Biology subjects

Girodat, D.

Publications and source records attributed to Girodat, D..

4 recordsLinked to original sources

bioRxiv2026

Phosphorylation of the Kv7.4 B helix reorganizes calmodulin interactions and reduces PIP2 binding

Voltage-gated Kv7 (KCNQ, M-type) potassium channels regulate cellular excitability through interactions with phosphatidylinositol 4,5-bisphosphate (PIP2;) and calmodulin (CaM). The distal B helix of Kv7.2-5 channels contains a conserved protein kinase C (PKC) phosphorylation site, suggesting that phosphorylation may regulate channel activity by altering CaM- and PIP2;-dependent mechanisms. Here, we investigated the effects of phosphorylation of Thr552 within the Kv7.4 B helix using electrophysiology, biophysical assays, NMR spectroscopy, and molecular dynamics simulations. Phosphomimetic substitution of Thr552 produced a loss-of-function phenotype characterized by reduced current density and a depolarizing shift in voltage-dependent activation without altering channel surface expression. Biophysical studies demonstrated that phosphorylation produced only modest effects on overall CaM association. However, NMR spectroscopy revealed phosphorylation-dependent changes in apoCaM interactions, and molecular dynamics simulations identified remodeling of the local interaction network surrounding the distal B-helix polybasic (KRK motif) region. In contrast, phosphorylation markedly reduced PIP2; binding to both the isolated B helix and CaM-associated Kv7.4 regulatory complexes. Mutation of the distal B-helix KRK motif similarly impaired PIP2; binding, identifying this region as an important determinant of lipid recognition. Together, these findings support a model in which phosphorylation of Thr552 suppresses Kv7.4 activity primarily by reducing PIP2; interactions while reorganizing, rather than disrupting, CaM binding. These results identify Thr552 as a critical regulatory site linking phosphorylation-dependent signaling to Kv7.4 channel gating.

biochemistry↗

bioRxiv2025

Human Protein Synthesis Requires aminoacyl-tRNA Pivoting During Proofreading

Rigorous studies have characterized the aa-tRNA selection mechanism in bacteria, which is essential for maintaining translational fidelity. Recent investigations have identified critical distinctions in humans, such as the requirement of subunit rolling and a tenfold slower proofreading step. Although these studies captured key intermediates involved in tRNA selection, they did not elucidate the transitions of aa-tRNA between intermediates. Here, we simulated 1,856 aa-tRNA accommodation events into the human ribosomal A site, revealing the requirement of a distinct [~]30{degrees} pivoting of aa-tRNA about the anticodon stem within the accommodation corridor. This pivoting is crucial for navigating the crowded accommodation corridor, which becomes more constrained due to subunit rolling. Subunit rolling-dependent crowding increases the steric contributions of the accommodation corridor during aa-tRNA accommodation, consistent with the 10-fold reduction in the rate of proofreading. The pivoting of the aa-tRNA enables precise alignment within the accommodation corridor, allowing it to traverse the narrower passage. Furthermore, we found that domain III of eEF1A interacts with the accommodating aa-tRNA through conserved basic residues, providing a steric block to prevent dissociation from the A site. Together, these findings provide a structural framework for understanding the distinctions between bacterial and human aa-tRNA selection and demonstrate that the alignment of the aa-tRNA relative to the ribosomal catalytic sites is a critical determinant of translational fidelity.

biophysics↗

bioRxiv2024

Alternate conformational trajectories in protein synthesis

Translocation in protein synthesis entails the efficient and accurate movement of the mRNA-[tRNA]2 substrate through the ribosome after peptide bond formation. An essential conformational change during this process is the swiveling of the small subunit head domain about two rRNA hinge elements. Using directed evolution and molecular dynamics simulations, we derive alternate hinge elements capable of translocation in vitro and in vivo and describe their effects on the conformational trajectory of the EF-G-bound, translocating ribosome. In these alternate conformational pathways, we observe a diversity of swivel kinetics, hinge motions, three-dimensional head domain trajectories and tRNA dynamics. By finding alternate conformational pathways of translocation, we identify motions and intermediates that are essential or malleable in this process. These findings highlight the plasticity of protein synthesis and provide a more thorough understanding of the available sequence and conformational landscape of a central biological process. Author SummaryTranslocation, the motion of the ribosome across its mRNA substrate, is an essential stage of protein synthesis. A key conformational change in this process is the rotation of the ribosome head domain about two rRNA hinges in the direction of translocation, repositioning the mRNA and tRNAs in their final states. Employing directed evolution, we obtain variant hinges capable of performing translocation in vitro and in vivo. Through molecular dynamics simulations, the different variant ribosome translocation conformational trajectories are described. This description reveals different possible conformational pathways to translocation, with varying dynamics, motions and intermediates. The understanding of this conformational malleability can increase our knowledge of protein synthesis function, disruption, evolution, and engineering.

synthetic biology↗

bioRxiv2019

Loss of macp{Psi} ribosomal RNA modification is a major feature of cancer

The ribosome is an RNA-protein complex essential for translation in all domains of life. The structural and catalytic core of the ribosome is its ribosomal RNA (rRNA). While mutations in ribosomal protein (RP) genes are known drivers of oncogenesis, oncogenic rRNA variants have remained elusive. We discovered a cancer-specific single nucleotide variation in 18S rRNA at nucleotide 1248.U in up to 45.9% of colorectal carcinoma (CRC) patients and present across >22 cancer types. This is the site of a unique hyper-modified base, 1-methyl-3--amino--carboxyl-propyl pseudouridine (m1acp3{Psi}), a >1 billion years conserved RNA modification at the ribosomes peptidyl decoding-site. A sub-set of CRC tumors we term hypo-m1acp3{Psi}, show sub-stoichiometric m1acp3{Psi}-modification unlike normal control tissues. A m1acp3{Psi} knockout model and hypo-m1acp3{Psi} patient tumors share a translational signature, characterized by highly abundant ribosomal proteins. Thus, m1acp3{Psi}-deficient rRNA forms an uncharacterized class of onco-ribosome which may serve as a chemotherapeutic target for treating cancer patients.

cancer biology↗