International Journal of Biochemistry and Biophysics Vol. 3(2), pp. 13 - 23
DOI: 10.13189/ijbb.2015.030202
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Insight into the LGP2 Helicase Domain – An in Silico Approach

Subhomoi Borkotoky , Chetan Kumar Meena , Aswathy Soman , Ayaluru Murali ^*
Bioinformatics Centre, School of Life Sciences, Pondicherry University, Puducherry, India

ABSTRACT

LGP2, a member of retinoic acid inducible gene–I like receptors (RLR), encoded by the gene DHX58 in human induces antiviral response against many RNA viruses. The LGP2 shares a considerable similarity to the amino acid sequence of Hef Helicase Domain, the helicase domain of RIG-I-like protein helicase-associated endonuclease (Hef), which is involved in RNA binding. Earlier studies suggest that RLR contains a conserved C-terminal domain (CTD), which is responsible for the binding specificity to the viral RNAs and C-terminal domain of LGP2 also takes part in RNA binding. The present study is aimed to explore the interactions of LGP2 and RNA, thereby finding the crucial residues for the interaction, with the help of in-silico tools. The predicted crucial residues were validated by docking and molecular dynamics simulation studies as well as by fitting the model on a LGP2 density map. Our results in this study suggest that the residues in the helicase domain of LGP2 are crucial for RNA binding and it is positioned around the groove region of LGP2. Though earlier experimental studies identified the RNA binding residues, but our in silico binding studies with the full length LGP2 predicted some additional residues that can be valuable

KEYWORDS
LGP2, Homology Modeling, Molecular Docking, Molecular Dynamics Simulation, Flexible Fitting

Cite This Paper in IEEE or APA Citation Styles
(a). IEEE Format:
[1] Subhomoi Borkotoky , Chetan Kumar Meena , Aswathy Soman , Ayaluru Murali , "Insight into the LGP2 Helicase Domain – An in Silico Approach," International Journal of Biochemistry and Biophysics, Vol. 3, No. 2, pp. 13 - 23, 2015. DOI: 10.13189/ijbb.2015.030202.

(b). APA Format:
Subhomoi Borkotoky , Chetan Kumar Meena , Aswathy Soman , Ayaluru Murali (2015). Insight into the LGP2 Helicase Domain – An in Silico Approach. International Journal of Biochemistry and Biophysics, 3(2), 13 - 23. DOI: 10.13189/ijbb.2015.030202.