Modeling and structural analysis of cellulases using Clostridium thermocellum as template

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...

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Detalles Bibliográficos
Autores principales: Kumar, Nathan Vinod, Rani, Mary Esther, Gunaseeli, Rathinasamy, Kannan, Narayanan Dhiraviam, Sridhar, Jayavel
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Biomedical Informatics 2012
Materias:
Hypothesis
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3523225/
https://www.ncbi.nlm.nih.gov/pubmed/23251045
http://dx.doi.org/10.6026/97320630081105
Descripción
Sumario: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.

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