γ-Tocopherol methyl transferase (γ-TMT) involved in synthesis of tocopherol (vitamin-E) methylates γ- and δ- tocopherols to form α- and β-tocopherols respectively. γ-TMT of soybean (Glycine max L.) was found to be a water soluble protein with the highest amount of polar amino acids contributing to its molecular surface hydrophilicity; the protein was found to be highly thermostable with half-life of < 5hr under in-vivo conditions. The isoelecric point (6.3) of the protein rendered the protein activity in the acidic buffer. We predicted three dimensional structure of γ-TMT as a monomer harboring majority of the α-helical structures and with the highest amount of hydrogen-bonded turns and extended strands in the β-ladder. Qualitative and quantitative analyses of the resulting model suggested the proposed model to be reliable with MPQS value of 1.24, an estimated native overlap at 3.5A0 of about 72.5%, a discrete optimized protein energy of - 0.48 and with a Z-score of 51.10. The predicted model was found to be stable taking into consideration more than 94.1% of the residues in the most favored regions. The structural superimposition of the predicted structure indicated a highly conserved structure despite its low amino acid similarity with the template protein. The results also led to the identification of the functional SAM/SAH binding sites such as HIS38, HIS40, GLY88 and ILE111 on γ-TMT and revealed the presence of the largest cleft on the surface which may play a major role during the ligand-protein interactions. Phylogenetic tree analysis revealed the Glycine max γ-TMT to be evolutionarily modified from photosynthetic bacterial MPBQ methyl transferase. Thus the predicted three dimensional structure and other related information generated in the present study have potential implications in better understanding of the molecular mechanisms and nature of methyl transferase related enzymatic reactions.

Classification analysis of microarray data is known to be hard because it involves thousands of features (genes) values, so it is necessary to reduce the number of features to obtain a manageable size of data for classification. In the present work two existing feature extraction/selection algorithms, namely Independent component analysis (ICA) and t-test are used which is a new combination of extraction/selection. The main objective of this paper is to rank the independent components of the DNA microarray data using t-test to improve the performance of Support Vector Machine (SVM)) classifier. To show the validity of the proposed method, it is applied to reduce the number of genes of five DNA microarray datasets then classify these datasets by using the SVM classifier. Experimental results on five datasets demonstrate that genes selected by proposed approach effectively improve the performance of SVM classifiers in terms of classification accuracy. We compare our proposed method with several existing methods and find that the proposed method can obtain better classification accuracy, using SVM classifier and accuracy increased up to 94.42 % of Acute leukemia data using the RBF kernel.

Correct folding is imperative for a protein to perform its function. Failing to fold correctly can result in a misfolded or inactive protein. Along with several other factors, molecular chaperones play an integral role in folding. Heat shock proteins (HSPs) are a specialized group of chaperone proteins synthesized in all living organisms in response to stress. Among different Hsps, Hsp60 forms the most conserved chaperone present in eukaryotes and eubacteria. Homology is one of the most important concepts in Evolutionary biology and proteomics. Identifying a distant structural ortholog designates a connection of common descent between entities. It will be great evolutionary significance to explore the distant homologs of this protein. Different biological databases were searched. With no reported valid structural ortholog, Fold based method was used. PGenTHREADER was intensively used to identify different templates sequentially. Hsp60 structure was modeled and validated using various servers. Phylogenetic analysis using ClustalW2 and Mega 5 was carried out to find the most relevant distant homologs from the PGenTHREADER templates. Sub structural comparative study was carried out between Hsp60 structure and the newly found template using UCSF-CHIMERA. The first equatorial, first intermediate and second equatorial regions of Hsp60 and Signal Recognition Particle 54kDa (SRP54) were observed to be much conserved. Some deletions have occurred in the apical and second equatorial region. This study sheds light on the highly conserved nature of the chaperonin which has not got much diversified in the course of evolution and a possible linkage with SRP54 in the light of evolution. Also, the conserved nature of Hsp60 is very much evident from their highly limited homologs reported in databases.

Polyphenol oxidases (PPOs) are copper-binding enzymes that oxidize polyphenols to quinones. PPOs are ubiquitous in plants, but, knowledge on their evolution and diversity in cereals is explored to a limited extent. This study reports their distribution and diversity in maize, sorghum, barley and millet. We have identified additional PPO proteins in the four crops than those previously reported. In all, 27 PPO were studied and an overall sequence identity across the species ranged between 30-99%. In addition to several variants of ‘HxxYC’ motif, a novel motif (HRxYxxFxER) that begins with third conserved histidine residue of ‘Copper A’ is reported. Another tri-peptide motif, ‘AGS’ was found to be 100% conserved. Twin-tyrosine (YxY) motif was substituted by ‘FTY’ or ‘YRF’ motif in four millet and one barley sequences. Among the 27 PPOs, 7 proteins were predicted to be synthesized via secretory pathway. PROSITE Scan analysis identified several domains including Zinc finger C2H2-type, Immunoglobulin [Ig]-like, and ‘TAT’ signal. Phylogenetic analysis revealed two major clades and also indicated a non-species specific diversification of the cereal PPOs investigated. Overall, our study analysed the diversity among the four cereal PPOs, it is observed that their number and distribution is consistent with their implications in different roles.