Deflating the RNA Mg bubble. Stereochemistry to the rescue!
Fiche publication
Date publication
décembre 2020
Journal
RNA (New York, N.Y.)
Auteurs
Membres identifiés du Cancéropôle Est :
Dr ENNIFAR Eric
Tous les auteurs :
Auffinger P, Ennifar E, D'Ascenzo L
Lien Pubmed
Résumé
Proper evaluation of the ionic structure of biomolecular systems remains challenging in X ray and cryo-EM techniques but is essential for advancing our understanding of complex structure/activity/solvent relationships. However, numerous studies overestimate the number of MgProper evaluation of the ionic structure of biomolecular systems remains challenging in X ray and cryo-EM techniques but is essential for advancing our understanding of complex structure/activity/solvent relationships. However, numerous studies overestimate the number of Mg in the deposited structures and underrate the importance of stereochemical rules to correctly assign these ions. Herein, we re-evaluate the PDBid 6QNR and 6SJ6 models of the ribosome ionic structure and establish that stereochemical principles need consideration when evaluating ion binding features, even when K anomalous signals are available as it is the case for 6QNR. Assignment errors can result in misleading conceptions of the solvent structure of ribosomes and other RNA systems and should therefore be avoided. Our analysis resulted in a significant decrease of the number of bound Mg in the 6QNR structure, suggesting that K and not Mg is the prevalent ion in the ribosome 1st solvation shell. We stress that the use of proper stereochemical guidelines is critical for deflating the current Mg bubble witnessed in many ribosome and other RNA structures. Herewith, we would like to draw the attention of the researchers interested in the ionic structure of biomolecular systems on the importance and complementarity of stereochemistry and other ion identification techniques such as those pertaining to the detection of anomalous signals of transition metals and K We also stress that for the identification of lighter ions such as Mg, Na, , stereochemistry coupled with high resolution structures remain the best currently available option. in the deposited structures and underrate the importance of stereochemical rules to correctly assign these ions. Herein, we re-evaluate the PDBid 6QNR and 6SJ6 models of the ribosome ionic structure and establish that stereochemical principles need consideration when evaluating ion binding features, even when K anomalous signals are available as it is the case for 6QNR. Assignment errors can result in misleading conceptions of the solvent structure of ribosomes and other RNA systems and should therefore be avoided. Our analysis resulted in a significant decrease of the number of bound Mg in the 6QNR structure, suggesting that K and not Mg is the prevalent ion in the ribosome 1 solvation shell. We stress that the use of proper stereochemical guidelines is critical for deflating the current Mg bubble witnessed in many ribosome and other RNA structures. Herewith, we would like to draw the attention of the researchers interested in the ionic structure of biomolecular systems on the importance and complementarity of stereochemistry and other ion identification techniques such as those pertaining to the detection of anomalous signals of transition metals and K We also stress that for the identification of lighter ions such as Mg, Na, , stereochemistry coupled with high resolution structures remain the best currently available option.
Mots clés
X-ray, cryo-EM, ionic atmosphere, solvent, validation
Référence
RNA. 2020 Dec 2;: