Protein structure determination of insulin of zebra fish (Danio rerio) by homology modeling and structure analysis

Abstract

The protein sequence of insulin of zebra fish is obtained from UniProt. Due to lack of their structure, structure prediction is necessary, because the structure of protein plays an important role in their function. Our work is based on the production of two protein structure, from the same sequence, by computational approach and finally validates these generated structures. In this work two different widely acceptable online web tool are used for generating structure from the protein sequences of insulin of zebra fish. These are Swiss Model web server and ESyPred3D web server. After getting structure from this two web tool, the structures are passed by a series of quality tests. ProQ web software is used for checking quality of these generated structures. 3d-ss web tool is used for superimposition between two generated structures. It can compare between two structures. The Ramachandran plot is calculated by using VegaZZ software. CASTp (Computer Atlas of Surface Topology of protein) is a web tool, used to predict active sides with their respective volume and area. Finally ProFunc tool is used for analysis of two structures. Key-Words: CASTp, Homology Modeling, ProQ, VegaZZ, Zebra fish insulin I. Introduction Insulin is a peptide hormone, produced by beta cells of the pancreas, and is central to regulating carbohydrate and fat metabolism in the body. Insulin causes cells in the liver, skeletal muscles, and fat tissue to absorb glucose from the blood. In the liver and skeletal muscles, glucose is stored as glycogen. Protein structure plays an important role in their function. There are many sequence of this protein are present in UniProt database. But due to their lack of structure, homology modeling is necessary. But this work is based on the insulin of the zebra fish. Homology modeling, also known as comparative modeling of protein, refers to constructing an atomic- resolution model of the target protein from its amino acid sequence and an experimental three-dimensional structure of a related homologous protein (the template). Homology modeling relies on the identification of one or more known protein structures likely to resemble the structure of the query sequence. Evolutionarily related proteins have similar sequences and naturally occurring homologous proteins have similar protein structure. It has been shown that three-dimensional protein structure is evolutionarily more conserved than would be expected on the basis of sequence conservation alone. The sequence alignment and template structure are then used to produce a structural model of the target. Because protein structures are more conserved than DNA sequences, detectable levels of sequence similarity usually imply significant structural similarity. The quality of the homology model is dependent on the quality of the sequence alignment and template structure. In this work two widely acceptable structure prediction tools are used, these are Swiss Model and ESyPred3D. Both are runs in windows environment. The structures are then validating using ProQ. Superimposition is done by 3d-ss. Ramachandran plot (also known as a Ramachandran diagram or a (φ,ψ) plot), originally developed in 1963 by G. N. Ramachandran, C. Ramakrishnan, and V. Sasisekharan, is a way to visualize backbone dihedral angles ψ against φ of amino acid residues in protein structure. Ramachandran plot is calculated by VegaZZ software. CASTp is used to predict active sides with their respective volume and area. The ProFunc server ( http://www.ebi.ac.uk/thornton-srv/databases/profunc/index.html ) had been developed to help identifying the likely biochemical function of a protein from its three-dimensional structure.