Login Register Cart 0
Generic placeholder image

Current Proteomics

Editor-in-Chief

ISSN (Print): 1570-1646
ISSN (Online): 1875-6247

Back
Journal Home About Journal Editorial Board Journal Insight Current Issue Volumes/Issues
Subscribe
Research Article

In Silico Structural and Functional Analysis of Bacillus Uricases

Author(s): Anand Kumar Nelapati, Shubham Meena, Aditya Kumar Singh, Narsimha Bhakta and JagadeeshBabu PonnanEttiyappan*

Volume 18, Issue 2, 2021

Published on: 12 May, 2020

Page: [124 - 142] Pages: 19

DOI: 10.2174/1570164617999200512081127

Price: $65

Abstract

Background: Excluding humans, the peroxisomal uricase is responsible for the catabolism of uric acid into allantoin in many species like microorganisms, plants, and invertebrates. Particularly in humans, the synthesis and excretion of uric acid are naturally balanced. When the uric acid concentration crosses 7 mg/dl, it results in conditions such as hyperuricemia and gout. Uricase is one of the potential sources for the reduction of uric acid in humans. Uricase is also widely used as a commercial diagnostic reagent in medical and clinical biochemistry to estimate the uric acid concentration in blood and other biological fluids. Computational approaches can be used for screening and investigation of uricase enzyme with desirable characteristics that can be employed in diverse industrial applications.

Objectives: The present study deals with computational-based structural, functional, and phylogenetic analyses of uricase enzymes from various Bacillus species.

Methods: Seventy uricase protein sequences from Bacillus species were selected for multiple sequence alignment, phylogenetic analysis, motif assessment, domain architecture examination, understanding of basic physicochemical properties and in silico identification of the composition of amino acids in uricase. Further, structural (secondary and tertiary structure prediction), and functional (CYS_REC, MOTIF scan, CD-search, STRING, SOSUI, and PeptideCutter) analyses of uricase were performed.

Results: Bacillus simplex (WP_063232385.1) was chosen as the representative species of the Bacillus genera. The three-dimensional (3D) structure of B. simplex uricase was predicted and validated using QMEAN, RAMPAGE, ERRAT, Verify 3D and PROQ servers. The analysis revealed that the tertiary structure of the selected uricase has good quality and acceptability.

Conclusion: Computational analysis of uricase from various Bacillus sources revealed that all the selected Bacillus uricases are active within acidic to a neutral environment, and thermally stable with a molecular weight ranging from 35.59-59.85kDa. The secondary structure analysis showed that all uricases are rich in alpha-helices and sheets. The CDD tool identified two conserved domains, one of which belongs to OHCU decarboxylase and another belongs to Uricase superfamily. The quality estimation of 3D modeled protein gave a high overall quality factor score of 94.64. Also, all Bacillus species of uricase enzyme and their corresponding genes showed a strong correlation from the phylogenetic comparison of the selected taxa. The present detailed computational investigation on the uricase protein could help in screening a suitable uricase producing microbe with desirable characteristics for industrial application.

Keywords: Uricase, Bacillus species, phylogenetic analysis, secondary structure, protein modeling, in silico, analysis.

