Title

Authors

Affiliation

¹Research Centre, Department of Botany and Microbiology, Lady Doak College, Madurai – 625002; ²Center for Environmental Studies, Lady Doak College, Madurai -625002; ³Department of Plant Biotechnology, School of Biotechnology, Madurai Kamaraj University, Madurai-625021; ⁴UGC-NRCBS, School of Biological Sciences, Madurai Kamaraj University, Madurai-625021

Email

ranimam@yahoo.com; *Corresponding author

Article Type

Hypothesis

Date

Received October 16, 2012; Accepted October 26, 2012; Published November 13, 2012

Cellulase is one of the most widely distributed enzymes with wide application. They are involved in conversion of biomass into simpler sugars. Cellulase of Trichoderma longibrachiatum, a known cellulolytic fungus was compared with Clostridium thermocellum [AAA23226.1] cellulase. Blastp was performed with AAA23226.1 as query sequence to obtain nine similar sequences from NCBI protein data bank. The physicochemical properties of cellulase were analyzed using ExPASy’s ProtParam tool namely ProtParam, SOPMA and GOR IV. Homology modeling was done using SWISS MODEL and checked quality by RMSD values using VMD1.9.1. Active sites of each model were predicted using automated active site prediction server of SCFBio. Study revealed instability of cellulase of two eukaryotic strains namely Trichoderma longibrachiatum [CAA43059.1] and Melanocarpus albomyces [CAD56665.1]. The negative GRAVY score value of cellulases ensured better interaction and activity in aqueous phase. It was found that molecular weight (M. Wt) ranges between 25-127.56 kDa. Iso-electric point (pI) of cellulases was found to be acidic in nature. GOR IV and SOPMA were used to predict secondary structure of cellulase, which showed that random coil, was dominated. Neighbor joining tree with C. thermocellum [AAA23226.1] cellulase as root showed that cellulases of Thermoaerobacter subterraneus [ZP_07835928] and C. thermocellum [CAA4305.1] were more similar to eukaryotic cellulases supported by least boot strap values. Pseudoalteromonas haloplanktis cellulase was found to be the ideal model supported by least RMSD score among the predicted structures. Trichoderma longibrachiatum cellulase was found to be the best compared to other cellulases, which possess high number of active sites with ASN and THR rich active sites. CYS residues were also present ensuring stable interaction and better bonding. Hydrophilic residues were found high in active sites of all analyzed models and template.

Citation

Kumar et al. Bioinformation 8(22): 1105-1110 (2012)
 

Edited by

P Kangueane

ISSN

0973-2063

Publisher

Biomedical Informatics

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.