International Journal on Recent and Innovation Trends in Computing and Communication ISSN: 2321-8169 Volume: 2 Issue: 10 3208 – 3215 _____________________________________________________________________________________ 3208 IJRITCC | October 2014, Available @ http://www.ijritcc.org ______________________________________________________________________________ Bioinformatic Analysis, Structure Modeling and Active Site Prediction of Aquaporin Protein from Catfish Heteropneustes fossilis Amisha Singh, Radha Chaube* Zoology Department, Mahila Mahavidyalaya, Banaras Hindu University, Varanasi – 221 005, India. *Corresponding author: chauberadha@rediffmail.com Tel: 091-0542-2317546, Fax: 091-0542-2368174 (BHU) Abstract- Aquaporins (AQPs) are membrane channel proteins which facilitate the rapid transport of water across cellular membrane and are of fundamental importance to the control of cell volume and transcellular water traffic. In the present study using bioinformatic tools an in silico modeling and analysis of aquaporin protein sequences of catfish Heteropneustes fossilis was conducted. Primary structure prediction and physiochemical characterization were performed by computing theoretical isoelectric point (pI), molecular weight, extinction coefficient, instability index and aliphatic index. Secondary structure assessment of aquaporin protein of Indian catfish using GOR IV reveals greater percentage of residues as alpha helix and random coils against the beta sheets. After performing homology modeling using MODELLER, a 3D structure of aquaporin of Indian catfish have been predicted from its amino acid sequence. After the prediction structure has been validated through various validation tools. This homology modeling based structure will provide an insite to its functional aspect and further studies which are based on tertiary structure of protein. Active site of aquaporin protein has been predicted using DoGSite scorer. Analysis of aquaporin active site will provide an insight to more précised functional characterization of this protein. In future, present study will allow the designing of mutant and inhibitors for the study of physiological role of aquaporin protein in Heteropneustes fossilis. Keywords- Aquaporin; catfish; physiochemical properties; structural comparison; RMSD; active site __________________________________________________*****_________________________________________________ I. INTRODUCTION Aquaporins are trans-membrane intergral proteins which belongs to the superfamily of major intrinsic protein (MIPs) which facilitate bi-directional and passive transport of water across the lipid bilayer of cell membrane. Another member of MIPs which plays similar role to aquaporin is aquaglycerophorin which transports small molecules and glycerol across the lipid bilayer [1-2]. Over 200 aquaporin sequences have been found over wide range of organisms [3]. These aquaporin channel proteins are found both in prokaryotes and eukaryotes and plays a major role in maintaining fluid homeostatsis [4]. Approximately 30 years ago, aquaporins were discovered when a study was carried out regarding the system involved in the rapid movement of water across the biological membrane in Rh cell antigen. Aquaporins are located as homo-tetramer with each subunit having individually functional waterpore [5]. Early studies of aquaporin 1 pointed to an “Hour Glass Model” in which repeated sequences were responsible for forming the pore. These repeated sequences are NPA (Asn-Pro-Ala) motif which is characteristic and identifying feature of aquaporin protein [6]. When we move towards the classification of aquaporin, till now 13 aquaorins (0-12) has been discovered in mammals, but in case of lower vertebrates less information is available. Some work has been carried out in zebrafish (Danio rerio) and 18 sequences has been reported which are structurally reported to the four superfamilies of tetrapod aquaporin. Aquaporins (AQP0, AQP1 and AQP4) are water transporter, aquaglycerophorins (AQP3 and AQP7-10), urea transporter (AQP8) and two unorthodox aquaporins (AQP11 & AQP12) [7]. Aquaporin protein have six membrane spanning alpha helices and both C and N termini facing the cytosol. Two loops are found in aquaporin protein: cytosolic domain and extracytosolic domain. Cytosolic loop lies between second and third transmembrane domain (B) and extracytosolic domain lies between the fifth and sixth transmembrane domain (E). These two loops form short hydrophobic helices that clip halfway into the membrane from opposite sides. These two loops generally contain conserved NPA (Asn-Pro-Ala) motif. Asparagine residues are key to the formation of water selective filter [8]. In case of mammals, 13 isoforms of aquaporins have been identified and studied but still less information is available regarding the aquaporin in fishes [9-11]. In the current study our focus is on the full in silico analysis and modeling i.e homology modeling of Aquaporin-1b (ovarian aquaporin) of Indian catfish Heteropneustes fossilis. Aquaporin 1b of Indian catfish belongs to class I of aquaporin obtained from ovary [12]. Aquatic animals and fishes face various osmotic challenges in maintaining body fluid homeostasis. So, the study of aquaporins in these animals is of great importance. Experimental techniques (NMR and X-ray Crystallorgaphy) used for predicting the 3D structure of proteins are very much tedious and