« Previous Next »
Graphical Abstract

[1]
Punnappuzha, A.; PonnanEttiyappan, J.; Nishith, R.S.; Hadigal, S.; Pai, P.G. Synthesis and characterization of polysialic acid-uricase conjugates for the treatment of hyperuricemia. Int. J. Pept. Res. Ther., 2014, 20, 465-472.
[http://dx.doi.org/10.1007/s10989-014-9411-2]
[2]
Khade, S.; Srivastava, S.K. Uricase and its clinical applications. Int. J. Biol. Med. Res., 2015, 6, 5211-5215.
[3]
Scott, J.T. New knowledge of the pathogenesis of gout. J. Clin. Pathol. Suppl.(R Coll Pathol), 1978, 12, 205-213.
[http://dx.doi.org/10.1002/art.30520] [PMID: 32192]
[4]
Zhu, Y.; Pandya, B.J.; Choi, H.K. Prevalence of gout and hyperuricemia in the US general population: the National Health and Nutrition Examination Survey 2007-2008. Arthritis Rheum., 2011, 63(10), 3136-3141.
[http://dx.doi.org/10.1002/art.30520] [PMID: 21800283]
[5]
Gliozzi, M.; Malara, N.; Muscoli, S.; Mollace, V. The treatment of hyperuricemia. Int. J. Cardiol., 2016, 213, 23-27.
[http://dx.doi.org/10.1016/j.ijcard.2015.08.087] [PMID: 26320372]
[6]
Freitas, D. S.; Spencer, P.J.; Vassão, R.C.; Abrahão-Neto, J. Biochemical and biopharmaceutical properties of PEGylated uricase. Int. J. Pharm., 2010, 387(1-2), 215-222.
[http://dx.doi.org/10.1016/j.ijpharm.2009.11.034] [PMID: 19969053]
[7]
Cammalleri, L.; Malaguarnera, M. Rasburicase represents a new tool for hyperuricemia in tumor lysis syndrome and in gout. Int. J. Med. Sci., 2007, 4(2), 83-93.
[http://dx.doi.org/10.7150/ijms.4.83] [PMID: 17396159]
[8]
Masera, G.; Jankovic, M.; Zurlo, M.G.; Locasciulli, A.; Rossi, M.R.; Uderzo, C.; Recchia, M. Urate-oxidase prophylaxis of uric acid-induced renal damage in childhood leukemia. J. Pediatr., 1982, 100(1), 152-155.
[http://dx.doi.org/10.1016/S0022-3476(82)80259-X] [PMID: 6948943]
[9]
Schiavon, O.; Caliceti, P.; Ferruti, P.; Veronese, F.M. Therapeutic proteins: a comparison of chemical and biological properties of uricase conjugated to linear or branched poly(ethylene glycol) and poly(N-acryloylmorpholine). Farmaco, 2000, 55(4), 264-269.
[http://dx.doi.org/10.1016/S0014-827X(00)00031-8] [PMID: 10966157]
[10]
Nanda, P.; Babu, P.E. Isolation, screening and production studies of uricase producing bacteria from poultry sources. Prep. Biochem. Biotechnol., 2014, 44(8), 811-821.
[http://dx.doi.org/10.1080/10826068.2013.867875] [PMID: 24279683]
[11]
Dabbagh, F.; Ghoshoon, M.B.; Hemmati, S.; Zamani, M.; Mohkam, M.; Ghasemi, Y. Engineering human urate oxidase: towards reactivating it as an important therapeutic enzyme. Curr. Pharm. Biotechnol., 2015, 17(2), 141-146.
[http://dx.doi.org/10.2174/1389201016666150907113055] [PMID: 26343133]
[12]
Wu, X.W.; Lee, C.C.; Muzny, D.M.; Caskey, C.T. Urate oxidase: primary structure and evolutionary implications. Proc. Natl. Acad. Sci. USA, 1989, 86(23), 9412-9416.
[http://dx.doi.org/10.1073/pnas.86.23.9412] [PMID: 2594778]
[13]
Howard, S.C.; Jones, D.P.; Pui, C.H. The tumor lysis syndrome. N. Engl. J. Med., 2011, 364(19), 1844-1854.
[http://dx.doi.org/10.1056/NEJMra0904569] [PMID: 21561350]
[14]
Nanda, P. JagadeeshBabu, P.E. Studies on the site-specific PEGylation induced interferences instigated in uricase quantification using the Bradford method. Int. J. Pept. Res. Ther., 2016, 22, 399-406.
[http://dx.doi.org/10.1007/s10989-016-9518-8]
[15]
Lucas, K.; Boland, M.J.; Schubert, K.R. Uricase from soybean root nodules: purification, properties, and comparison with the enzyme from cowpea. Arch. Biochem. Biophys., 1983, 226(1), 190-197.
[http://dx.doi.org/10.1016/0003-9861(83)90284-9] [PMID: 6685457]
[16]
Capote-Maínez, N.; Sánchez, F. Characterization of the common bean uricase II and its expression in organs other than nodules. Plant Physiol., 1997, 115(4), 1307-1317.
