International Journal of Computational Bioinformatics and In Silico Modeling
ABSTRACT: Cocoonase is proteolytic enzyme having capacity to hydrolyze sericin of the cocoons. It is secreted by emerging silk moth during pupal-adult development which allows the exit of moth from the cocoon. Cocoonase hydrolyses
the interstitial matrix of cocoon that is composed of fibroin and sericin protein and acts on sericin without
affecting the fibroin. However, as a ruling practice, softening of tasar cocoon is generally performed in alkaline
solution by using soap, soda, H2O2, and alkali etc. which adversely affects the natural color and softness of tasar
silk. Seeking the importance of this enzyme in cocoon softening we aim to see the presence of cocoonase in other
sericigenous insects and do the phylogenetic analysis and conserved domain prediction. For this analysis
nucleotide and protein sequences of this enzyme were retrieved from NCBI. Phylogenetic analysis was
performed using MEGA 5.1Beta4 software. Presence of conserved domain in all retrieved protein sequences was
identified by the online SMART software. Further, presence of conserved domain in Antheraea pernyi cocoonase
protein sequence was identified by InterProScan and the 3D structure prediction was performed by I-TASSER.
Total fourteen nucleotide and fourteen protein sequences of cocoonase were retrieved from NCBI. Phylogenetic
analysis revealed that Bombyx mori and B. mandarina cocoonase mRNA sequences are closely related while A.
pernyi cocoonase mRNA sequence showed little variation. It is evident that, although both (Bombyx and
Antheraea) are sericigenous insects but divergence in mRNA sequences were observed. Moreover, on the other
hand, all the cocoonase mRNA sequences have common conserved region of trypsin like serine protease and
Peptidase S1 domain was identified by InterProScan in A. pernyi. 3D structure prediction of A. pernyi cocoonase
protein was carried out using 2ANY (plasma kallikrein protein) as template..
KeyWords: Antheraea pernyi, Antheraea mylitta, cocoon, cocoonase, cooking, fibroin, sericin, trypsin, 3D structure.
How to cite: Smita Lata et. al. Int J Comput Bioinfo In Silico Model. 2(4) 2013: 141-146
ABSTRACT: Identification of in silico observation and development of high through put technologies are easier to predict cancer in early stages. So there is a need to establish biomarkers for prediction and detection of breast cancer at first stage. A biomarker is an indicator of a biological state in this project. In bioinformatics it can be used to
study cancers to identify novel gene/protein which can be used as biomarker. Bioinformatics approaches can be
used in effective identification of biomarkers. In this study a combined advance approach using gene expression
analysis and bioinformatics were implemented to identify a novel biomarker for breast cancer. In this study we
predicted gene ADIPOQ, associated with breast fibroepithelial neoplasia, CD36 and GHR associated with
precancerous condition intraepithelial neoplasia. ADIPOQ and PTPN are associated with Myelodysplastic
syndrome. All these marker genes can be used in prognosis of specific conditions of cancer.
KeyWords: Breast Cancer, High throughput data analysis, Microarray Data Analysis, Biomarkers
How to cite: Jyotsana Pandey et. al. Int J Comput Bioinfo In Silico Model. 2(4) 2013: 147-151
ABSTRACT: The G8 (for eight conserved glycine residues) domain act as half ABC trasporter is widely distributed, found in Homo sapiens. Uncharacterized Homolgs of this protein was obtained by sequence similarity search using BLAST and further analysed by multiple sequence alignment in Pan troglodytes, Nomascus leucogenys, Pongo abelii and
Nomascus leucogenys. Phylogenetic results indicate that G8 protein of Homo sapiens is highly similar to G8
protein of Pan troglodytes, Nomascus leucogenys and closely related. Structure Modelling is done to predict
structural similarities among transmembrane regions and its role as a transporter protein. Transmembrane
prediction shows it is non-cytoplasmic in all organisms. Multiple sequence alignment analysis of transmembrane
region indicates significant similarity except few amino acids, proline at 20th and histidine at 42nd position are
present in human protein but leucine and arginine are present respectively in protein of Pan troglodyte. SSCH(R)
LI motif is predicted among four sequences except in GIR3J8 protein of Nomascus leucogenys. Modeled structure
of G8 proteins of Homo sapiens shows close similarities with its homologues in other three organisms.
Transmembrane region LLWYLVFQYLLPGAGYILR using HMMPLOT is G1R3J8_NOMLE protein of Nomascus
leucogenys but not in other sequences. Human G8 protein shows similarity to subunit an isoform 1 Q9Z1G4Vtype
proton ATPase (116 kDa) in Mus musculus which contain V type domain and Vacuolar proton translocating
ATPase protein (Q93050) in Homo sapiens.
