Biology subjects

Rich-New, S. T.

Publications and source records attributed to Rich-New, S. T..

3 recordsLinked to original sources

bioRxiv2024

Structural diversity and clustering of bacterial flagellar outer domains

Supercoiled flagellar filaments function as mechanical propellers within the bacterial flagellum complex, playing a crucial role in motility. Flagellin, the building block of the filament, features a conserved inner D0/D1 core domain across different bacterial species. In contrast, approximately half of the flagellins possess additional, highly divergent outer domain(s), suggesting varied functional potential. In this study, we elucidate atomic structures of flagellar filaments from three distinct bacterial species: Cupriavidus gilardii, Stenotrophomonas maltophilia, and Geovibrio thiophilus. Our findings reveal that the flagella from the facultative anaerobic G. thiophilus possesses a significantly more negatively charged surface, potentially enabling adhesion to positively charged minerals. Furthermore, we analyzed all AlphaFold predicted structures for annotated bacterial flagellins, categorizing the flagellin outer domains into 682 structural clusters. This classification provides insights into the prevalence and experimental verification of these outer domains. Remarkably, two of the flagellar structures reported herein belong to a previously unexplored cluster, indicating new opportunities on the study of the functional diversity of flagellar outer domains. Our findings underscore the complexity of bacterial flagellins and open up possibilities for future studies into their varied roles beyond motility.

microbiology↗

bioRxiv2023

Protein-Ligand Binding Site Prediction and de Novo Ligand Generation from Cryo-EM Maps

Identification of protein-ligand binding sites is one of the most challenging tasks in drug discovery and design. Recent advances in machine learning community, particularly deep learning, inspired considerable research into deep learning-based methods for protein ligand binding site prediction (PLBP) and have achieved promising results. However one limitation of these methods and models is that they are developed and evaluated using conventional databases consisting of relatively small protein structures determined from X-ray crystallography and NMR with high resolution. When current PLBP methods are directly applied to large protein complexes, they either fail or produce very poor results. Given the increasing popularity of protein structures determined from Cryo-EM maps, which usually capture large protein complexes at relatively low resolution, there is a strong need to apply PLBP methods to Cryo-EM maps. For this purpose, we created a novel database (EMD-Ligand Dataset) consisting of Cryo-EM maps and information about their ligand-binding partners. Our study of several state-of-the-art PLBP methods show that even though they perform reasonably well on conventional databases, they do poorly on the novel EMD-Ligand Dataset, which calls for more research and work to be done by the community. As current methods for determining protein structures experimentally from Cryo-EM maps are time-consuming and expensive, we integrated PLBP methods with DeepTracer, an automatic and fast, de novo Cryo-EM protein structure modeling method, and established an end-to-end system capable of predicting ligand binding sites directly from Cryo-EM maps. Additionally, we leveraged an existing ligand generator to generate drug-like ligands from our predicted ligand-binding pockets and demonstrated its effectiveness.

bioinformatics↗

bioRxiv2023

Two dramatically distinct archaeal type IV pili structures formed by the same pilin

Type IV pili (T4P) represent one of the most common varieties of surface appendages in archaea. These filaments, assembled from relatively small pilin proteins, can be many microns long and serve diverse functions, including adhesion, biofilm formation, motility, and intercellular communication. Using cryo-electron microscopy (cryo-EM), we determined atomic structures of two dramatically different T4P from Saccharolobus islandicus REY15A. Unexpectedly, both pili were assembled from the same pilin protein but under different growth conditions. One filament, denoted mono-pilus, conforms to canonical archaeal T4P structures where all subunits are equivalent, whereas in the other filament, the tri-pilus, the same protein exists in three different conformations. The three conformations involve different orientations of the outer immunoglobulin (Ig)-like domains, mediated by a very flexible linker, and all three of these conformations are very different from the single conformation found in the mono-pilus. Remarkably, the outer domains rotate nearly 180{degrees} between the mono- and tri-pilus conformations, formally similar to what has been shown for outer domains in bacterial flagellar filaments, despite lack of homology between bacterial flagella and archaeal T4P. Interestingly, both forms of pili require the same ATPase and TadC-like membrane pore for assembly, indicating that the same secretion system can produce structurally very different filaments. However, the expression of the ATPase and TadC genes was significantly different under the conditions yielding mono- and tri-pili. While archaeal T4P are homologs of archaeal flagellar filaments, our results show that in contrast to the rigid supercoil that the flagellar filaments must adopt to serve as helical propellers, archaeal T4P are likely to have fewer constraints on their structure and enjoy more internal degrees of freedom.

microbiology↗