International Journal of Science and Research (IJSR) ISSN (Online): 2319-7064 Index Copernicus Value (2013): 6.14 | Impact Factor (2015): 6.391 Volume 5 Issue 4, April 2016 www.ijsr.net Licensed Under Creative Commons Attribution CC BY Homology Modeling, Docking Studies and Functional Site Analysis of Various Accessory Interacting Proteins of MnSOD of Nostoc PCC7120 and FeSOD of Thermosynechococcus elongatus Bikash Thakuria, Phiralang Diengdoh, *Samrat Adhikari 3 Bioinformatics Centre, Department of Biotechnology, St. Edmund’s College, Shillong, Meghalaya, India Abstract: Antioxidant enzymes studies have been evolved to be a potent area of study in context to bioinformatics tools. These antioxidant enzymes are produced by the cell to scavenging the stress effect of and external stimuli. In context to the present study, FeSOD and MnSOD have been investigated using bioinformatics tools. The complex biological systems and their behaviours have now become easy to study via the available bioinformatics tools. Homology modelling has emerged as a powerful tool in predicting an unknown structure of a protein and through phylogenetic analysis we can predict a relationship between the two species of cyanobacteria taken in our current study. Modelling and molecular docking studies is an important step in systems biology study. Despite availability of hundreds of known protein sequences, accurate information about their role in pathways is still largely inaccurate. Here, an attempt is made to explore the structural and the interactions of the accessory proteins with the two enzymes viz. MnSOD (from Nostoc sp. PCC7120) and FeSOD (from Thermosynechococcus elongates) based on the maps available from STRING database with the help of molecular docking studies. Keywords: Homology modelling, protein motifs, physiological characterization, pathway analysis,molecular docking 1. Introduction Cyanobacteria, also referred to as blue–green algae are a large and morphologically diverse group of oxygenic phototrophic prokaryotes, which occur in almost every habitat on earth (Thajuddin, N., Subramanian, G., 2005). These groups of bacteria have both beneficial and detrimental properties when judged from a human perspective. Their extensive growth can create considerable nuisance for management of inland waters and at the same time they might be highly toxic (Gorham, P.R., Carmichael J.I.., 1988). As a consequence, the negative aspects of cyanobacteria have gained more research attention and public concern not only concluding them as a potential candidate for bioremediation activities but also throws a limelight intro their deep assets for scavenging the cell vitality & viability by production of oxidative stress enzymes at intracellular levelfor maintaining cell integrity.This process of induction of oxidative stress is generally linked with the generation of free reactive oxygen radicals causing inhibition of microorganism development. Molecular oxygen is however unreactive, but when activated through reduction, forms reactive oxygen species (ROS) such as superoxide radical (O 2 - ), hydrogen peroxide (H 2 O 2 ) and hydroxyl radical (OH - ). ROS interact rapidly with biological molecules (proteins, lipids, DNA) causing oxidative stress which can result in cell death via apoptosis or necrosis (Kannan, K, Jain, S.K., 2000). One among them is the enzyme named Superoxide dismutase (SOD, EC 1.15.1.1) which belongs to a large and ubiquitous family of metalloenzymes that catalyzes the dismutation of a highly toxic and reactive superoxide radical (O 2 - ) to hydrogen peroxide (H 2 O 2 ) and oxygen (O 2 ) molecule through a cyclic oxidation-reduction mechanism. It is an efficient antioxidant enzyme that is found in virtually all O 2 respiring organisms and acts as the preliminary basis of defense mechanism to surpass the oxidative stress rendered by external stimuli (McCord, J.M., Fridovich, I., 1969). Superoxide anion (O 2 - ) and nitric oxide (NO) have been involved as apoptosis inducers (Richter C., 1993, Estevez, A.G., Radi, R., Barbeito, L. et al., 1995,Raiji, L., Baylis, C., 1995,Susin, S.A., Zamazami, N., Kroemer, G., 1998) and as an anti-oxidant protective effect of SOD during oxidative stress have also been also reported (Yen, H.C., Oberley T.D., Vichitbandhan S. et al., 1996, Ho Y. S., Magnenat J. L., Gargano M. et al., 1998). These enzymes particularly catalyzes the disproportionation of superoxide anion radical to hydrogen peroxide and molecular oxygen to protect the cells against oxidative damage and regulate the cellular concentration of O 2 − and its reactive progeny under both physiological and pathological conditions (Balasubramanian, A., Das, S., Bora, A. et al., 2012). Generally, SODs have been classified into four major canonical forms depending on the catalytic metals availability, FeSOD, MnSOD, Cu/ZnSOD and NiSOD. Besides these four, a cambialistic Fe/MnSOD also exists (Meier, B., Barra, D., Bossa, F. et al., 1982). The MnSOD enzyme is involved in maintaining nanomolar, physiological levels of O 2 − and its progeny. In a very elegant and comprehensible analysis a more complex role of MnSOD in establishing cellular redox environment and thus biological state of the cell has been evaluated based on thermodynamic and kinetic grounds (Buettner, G.R., Ng, C.F., Wang, M. et al., 2006, Buettner, G.R., 2011).FeSOD is found in prokaryotes and in eukaryotes. In eukaryotes it has been isolated from Euglena gracilis(Kanematsu, S., Asada K., 1990) and higher plants. There are two distinct groups of FeSOD the first group is a homodimer formed from two identical 20kDa subunit proteins, with 1-2 gram atom of iron in the active centre and the second is prevalent in most higher plants, as a tetramer of four equal subunits with a molecular weight of 80-9- kDa. Members of this family contain 2-4 gram atoms of iron in the active centre (Alscher, R.G., Erturk, N., Heath, L.S., 2002). Although SOD enzymes Paper ID: NOV162782 1150