Su Y, Guo J, Ling H, Chen S, Wang S, Xu L, Allan AC, Que Y (2014) Isolation of a novel peroxisomal catalase gene from sugarcane, which is responsive to biotic and abiotic stresses. PLoS One 9(1):1–11. https://doi.org/10.1371/journal.pone.0084426
Takio N, Yadav M, Yadav HS (2021) Catalase-mediated remediation of environmental pollutants and potential application – a review. Biocatal Biotransform 39(6):389–407. https://doi.org/10.1080/10242422.2021.1932838
Ashokan KV, Mundaganur DS, Mundaganur YD (2011) Catalase: phylogenetic characterization to explore protein cluster. J Res Bioinform 1:001–008
Garcia R, Kaid N, Vignaud C, Nicolas J (2000) Purification and some properties of catalase from wheat germ (Triticum aestivum L.). J Agric Food Chem 48:1050–1057. https://doi.org/10.1021/jf990933i
Keyham J, Keyhani E, Kamali J (2002) Thermal stability of catalases active in dormant saffron corms. Mol Rep 29(1-2):125–128. https://doi.org/10.1023/A:1020301107228
Lee SH, An CS (2005) Differential expression of three catalase genes in hot pepper. Mol Cell 20(2):247–255
Purev M, Kim YJ, Kim MK, Pulla RK, Yang DC (2010) Isolation of a novel catalase (Cat1) gene from Panax ginseng and analysis of the response of this gene to various stresses. Plant Physiol Biochem 48(6):451–460. https://doi.org/10.1016/j.plaphy.2010.02.005
Chen HJ, Wu SD, Huang GJ, Shen CY, Afiyanti M, Li WJ, Lin YH (2012) Expression of a cloned sweet potato catalase SPCAT1 alleviates ethephon-mediated leaf senescence and H2O2 elevation. J Plant Physiol 169(1):86–97. https://doi.org/10.1016/j.jplph.2011.08.002
Du Y, Wang P, Chen J, Song C (2008) Comprehensive functional analysis of the catalase gene family in Arabidopsis Thaliana. J Integr Plant Biol 50(10):1318–1326. https://doi.org/10.1111/j.1744-7909.2008.00741.x
Guan Z, Chai T, Zhang Y, Xu J, Wei W (2009) Enhancement of Cd tolerance in transgenic tobacco plants overexpressing a Cd-induced catalase CDNA. Chemosphere 76(5):623–630. https://doi.org/10.1016/j.chemosphere.2009.04.047
Sheoran SB, Pandey P, Sharma S, Narwal R et al (2013) Insilico comparative analysis and expression profile of antioxidant proteins in plants. Genet Mol Res 12(1):537–551
Hoseinian GA, Ghaemi N, Rahimi F (2006) Partial purification and properties of catalase from Brassiaoleracea capitata. Asian J Plant Sci 5:827–831
Linka B, Szakonyi G, Petkovits T, Nagy LG, Papp T, Vágvölgyi C, Benyhe S, Ötvös F (2012) Homology modeling and phylogenetic relationships of catalases of an opportunistic pathogen Rhizopus Oryzae. Life Sci 91(3–4):115–126. https://doi.org/10.1016/j.lfs.2012.06.016
Lai J, Jin J, Kubelka J, Liberles DA (2012) A phylogenetic analysis of normal modes evolution in enzymes and its relationship to enzyme function. J Mol Biol 422(3):442–459. https://doi.org/10.1016/j.jmb.2012.05.028
Yadav M, Yadav S, Yadav D, Yadav K (2017) In-silico analysis of manganese peroxidases from different fungal sources. Curr Proteomics 14(3):1–13. https://doi.org/10.2174/1570164614666170203165022
Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4(4):406–425. https://doi.org/10.1093/oxfordjournals.molbev.a040454
Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, Ren J, Li WW, Noble WS (2009) MEME Suite: tools for motif discovery and searching. Nucleic Acids Res 37:202–208. https://doi.org/10.1093/nar/gkp335
Geourjon C, Deléage G (1995) SOPMA: significant improvements in protein secondary structure prediction by consensus prediction from multiple alignments. Comput Appl Biosci 11(6):681–684. https://doi.org/10.1093/bioinformatics/11.6.681
Levin JM, Robson B, Garnier J (1986) An algorithm for secondary structure determination in proteins based on sequence similarity. FEBS Lett 205(2):303–308. https://doi.org/10.1016/0014-5793(86)80917-6
Arnold K, Bordoli L, Kopp J, Schwede T (2006) The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling. Bioinformatics 22(2):195–201. https://doi.org/10.1093/bioinformatics/bti770
MacArthur MW, Laskowski RA, Thornton JM (1994) Knowledge-based validation of protein structure coordinates derived by X-ray crystallography and NMR spectroscopy. Curr Opin Struct Biol 4(5):731–737. https://doi.org/10.1016/S0959-440X(94)90172-4
