloti nifH promoter”, Journal of Bacteriology, Vol. 171, Issue 6, pp. 3354-3365, 1989.
[24] A. Roy, A. Kucukural, Y. Zhang, “I-TASSER: unified platform for automated protein structure and function prediction”, Nature Protocols, Vol. 5, pp. 725–738, 2010.
[25] Y. Zhang, “I-TASSER server for protein 3D structure prediction”, BMC Bioinformatics, Vol. 9, pp. 40, 2008.
[26] J. Yang, R. Yan, A. Roy, D. Xu, J. Poisson, Y. Zhang, “I-TASSER Suite: Protein structure and function prediction”, Nature Methods, Vol. 12, pp. 78–85, 2015.
[27] M. Kallberg, H. Wang, S. Wang, et al., “Template- based protein structure modeling using the RaptorX web server”, Nature Protocols, Vol. 7, Issue 8, pp. 1511-1522, 2012.
[28] D. Bhattacharya, J. Nowotny, R. Cao, J. Cheng, “3Drefine: interactive web server for efficient protein structure refinement”, Nucleic Acids Research, Vol. 44(W1), pp. 406-409, 2016. doi: 10.1093/nar/gkw336
[29] R.W.W. Hooft, C. Sander, G. Vriend, “Objectively judging the quality of a protein structure from a Ramachandran plot”, Bioinformatics, Vol. 13, pp. 425–430, 1997.
[30] U.S. Bhalla, R. Iyengar, “Emergent properties of networks of biological signaling pathways”, Science, Vol. 283, pp. 381–387, 1999.
[31] H. Jeong, B. Tombor, R. Albert, Z.N. Oltvai, A.-L. Barabasi, “The large-scale organization of metabolic networks”, Nature, Vol. 407, pp. 651–654, 2000.
[32] J. Pražnikar, M. Tomi?, D. Turk, “Validation and quality assessment of macromolecular structures using complex network analysis”, Scientific Reports, Vol. 9, pp. 1678, 2019. https://doi.org/10.1038/s41598-019-38658-9
[33] R. Farmer, B. Gautam, S. Singh, P.K. Yadav, P.A. Jain, “Virtual screening of AmpC/ß–lactamase for antimicrobial resistance in Pseudomonas aeruginosa”, Bioinformation, Vol. 4, pp. 290–294, 2010.
[34] P.K. Yadav, G. Singh, B. Gautam, S. Singh, M. Yadav, U. Srivastav, B. Singh, “Molecular modeling, dynamics studies and virtual screening of fructose 1,6- biphosphate aldolase-II in community acquired-methicillin resistant Staphylococcus aureus (CA-MRSA)”, Bioinformation, Vol. 9, pp. 158–164, 2013.
[35] K. Pramanik, P.K. Ghosh, S. Ray, A. Sarkar, S. Mitra, T.K. Maiti, “In silico structural, functional and phylogenetic analysis with three dimensional protein modeling of alkaline phosphatase enzyme of Pseudomonas aeruginosa”; Journal of Genetic Engineering and Biotechnology, Vol. 15, pp. 527–537, 2017b.
[36] R. Pathak, P. Narang, M. Chandra, R. Kumar, P.K. Sharma, H.K. Gautam, “Homology modeling and comparative profiling of superoxide dismutase among extremophiles: Exiguobacterium as model organism”, Indian Journal of Microbiology, Vol. 54, pp. 450-458, 2014. https://doi.org/10.1007/s12088-014-0482-8
[37] K. Pramanik, T. Soren, S. Mitra, T.K. Maiti, “In silico structural and functional analysis of Mesorhizobium ACC deaminase”, Computational Biological Chemistry, Vol. 68, pp. 12–21, 2017a. http://dx.doi.org/10.1016/j.compbiolchem.2017.02.005
[38] P.K.K. Mishra, R. Nimmanapalli, “In silico characterization of Leptospira interrogans DNA ligase and delineation of its antimicrobial stretches”, Annals of Microbiology, Vol. 69, pp. 1329–1350, 2019. https://doi.org/10.1007/s13213-019-01516-0
[39] R. Adiyaman, L.J. McGuffin, “Methods for the refinement of protein structure 3D models”, International Journal of Molecular Sciences, Vol. 20, Issue 9, pp. 2301, 2019. https://doi.org/10.3390/ijms20092301
[40] L.R. Jarboe, X. Zhang, X. Wang, J.C. Moore, K.T. Shanmugam, L.O. Ingram, “Metabolic engineering for production of biorenewable fuels and chemicals: Contributions of synthetic biology”, Journal of Biomedicine and Biotechnology, Vol. 2010, 761042, pp. 18, 2010. doi:10.1155/2010/761042
[41] R.W. Bradley, M. Buck, B. Wang, “Tools and principles for microbial circuit engineering”, Journal of Molecular Biology, Vol. 428, Issue 5, pp. 862– 888, 2016.
