Research Activities in 2013

• Molecular evolution: Nucleotide and codon composition in genomes

We are interested to find out evolutionary selection mechanism on codon usage bias in bacteria. A new method has been developed to find out selection on codon usage bias. Using the method, we have found out that GGU and CGU codons in Gly and Arg family are selected in genome with high G+C%. Our result is also in aggrement with the findings of Wang et al (2011), Wald et al (2012) and Ran & Higgs(2010). So our result is in support of the finding that selection on optimal codons is not essentially in the direction of genome composition unlike the report by Hershberg and Petrov (2009). Using our result , we are able to find out selection mechanism in G+C high bacteria that were previously reported by Sharp et al (2005)to have a low selection using WWY codons.



• Computer Aided Drug Design

Finding out novel drugs against bacteria is one of the major challenges in front of bioinformatics research. We are targeting vital metabolism functions in bacteria for this purpose. One of such targets we have taken is anticodon modification enzymes in bacteria. We have visualized the structure of the enzyme thoroghly using Chimera, VMD softwares. The structure of different ligand used was minimized using Argus Lab. Then using Molegro Virtual Docker software the docking study was performed.



• Computational studies of Intrinsically Disordered Regions of proteins:SRP19 of Human and Pectatelyase KSM-P15 of Bacillus sp

In the recent times, IDPs have a new mark in the study of protein structure -function relationship. It has become evident that these proteins do not require a stable structure even under physiological conditions in order to do their biological role. A number of such proteins have been identified which lack a well -defined tertiary structure and exhibit a number of slighyly different conformations that dynamically change over time and population. In our work, we have chosen two completely different proteins:



• The first selected protein is Human SRP19kD, which has ten amino acid long disordered region. This disorder region has been modelled to find the secondary structure information propensity of the disorder region amino acid sequences. The successful modelling and the energy minimization of the unstructured region have given a message that the disordered region can form a secondary structure at the cost of performing only a single function.


• In another case, we have taken Pectate Lyase of Bacillus species KSM-P15. We have analyzed the role of disordered region in a protein function by performing the docking studies of the protein with Pectic acid, which is a known substrate to bind with this protein.
  In summary, present analysis has shown the functional importance of the disordered region in IDPs. The multifunction characteristics of these proteins come from the flexible part and this might get affected in case that region can attain a certain level of secondary structure. The results and the observations from this work can help in understanding of the Intrinsically Disordered Proteins (IDPs)