Biology subjects

Kumariya, R.

Publications and source records attributed to Kumariya, R..

3 recordsLinked to original sources

bioRxiv2026

More insights into the dynamic assembly and rotation of the archaellum motor machinery

Archaea use the archaellum for swimming motility. Rotation of the archaellum is driven by the ATPase ArlI and the membrane platform protein ArlJ. Structural studies suggest that conformational changes in ArlI power the rotation of ArlJ. However, how ATP hydrolysis is converted into rotation remains poorly under-stood. Using single-molecule total internal reflection fluorescence (TIRF) microscopy, we show that dimeric ArlJ forms a complex with ArlI. Combining conservation analysis, AlphaFold3 predictions and co-purifications, we identified conserved ArlJ residues required for interaction with ArlI, including a structural-ly rigid loop and the critical residue R341 at the ArlI interface. Motility assays in Haloferax volcanii confirmed these findings. Together, these findings support a model in which a dimeric ArlJ is interacting with ArlI via conserved residues to generate torque.

microbiology↗

bioRxiv2025

Evaluation of Alphafold modeling for elucidation of nanobody-peptide epitope interactions

Models of Ab-antigen complexes can be used to understand interaction mechanisms and for improving affinity. This study evaluates the use of the protein structure prediction algorithm AlphaFold (AF) for exploration of interactions between peptide epitope tags and the smallest functional antibody fragments, nanobodies (Nbs). Although past studies of AF for modeling antibody-target (antigen) interactions suggested modest algorithm performance, those were primarily focused on Ab-protein interactions, while the performance and utility of AF for Nb-peptide interactions, which are generally less complex due to smaller antigens, smaller binding domains, and fewer chains, is less clear. In this study we evaluated the performance of AF for predicting the structures of Nbs bound to experimentally validated, linear, short peptide epitopes (Nb-tag pairs). We expanded the pool of experimental data available for comparison through crystallization and structural determination of a previously reported Nb-tag complex (Nb127). Models of Nb-tag pair structures generated from AF were variable with respect to consistency with experimental data, with good performance in just over half (4 out of 6) of cases. Even among Nb-tag pairs successfully modeled in isolation, efforts to translate modeling to more complex contexts failed, suggesting an underappreciated role of the size and complexity of inputs in AF modeling success. Finally, the model of a Nb-tag pair with minimal previous characterization was used to guide the design of a peptide-electrophile conjugate that undergoes covalent crosslinking with Nb upon binding. These findings highlight the utility of minimized antibody and antigen structures to maximize insights from AF modeling.

biochemistry↗

bioRxiv2021

Autophosphorylation of the KaiC-like protein ArlH inhibits oligomerisation and interaction with ArlI, the motor ATPase of the archaellum

Motile archaea are propelled by the archaellum, whose motor complex consists of the membrane protein ArlJ, the ATPase ArlI, and the ATP-binding protein ArlH. Despite its essential function and the existence of structural and biochemical data on ArlH, the role of ArlH in archaellum assembly and function remains elusive. ArlH is a structural homolog of KaiC, the central component of the cyanobacterial circadian clock. Similar to KaiC, ArlH exhibits autophosphorylation activity, which was observed for both ArlH of the euryarchaeon Pyrococcus furiosus (PfArlH) and the crenarchaeon Sulfolobus acidocaldarius (SaArlH). Using a combination of single molecule fluorescence measurements and biochemical assays, it is shown that autophosphorylation of ArlH is closely linked to the oligomeric state of ArlH bound to ArlI. These experiments also strongly suggest that ArlH is a hexamer in its functional ArlI bound state. Mutagenesis of the putative catalytic residue Glu-57 in SaArlH results in a reduced autophosphorylation activity and abolished archaellation and motility, suggesting that optimum phosphorylation activity of ArlH is essential for both archaellation and motility.

microbiology↗