KeyWords: G8 protein; ABC half transporter; Modelling; Pan troglodytes; Nomascus leucogenys;
How to cite: Mamta Sagar et. al. Int J Comput Bioinfo In Silico Model. 2(4) 2013: 152-158
ABSTRACT: Resistance to the commonly used antiviral drugs (namely Acyclovir) is posing a problem among Herpes simplex virus infections. Mutations in the thymidine kinase gene have been identified to be responsible for the resistance
expressed by these viruses. In this study we have characterized the phenotypic and genotypic drug resistance of
two ocular isolates, which have been further studied by in-silico methods. The phenotypic susceptibility of the
isolate was studied by Plaque Reduction Assay method. The Thymidine kinase gene (UL23) of the isolates was
amplified and further sequenced to detect mutations. The structure of wild type and mutant type thymidine
kinase were elucidated by molecular modeling and the structural deviations between them were studied. The
binding energies of Acyclovir with mutant and wild type thymidine kinase were analyzed from docking studies.
PRA result showed that the isolate was resistant to 400 μg/ml of the drug. Targeted sequencing results revealed
11 mutations, of which two were novel mutations (Leu43Pro and Gln89Arg.). The structure of mutant TK was in
more open conformation compared to wild TK structure. Docking studies infer the greater affinity of Acyclovir
binding to wild TK in comparison to mutant TK.
KeyWords: Herpes simplex virus 1, UL23, Thymidine kinase, Molecular modeling, Docking studies
How to cite: Samson Moses et. al. Int J Comput Bioinfo In Silico Model. 2(4) 2013: 159-166
ABSTRACT: Invertases are highly regulated enzymes with essential functions in carbohydrate transport and partitioning, sugar signalling, seed development and plant development. Plant possess three types of invertases, which are
located in the apoplast, the cytoplasm and the vacuole, respectively. Homology model of Solanum tuberosum
vacuolar acid invertase (St-vaINV) was constructed using Arabidopsis cell-wall invertase (At-cwINV1) and
Cichorium intybus (1-FEH IIa ) as a template which showed its overall structure was similar to the glycoside
hydrolase family 32 (GH32) enzymes. The three highly conserved motifs, NDPNG, RDP and EC, were located
within the active site and involved in catalyzing sucrose hydrolysis. The residues N22, D23, R148, E203, D149
and D239, together with the conserved W20, W47 and W82 residues forming a hydrophobic zone, were
necessary to create the ideal sucrose-binding pocket. The docking studies suggested that the sucrose binding
catalytic domain of St-vaINV had several minor but potentially important structural differences to that AtcwINV1
resulting in altered affinity for sucrose binding.
KeyWords: Invertase; homology modelling; modeller; sucrose; docking
How to cite: Ritu Singh et. al. Int J Comput Bioinfo In Silico Model. 2(4) 2013: 167-172
ABSTRACT: The protein sequence analysis in bioinformatics is done by comparing the sequences residue wise. For pair wise sequence analysis or for multiple sequence analysis, the protein sequences are compared amino acid by amino
acid. But the elemental composition of proteins gives the basic level of its organization. All the twenty amino
acids are made basically from the five atoms namely – Carbon, Nitrogen, Hydrogen, Sulphur and Oxygen.
Amongst all, carbon is the main element that contributes majorly to all hydrophobic reactions. The protein
sequence analysis cannot be done by solely comparing their amino acids, but it could be done by going one more
step down and comparing the atoms. The present review shows an insight to the upcoming atom level
comparison and its potential effects on sequence analysis.
KeyWords: Carbon; hydrophobicity; protein sequence analysis
How to cite: Parul Johri. Int J Comput Bioinfo In Silico Model. 2(4) 2013: 173-179
ABSTRACT: Vaccinomics is new branch of bioinformatics that deals with the designing of a candidate vaccine against a pathogen which is produced in less time as that of conventional vaccinology. This new beginning of the vaccine
research in past few decades has led to several new approaches towards vaccine development. These include
synthetic peptides that able to stimulate immune system of host. Hence epitope prediction and epitope mapping
are most important steps in designing of the synthetic vaccine. Epitope prediction and Epitope mapping can be
done by various tools and software that runs on various algorithms that are most useful for prediction; giving
appropriate value by considering each amino acid.
