Study of the Langat virus RNA-dependent RNA polymerase through homology modeling

Authors

  • Kalliopi Io Diakou Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 75 Iera Odos, 11855 Athens
  • Thanasis Mitsis Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 75 Iera Odos, 11855 Athens
  • Katerina Pierouli Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 75 Iera Odos, 11855 Athens
  • Eleni Papakonstantinou Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 75 Iera Odos, 11855 Athens
  • Vasileios Megalooikonomou Computer Engineering and Informatics Department, School of Engineering, University of Patras, Patras
  • Aspasia Efthimiadou Department of Soil Science of Athens, Institute of Soil and Water Resources, Hellenic Agricultural Organization- Demeter, Sofokli Venizelou 1, Lycovrissi, 14123, Attica
  • Dimitrios Vlachakis Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 75 Iera Odos, 11855 Athens, Greece Lab of Molecular Endocrinology, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Greece Department of Informatics, Faculty of Natural and Mathematical Sciences, King’s College London, Strand, London WC2R 2LS, United Kingdom

DOI:

https://doi.org/10.14806/ej.26.1.944

Keywords:

viral protein, homology modeling, polymerase, langat virus

Abstract

Langat virus is a member of the Flaviviridae family and a close relative of a group of important tick-borne viruses that cause human encephalitis. RNA-dependent RNA polymerase is a significant component of the replication mechanism of the Flaviviridae viral family. In the present work, a three-dimensional model of the Langat virus RNA-dependent RNA polymerase was designed through homology modeling. The experimentally determined structure of the RNA-dependent RNA polymerase of Dengue virus type II, another member of the same viral family, was employed as template for the homology modeling process. The resulting model underwent a series of optimisations and its quality was verified using the Verify3D algorithm. Important functional characteristics of the family of viral RNA-dependent RNA polymerases were identified in the generated model, thus affirming the potential for its use in the possible design of anti-viral agents for Langat virus.

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Published

2021-06-29

Issue

Vol. 26: Special issue to Biostatistics and Mathematical Modelling in Bioinformatics

Section

Research Papers

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