Role of motif B loop in allosteric regulation of RNA-dependent RNA polymerization activity

Damià Garriga, Cristina Ferrer-Orta, Jordi Querol-Audí, Baldo Oliva, Núria Verdaguer

Research output: Contribution to journalReview ArticleResearchpeer-review

50 Citations (Scopus)


Increasing amounts of data show that conformational dynamics are essential for protein function. Unveiling the mechanisms by which this flexibility affects the activity of a given enzyme and how it is controlled by other effectors opens the door to the design of a new generation of highly specific drugs. Viral RNA-dependent RNA polymerases (RdRPs) are not an exception. These enzymes, essential for the multiplication of all RNA viruses, catalyze the formation of phosphodiester bonds between ribonucleotides in an RNA-template-dependent fashion. Inhibition of RdRP activity will prevent genome replication and virus multiplication. Thus, RdRPs, like the reverse transcriptase of retroviruses, are validated targets for the development of antiviral therapeutics. X-ray crystallography of RdRPs trapped in multiple steps throughout the catalytic process, together with NMR data and molecular dynamics simulations, have shown that all polymerase regions contributing to conserved motifs required for substrate binding, catalysis and product release are highly flexible and some of them are predicted to display correlated motions. All these dynamic elements can be modulated by external effectors, which appear as useful tools for the development of effective allosteric inhibitors that block or disturb the flexibility of these enzymes, ultimately impeding their function. Among all movements observed, motif B, and the B-loop at its N-terminus in particular, appears as a new potential druggable site.

Original languageEnglish
Pages (from-to)2279-2287
Number of pages9
JournalJournal of Molecular Biology
Issue number13
Publication statusPublished - 10 Jul 2013
Externally publishedYes


  • antiviral therapy
  • drug discovery
  • RNA viruses
  • RNA-dependent RNA polymerase
  • viral enzymes

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