Project titles for:
Project titles for: 2008-10
- In silico analysis of Larger subunit of AGPase in Rice and Maize
- In silico Analysis of mutated in Larger subunit of AGPase in Maize
- Structural Comparison of Betaine Aldehyde Dehydrogenase-1 of Barley and Rice
- Analysis of Gene Expression Database of Skin Cancer
- Evaluation of Sequence Alignment Tools
- Phylogenetic analysis of Drb 3.2 gene
- Modelling of Smaller subunit of AGPase in Rice and Maize
- Prediction of Protein structure from sequence
- Development of Clinical Information Database of domestic animals
- To identify distant relationship between flavoprotein superfamily
- Promoters comparison in bacteria
- Transport protein features analysis
- Genome deciphering and comparative genomics of Solanaceous genome
- Computational approach in deciphering effect of gene alteration in Arabidopsis Thaliana
- Simulation of conformational changes in protein
We have two types of methods for predicting tertiary structure of proteins. Ab initio modeling are the first class methods predicting tertiary structures from sequence alone. Without relying on similarity at the fold level between the modeled sequence and any of the known structures. The second class of methods includes threading and comparative modeling. These second class methods rely on the detectable similarity between most of the modeled sequence and at least one known structure. Comparative protein structure modeling build a three dimensional model for a protein of unknown structure based on one or more related proteins of known structure. Threading methods relies on pairwise comparison of a protein sequence and a protein structure, i.e. structure information is used for the one of the two proteins that are being compared and the target sequence is threaded through a library of 3D profiles. In this project, work has been carried out to model 3D structure of human kallikrein 8 (hk8) in silico using homology modeling. KLK8 is the gene encoding protein human kallikrein 8 (hk8). Chromosomal location of this gene is 19q13.3-q13.4. Study of this protein is important because of its involvement in various diseases such as Alzheimer disease, Psoriasis vulgaris, Squamous cell carcinoma, lichen planus and it is found to be over expressed in ovarian carcinoma. Researchers used this protein as biomarker for cancer. 3D Structure of this protein may provide more insight into its role in cancer and help in inhibiting its pro neoplastic action The amino acid sequence of hk8 protein (gi 116006732) was obtained from NCBI’s protein database. Amino acid sequence was submitted to BLASTp. From results of BLASTp it was clear that 1NPM_A shows highest identity with target sequence. Therefore, it was chosen as template . Four different programs were used to generate 3D structure of this protein . Two with the help of servers PHYRE and SWISS-MODEL. Other two structures were generated with the help of software modeller and Prime suite 33 in Maestro. Phyre, Swiss-Model and Prime did not consider first 32 residues at the beginning because these residues belong to cleavage site but Modeller consider these first 32 residues. All four structures consist of two adjoining six-stranded beta-barrels and three alpha helices. After model generation, model refinement was performed by removing unfavorable non-bonded contacts with the help of Swiss-pdb viewer. The models were improved by using programs Complete a structure and Prepare PDB file for Docking programs of WHATIF server. In addition the models were verified with various computational methods from the same server namely, Coarse packing quality control, Planarity, Anomalous bond lengths and Anomalous bond angles. All models were evaluated from structural analysis and verification server including PROCHECK, ERRAT, VERIFY3D. All four structures pass this verification. The models had appropriate helixes and sheets that confirm secondary structure well. There was no heteroatom found in any of the models.