Biology subjects

Gomez-Mulas, A.

Publications and source records attributed to Gomez-Mulas, A..

4 recordsLinked to original sources

bioRxiv2026

K-Ras controls asymmetric cell divisions from the primary cilium

The Ras-MAPK pathway drives central cellular processes, including cell proliferation and differentiation. How exactly Ras controls differentiation is however not understood. Supported by mathematical modelling and single-cell RNA sequencing we show that K-Ras4B sustains ciliation during differentiation thus restricting commitment of skeletal muscle stem and progenitor cells during asymmetric cell divisions. Modulation of K-Ras4B abundance or expression of oncogenic K-Ras4B-G12C perturb normal differentiation. K-Ras4B, but not N-Ras and H-Ras, localizes to the primary cilium and its abundance there depends on the ciliary trafficking chaperone PDE6D. The presence of B-Raf and active MEK at the base of and active ERK inside the cilium suggests that K-Ras4B is active there. Conditions that localize a K-Ras4B mutant only to the cilium are sufficient to sustain ciliation and normal differentiation. Finally, in vivo modulation of K-Ras4B activity during zebrafish embryogenesis perturbs ciliation-dependent heart-looping. Our results thus imply a novel fundamental role of K-Ras4B in controlling ciliation and differentiation and suggest an explanation for the phenotypic similarities between RASopathies and ciliopathies.

cell biology↗

bioRxiv2025

Development of a genetically encoded and potent PDE6D inhibitor

PDE6D is a trafficking chaperone of prenylated proteins, such as small GTPases. Several small molecule inhibitors have been developed against it, given that the oncogene K-Ras is one of the cargo proteins. Inhibitor development suffered from the fact that inhibitors against the hydrophobic pocket of PDE6D were typically poorly water-soluble. Here we describe the development of genetically encoded inhibitors that are inspired by high-affinity natural cargo of PDE6D. Our most potent inhibitor, SNAP-STI, encodes merely a farnesylated tetra-peptide, which efficiently blocks PDE6D binding of farnesylated cargo. Direct comparison with small molecule PDE6D inhibitors suggests its higher potency. We show that inhibition of K-Ras membrane anchorage and K-RasG12C-dependent MAPK-signaling by SNAP-STI is weak, consistent with what is observed after PDE6D knockdown. Our data therefore further support that PDE6D is not a suitable surrogate target for efficient inhibition of K-Ras membrane anchorage and MAPK-activity. Nonetheless, by exploiting contacts at the pocket entry, we established a generalizable strategy to design high-affinity PDE6D inhibitors, providing powerful tools for PDE6D biology and target validation.

biochemistry↗

bioRxiv2024

The lack of trade-off between conformational stability and binding affinity in a nanobody with therapeutic potential for a misfolding disease

To improve protein pharmaceuticals, we need to balance protein stability and binding affinity with in vivo efficiency. We have recently developed a nanobody (NB-AGT-2) against the alanine:glyoxylate aminotransferase with high stability (Tm[~]85{degrees}C) that may be useful to treat a misfolding disease called primary hyperoxaluria type 1. In this work, we characterize the relationships between protein stability and binding affinity in NB-AGT-2 by generating single and double cavity-creating mutants in its hydrophobic core. These mutations decrease thermal stability by 10-20 {degrees}C, reflecting changes in thermodynamic stability of up to 8 kcal{middle dot}mol-1, hardly affecting their binding affinity for its target. Our results thus show that NB stability can be challenged without an effect on its binding.

biophysics↗

bioRxiv2024

Thermodynamic versus kinetic basis for the high conformational stability of nanobodies for therapeutic applications

Single domain nanobodies (NB) are powerful tools for biotechnological and therapeutic applications. They strongly bind to their targets and are very stable. Early studies showed that NB unfolding is reversible and can be analyzed by equilibrium thermodynamics whereas more recent studies focused on their kinetic stability in very harsh conditions, far from storage or physiological temperatures (4-37{degrees}C). Here we reinforce the thermodynamic view in which a simple two-state denaturation model is applicable. We found that thermal stability of NB actually reflect thermodynamic stabilities in wide range of temperatures (18-100{degrees}C). We also modeled their structure observing subtle differences. We expect that our approach will be helpful to improve our capacity to enhance structure-function-stability relationships of NB.

biophysics↗