Eisenberg D, Lüthy R, Bowie JU (1997) VERIFY3D: assessment of protein models with three-dimensional profiles. Methods Enzymol 277:396–404. https://doi.org/10.1016/s0076-6879(97)77022-8
Laskowski RA, MacArthur MW, Moss DS, Thornton JM (1993) PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Crystallogr 26(2):283–291. https://doi.org/10.1107/S0021889892009944
Szklarczyk D, Franceschini A, Wyder A et al (2015) STRING v10: protein-protein interaction networks, integrated over the tree of life. Nucleic Acids Res 43:D447–D452. https://doi.org/10.1093/nar/gku1003
Purwar S, Gupta A, Vajpayee G, Sundaram S (2014) Isolation and in-silico characterization of peroxidase isoenzymes from wheat (Triticum aestivum) against Karnal Bunt (Tilletia indica). Bioinformation 10(2):87. https://doi.org/10.6026/97320630010087
Mathé C, Fawal N, Roux C, Dunand C (2019) In silico definition of new ligninolytic peroxidase sub-classes in fungi and putative relation to fungal life style. Sci Rep 9(1):1–14. https://doi.org/10.1038/s41598-019-56774-4
Singh AK, Katari SK, Umamaheswari A, Raj A (2021) In silico exploration of lignin peroxidase for unraveling the degradation mechanism employing lignin model compounds. RSC Adv 11(24):14632–14653. https://doi.org/10.1039/d0ra10840e
Morya VK, Yadav VK, Yadav S, Yadav D (2016) Active site characterization of proteases sequences from different species of Aspergillus. Cell Biochem Biophys 74:327–335. https://doi.org/10.1007/s12013-016-0750-9
Hoda A, Tafaj M, Sallaku E (2021) In silico structural, functional and phylogenetic analyses of cellulase from Ruminococcus Albus. J Genet Eng Biotechnol 19(1):58. https://doi.org/10.1186/s43141-021-00162-x
Alam NB, Ghosh A (2018) Comprehensive analysis and transcript profiling of Arabidopsis thaliana and Oryza sativa catalase gene family suggests their specific roles in development and stress responses. Plant Physiol Biochem 123:54–64. https://doi.org/10.1016/j.plaphy.2017.11.018
Ikai A (1980) Thermostability and aliphatic index of globular proteins. J Biochem 88(6):1895–1898. https://doi.org/10.1093/oxfordjournals.jbchem.a133168
Kaur A, Pati PK, Pati AM, Nagpal AK (2020) Physico-chemical characterization and topological analysis of pathogenesis-related proteins from Arabidopsis thaliana and Oryza sativa using in-silico approaches. PLoS One 5:1–15. https://doi.org/10.1371/journal.pone.0239836
Gamage DG, Gunaratne A, Periyannan GR, Russell TG (2019) Applicability of instability index for in vitro protein stability prediction. Protein Pept Lett 26(5):339–347
Huson DH, Bryant D (2006) Application of phylogenetic networks in evolutionary studies. Mol Biol Evol 23(2):254–267. https://doi.org/10.1093/molbev/msj030
Huelsenbeck JP, Bollback JP (2008) Application of the likelihood function in phylogenetic analysis. In: Handbok of Statistical Genetics, vol 1, 3rd edn, pp 460–488. https://doi.org/10.1002/9780470061619.ch15
Alam MT, Merlo ME, Takano E, Breitling R (2010) Genome-based phylogenetic analysis of Streptomyces and its relatives. Mol Phylogenet Evol 54(3):763–772. https://doi.org/10.1016/j.ympev.2009.11.019
Ong Q, Nguyen P, Phuong Thao N, Le L (2016) Bioinformatics approach in plant genomic research. Curr Genomics 17(4):368–378
Smeets HJM, Brunner HG, Ropers HH, Wieringa B (1989) Use of variable simple sequence motifs as genetic markers: application to study of myotonic dystrophy. Hum Genet 83(3):245–251. https://doi.org/10.1007/BF00285165
Nettling M, Treutler H, Grau J, Keilwagen J, Posch S, Grosse I (2015) DiffLogo: a comparative visualization of sequence motifs. BMC Bioinformatics 16(1):1–9. https://doi.org/10.1186/s12859-015-0767-x
Bork P, Koonin EV (1996) Protein sequence motifs. Curr Opin Struct Biol 6(3):366–376. https://doi.org/10.1016/s0959-440x(96)80057-1
Morris AL, MacArthur MW, Hutchinson E.G., Thornton J.M. (1992) Stereochemical quality of protein structure coordinates. Proteins: Struct. Funct. Genet. 12(4):345-364. https://doi.org/10.1002/prot.340120407.