[http://dx.doi.org/10.1104/pp.115.4.1307] [PMID: 9414545]
[17]
Kai, L.; Ma, X.H.; Zhou, X.L.; Jia, X.M.; Li, X.; Guo, K.P. Purification and characterization of a thermostable uricase from microbacterium sp. strain ZZJ4-1. World J. Microbiol. Biotechnol., 2008, 24, 401-406.
[http://dx.doi.org/10.1007/s11274-007-9489-1]
[18]
Li, W.; Xu, S.; Zhang, B.; Zhu, Y.; Hua, Y.; Kong, X.; Sun, L.; Hong, J. Directed evolution to improve the catalytic efficiency of urate oxidase from Bacillus subtilis . PLoS One, 2017, 12(5), e0177877.
[http://dx.doi.org/10.1371/journal.pone.0177877] [PMID: 28531234]
[19]
Pfrimer, P.; de Moraes, L.M.P.; Galdino, A.S.; Salles, L.P.; Reis, V.C.B.; De Marco, J.L.; Prates, M.V.; Bloch, C., Jr; Torres, F.A.G. Cloning, purification, and partial characterization of Bacillus subtilis urate oxidase expressed in Escherichia coli . J. Biomed. Biotechnol., 2010, 2010, 674908.
[http://dx.doi.org/10.1155/2010/674908] [PMID: 20168977]
[20]
Zhou, X.; Ma, X.; Sun, G.; Li, X.; Guo, K. Isolation of a thermostable uricase-producing bacterium and study on its enzyme production conditions. Process Biochem., 2005, 40, 3749-3753.
[http://dx.doi.org/10.1016/j.procbio.2005.05.002]
[21]
Adámek, V.; Králová, B.; Süchová, M.; Valentová, O.; Demnerová, K. Purification of microbial uricase. J. Chromatogr. A, 1989, 497, 268-275.
[http://dx.doi.org/10.1016/0378-4347(89)80028-3] [PMID: 2625463]
[22]
Bomalaski, J.S.; Holtsberg, F.W.; Ensor, C.M.; Clark, M.A. Uricase formulated with polyethylene glycol (uricase-PEG 20): biochemical rationale and preclinical studies. J. Rheumatol., 2002, 29(9), 1942-1949.
[PMID: 12233890]
[23]
Beedkar, S.D.; Khobragade, C.N.; Bodade, R.G.; Vinchurkar, A.S. Comparative structural modeling and docking studies of uricase: possible implication in enzyme supplementation therapy for hyperuricemic disorders. Comput. Biol. Med., 2012, 42(6), 657-666.
[http://dx.doi.org/10.1016/j.compbiomed.2012.03.001] [PMID: 22537975]
[24]
Colloc’h, N.; el Hajji, M.; Bachet, B.; L’Hermite, G.; Schiltz, M.; Prangé, T.; Castro, B.; Mornon, J.P. Crystal structure of the protein drug urate oxidase-inhibitor complex at 2.05 A resolution. Nat. Struct. Biol., 1997, 4(11), 947-952.
[http://dx.doi.org/10.1038/nsb1197-947] [PMID: 9360612]
[25]
Caves, M.S.; Derham, B.K.; Jezek, J.; Freedman, R.B. Thermal inactivation of uricase (urate oxidase): mechanism and effects of additives. Biochemistry, 2013, 52(3), 497-507.
[http://dx.doi.org/10.1021/bi301334w] [PMID: 23237426]
[26]
Takénaka, A.; Hossain, M.T.; Magat Juan, E.C.; Suzuki, K.; Yamamoto, T.; Imamura, S.; Sekiguchi, T. Crystal structures of uricase complexed with its real substrate and product. Acta Crystallogr. A, 2005, 61, c496-c496.
[http://dx.doi.org/10.1107/S0108767305079535]
[27]
Nelapati, A.K.; Das, B.K.; Ponnan Ettiyappan, J.B.; Chakraborty, D. In-silico epitope identification and design of uricase mutein with reduced immunogenicity. Process Biochem., 2020, S1359511319311808.
[28]
Retailleau, P.; Colloc’h, N.; Vivarès, D.; Bonneté, F.; Castro, B.; El-Hajji, M.; Mornon, J-P.; Monard, G.; Prangé, T. Complexed and ligand-free high-resolution structures of urate oxidase (Uox) from Aspergillus flavus : a reassignment of the active-site binding mode. Acta Crystallogr. D Biol. Crystallogr., 2004, 60(Pt 3), 453-462.
[http://dx.doi.org/10.1107/S0907444903029718] [PMID: 14993669]
[29]
Gruia, F.; Parupudi, A.; Baca, M.; Ward, C.; Nyborg, A.; Remmele, R.L., Jr; Bee, J.S. Impact of mutations on the higher order structure and activity of a recombinant uricase. J. Pharm. Sci., 2017, 106(4), 1018-1024.
[http://dx.doi.org/10.1016/j.xphs.2016.12.028] [PMID: 28063825]
