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Search: authors:"Westhof, Eric"

6 papers found.
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Mining for recurrent long-range interactions in RNA structures reveals embedded hierarchies in network families

The wealth of the combinatorics of nucleotide base pairs enables RNA molecules to assemble into sophisticated interaction networks, which are used to create complex 3D substructures. These interaction networks are essential to shape the 3D architecture of the molecule, and also to provide the key elements to carry molecular functions such as protein or ligand binding. They are...

Prediction of nucleic acid binding probability in proteins: a neighboring residue network based score

We describe a general binding score for predicting the nucleic acid binding probability in proteins. The score is directly derived from physicochemical and evolutionary features and integrates a residue neighboring network approach. Our process achieves stable and high accuracies on both DNA- and RNA-binding proteins and illustrates how the main driving forces for nucleic acid...

The ribosome prohibits the G•U wobble geometry at the first position of the codon–anticodon helix

Precise conversion of genetic information into proteins is essential to cellular health. However, a margin of error exists and is at its highest on the stage of translation of mRNA by the ribosome. Here we present three crystal structures of 70S ribosome complexes with messenger RNA and transfer RNAs and show that when a G•U base pair is at the first position of the codon...

Classification of pseudo pairs between nucleotide bases and amino acids by analysis of nucleotide–protein complexes

Nucleotide bases are recognized by amino acid residues in a variety of DNA/RNA binding and nucleotide binding proteins. In this study, a total of 446 crystal structures of nucleotide–protein complexes are analyzed manually and pseudo pairs together with single and bifurcated hydrogen bonds observed between bases and amino acids are classified and annotated. Only 5 of the 20 usual...

Frequency and isostericity of RNA base pairs

Most of the hairpin, internal and junction loops that appear single-stranded in standard RNA secondary structures form recurrent 3D motifs, where non-Watson–Crick base pairs play a central role. Non-Watson–Crick base pairs also play crucial roles in tertiary contacts in structured RNA molecules. We previously classified RNA base pairs geometrically so as to group together those...