Advances in Synthetic Biology by Unknown

Author:Unknown
Language: eng
Format: epub
ISBN: 9789811500817
Publisher: Springer Singapore

11.4.3 Ligand Recognition

The structural determinants of ligand recognition by riboswitches vary with the type and source of organisms. Basically, the aptamer domain is folded into a three-way junction and forms a ligand-binding site. This region is being exploited in synthetic chemistry to make random fragments followed by selection of the potent ones. This can be seen naturally by the existence of only four classes of riboswitches for many decades while there are more than 30 different structural architectures for binding different ligands (Weinberg et al. 2017). Here, bioinformatics approach becomes more efficient in the prediction of ligand-binding sequences and calculation of ligand-binding energy. Molecular dynamics simulations have also become a robust approach to assess the stability of the riboswitch-ligand complexes. A study by Micura et al. (Haller et al. 2013) explained the molecular mechanism of TPP riboswitch binding to the ligand through a three-state model which was earlier proposed by SAXS (Ali et al. 2010; Baird and Ferre-D’Amare 2010). Further, Velmurugan and co-workers (Kesherwani et al. 2018) explained the molecular mechanism of the TPP riboswitch and the nucleotides that are crucial for stability and ligand binding. Similarly, the recognition mechanism can be referred in the literature for other riboswitches as well (Gilbert et al. 2006; Kim and Breaker 2008; Mulhbacher and Lafontaine 2007; Serganov 2010; Serganov and Patel 2009).

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