[30]
Tan, Q.; Zhang, J.; Wang, N.; Li, X.; Xiong, H.; Teng, Y.; He, D.; Wu, J.; Zhao, C.; Yin, H.; Zhang, L. Uricase from Bacillus fastidious loaded in alkaline enzymosomes: enhanced biochemical and pharmacological characteristics in hypouricemic rats. Eur. J. Pharm. Biopharm., 2012, 82(1), 43-48.
[http://dx.doi.org/10.1016/j.ejpb.2012.06.002] [PMID: 22705639]
[31]
Yamamoto, K.; Kojima, Y.; Kikuchi, T.; Shigyo, T.; Sugihara, K.; Takashio, M.; Emi, S. Nucleotide sequence of the uricase gene from Bacillus sp. TB-90. J. Biochem., 1996, 119(1), 80-84.
[http://dx.doi.org/10.1093/oxfordjournals.jbchem.a021219] [PMID: 8907179]
[32]
Huang, S-H.; Wu, T-K. Modified colorimetric assay for uricase activity and a screen for mutant Bacillus subtilis uricase genes following StEP mutagenesis. Eur. J. Biochem., 2004, 271(3), 517-523.
[http://dx.doi.org/10.1046/j.1432-1033.2003.03951.x] [PMID: 14728678]
[33]
Feng, J.; Li, X.; Yang, X.; Zhang, C.; Yuan, Y.; Pu, J.; Zhao, Y.; Xie, Y.; Yuan, H.; Bu, Y.; Liao, F. A new practical system for evaluating the pharmacological properties of uricase as a potential drug for hyperuricemia. Arch. Pharm. Res., 2010, 33(11), 1761-1769.
[http://dx.doi.org/10.1007/s12272-010-1108-2] [PMID: 21116779]
[34]
Rahmatabadi, S.S.; Sadeghian, I.; Nezafat, N.; Negahdaripour, M.; Hajighahramani, N.; Hemmati, S.; Ghasemi, Y. In silico investigation of pullulanase enzymes from various bacillus species . Curr. Proteomics, 2017, 14, 175-185.
[http://dx.doi.org/10.2174/1570164614666170306164830] [PMID: 20134095]
[35]
Pustake, S.O.; Bhagwat, P.K.; Dandge, P.B. Statistical media optimization for the production of clinical uricase from Bacillus subtilisstrain SP6. Heliyon, 2019, 5(5), e01756.
[http://dx.doi.org/10.1016/j.heliyon.2019.e01756] [PMID: 31193400]
[36]
Nanda, P.P.E.J; Raju, J.R. Production and optimization of site-specific monoPEGylated uricase conjugates using MPEG-maleimide through RP-HPLC methodology. J. Pharm. Innov., 2016, 11, 279-288.
[http://dx.doi.org/10.1007/s12247-016-9251-z]
[37]
Zhao, Y.; Zhao, L.; Yang, G.; Tao, J.; Bu, Y.; Liao, F. Characterization of a uricase from Bacillus fastidious A.T.C.C. 26904 and its application to serum uric acid assay by a patented kinetic uricase method. Biotechnol. Appl. Biochem., 2006, 45(Pt 2), 75-80.
[http://dx.doi.org/10.1042/BA20060028] [PMID: 16689679]
[38]
Koteswara Reddy, G.; Nagamalleswara Rao, K.; Yarrakula, K. Insights into structure and function of 30S ribosomal protein S2 (30S2) in Chlamydophila pneumoniae: A potent target of pneumonia. Comput. Biol. Chem., 2017, 66, 11-20.
[http://dx.doi.org/10.1016/j.compbiolchem.2016.10.014] [PMID: 27866051]
[39]
Nezafat, N.; Negahdaripour, M.; Gholami, A.; Ghasemi, Y. Computational analysis of collagenase from different Vibrio, Clostridium and Bacillus strains to find new enzyme sources. Available from: https://www.ingentaconnect.com/content/doaj/24235652/ 2015/00000001/00000004/art00005 (accessed Jun 11, 2019)
[40]
Artimo, P.; Jonnalagedda, M.; Arnold, K.; Baratin, D.; Csardi, G.; de Castro, E.; Duvaud, S.; Flegel, V.; Fortier, A.; Gasteiger, E.; Grosdidier, A.; Hernandez, C.; Ioannidis, V.; Kuznetsov, D.; Liechti, R.; Moretti, S.; Mostaguir, K.; Redaschi, N.; Rossier, G.; Xenarios, I.; Stockinger, H. ExPASy: SIB bioinformatics resource portal. Nucleic Acids Res., 2012, 40(Web Server issue), W597-603.
[PMID: 22661580]
[41]
Pundir, S.; Martin, M.J.; O’Donovan, C. UniProt protein knowledgebase. Methods Mol. Biol., 2017, 1558, 41-55.
[http://dx.doi.org/10.1007/978-1-4939-6783-4_2] [PMID: 28150232]
[42]
Kumar, S.; Stecher, G.; Tamura, K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol. Biol. Evol., 2016, 33(7), 1870-1874.
