Biology subjects

Uday, A. B.

Publications and source records attributed to Uday, A. B..

5 recordsLinked to original sources

bioRxiv2026

Structural tuning of native type V fimbriae shapes mechanical specialization in Porphyromonas gingivalis

Fimbriae are proteinaceous filaments central to bacterial adhesion, colonization, and biofilm formation. Porphyromonas gingivalis, a keystone periodontal pathogen, utilizes two type V fimbriae systems, the major Fim and the minor Mfa fimbriae, that support distinct adhesive and biofilm-associated functions. Here, we determine the high-resolution cryo-electron microscopy structures of natively assembled FimA and Mfa1 stalks purified directly from P. gingivalis. Despite a shared donor-strand exchange mechanism, the two stalks exhibit distinct helical geometries and donor-strand environments. FimA has a larger helical pitch, whereas the Mfa1 donor strand is more extensively buried and further shielded by an ordered N-terminal latch. Comparison with monomeric stalk pilin structures reveals distinct assembly-associated remodeling around the donor-strand interface. Deletion of the Mfa1 latch reduces heat-resistant oligomer accumulation and produces species consistent with incomplete processing, yet recovered filaments retain the donor-strand-exchanged stalk architecture and exhibit initial force peaks comparable to native Mfa1 during simulated axial extension. Atomic force microscopy reveals greater apparent local stiffness of FimA under indentation, whereas steered molecular dynamics simulations show multiple lower-force axial transitions in FimA but a dominant higher-force transition in Mfa1. In both systems, the exchanged donor strands remain engaged during simulated extension while distinct surrounding contact networks rearrange. Together, these findings demonstrate how a conserved polymerization linkage can support structurally and mechanically distinct adhesive filaments, providing a molecular basis for mechanical diversification of type V fimbriae.

molecular biology↗

bioRxiv2026

Structural basis of substrate recognition for proteasome degradation by prokaryotic ubiquitin-like protein ligase PafA

Selective protein degradation in some bacteria is performed by the Pup-proteasome system, in which the ligase PafA tags hundreds of substrates for proteasomal degradation. How a single enzyme achieves such broad substrate specificity in the absence of conserved sequence motifs has remained unclear. Here we determine structures of PafA in complex with a pupylated substrate and show that substrate recognition is mediated by a minimal and highly distributed interface. PafA samples an ensemble of closely related conformations that collectively position the target lysine residue for modification. This recognition mechanism arises from a combination of structured contacts and dynamic elements on both the enzyme and substrate, enabling geometric compatibility rather than sequence-specific interactions. These findings reveal an ensemble-driven mechanism of molecular recognition that explains how broad substrate specificity is achieved and provides a framework for understanding selective protein degradation in prokaryotes.

biochemistry↗

bioRxiv2024

Mechanism of allosteric activation in human mitochondrial ClpP protease

Human ClpP protease contributes to mitochondrial protein quality control by degrading misfolded proteins. ClpP is overexpressed in cancers such as acute myeloid leukemia (AML), where its inhibition leads to the accumulation of damaged respiratory chain subunits and cell death. Conversely, hyperactivating ClpP with small-molecule activators, such as the recently-discovered ONC201, disrupts mitochondrial protein degradation and impairs respiration in cancer cells. Despite its critical role in human health, the mechanism underlying the structural and functional properties of human ClpP remain elusive. Notably, human ClpP is paradoxically activated by active-site inhibitors. All available structures of human ClpP published to date are in the inactive compact or compressed states, surprisingly even when ClpP is bound to an activator molecule such as ONC201. Here, we present the first structures of human mitochondrial ClpP in the active extended state, including a pair of structures where ClpP is bound to an active-site inhibitor. We demonstrate that amino acid substitutions in the handle region (A192E and E196R) recreate a conserved salt bridge found in bacterial ClpP, stabilizing the extended active state and significantly enhancing ClpP activity. We elucidate the ClpP activation mechanism, highlighting a hormetic effect where sub-stoichiometric inhibitor binding triggers an allosteric transition that drives ClpP into its active extended state. Our findings link the conformational dynamics of ClpP to its catalytic function and provide high-resolution structures for the rational design of potent and specific ClpP inhibitors, with implications for targeting AML and other disorders with ClpP involvement. Significance statementHuman ClpP protease is essential for maintaining mitochondrial protein quality by degrading damaged proteins. In cancers like acute myeloid leukemia (AML), ClpP is overexpressed, and inhibiting it causes cancer cell death by disrupting mitochondrial function. Conversely, activating ClpP with small molecules, such as ONC201, also leads to cancer cell death by impairing mitochondrial respiration. However, the structural details of ClpP activation have been elusive. Our research presents the first structures of human ClpP in its active state, revealing a novel activation mechanism where inhibitors unexpectedly trigger activity through allosteric changes. These insights provide a foundation for designing targeted therapies for AML and other diseases where ClpP plays a crucial role.

biochemistry↗

bioRxiv2024

Structural basis for allosteric regulation of the proteasome core particle

Intracellular protein degradation is vital across all domains of life1. In eukaryotes, the ubiquitin proteasome system performs most non-lysosomal protein degradation and influences numerous cellular processes. Some bacteria, including the human pathogen Mycobacterium tuberculosis (Mtb), encode a proteasome system that selectively degrades damaged or misfolded proteins crucial for the pathogens survival within host macrophages2-7. Consequently, the 20S core particle (CP), the central component of the proteasome system, has emerged as a viable target for tuberculosis treatment strategies2,8-10. Both eukaryotic and Mtb proteasome systems are allosterically regulated11-13, yet the specific conformations involved have not been captured in high-resolution structures to date. Here we present the first structure of Mtb 20S CP, and indeed any 20S CP, in an inactive state called 20SOFF, distinguished from the canonical active state, 20SON, by the conformation of switch helices I and II. The rearrangement of these helices collapses the S1 pocket, effectively inhibiting substrate binding. The switch helices are conserved and regulate the activity of HslV protease, the proteasomes ancestral enzyme in bacteria, and a diverse family of serine/threonine protein phosphatases. Our results highlight the potential of harnessing allostery to develop therapeutics against the 20S CP in Mtb and eukaryotic systems.

biochemistry↗

bioRxiv2023

Atomic structure of wheat ribosome reveals unique features of the plant ribosomes

Ribosomes from plants have unique plant-specific features that may aid in rapid gene expression and regulation in response to changing environmental conditions due to their sessile nature. Here, we present high-resolution cryo-electron microscopy structures of the 60S and 80S ribosomes from wheat, a monocot staple crop plant (Triticum aestivum). We compare wheat ribosome with closely related ribosomes from a dicot plant and other eukaryotes from yeast to humans. While plant ribosomes have unique plant-specific rRNA modification (Cm1847) in peptide exit tunnel, Zinc-finger motif in eL34 is absent and uL4 is extended making an exclusive interaction network. We note striking differences in eL15-Helix 11 (25S) interaction network, eL6-Expansion segment 7 assembly and certain rRNA chemical modifications between monocot and dicot ribosomes. Among eukaryotic ribosomes, we observe that rRNA modification (Gm75) in 5.8S rRNA is highly conserved and a base flipping (G1506) in peptide exit tunnel, and these features are likely involved in sensing nascent peptide. Finally, we discuss importance of universal conservation of three consecutive rRNA modifications in all ribosomes for their interaction with A-site aminoacyl-tRNA.

plant biology↗