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Ploskon, E.

Publications and source records attributed to Ploskon, E..

3 recordsLinked to original sources

Structural and functional examination of Neisseria gonorrhoeae TfpC reveals a dynamic two-domain architecture required for type IV pilus function

The Neisseria gonorrhoeae (Gc) Type IV pilus (T4p) is a critical apparatus for colonization and virulence. This molecular machine resides at the host-pathogen interface and mediates adherence to host cells, twitching motility, natural transformation, and resistance to oxidative agents. Previously, we identified a DUF4124 family, T4p component, TfpC. TfpC is required for full T4p elaboration, and deleting the tfpC gene reduced natural transformation competence and resulted in an under-piliated colony morphology. Our earlier models suggested TfpC is composed of an N-terminal transmembrane helix and a proline-rich disordered region followed by a C-terminal coiled-coil. Here, we used targeted structural and genetic approaches to define TfpC's molecular structure. Our new data show that TfpC's N-terminal domain forms a novel, dynamic three-stranded {beta}-sheet structure. These data indicate that the flexible disordered region acts as a linker between the N- and C-terminal domains. Functionally, we illustrate TfpC requires an acidic face within the C-terminal coiled-coil domain to mediate pilus biogenesis and function. This study characterizes a unique protein fold and family and defines the contributions of TfpC's domains to its function.

microbiology↗

The NMR Exchange Format (NEF): Specification and Applications

The NMR Exchange Format (NEF) is a community-driven standard for representing NMR experimental data in a consistent, interoperable, and machine-readable form. Built on the STAR syntax, NEF provides a structured framework for storing and exchanging chemical shifts, peak lists, various types of structural restraints, and related metadata, thus allowing for data exchange across software platforms. By enabling direct, lossless transfer of information, NEF simplifies multi-software workflows, improves reproducibility, and supports FAIR (Findable, Accessible, Interoperable, Reusable) data principles. We describe the NEF specification, its current implementation across commonly used NMR software packages, and its application in areas including biomolecular structure determination, metabolomics, and ligand screening. Testing demonstrates that NEF can be used to exchange complete datasets between programs without loss of information or functionality. We also outline recent developments and future directions, such as inclusion of NMR relaxation data and support for non-standard residue topologies. NEFs growing adoption highlights its potential as a unifying standard for NMR data, enabling more efficient, transparent and collaborative research.

biochemistry↗

Restraint Validation of Biomolecular Structures Determined by NMR in the Protein Data Bank

Biomolecular structure analysis from experimental NMR studies generally relies on restraints derived from a combination of experimental and knowledge-based data. A challenge for the structural biology community has been a lack of standards for representing these restraints, preventing the establishment of uniform methods of model-vs-data structure validation against restraints and limiting interoperability between restraint-based structure modeling programs. The NMR exchange (NEF) and NMR-STAR formats provide a standardized approach for representing commonly used NMR restraints. Using these restraint formats, a standardized validation system for assessing structural models of biopolymers against restraints has been developed and implemented in the wwPDB OneDep data deposition-validation-biocuration system. The resulting wwPDB Restraint Violation Report provides a model vs. data assessment of biomolecule structures determined using distance and dihedral restraints, with extensions to other restraint types currently being implemented. These tools are useful for assessing NMR models, as well as for assessing biomolecular structure predictions based on distance restraints. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=100 SRC="FIGDIR/small/575520v2_ufig1.gif" ALT="Figure 1"> View larger version (20K): org.highwire.dtl.DTLVardef@bac5eforg.highwire.dtl.DTLVardef@190cdborg.highwire.dtl.DTLVardef@9b3d83org.highwire.dtl.DTLVardef@1e38ccc_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIPDB Structure Validation Report expanded to include Restraint Analysis C_LIO_LINMR Exchange Format (NEF) and NMR-STAR for distance restraint representation C_LIO_LIStandard distance and dihedral restraint formats for model vs. restraint assessment C_LIO_LIStandardized restraint formats provide interoperability between modeling programs C_LI

bioinformatics↗