[http://dx.doi.org/10.1093/molbev/msw054] [PMID: 27004904]
[43]
Yadav, P.K.; Singh, V.K.; Yadav, S.; Yadav, K.D.S.; Yadav, D. In silico analysis of pectin lyase and pectinase sequences. Biochemistry (Mosc.), 2009, 74(9), 1049-1055.
[http://dx.doi.org/10.1134/S0006297909090144] [PMID: 19916917]
[44]
Saitou, N.; Nei, M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol., 1987, 4(4), 406-425.
[PMID: 3447015]
[45]
Felsenstein, J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution, 1985, 39(4), 783-791.
[http://dx.doi.org/10.1111/j.1558-5646.1985.tb00420.x] [PMID: 28561359]
[46]
Bailey, T.L.; Boden, M.; Buske, F.A.; Frith, M.; Grant, C.E.; Clementi, L.; Ren, J.; Li, W.W.; Noble, W.S. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res., 2009, 37(Web Server issue), W202-208.
[http://dx.doi.org/10.1093/nar/gkp335] [PMID: 19458158]
[47]
Bailey, T.L.; Elkan, C. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc. Int. Conf. Intell. Syst. Mol. Biol., 1994, 2, 28-36.
[PMID: 7584402]
[48]
Finn, R.D.; Bateman, A.; Clements, J.; Coggill, P.; Eberhardt, R.Y.; Eddy, S.R.; Heger, A.; Hetherington, K.; Holm, L.; Mistry, J.; Sonnhammer, E.L.L.; Tate, J.; Punta, M. Pfam: the protein families database. Nucleic Acids Res., 2014, 42(Database issue), D222-D230.
[http://dx.doi.org/10.1093/nar/gkt1223] [PMID: 24288371]
[49]
Pooja, K.; Rani, S.; Kanwate, B.; Pal, G.K. Physico-chemical, sensory and toxicity characteristics of dipeptidyl peptidase-IV inhibitory peptides from rice bran-derived globulin using computational approaches. Int. J. Pept. Res. Ther., 2017, 23, 519-529.
[http://dx.doi.org/10.1007/s10989-017-9586-4]
[50]
Rani, S.; Pooja, K.; Pal, G.K. Exploration of potential angiotensin converting enzyme inhibitory peptides generated from enzymatic hydrolysis of goat milk proteins. Biocatal. Agric. Biotechnol., 2017, 11, 83-88.
[http://dx.doi.org/10.1016/j.bcab.2017.06.008]
[51]
Gasteiger, E.; Hoogland, C.; Gattiker, A.; Duvaud, S.; Wilkins, M.R.; Appel, R.D.; Bairoch, A. Protein identification and analysis tools on the ExPASy server.The Proteomics Protocols Handbook; Walker, J.M., Ed.; Humana Press: Totowa, NJ, 2005, pp. 571-607.
[http://dx.doi.org/10.1385/1-59259-890-0:571]
[52]
Gill, S.C.; von Hippel, P.H. Calculation of protein extinction coefficients from amino acid sequence data. Anal. Biochem., 1989, 182(2), 319-326.
[http://dx.doi.org/10.1016/0003-2697(89)90602-7] [PMID: 2610349]
[53]
Guruprasad, K.; Reddy, B.V.B.; Pandit, M.W. Correlation between stability of a protein and its dipeptide composition: a novel approach for predicting in vivo stability of a protein from its primary sequence. Protein Eng., 1990, 4(2), 155-161.
[http://dx.doi.org/10.1093/protein/4.2.155] [PMID: 2075190]
[54]
Ikai, A. Thermostability and aliphatic index of globular proteins. J. Biochem., 1980, 88(6), 1895-1898.
[PMID: 7462208]
[55]
Kyte, J.; Doolittle, R.F. A simple method for displaying the hydropathic character of a protein. J. Mol. Biol., 1982, 157(1), 105-132.
[http://dx.doi.org/10.1016/0022-2836(82)90515-0] [PMID: 7108955]
[56]
Bjellqvist, B.; Basse, B.; Olsen, E.; Celis, J.E. Reference points for comparisons of two-dimensional maps of proteins from different human cell types defined in a pH scale where isoelectric points ent human cell types defined in a pH scale where isoelectric points correlate with polypeptide compositions. Electrophoresis, 1994, 15(3-4), 529-539.
[http://dx.doi.org/10.1002/elps.1150150171] [PMID: 8055880]
[57]
Bjellqvist, B.; Hughes, G.J.; Pasquali, C.; Paquet, N.; Ravier, F.; Sanchez, J.C.; Frutiger, S.; Hochstrasser, D. The focusing positions of polypeptides in immobilized pH gradients can be predicted from their amino acid sequences. Electrophoresis, 1993, 14(10), 1023-1031.