Mugilan A, Ajitha MC, Devi, Thinagar (2010) Insilico secondary structure prediction method (Kalasalingam University Structure Prediction Method) using comparative analysis. Trends Bioinformatics 3(1):11–19. https://doi.org/10.3923/tb.2010.11.19
Waterhouse A, Bertoni M, Bienert S, Studer G, Tauriello G, Gumienny R, Heer FT, De Beer TAP, Rempfer C, Bordoli L, Lepore R, Schwede T (2018) SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Res 46(W1):W296–W303. https://doi.org/10.1093/nar/gky427
Kikuchi O (1978) A molecular orbital study of the conformation and g-factors of the HSSH− radical anion. Bull Chem Soc Jpn 51(1):315–316. https://doi.org/10.1246/bcsj.51.315
Tran NT, Jakovlić I, Wang WM (2015) In silico characterisation, homology modelling and structure-based functional annotation of blunt snout bream (Megalobrama amblycephala) Hsp70 and Hsc70 proteins. J Anim Sci Technol 57(1):1–9. https://doi.org/10.1186/s40781-015-0077-x
Aslanzadeh V, Ghaderian M (2012) Homology modeling and functional characterization of PR-1a protein of Hordeum vulgare subsp. Vulgare. Bioinformation 8(17):807. https://doi.org/10.6026/97320630008807
Messaoudi A, Belguith H, Ben Hamida J (2013) Homology modeling and virtual screening approaches to identify potent inhibitors of VEB-1 β-lactamase. Theor Biol Med Model 10(1):1–0. https://doi.org/10.1186/1742-4682-10-22
Pramanik K, Ghosh PK, Ray S, Sarkar A, Mitra S, Maiti TK (2017) An in silico structural, functional and phylogenetic analysis with three-dimensional protein modeling of alkaline phosphatase enzyme of Pseudomonas aeruginosa. J Genet Eng Biotechnol 15(2):527–537. https://doi.org/10.1016/j.jgeb.2017.05.003
Hoda A, Tafaj M, Sallaku E (2021) In silico structural, functional and phylogenetic analysis of cellulase from Ruminococcus albus. J Genet Eng Biotechnol 19:58. https://doi.org/10.1186/s43141-021-00162-x
Panda S, Chandra G (2012) Physicochemical characterization and functional analysis of some snake venom toxin proteins and related non-toxin proteins of other chordates. Bioinformation 8(18):891–896
Enany S (2014) Structural and functional analysis of hypothetical and conserved proteins of Clostridium tetani. J Infect Public Health 7:296–307
Zhang B, Li J, Lü Q (2018) Prediction of 8-state protein secondary structures by a novel deep learning architecture. BMC Bioinformatics 19:293
Rodwell VW, Kenelly PJ, Bender D, Botham K, Weil PA (2018) Harper’s Illustrated Biochemistry 31/e. McGraw-Hill Education McGraw-Hill Companies, New York, Blacklick
Krieger F, Moglich A, Kiefhaber T (2005) Effect of proline and glycine residues on dynamics and barriers of loop formation in polypeptide chains. J Am Chem Soc 127:3346–3352. https://doi.org/10.1021/ja042798i
Damian S, Annika LG, David L, Alexander J, Stefan W, Jaime HC, Milan S, Nadezhda TD, John HM, Peer B, Lars JJ, Christian VM (2019) STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res 47(D1):D607–D613. https://doi.org/10.1093/nar/gky1131
Rights and permissions
Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.
Disclaimer:
This article is autogenerated using RSS feeds and has not been created or edited by OA JF.
Click here for Source link (https://www.springeropen.com/)
