International Journal of Bioinformatics Research

4-13

Authors: Ashwin Kumar Dakshinamurthi, Manthira Vasagam Chidambaram, Vivek Anand Manivel, Swaminathan Detchanamurthy

Interleukin-2 (IL-2) is an immunoregulatory cytokine whose biological effects are mediated through interaction with specific receptors on the surface of target cells. Due to its presumed role in generating a normal immune response, IL-2 is being evaluated for the treatment of a variety of tumors, in addition to infectious diseases. Main drawback of human IL-2 is that the molecule is relatively unstable. Therefore, with the objective of increasing the stability of the molecule, site directed mutagenesis of human IL-2 gene was carried out. Early studies indicated that mutations at three Cysteine residues (58, 105, 125) which are in the active sites of human IL-2 resulted in the reduced stability as well as the biological activity of the molecule. Therefore, mutations were carried out at the positions of amino acid other than the receptor binding sites at 111Valine to Arginine, 117Lysine to Glutamine and 133 Threonine to Asparagine of the human sequence by comparing it with the bovine sequence which has higher stability than the human counterpart, using SWISS PDB tool. To understand the biological activity of the mutated IL-2, energy minimization studies were carried out using SWISS-PDB. Docking studies were performed to check the reliability of the results using HEX DOCK, ARGUS LAB and PATCH DOCK between the IL-2 receptor and its mutated Ligand. These docking results also confirmed that the reliability of these mutated IL-2 gene. Stability, half life and ADME characteristics of these mutants can be studied in a detailed manner in the in vivo studies.

27-36

Authors: B. Uma Reddy

The present study was undertaken to assess the role of plastid-rbcL (ribulose-1, 5-bisphosphate carboxylase large-subunit) gene sequences in addressing the evolutionary relationships within the angiosperms at inter and intra-familial levels using computational experiment. In order to elucidate the relationships, a set of 92 chloroplast rbcL sequences representing from 90 taxa of 12 genera and 10 angiospermic plant families (dicot and monocots) were withdrawn from the GenBank database. The multiple sequence alignment was performed using Genebee-ClustalW service to findout the regions of conserved or indels among the sequences. The phylogenetic tree was inferred from these sequences by employing Bootstrap method of UPGMA (Unweighted Pair Group Method with Arithmetic Mean) using MEGA (Molecular Evolutionary Genetics Analysis) software. The consistency of these generic-wise groupings was further confirmed by the MP (Maximum-Parsimony), ME (Minimum-Evolution) and NJ (Neighbor-Joining) methods. The analysis of these studies strongly indicates that, out of the 12 selected genera Trichosanthes (Cucurbitaceae), Phyllanthus (Phyllanthaceae), Austrobryonia (Cucurbitaceae), Solanum (Solanaceae), Piper (Piperaceae) and Saxifraga (Saxifragaceae) are grouped into separate clusters and exhibiting monophyletic conditions. Where as, Drypetes (Putranjivaceae), Asparagus (Asparagaceae), Cassia (Caesalpinioideae, sub-family), Canna (Cannaceae), Mentha (Lamiaceae), are paraphyletic and the members of the Salvia (Lamiaceae) are distributed throughout these hiraeoid clades, confirming the polyphyly of this large genus. Similar observations were noticed in all four methods. Thus, chloroplast rbcL gene sequences can unambiguously resolve the relationships, as well as provided a good indication of major supra-generic groupings among the selected angiospermic plant families and also gave many clues for future studies.

47-53

Authors: B. Uma Reddy

MaturaseK gene (matK) of chloroplast is highly conserved in plant systematics which is involved in Group-II intron splicing. The size of the gene is approximately 1500 base pairs in length, located with in the intron of trnK. In the present study, matK gene from Cucurbitaceae was taken for the analysis of variants, parsimony site, patterns, transition/ transversion rate and phylogeny. The family Cucurbitaceae comprises over 120 genera and 825 species with medicinal values. The matK gene sequences have been withdrawn from GenBank and used for the analysis. The multiple sequence alignments were performed by Genebee-ClustalW. The phylogenetic analyses were carried out by MEGA (Molecular Evolutionary Genetics Analysis) software package based on Unweighted Pair Group Method with Arithmetic Mean (UPGMA) and Maximum Parsimony (MP) methods. The results indicated that the Trichosanthes, Austrobryonia, Momordica, Neoalsomitra, Gomphogyne, Sicyos genera showed polyphyletic condition. The overall invariants between the 88 taxa are 28.5%, average composition of nucleotides among taxa are found to be approximately, A-0.30, T-0.37, G-0.15, C-0.17 and the ratio of transition and transversion is 0.824. Phylogenetic tree was designed to identify the ideal regions that could be used for defining the inter and intra-generic relationships. From this study, it could be concluded that, the chloroplast matK gene sequences can unambiguously resolve the relationships, as well as provided a good indication of major supra-generic groupings among the selected members of the family Cucurbitaceae.

