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In silico characterization of Leptospira interrogans DNA ligase A and delineation of its antimicrobial stretches

  • Prasanta Kumar Koustasa MishraEmail author
  • Ramadevi Nimmanapalli
Original Article
  • 5 Downloads

Abstract

Purpose

In the present study, an attempt is being made to characterize the DNA ligase A (LigA) of Leptospira interrogans by computational methods.

Methods

Several prediction servers (SwissProt, MoByle, TMHMM, PSIPRED, SignalP, etc.) were used to predict and interpret the physico-chemical parameters associated with LigA. A three-dimensional (3D) structure of the protein was created by homology-based modeling (I-TASSER). DNA-binding regions (PATCHDOCK) and interactome (STRINGS) of the protein were also predicted. A phylogenetic tree was constructed by MEGA version X. Finally, amino acid residues with antimicrobial activity were determined from the LigA sequence by AntiBP server.

Results

Domains responsible for oligonucleotide binding (OB), BRCT (BRCA1 carboxy-terminal), and motifs like helix hairpin helix (HhH) were found to be present in the protein designating the super family it belongs to. Moreover, consensus residues, i.e., -KX/IDG- responsible for adenylation, are also found to be conserved within the amino acid sequence. In silico mutational analysis suggested that replacing any of the charged residues in the consensus (K or D) can lead to catalytic instability of the enzyme. Further, the protein was scanned for antimicrobial peptide (AMPs). Ten different stretches were found to have a potential bactericidal effect with significant scores.

Conclusions

LigA of Leptospira interrogans is an acidic protein rich in alpha helixes which also contain 10 potential antimicrobial peptides in its amino acid sequence.

Keywords

DNA ligase Structural co-ordinates In silico Antimicrobial peptides Leptospira 

Notes

Acknowledgments

The authors are highly thankful to the Dean, FVAS, RGSC-BHU, and Vice-Chancellor, Banaras Hindu University, for providing the required supports during the analysis.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Research involving human participants and/or animals

N/A

Informed consent

N/A

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Copyright information

© Università degli studi di Milano 2019

Authors and Affiliations

  1. 1.Department of Veterinary Physiology and Biochemistry, Faculty of Veterinary and Animal Sciences, Rajiv Gandhi South CampusBanaras Hindu UniversityMirzapurIndia

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