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Articles by Nicholas Sofos
Structure of a contractile injection system in Salmonella enterica subsp. salamae
Abstract Extracellular contractile injection systems (eCISs) are phage-derived nanomachines used by bacteria to deliver effectors into target cells. Well-studied examples include the Photorhabdus asymbiotica virulence cassettes and the antifeeding prophage from Serratia entomophila, which have been engineered for heterologous cargo delivery.
RBPseg: Toward a complete phage tail fiber structure atlas
Abstract Bacteriophages use receptor-binding proteins (RBPs) to adhere to bacterial hosts, yet their sequence and structural diversity remain poorly understood. Tail fibers, a major class of RBPs, are elongated and flexible trimeric proteins, making their full-length structures difficult to resolve experimentally. Advances in deep learning–based protein structure prediction, such as AlphaFold2-multimer (AF2M) and ESMFold, provide opportunities for studying these challenging proteins.
Towards a complete phage tail fiber structure atlas.
Abstract Bacteriophages use receptor-binding proteins (RBPs) to adhere to bacterial hosts. Understanding the structure of these RBPs can provide insights into their target interactions. Tail fibers, a prominent type of RBP, are typically elongated, flexible, and trimeric proteins, making it challenging to obtain high-resolution experimental data of their full-length structures.
Conformational landscape of the type V-K CRISPR-associated transposon integration assembly
Highlights • Landscape of assemblies of the V-K CAST post-transposition complex by cryo-EM • The stem loop of the sgRNA is inserted between two hairpin loops of TnsC filament • TnsC hairpin loop and LE and RE TnsB-binding sites mutants enhance activity • The length of the TnsB linker and the TnsC filament affect the PAM-to-att distance Summary CRISPR-associated transposons (CASTs) are mobile genetic elements that co-opt CRISPR-Cas systems for RNA-guided DNA transposition.
Structures of the Cmr-β Complex Reveal the Regulation of the Immunity Mechanism of Type III-B CRISPR-Cas
Highlights • The stalk loop is an allosteric sensor signaling the self- versus non-self-recognition • Dynamics of the stalk loop key in triggering Cmr2 (Cas10)-dependent activities • The HD domain of SisCmr2 cleaves non-complementary UA ssRNA • The Cmr7 subunit modulates the cleavage activities and cOA generation Summary Cmr-β is a type III-B CRISPR-Cas complex that, upon target RNA recognition, unleashes a multifaceted immune response against invading genetic elements, including...
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