[http://dx.doi.org/10.1002/elps.11501401163] [PMID: 8125050]
[58]
Geourjon, C.; Deléage, G. SOPMA: significant improvements in protein secondary structure prediction by consensus prediction from multiple alignments. Comput. Appl. Biosci., 1995, 11(6), 681-684.
[http://dx.doi.org/10.1093/bioinformatics/11.6.681] [PMID: 8808585]
[59]
Combet, C.; Blanchet, C.; Geourjon, C.; Deléage, G. NPS@: network protein sequence analysis. Trends Biochem. Sci., 2000, 25(3), 147-150.
[http://dx.doi.org/10.1016/S0968-0004(99)01540-6] [PMID: 10694887]
[60]
Jones, D.T. Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol., 1999, 292(2), 195-202.
[http://dx.doi.org/10.1006/jmbi.1999.3091] [PMID: 10493868]
[61]
McGuffin, L.J.; Bryson, K.; Jones, D.T. The PSIPRED protein structure prediction server. Bioinformatics, 2000, 16(4), 404-405.
[http://dx.doi.org/10.1093/bioinformatics/16.4.404] [PMID: 10869041]
[62]
Ashok Kumar, T. CFSSP: Chou and Fasman secondary structure prediction server. Wide Spect, 2013, 1(9), 15-19.
[63]
Kelley, L.A.; Mezulis, S.; Yates, C.M.; Wass, M.N.; Sternberg, M.J.E. The Phyre2 web portal for protein modeling, prediction and analysis. Nat. Protoc., 2015, 10(6), 845-858.
[http://dx.doi.org/10.1038/nprot.2015.053] [PMID: 25950237]
[64]
Schwede, T.; Kopp, J.; Guex, N.; Peitsch, M.C. SWISS-MODEL: an automated protein homology-modeling server. Nucleic Acids Res., 2003, 31(13), 3381-3385.
[http://dx.doi.org/10.1093/nar/gkg520] [PMID: 12824332]
[65]
Pramanik, K.; Saren, S.; Mitra, S.; Ghosh, P.K.; Maiti, T.K. Computational elucidation of phylogenetic, structural and functional characteristics of pseudomonas lipases. Comput. Biol. Chem., 2018, 74, 190-200.
[http://dx.doi.org/10.1016/j.compbiolchem.2018.03.018] [PMID: 29627694]
[66]
Pramanik, K.; Ghosh, P.K.; Ray, S.; Sarkar, A.; Mitra, S.; Maiti, T.K. An in silicostructural, functional and phylogenetic analysis with three dimensional protein modeling of alkaline phosphatase enzyme of Pseudomonas aeruginosa. J. Genet. Eng. Biotechnol., 2017, 15(2), 527-537.
[http://dx.doi.org/10.1016/j.jgeb.2017.05.003] [PMID: 30647696]
[67]
Pramanik, K.; Soren, T.; Mitra, S.; Maiti, T.K. In silico structural and functional analysis of mesorhizobium ACC deaminase. Comput. Biol. Chem., 2017, 68, 12-21.
[http://dx.doi.org/10.1016/j.compbiolchem.2017.02.005] [PMID: 28214450]
[68]
Benkert, P.; Künzli, M.; Schwede, T. QMEAN server for protein model quality estimation. Nucleic Acids Res., 2009, 37(Web Server issue), W510-514.
[http://dx.doi.org/10.1093/nar/gkp322] [PMID: 19429685]
[69]
Benkert, P.; Biasini, M.; Schwede, T. Toward the estimation of the absolute quality of individual protein structure models. Bioinformatics, 2011, 27(3), 343-350.
[http://dx.doi.org/10.1093/bioinformatics/btq662] [PMID: 21134891]
[70]
Colovos, C.; Yeates, T.O. Verification of protein structures: patterns of nonbonded atomic interactions. Protein Sci., 1993, 2(9), 1511-1519.
[http://dx.doi.org/10.1002/pro.5560020916] [PMID: 8401235]
[71]
Bowie, J.U.; Lüthy, R.; Eisenberg, D. A method to identify protein sequences that fold into a known three-dimensional structure. Science, 1991, 253(5016), 164-170.
[http://dx.doi.org/10.1126/science.1853201] [PMID: 1853201]
[72]
Lüthy, R.; Bowie, J.U.; Eisenberg, D. Assessment of protein models with three-dimensional profiles. Nature, 1992, 356(6364), 83-85.
[http://dx.doi.org/10.1038/356083a0] [PMID: 1538787]
[73]
Lovell, S.C.; Davis, I.W.; Arendall, W.B., III; de Bakker, P.I.W.; Word, J.M.; Prisant, M.G.; Richardson, J.S.; Richardson, D.C. Structure validation by Calpha geometry: phi, psi and Cbeta deviation. Proteins, 2003, 50(3), 437-450.
