April Journal-2009.p65 - Association of Biotechnology and Pharmacy

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Current Trends in Biotechnology and Pharmacy Vol. 3 (2) 210-218, April 2009. ISSN 0973-8916 212 was carried out. The predicted structure contains a fold (â/á) 8 shape at the core. The secondary structure tells about the possible alpha helices, beta sheets and coiled regions in the CtGH39. The Ramachandran plot tells about the residues which have favourable conformation for psi and phi angles which will further help in understanding the mechanism of cellulolysis. Materials and Methods The amino acid sequence of CtGH39 (UniProt id A3DHB2) was first subjected to analysis by HHpred with 8 iterations of PSI- BLAST (16) for homology, it could also build a phylogenetic tree based on alignment scores so that evolutionary relationship among closely matching sequences can be understood. Thereafter, very closely resembling sequences with better E score
Current Trends in Biotechnology and Pharmacy Vol. 3 (2) 210-218, April 2009. ISSN 0973-8916 Fig. 1. Phylogenetic tree generated (showing distance) using BLASTp shows that CtGH39 comes from dockerin type cellulosome enzyme complex from Clostridium thermocellum ATCC 27405 and a hypothetical protein from Thermotoga petrophila must be its closest neighbour. 213 stereothermophilus (1w91), Thermoanaero bacterium saccharolyticum (1uhv) and Bacillus stereothermophilus (1qw9) (Fig. 2). High consensus portions shown in red are identical amino acids in all 5 sequences (Fig. 2). Those regions represented in blue are the conserved amino acids at least 4 out of 5 sequences and the neutral portions are shown in black (Fig. 2). Multiple sequence alignment (MSA) is often used to assess sequence conservation of protein domains, tertiary and secondary structures and even individual amino acids or nucleotides (17). The MSA results of CtGH39 using HHpred and MultAlin (17,18) showed the conserved regions that are present among the closely matching sequences and these sequences helped in further model building or structure prediction (Fig. 2). Fig. 2. Multiple sequence alignment analysis of CtGH39 using ClustalX. Multiple sequence alignment analysis of CtGH39 using MultAlin and HHpred showed above 90% similarities with protein sequences of Thermotoga petriphila (Hypothetical protein), Geobacillus stereothermophilus (1w91), Thermoanaerobacterium saccharolyticum (1uhv) and Bacillus stereothermophilus (1qw9) from the PDB database. High consensus portions shown in red (>90%) are identical amino acids in all 5 sequences. Blue regions (>50%) are the conserved amino acids in at least 4 out of 5 sequences and the neutral portions are shown in black. Ahmed et al
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April Journal-2009.p65 - Association of Biotechnology and Pharmacy

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