ABSTRACT
Aims: To make three dimensional structure of native and mutated matrix protein (M) of Nipah Virus (NiV) and to establish conformational and functional comparison between the two. Study Design: All in-silico analysis were performed using various online and offline software. Place and Duration of Study: Department of Biotechnology and Bioinformatics, Padmashree Dr. D.Y.Patil Vidyapeeth, Navi Mumbai, February 2013. Methodology: The protein’s physicochemical properties were characterized and 3D model of both the normal and the mutated protein were created using Phyre2. Single point mutation of S147G is recorded which leads to altered structure formation. Both the models were evaluated and compared conformationally. Results: 4G1GB based structures were modeled by phyre2 and minimized energies recorded were-16760.041 kJ/mol for native and -16563.029 kJ/mol for the mutated protein. Structure validation proved that both the native and mutated structures were reliable. Formation of 3 H-bonds make mutated M structure slightly more stable than the native one. Conclusion: NiV, one of deadliest pathogen, needs to be checked immediately. More information gain is needed by performing wet lab analysis. This work might help understand the functional difference between native and mutated M protein and can be used as the potent drug target via applying rational drug designing approach.
ABSTRACT
Objective: To analyze the amino acid sequence composition, secondary structure, the spatial conformation of its domain and other characteristics of Argonaute protein. Methods:Bioinformatics tools and the internet server were used. Firstly, the amino acid sequence composition features of the Argonaute protein were analyzed, and the phylogenetic tree was constructed. Secondly, Argonaute protein’s distribution of secondary structure and its physicochemical properties were predicted. Lastly, the protein functional expression form of the domain group was established through the Phyre-based analysis on the spatial conformation of Argonaute protein domains. Results: 593 amino acids were encoded by Argonaute protein, the phylogenetic tree was constructed, and Argonaute protein’s distribution of secondary structure and its physicochemical properties were obtained through analysis. In addition, the functional expression form which comprised the N-terminal PAZ domain and C-terminal Piwi domain for the Argonaute protein was obtained with Phyre. Conclusions: The information relationship between the structure and function of the Argonaute protein can be initially established with bioinformatics tools and the internet server, and this provides the theoretical basis for further clarifying the function of Schistosoma Argonaute protein.
ABSTRACT
<p><b>OBJECTIVE</b>To analyze the amino acid sequence composition, secondary structure, the spatial conformation of its domain and other characteristics of Argonaute protein.</p><p><b>METHODS</b>Bioinformatics tools and the internet server were used. Firstly, the amino acid sequence composition features of the Argonaute protein were analyzed, and the phylogenetic tree was constructed. Secondly, Argonaute protein's distribution of secondary structure and its physicochemical properties were predicted. Lastly, the protein functional expression form of the domain group was established through the Phyre-based analysis on the spatial conformation of Argonaute protein domains.</p><p><b>RESULTS</b>593 amino acids were encoded by Argonaute protein, the phylogenetic tree was constructed, and Argonaute protein's distribution of secondary structure and its physicochemical properties were obtained through analysis. In addition, the functional expression form which comprised the N-terminal PAZ domain and C-terminal Piwi domain for the Argonaute protein was obtained with Phyre.</p><p><b>CONCLUSIONS</b>The information relationship between the structure and function of the Argonaute protein can be initially established with bioinformatics tools and the internet server, and this provides the theoretical basis for further clarifying the function of Schistosoma Argonaute protein.</p>