[http://dx.doi.org/10.1002/prot.10286] [PMID: 12557186]
[74]
Cristobal, S.; Zemla, A.; Fischer, D.; Rychlewski, L.; Elofsson, A. A study of quality measures for protein threading models. BMC Bioinformatics, 2001, 2, 5.
[http://dx.doi.org/10.1186/1471-2105-2-5] [PMID: 11545673]
[75]
Roy, S.; Maheshwari, N.; Chauhan, R.; Sen, N.K.; Sharma, A. Structure prediction and functional characterization of secondary metabolite proteins of Ocimum. Bioinformation, 2011, 6(8), 315-319.
[http://dx.doi.org/10.6026/97320630006315] [PMID: 21769194]
[76]
Singh, S.; Singh, G.; Sagar, N.; Yadav, P.K.; Jain, P.A.; Gautam, B.; Wadhwa, G. Insight into trichomonas vaginalis genome evolution through metabolic pathways comparison. Bioinformation, 2012, 8(4), 189-195.
[http://dx.doi.org/10.6026/97320630008189] [PMID: 22419839]
[77]
Szklarczyk, D.; Franceschini, A.; Wyder, S.; Forslund, K.; Heller, D.; Huerta-Cepas, J.; Simonovic, M.; Roth, A.; Santos, A.; Tsafou, K.P.; Kuhn, M.; Bork, P.; Jensen, L.J.; von Mering, C. STRING v10: protein-protein interaction networks, integrated over the tree of life. Nucleic Acids Res., 2015, 43(Database issue), D447-D452.
[http://dx.doi.org/10.1093/nar/gku1003] [PMID: 25352553]
[78]
Hirokawa, T.; Boon-Chieng, S.; Mitaku, S. SOSUI: classification and secondary structure prediction system for membrane proteins. Bioinformatics, 1998, 14(4), 378-379.
[http://dx.doi.org/10.1093/bioinformatics/14.4.378] [PMID: 9632836]
[79]
Appaiah, P.; Vasu, P. In silico designing of protein rich in large neutral amino acids using bovine as1 casein for treatment of phenylketonuria. J. Proteomics Bioinform., 2016, 9, 287-297.
[80]
Dubey, A.K.; Yadav, S.; Kumar, M.; Singh, V.K.; Sarangi, B.K.; Yadav, D. In silico characterization of pectate lyase protein sequences from different source organisms. Enzyme Res., 2010, 2010, 950230.
[http://dx.doi.org/10.4061/2010/950230] [PMID: 21048874]
[81]
Niño-Gómez, D.C.; Rivera-Hoyos, C.M.; Morales-Álvarez, E.D.; Reyes-Montaño, E.A.; Vargas-Alejo, N.E.; Ramírez-Casallas, I.N.; Erkan Türkmen, K.; Sáenz-Suárez, H.; Sáenz-Moreno, J.A.; Poutou-Piñales, R.A.; González-Santos, J.; Arévalo-Galvis, A. In silico characterization of 3-phytase A and 3-phytase B from Aspergillus niger. Enzyme Res., 2017, 2017, 9746191.
[http://dx.doi.org/10.1155/2017/9746191] [PMID: 29348934]
[82]
Irajie, C.; Mohkam, M.; Nezafat, N.; Hosseinzadeh, S.; Aminlari, M.; Ghasemi, Y. In silico analysis of glutaminase from different species of Escherichia and bacillus . Iran. J. Med. Sci., 2016, 41(5), 406-414.
[PMID: 27582590]
[83]
Pramanik, K.; Kundu, S.; Banerjee, S.; Ghosh, P.K.; Maiti, T.K. Computational-based structural, functional and phylogenetic analysis of enterobacter phytases. 3 Biotech, 2018, 8, 262.
[84]
Dutta, B.; Banerjee, A.; Chakraborty, P.; Bandopadhyay, R. In silicostudies on bacterial xylanase enzyme: structural and functional insight. J. Genet. Eng. Biotechnol., 2018, 16(2), 749-756.
[http://dx.doi.org/10.1016/j.jgeb.2018.05.003] [PMID: 30733796]
[85]
Dabbagh, F.; Moradpour, Z.; Ghasemian, A.; Ghasemi, Y. Phylogeny of urate oxidase producing bacteria: on the basis of gene sequences of 16S RRNA and uricase protein. Indian J. Pharm. Sci., 2012, 8, 99-102.
[86]
Pandey, S.; Kumar Negi, Y.; Marla, S. Comparative in silico analysis of ascorbate peroxidase protein sequences from different plant species. J. Bioeng. Biomed. Sci., 2011, 1, 1000103.
[87]
Bose, R.; Arora, S.; Dwivedi, V.D.; Pandey, A. Amino acid sequence based in silico analysis of β- galactosidases. Int. J. Bioinformat. Biosci., 2013, 3, 37-44.
[http://dx.doi.org/10.5121/ijbb.2013.3204]
[88]
