Biology subjects

Diercks, T.

Publications and source records attributed to Diercks, T..

5 recordsLinked to original sources

bioRxiv2026

Native virion structure reveals stochastic genome assortment underlying dose-dependent Orsay virus infection

Orsay virus (OrV), infecting Caenorhabditis elegans, is a valuable model for studying host-virus interactions, yet its bipartite RNA genome packaging and assembly mechanisms remain unclear. To investigate these mechanisms, we combine infection assays, single-molecule imaging, and cryo-electron microscopy. We find that the two RNA segments accumulate asymmetrically, and that productive infection depends on coinfection by multiple particles. We therefore asked whether unequal segment availability generates heterogeneous virions. Cryo-EM analysis of OrV, including symmetric and asymmetric reconstructions to 2.5 [A] resolution, unveils uniform internal density, excluding large populations of empty or semi-empty particles. We show the genome forms a semi-ordered network contacting the electropositive capsid interior through sequence-independent interactions with the N-terminus and penton region. We also resolve the capsid-8 linker, identifying the penton as a likely site coordinating capsid assembly. Together, we propose a model in which stochastic genome assortment emerges during assembly modulated by segment-specific replication dynamics.

microbiology↗

bioRxiv2023

Probing Altered Receptor Specificities of Antigenically Drifting Human H3N2 Viruses by Chemoenzymatic Synthesis, NMR and Modeling

Prototypic receptors for human influenza viruses are cell surface N-glycans carrying 2,6-linked sialosides. Under immune pressure, A/H3N2 influenza viruses have emerged with altered receptor specificities that appear to recognize 2,6-linked sialosides presented on extended N-acetyl-lactosamine (LacNAc) moieties. Here, molecular recognition features of such drifted hemagglutinins (HAs) are examined by chemoenzymatic synthesis of complex N-glycans having 13C-labeled monosaccharides at strategic positions. The labeled glycans were employed in 2D STD-1H and 13C-HSQC NMR experiments to pinpoint which monosaccharides of the extended LacNAc chain engage with evolutionarily distinct HAs. The NMR data in combination with computational and mutagenesis studies demonstrate that mutations distal to the receptor binding domain of recent HAs have created an extended binding site that can directly interact with the extended LacNAc chain. A fluorine containing sialyl-LacNAc derivative is used as NMR probe to derive relative binding affinities and confirmed the contribution of the extended LacNAc chain for binding.

biochemistry↗

bioRxiv2022

A glutamine-based single α-helix scaffold to target globular proteins

The binding of intrinsically disordered proteins to globular ones often requires the folding of motifs into [a]-helices. These interactions offer opportunities for therapeutic intervention but their modulation with small molecules is challenging because they bury large surfaces. Linear peptides that display the residues that are key for binding can be targeted to globular proteins when they form stable helices, which in most cases requires their chemical modification. Here we present rules to design peptides that fold into single [a]-helices by instead concatenating glutamine side chain to main chain hydrogen bonds recently discovered in polyglutamine helices. The resulting peptides are uncharged, contain only natural amino acids, and their sequences can be optimized to interact with specific targets. Our results provide design rules to obtain single [a]-helices for a wide range of applications in protein engineering and drug design.

biophysics↗

bioRxiv2020

A conserved rRNA switch is central to decoding site maturation on the small ribosomal subunit

While a structural description of the molecular mechanisms guiding ribosome assembly in eukaryotic systems is emerging, bacteria employ an unrelated core set of assembly factors for which high-resolution structural information is still missing. To address this, we used single-particle cryo-EM to visualize the effects of bacterial ribosome assembly factors RimP, RbfA, RsmA, and RsgA on the conformational landscape of the 30S ribosomal subunit and obtained eight snapshots representing late steps in the folding of the decoding center. Analysis of these structures identifies a conserved secondary structure switch in the 16S rRNA central to decoding site maturation, and suggests both a sequential order of action and molecular mechanisms for the assembly factors in coordinating and controlling this switch. Structural and mechanistic parallels between bacterial and eukaryotic systems indicate common folding features inherent to all ribosomes.

microbiology↗

bioRxiv2018

Side chain to main chain hydrogen bonds stabilize polyglutamine helices in transcription factors

Polyglutamine (polyQ) tracts are regions of low sequence complexity of variable length found in more than one hundred human proteins. These tracts are frequent in activation domains of transcription factors and their length often correlates with transcriptional activity. In addition, in nine proteins, tract elongation beyond specific thresholds causes polyQ disorders. To study the structural basis of the association between tract length, transcriptional activity and disease, here we addressed how the conformation of the polyQ tract of the androgen receptor (AR), a transcription factor associated with the polyQ disease spinobulbar muscular atrophy (SBMA), depends on its length. We found that the tract folds into a helical structure stabilized by unconventional hydrogen bonds between glutamine side chains and main chain carbonyl groups. These bonds are bifurcate with the conventional main chain to main chain hydrogen bonds stabilizing -helices. In addition, since tract elongation provides additional interactions, the helicity of the polyQ tract directly correlates with its length. These findings suggest a plausible rationale for the association between polyQ tract length and AR transcriptional activity and have implications for establishing the mechanistic basis of SBMA.

biophysics↗