Faculty Publications

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Bio-conjugation of Bacillus Fastidiosus-Uricase with methoxy polyethylene glycol derivative and study of physiochemical properties
(2012) Nanda, P.; JagadeeshBabu, P.E.; Tekalkote, S.; Kunnummal, B.M.; Kaleekkal, N.
Uricase (EC 1.7.3.3, UC) is an enzyme belonging to the class of oxidoreductases and catalyses the oxidation of uric acid to allantoin, carbon dioxide and hydrogen peroxide. In this present work, Uricase from Bacillus fastidisous was conjugated with methoxypolyethyleneglycol p-nitrophenyl carbonate (mPEG-np) a polyethylene glycol derivative, in order to improve the pharmaceutical properties of therapeutic enzyme uricase. The PEGylated conjugates (uricase-mPEG-np) were synthesized using various ratios of uricase and mPEG-np to get maximum residual activity. The PEGylated uricase showed maximum residual uricolytic activity of 90.9% compared to the unmodified uricase, which was achieved at a ratio of 1:17 of uricase to mPEG-np. PEGylated uricase was further characterized using SDS-PAGE to determine its final molecular weight and approximate number of mPEG molecules attached. The result showed that the molecular weight was increased to 79.4 KDa and the number of mPEG molecules bound per subunit of uricase was approximately 9. Stability of the PEGylated uricase at various temperature and pH was studied and found to be 32°C and pH of 9.0. Further the mechanism of binding and possible sites of binding were studied using molecular modeling and docking software tool ArgusLab 4.0.1 and the two-dimensional image of docked uricase were generated.
Studies on the Site-specific PEGylation Induced Interferences Instigated in Uricase Quantification Using the Bradford Method
(Springer Netherlands, 2016) Nanda, P.; JagadeeshBabu, P.E.
Uricase from Bacillus fastidiosus was site-specifically PEGylated using methoxypolyethyleneglycol-maleimide (mPEG-mal) of different molecular weights (750 Da, 5 kDa, 10 kDa) via Thiol PEGylation strategy. The obtained monoPEGylated uricase conjugates were characterized using sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) and the molecular weight of single subunit of the conjugate was found to be 42.6, 48.1 and 56.3 kDa with respect to different molecular weights of m-PEG-mal. The influence of PEGylation on the quantification of uricase using protein quantification techniques like Bradford assay, RP-HPLC detection and Dumbroff method has been evaluated. A gradual decline in the absorbance value was observed with the advancement of the PEGylation reaction, indicating an interferences in the protein quantification due to PEGylation. The extent of interference highly dependence on mPEG-mal concentration and its chain length. The present study indicates that the quantification of PEGylation induced interferences caused in protein measured ought to be prudently measured at every discrete step of the PEGylation process. © 2016, Springer Science+Business Media New York.
In silico structural and functional analysis of bacillus uricases
(Bentham Science Publishers, 2021) Nelapati, A.K.; Meena, S.; Singh, A.K.; Bhakta, N.; JagadeeshBabu, P.E.
Background: Excluding humans, the peroxisomal uricase is responsible for the catabolism of uric acid into allantoin in many species like microorganisms, plants, and inverte-brates. 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 esti-mate 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 uric-ase 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 do-mains, 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. Al-so, 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. © 2021 Bentham Science Publishers.

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