[42] S. Sindhu, D. Sindhu, “Development of computational tools for metabolic engineering”, International Journal of Innovative Research in Computer and Communication Engineering, Vol. 4, Issue 5, pp. 9208– 9217, 2016.
[43] X.G. Zhu, J.P. Lynch, D.S. LeBauer, A.J. Millar, M. Stitt, S.P. Long, “Plants in silico: Why, why now and what? - an integrative platform for plant systems biology research”, Plant Cell Environment, Vol. 39, pp. 1049–1057, 2016. doi: 10.1111/pce.12673
[44] S. Sindhu, D. Sindhu, “Information dissemination using computer and communication technologies for improving agriculture productivity”, International Journal of Emerging Trends and Technology in Computer Sciences, Vol. 6, Issue 6, pp. 143–152, 2017.
[45] R. Takors, “Biochemical engineering provides mindset, tools and solutions for the driving questions of a sustainable future”, Engineering in Life Sciences, Vol. 20, pp. 5-6, 2019. doi:10.1002/elsc.201900150
Citation
Divya Sindhu, S.K. Yadav, "Ramachandran plot analysis: Conformational validation of NifA protein structure in nitrogen-fixing Azorhizobium caulinodans," International Journal of Computer Sciences and Engineering, Vol.8, Issue.6, pp.116-121, 2020.
Drought Forecasting, using Artificial Neural Network (ANN) and Predict Values of Drought Condition Derived using Rainfall Data
Research Paper | Journal Paper
Vol.8 , Issue.6 , pp.122-125, Jun-2020
CrossRef-DOI: https://doi.org/10.26438/ijcse/v8i6.122125
Abstract
This paper focuses on drought forecasting, using Artificial Neural Network (ANN) and predicts the values of drought condition derived using Rainfall data of Indore (M.P). We have used the Rainfall data as input data of ANN model for drought forecasting, and determine Standardized Precipitation Index (SPI). Artificial Neural networks operate on the principle of learning from a training set. There is a large variety of neural network models and learning procedures. Two classes of neural networks that are usually used for prediction applications are feed-forward networks and recurrent networks. They often train both of these networks using back-propagation algorithm.
Key-Words / Index Term
Artificial Neural Networks (ANNs), SPI.
References
[1]. Agnew, C. T.: Using the SPI to identify drought. Drought Network News, Vol.12, Issue.1, pp.6–11, 1999.
[2]. Bankert, R. L.: Cloud classification of AVHRR Imagery in maritime regions using a probabilistic neural network, J. Appl. Meteorol., 33, pp.909–918, 1994.
[3]. Marzban, C. and Stumpf, G. J.: A neural network for tornado prediction based on Doppler radar-derived attributes. J. Appl. Meteor., 35, pp.617–626, 1996.
[4]. Mu¨ller, B., and Reinhardt, J.: Neural Networks: An Introduction, the Physics of Neural Networks Series, Springer-Verlag, 2, pp.266, 1991.
[5]. McKee, T. B., Doesken, N. J. and Kleist J.: The relation of drought frequency and duration to time scales, Proceedings of the Eighth Conference on Applied Climatology, American Meteorological Society, Boston. pp.179-184, 1993.
[6]. McKee, T. B., Doesken, N. J. and Kleist, J.: Drought monitoring with multiple time scales. Proceedings of the Ninth Conference on Applied Climatology; American Meteorological Society, Boston. pp.233–236, 1995.
Citation
Rajesh Kumar Sharma, Mayank Rajput, Rahul Sharma, "Drought Forecasting, using Artificial Neural Network (ANN) and Predict Values of Drought Condition Derived using Rainfall Data," International Journal of Computer Sciences and Engineering, Vol.8, Issue.6, pp.122-125, 2020.