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Insights from the molecular docking aided interaction analysis of HfQ with small RNAs


Rajkumar Praveen, Johni Rexliene, Ashwini Karuppaswamy, Murugesan Rajeshkannan, Viswanathan Balaji & Jayavel Sridhar*



Department of Biotechnology (DDE), Madurai Kamaraj University, Madurai-625021, Tamilnadu, INDIA; *Corresponding author



Rajkumar Praveen - E-mail: n.r.praveen9909@gmail.com, Phone: +91 9597769909

Johni Rexliene - E-mail: rexliene@gmail.com, Phone: +91 8124379780

Ashwini Karuppaswamy - E-mail: ashwinimicro2015@gmail.com, Phone: +91 9486365930

Murugesan Rajeshkannan - E-mail: rajeshlifescience@gmail.com, Phone: +91 9786846757 Viswanathan Balaji - E-mail: balajilabnagai@gmail.com, Phone: +91 9843545547

Jayavel Sridhar - E-mail: jsridhar@nrcbsmku.org & jsridharbiotech@mkuniversity.ac.in, Phone: +91 9751648767


Article Type

Research Article



Received March 1, 2022; Revised April 30, 2022; Accepted April 30, 2022, Published April 30, 2022



Hfq, RNA binding protein, is widely found in most of the prokaryotes. It plays a key role in gene regulation by binding with small RNA and facilitates mRNA pairing there by suppress or boost translation according to RNA structures. Interaction between sRNAs and HfQ in Salmonella SL1344 were screened using Co-Immuno Precipitation (HfQ-CoIP) studies earlier. We have formulated an In silico approach, to model the 3D structures of 155 sRNA and studied their interactions with HfQ proteins. We have reported the key interacting PHE42, LEU7, VAL27, PHE39 and PRO21 residues of HfQ binds with many small RNAs. Further mutation of PHE42 in to ALA42 in HfQ leads to loss of sRNA binding efficiency. We have differentiated the interactions in to HfQ binding and non-binding sRNAs, based on Atomic Contact Energy and area. This methodology may be applied generically for functional grouping of small RNAs in any organism.



HfQ, small RNA, Co-IP, RNA-SEQ, reads



Praveen et al. Bioinformation 18(4): 425-431 (2022)


Edited by

P Kangueane






Biomedical Informatics



This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.