Biology subjects

Auffinger, P.

Publications and source records attributed to Auffinger, P..

3 recordsLinked to original sources

bioRxiv2025

Cat_Wiz: A stereochemistry-guided toolkit for locating, diagnosing and annotating Mg2+ ions in RNA structures.

Misassigned Mg2+ ions are pervasive in RNA structural databases, obscuring mechanistic interpretation, undermining comparative analyses and compromising machine-learning training sets. Here, we present Cat_Wiz, a Coot-integrated, stereochemistry guided toolkit that facilitates the localization, diagnosis, correction and annotation of Mg2+ binding sites. Cat_Wiz comprises three modules: MG_diagnosis which validates and regularizes existing assignments; MG_detect which identifies unmodelled ion binding sites; and MG_clamp which classifies recurrent Mg2+ clamp motifs. Cat_Wiz also includes a complete binding site annotation system. The stereochemical principles implemented in Cat_Wiz were derived from an earlier analysis of the 1.55 [A] resolution Escherichia coli ribosome and from surveys of the Cambridge Structural Database. These principles provide a robust experimental foundation for characterizing Mg2+ binding sites. Applications to ribosomes, hammerhead ribozymes, group I introns, and quaternary RNA assemblies demonstrate that Cat_Wiz rapidly locates overlooked ions, corrects misassignments, and improves stereochemical fidelity in hours rather than days. Beyond refinement, Cat_Wiz generates curated data that can seed diverse machine-learning and AI models. This transparent, cost-effective framework establishes reproducible standards for RNA-ion assignments and will drive progress in the design of RNA 3D architectures through the identification of unique Mg2+-dependent backbone folds. Cat_Wiz is also applicable to Mg2+ binding sites in proteins and all related biomolecular systems since it is based on universal stereochemical principles.

molecular biology↗

bioRxiv2024

Principles of ion binding to RNA inferred from the analysis of a 1.55 A resolution bacterial ribosome structure - Part I: Mg2+

The importance of Mg2+ ions for RNA structure and function can difficultly be overstated. Several attempts were made to establish a comprehensive Mg2+ binding site classification. However, such descriptions were hampered by poorly modelled ion binding sites. Recently, ribosome cryo-EM structures with resolutions < 2.0 [A] allowed better descriptions of site-bound ions. However, in a recent cryo-EM 1.55 [A] E. coli ribosome structure, incomplete ion assignments prevented a full understanding of their binding modes. We revisited this model to establish general binding principles applicable to any RNA of sufficient resolution. These principles rely on the 2.9 [A] distance separating two Mg2+-bound cis-water molecules. By applying these rules, we could assign all Mg2+ ions bound with 2 to 4 non-water oxygens. We also uncovered unanticipated motifs where up to five adjacent nucleotides wrap around a single ion. The formation of these complex motifs involves a hierarchical dehydration of the Mg2+ ions, a process that plays a significant role in ribosome biogenesis and in the folding of large RNAs. These binding principles enhance our understanding of the roles of ions in RNA structure and will help refining the solvation shell of different ribosomes and of RNAs with complex topologies.

molecular biology↗

bioRxiv2020

Deflating the RNA Mg2+ bubble. Stereochemistry to the rescue!

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 Mg2+ 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 should always be considered 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 bound Mg2+ ions in the 6QNR structure, suggesting that K+ and not Mg2+ 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 Mg2+ 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 Mg2+, Na+, ..., stereochemistry coupled with high resolution structures remain the best currently available option.

biochemistry↗