KeyWords: Vaccinomics; synthetic peptides; Epitope prediction; epitope mapping; algorithms
How to cite: AM Kanampalliwar et. al. Int J Comput Bioinfo In Silico Model. 2(4) 2013: 180-185
ABSTRACT: Potato virus Y (PVY) is one of the most prevalent and important viruses that affect potatoes. The virus can be acquired from the infePotato virus Y (PVY) is one of the most prevalent and important viruses that affect potatoes. The virus can be acquired from the infected plant within seconds, and transmitted to a healthy plant just as fast. PVY can also be transmitted mechanically by machinery, tools, and damaging plants while walking through the field. Its strains can interact with other potato viruses such as Potato virus A (PVA) and Potato virus X (PVX) to result in heavier losses. As PVY is a non-persistent virus so the use of insecticides to control spread is generally not effective. The best strategy to control PVY is to use seed potatoes certified to have low virus content. Analysis showed that peptide fragments of this antigenic coat protein of Potato Y virus contain 203 amino acids which point out 195 nonamers. These nonamers can be focused for designing a sero-diagnostic tool to detect PVY infection. By analyzing antigenecity, hydrophilicity, solvent accessibility and exposed surface area, we found the location potential epitopes at the sequences 181-MPRYGLVRN-189, 41-THTVPRIKAI-50 and 94-YEAVQLAYDIGETEM-108, and may be sufficient for eliciting immune response and targeting for virus detection. Apart from these, the high affinity TAP transporter peptide regions were found which were predicted by using cascade Support Vector Machine (SVM) and Position Specific Scoring Matrices (PSSM). These high efficiency binding fragments are found to tightly bind to the HLA receptors by in silico molecular docking and therefore, be used in cross protection and to develop host specific antibodies. We Predicted MHC class-I and class-II binding peptides of antigen protein from Potato Y virus which can be important determinant in sero-diagonostic issue. Besides, we operated AllerHunter for predicting allergenicity and it predicted Potato Y virus as non allergen protein with significant scores based on the structural and physicochemical properties of whole protein. Although the computational predictions made here are based on concrete confidence hence we have developed a hypothetical immunization based detection tool which demands more validation and in vivo experiments to validate such in silico approaches.
KeyWords: Antigenic protein; Nonamers; Epitope; Support vector machine; PSSM
How to cite: Md. Jibran Alam et. al. Int J Comput Bioinfo In Silico Model. 2(4) 2013: 186-198
ABSTRACT: Rice and other higher plants like wheat, maize, sorghum etc. are highly silicon accumulating species and show differences in silicon accumulation. This difference is due to both physiologic and molecular distinction between intra and interspecies capacity to uptake silicon by silicon transporter in the form of silicic acid. To understand the complete mechanism of silicon or silicic acid uptake, it is necessary to study the 3D structure of transporter protein of the plants. 3D structure prediction for these silicon transporters by I-TASSER and validation by RAMPAGE are initial steps. The 3D models those showed over 90% residues in favorable regions are considered in this study. This work will lead to design a better plant which has maximum silicon uptake capacity.
KeyWords: Silicon transporter; biotic stress; abiotic stress; 3D structure
How to cite: Mohammad Arif Ashraf et. al. Int J Comput Bioinfo In Silico Model. 2(4) 2013: 199-205
ABSTRACT: In the present study, we performed in silico analyses of the ligand-residue interaction energies between P-glycoprotein (P-gp) and 6-(methylsulfinyl)hexyl isothiocyanate (6MITC) and its analogs to predict possible inhibitory effect of the ITCs on P-gp. In total, 12 residues were identified as the preferred interaction residues in P-gp. Possible involvement of the moieties at C6 of the ITCs in forming hydrogen bonds in the ITC/P-gp complexes was revealed. Five of the eight tested ITCs had hydrogen bonds with either Asn-721 or Gln-725, indicating that these residues may play important roles in the ITC/P-gp interactions. Further, on the basis of the highest values for the ITC/P-gp interaction energies, the possible accumulation of the ITCs in cells was predicted in the order of 6MITC > 2b > 2e > 2c ≈ 2d ≈ 2h ≈ 2f ≈ 2g. To the best of our knowledge, this is the first report to predict possible inhibitory effect of ITCs on P-gp with in silico structural analyses of the ligand-receptor interaction between ITCs and P-gp.
KeyWords: 6-(Methylsulfinyl)hexyl isothiocyanate (6MITC); ATP-binding cassette (ABC) transpoters; in silico; P-glycoprotein (P-gp); structural analysis
How to cite: Hideaki Yamaguchi et. al. Int J Comput Bioinfo In Silico Model. 2(4) 2013: 206-212