Eric Westhof

Publication de Eric Westhof

• Introduction
• Inhibition of Aminoglycoside-Deactivating Enzymes APH(3')-IIIa and AAC(6')-Ii by Amphiphilic Paromomycin O2''-Ether Analogues.
• Perspectives and Pitfalls in Nucleic Acids Crystallography
• Classification of pseudo pairs between nucleotide bases and amino acids by analysis of nucleotide-protein complexes.
• Editorial overview: Protein nucleic acid interactions: order, ambiguities and disorder in recognition and complex formation between proteins and nucleic acids
• Des ARN régulateurs chez les bactéries.
• Hierarchy and Dynamics of Rna Folding
• New dimensions of RNA in molecular recognition and catalysis.
• Modeling RNA Molecules
• Ribozymes, catalytically active RNA molecules. Introduction.
• Mutation in a primate-conserved retrotransposon reveals a noncoding RNA as a mediator of infantile encephalopathy.
• RNA modeling, naturally
• Hydration of RNA Base Pairs
• Predicting and modeling RNA architecture
• Biogenesis of Circular RNAs.
• Comparative genomics of protoploid Saccharomycetaceae.
• Identification and annotation of noncoding RNAs in Saccharomycotina.
• Prediction of nucleic acid binding probability in proteins: a neighboring residue network based score.:
• Handbook of RNA biochemistry: Second, Completely Revised and Enlarged Edition
• Self-assembled RNA nanostructures.
• Exploration of metal ion binding sites in RNA folds by Brownian-dynamics simulations
• A Large-Scale Assessment of Nucleic Acids Binding Site Prediction Programs.
• Speciation of a group I intron into a lariat capping ribozyme.
• Mutant MRPS5 affects mitoribosomal accuracy and confers stress‐related behavioral alterations
• RNA 3D Structure Analysis and Prediction
• RNA structure from deep sequencing.
• Structure of an A-form RNA duplex obtained by degradation of 6S RNA in a crystallization droplet
• Mining for recurrent long-range interactions in RNA structures reveals embedded hierarchies in network families
• A PNPase Dependent CRISPR System in Listeria.
• Recent advances in mitochondrial aminoacyl-tRNA synthetases and disease
• Isostericity and tautomerism of base pairs in nucleic acids.
• Specific features of telomerase RNA from Hansenula polymorpha.
• RNA structure analysis of human spliceosomes reveals a compact 3D arrangement of snRNAs at the catalytic core.
• Loop-loop interactions involved in antisense regulation are processed by the endoribonuclease III in Staphylococcus aureus.
• Structure-activity relationships among the kanamycin aminoglycosides: role of ring I hydroxy and amino groups. :
• RNase P: At last, the key finds its lock.
• La structure atomique du ribosome en pleine lumière [The atomic structure of the ribosome into the spotlight]
• Simulations of the molecular dynamics of nucleic acids
• The Endless Subtleties of RNA-Protein Complexes.
• Comparative genomics of emerging pathogens in the Candida glabrata clade.
• Rules governing the orientation of the 2′-hydroxyl group in RNA
• A quantitative RNA code for mRNA target selection by the germline fate determinant GLD-1
• RNA as a Drug Target: The Case of Aminoglycosides
• The RNA ontology (RNAO) : An ontology for integrating RNA sequence and structure data:
• Modelling the three-dimensional structure of ribonucleic acids
• RNA-Puzzles: A CASP-like evaluation of RNA three-dimensional structure prediction.:
• The modular structure of Escherichia coli threonyl-tRNA synthetase as both an enzyme and a regulator of gene expression
• Metal ion binding to RNA
• S2S-Assemble2: a Semi-Automatic Bioinformatics Framework to Study and Model RNA 3D Architectures.:
• RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures.