Dwivedi, V.D.; Arora, S.; Kumar, A.; Mishra, S.K. Computational analysis of xanthine dehydrogenase enzyme from different source organisms. Netw. Model. Anal. Health Inform. Bioinform., 2013.
[http://dx.doi.org/10.1007/s13721-013-0029-7]
[89]
Dwivedi, V.D.; Mishra, S.K. In silico analysis of L-asparaginase from different source organisms. Interdiscip. Sci., 2014, 6(2), 93-99.
[http://dx.doi.org/10.1007/s12539-012-0041-0] [PMID: 25172447]
[90]
Ramya, L.N.; Pulicherla, K.K. Molecular insights into cold active polygalacturonase enzyme for its potential application in food processing. J. Food Sci. Technol., 2015, 52(9), 5484-5496.
[http://dx.doi.org/10.1007/s13197-014-1654-6] [PMID: 26344963]
[91]
Imhoff, R.D.; Power, N.P.; Borrok, M.J.; Tipton, P.A. General base catalysis in the urate oxidase reaction: evidence for a novel Thr-Lys catalytic diad. Biochemistry, 2003, 42(14), 4094-4100.
[http://dx.doi.org/10.1021/bi027377x] [PMID: 12680763]
[92]
Ito, M.; Kato, S.; Nakamura, M.; Go, M.; Takagi, Y. Identification of an amino acid residue involved in the substrate-binding site of rat liver uricase by site-directed mutagenesis. Biochem. Biophys. Res. Commun., 1992, 187(1), 101-107.
[http://dx.doi.org/10.1016/S0006-291X(05)81464-0] [PMID: 1520291]
[93]
Verma, A.; Singh, V.K.; Gaur, S. Computational based functional analysis of Bacillus phytases. Comput. Biol. Chem., 2016, 60, 53-58.
[http://dx.doi.org/10.1016/j.compbiolchem.2015.11.001] [PMID: 26672917]
[94]
Malviya, N.; Srivastava, M.; Diwakar, S.K.; Mishra, S.K. Insights to sequence information of polyphenol oxidase enzyme from different source organisms. Appl. Biochem. Biotechnol., 2011, 165(2), 397-405.
[http://dx.doi.org/10.1007/s12010-011-9259-2] [PMID: 21523355]
[95]
Morya, V.K.; Yadav, S.; Kim, E-K.; Yadav, D. In silico characterization of alkaline proteases from different species of Aspergillus . Appl. Biochem. Biotechnol., 2012, 166(1), 243-257.
[http://dx.doi.org/10.1007/s12010-011-9420-y] [PMID: 22072140]
[96]
Yadav, M.; Yadav, S.; Yadav, D.; Yadav, K. In- silico analysis of manganese peroxidases from different fungal sources. Curr. Proteomics, 2017, 14, 201-213.
[http://dx.doi.org/10.2174/1570164614666170203165022]
[97]
Nelapati, A.K. PonnanEttiyappan, J. Computational analysis of therapeutic enzyme uricase from different source organisms. Curr. Proteomics, 2020, 17(1), 59-77.
[98]
Rani, S.; Pooja, K. Elucidation of structural and functional characteristics of collagenase from Pseudomonas aeruginosa. Process Biochem., 2018, 64, 116-123.
[http://dx.doi.org/10.1016/j.procbio.2017.09.029]
[99]
Berman, H.M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T.N.; Weissig, H.; Shindyalov, I.N.; Bourne, P.E. The protein data bank. Nucleic Acids Res., 2000, 28(1), 235-242.
[http://dx.doi.org/10.1093/nar/28.1.235] [PMID: 10592235]
[100]
Zobayer, N.; Hossain, A.B.M.A. In silico characterization and homology modeling of histamine receptors. J. Biol. Sci., 2018, 18, 178-191.
[http://dx.doi.org/10.3923/jbs.2018.178.191]
[101]
Tamboli, A.S.; Rane, N.R.; Patil, S.M.; Biradar, S.P.; Pawar, P.K.; Govindwar, S.P. Physicochemical characterization, structural analysis and homology modeling of bacterial and fungal laccases using in silico methods. Netw. Model. Anal. Health Inform. Bioinform., 2015, 4, 17.
[http://dx.doi.org/10.1007/s13721-015-0089-y]
[102]
Pramanik, K.; Pal, P.; Soren, T.; Mitra, S.; Ghosh, P.K.; Sarkar, A.; Maiti, T.K. In silico structural, functional and phylogenetic analysis of Klebsiella phytases. J. Plant Biochem. Biotechnol., 2018, 27, 362-372.
[http://dx.doi.org/10.1007/s13562-018-0445-y]

Rights & Permissions Print Cite
Article Metrics
31
2
© 2024 Bentham Science Publishers | Privacy Policy