58-64

Authors: B. Uma Reddy

The rbcL gene and protein sequences have been used in addressing systematic questions among the few selected members of the family Cucurbitaceae has been investigated. In order to elucidate the systematic positions, a set of chloroplast-rbcL nucleotide sequences (from 42 taxa of 7 genera) and aminoacid sequences (from 52 taxa of 10 genera) were withdrawn from GenBank and GenPept databases, respectively. The evolutionary distance was inferred from these sequences by employing Bootstrap method of UPGMA (Unweighted Pair Group Method with Arithmetic Mean) and MP (Maximum Parsimony) using MEGA (Molecular Evolutionary Genetic Analysis) software. From the separate analysis produced almost similar although not identical results, no strongly supported incongruent results. The members of the genus Austrobryonia showed strictly monophyletic, Trichosanthes, Luffa, Momordica and Coccinia are found to be paraphyletic. But the members of the genus Cucumis are distributed throughout these hiraeoid clades, confirming the polyphyly of this large genus observed in both the family trees. From the results, it is also clear that, the chloroplast-rbcL gene and aminoacid sequences resolved the relationships, as well as provided a good indication of major supra-generic groupings among the selected members of the family Cucurbitaceae. These results provide the necessary frame work and explicit phylogenetic hypotheses from which further reversionary and other systematic studies can proceed.

70-80

Authors: Mahalakshmi T., Achuthsankar S. Nair

Protein-Protein Interaction (PPI) networks are important as they provide clues about the functions of individual proteins as well as enable system level analyses of cellular processes. Predicting hub proteins, the highly connected proteins in PPI networks, is a challenging computational problem. This paper proposes a method for predicting hub proteins from sequence information with 76% accuracy, 84% sensitivity and 71% specificity. In this method, a biodiversity measure, Shannon Index, is used along with an amino acid attribute Transfer Free Energy to Surface (TFES) to distinguish hub proteins from non-hub proteins. Also an analysis of disorderliness in hub proteins revealed that some amino acids have higher composition in hub than in non-hub.

85-92

Authors: Rakesh S., Pradhan D. , Umamaheswari A.

Leptospirosis continues to have major impacts on people of developing countries with inestimable morbidity and mortality. As current leptospirosis vaccination is relatively unsuccessful, development of efficacious vaccines through novel means became utmost priority for prevention of frequent outbreaks of the disease. Herein, MHC class II restricted peptide epitopes were identified from pathogenic Leptospiral membrane proteins to suggest T-cell epitope driven leptospirosis vaccines through reverse vaccinology. The proteome of Leptospira interrogans serovar Lai was screened to select 137 membrane proteins. Jemboss Antigenic server was employed to find antigenic peptides, followed by ProPred analysis to predict 30 short peptides having strong binding affinity with HLA DRB1*0101, DRB1*0401 and DRB1*1501 alleles. Predictions were revised to pick antigenic peptides with same core region binding with the selected HLADRB1 alleles and ten such peptides were found from seven proteins. Further, to confirm the interaction at structure level, Leptospira excinuclease ABC subunit B protein having short T-cell antigenic peptide (133-REDVVIVSSVSCIYGLG-149) was modeled using Modeller9v7. The model reliability was evaluated through Procheck, ProSA and ProQ. Docking calculations for selected HLA DRB1 alleles (receptor) and modelled Leptospira excinuclease ABC subunit B protein (ligand) were carried out using Hex 5.1. The protein –protein interaction revealed that the core region (136-VVIVSSVSC-144) of the antigenic peptide (133-REDVVIVSSVSCIYGLG-149) was well interacting with the receptors. Through the reverse vaccinology approach and docking studies, the short antigenic peptide 133-REDVVIVSSVSCIYGLG-149 of Leptospira excinuclease ABC subunit B is proposed as a potential novel T-cell driven subunit vaccine against leptospirosis.