• Crystal Structure of Geneticin Bound to a Bacterial 16S Ribosomal RNA A Site Oligonucleotide
• Assemble: an interactive graphical tool to analyze and build RNA architectures at the 2D and 3D levels
• RNA-Puzzles toolkit: a computational resource of RNA 3D structure benchmark datasets, structure manipulation, and evaluation tools
• Structural basis for the specificity of the initiation of HIV‐1 reverse transcription
• Transfer RNA structure
• Hydration of transfer RNA molecules: a crystallographic study
• Loop stereochemistry and dynamics in transfer RNA.
• New Structural Insights into Translational Miscoding.
• Translation of non-standard codon nucleotides reveals minimal requirements for codon-anticodon interactions
• Structural insights into the translational infidelity mechanism.
• Hydration of C—H groups in tRNA
• An extended structural signature for the tRNA anticodon loop
• The 9/4 secondary structure of eukaryotic selenocysteine tRNA: More pieces of evidence
• The conformation of the initiator tRNA and of the 16S rRNA from Escherichia coli during the formation of the 30S initiation complex
• RNA hydration: three nanoseconds of multiple molecular dynamics simulations of the solvated tRNAAsp anticodon hairpin11Edited by J. Karn
• Studies on Anticodon-anticodon Interactions: Hemi-protonation of Cytosines Induces Self-pairing Through the GCC Anticodon of E. Coli tRNA-Gly
• Modified nucleotides of tRNAPro restrict interactions in the binary Primer/Template complex of M-MuLV11Edited by J. Karn
• Dimerization confers increased stability to nucleases in 5' halves from glycine and glutamic acid tRNAs
• Mapping post-transcriptional modifications in Staphylococcus aureus tRNAs by nanoLC/MSMS
• High-resolution cryo-electron microscopy structure of the Trypanosoma brucei ribosome.
• In-line alignment and Mg(2+) coordination at the cleavage site of the env22 twister ribozyme.
• RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers
• Comparative patterns of modified nucleotides in individual tRNA species from a mesophilic and two thermophilic archaea
• The multiple flavors of GoU pairs in RNA
• 2,6-Diaminopurine as a highly potent corrector of UGA nonsense mutations
• A new understanding of the decoding principle on the ribosome.
• Ribosomal mistranslation leads to silencing of the unfolded protein response and increased mitochondrial biogenesis
• Unique secondary and tertiary structural features of the eucaryotic selenocysteine tRNASec
• Unusual tertiary pairs in eukaryotic tRNA-Ala
• Using droplet-based microfluidics to improve the catalytic properties of RNA under multiple-turnover conditions.
• Molecular mimicry in translational control of E.coli threonyl-tRNA synthetase gene. Competitive inhibition in tRNA aminoacylation and operator-repressor recognition switch using tRNA identity rules
• Usefulness of functional and structural solution data for the modeling of tRNA-like structures.
• RNA-RNA interaction is required for the formation of specific bicoid mRNA 3' UTR-STAUFEN ribonucleoprotein particles
• Transfer RNA identity rules and conformation of the tyrosine tRNA-like domain of BMV RNA imply additional charging by histidine and valine.
• A structural module in RNase P expands the variety of RNA kinks.
• An integrated, structure- and energy-based view of the genetic code.
• The viral protein NSP1 acts as a ribosome gatekeeper for shutting down host translation and fostering SARS-CoV-2 translation
• Non-canonical substrates of aminoacyl-tRNA synthetases: the tRNA-like structure of brome mosaic virus genomic RNA.
• iSpinach: a fluorogenic RNA aptamer optimized for in vitro applications.
• Recognition of Watson-Crick base pairs: constraints and limits due to geometric selection and tautomerism
• Automated prediction of three-way junction topological families in RNA secondary structures.
• A central pseudoknotted three-way junction imposes tRNA-like mimicry and the orientation of three 5' upstream pseudoknots in the 3' terminus of tobacco mosaic virus RNA.
• Pseudouridines or how to draw on weak energy differences
• Transcriptome-wide identification of A > I RNA editing sites by inosine specific cleavage.
• Sequence-based identification of 3D structural modules in RNA with RMDetect
• Solution structure of the 3'-end of brome mosaic virus genomic RNAs. Conformational mimicry with canonical tRNAs.
• New structural insights into the decoding mechanism: Translation infidelity via a G·U pair with Watson-Crick geometry.
• Crystal Structure of the Bacterial Ribosomal Decoding Site Complexed with a Synthetic Doubly Functionalized Paromomycin Derivative: a New Specific Binding Mode to an A-Minor Motif Enhances in vitro Antibacterial Activity
• The solution structure of the Escherichia coli initiator tRNA and its interactions with initiation factor 2 and the ribosomal 30 S subunit.
• Multiple molecular dynamics simulations of the anticodon loop of tRNA^Asp in aqueous solution with counterions
• Search of essential parameters for the aminoacylation of viral tRNA-like molecules. Comparison with canonical transfer RNAs.
• How to fold and protect mitochondrial ribosomal RNA with fewer guanines
• The nature of the purine at position 34 in tRNAs of 4-codon boxes is correlated with nucleotides at positions 32 and 38 to maintain decoding fidelity
• Solution Conformation of tRNAs: Correlation with Crystal Structures
• Phylogenetic analysis of tmRNA genes within a bacterial subgroup reveals a specific structural signature
• Tautomeric G*U pairs within the molecular ribosomal grip and fidelity of decoding in bacteria
• The ribosome prohibits the G•U wobble geometry at the first position of the codon-anticodon helix.
• Novel base-pairing interactions at the tRNA wobble position crucial for accurate reading of the genetic code.
• Molecular recognition of aminoglycoside antibiotics by ribosomal RNA and resistance enzymes: An analysis of x-ray crystal structures
• Importance of potassium ions for ribosome structure and function revealed by long-wavelength X-ray diffraction
• Twenty years of RNA crystallography.
• Solution structure of a tRNA with a large variable region: Yeast tRNASer
• Genome evolution in yeasts.
• GU Base Pairs and Variable Loop in Yeast tRNAAsp
• Structure function relationship in the tRNAAsp/AspRS system from yeast
• Molecular Dynamics Simulations of Solvated Yeast tRNAAsp
• Dynamics in tRNA - Yeast tRNAPhe and tRNAAsp the models for free and mRNA bound tRNAs
• The tRNAAsp-AspRS system from yeast: Structural and functional studies
• Crystallographic refinement of yeast aspartic acid transfer RNA
• Restrained refinement of two crystalline forms of yeast aspartic acid and phenylalanine transfer RNA crystals
• Pichia sorbitophila, an Interspecies Yeast Hybrid, Reveals Early Steps of Genome Resolution After Polyploidization.
• Crystallography of the tRNAAsp-aspartyl-tRNA synthetase system from yeast
• The structure of yeast tRNAAsp. A model for tRNA interacting with messenger RNA
• Binding of tobramycin leads to conformational changes in yeast tRNA(Asp) and inhibition of aminoacylation.
• The versatile transfer RNA molecule: Crystallography of yeast tRNAAsp
• Structure of Monomeric Yeast and Mammalian Sec61 Complexes Interacting with the Translating Ribosome
• The complete genome of Blastobotrys (Arxula) adeninivorans LS3 - a yeast of biotechnological interest
• Génolevures: protein families and synteny among complete hemiascomycetous yeast proteomes and genomes.
• Yeast tRNAAsp tertiary structure in solution and areas of interaction of the tRNA with aspartyl-tRNA synthetase: A comparative study of the yeast phenylalanine system by phosphate alkylation experiments with ethylnitrosourea
• Molecular dynamics of yeast tRNAAsp
• Crystal structure of yeast tRNAAsp: atomic coordinates
• Anticodon-Anticodon interactions in solution - Studies of the self-association of yeast or E coli tRNA(Asp) and of E coli transfer RNA(Gly).
• Correlation Between Crystal and Solution Structures in tRNA. Yeast tRNAPhe and tRNAAsp the Models for Free and Messenger RNA Bound tRNAs
• Anticodon-anticodon interaction induces conformational changes in tRNA: yeast tRNAAsp, a model for tRNA-mRNA recognition