Biology subjects

Cuevas-Velazquez, C. L.

Publications and source records attributed to Cuevas-Velazquez, C. L..

3 recordsLinked to original sources

bioRxiv2026

A molecular grammar for environmental sensitivity in intrinsically disordered protein regions

Cells must continuously sense and respond to changes in their physicochemical environment, yet the molecular mechanisms underlying this process remain incompletely understood. Intrinsically disordered protein regions (IDRs) constitute a substantial fraction of the eukaryotic proteome and participate in nearly every major cellular process. IDRs exist as dynamic conformational ensembles whose properties are strongly influenced by both amino acid sequence and the physicochemical environment. Although this intrinsic sensitivity has suggested that IDRs may contribute to environmental sensing of the cellular environment, the sequence-encoded principles that enable such sensing remain poorly understood. Here we identify a molecular grammar that captures key sequence features underlying variation in environmental ensemble sensitivity across diverse IDRs. Using 188 IDRs derived from organisms across all kingdoms of life, we systematically quantify changes in ensemble properties in response to hyperosmotic stress in living cells. We show that ensemble sensitivity is significantly associated with specific sequence features and predicted ensemble dimensions, with homogeneous patterning of oppositely charged residues emerging as a strong predictor of high sensitivity in charged IDRs. This sequence organization is necessary for high sensitivity in naturally-occurring IDRs and sufficient to confer high responsiveness in de novo designed low-complexity sequences. We further demonstrate that the presence of additional structured domains within IDR-containing proteins can substantially modulate ensemble sensitivity relative to isolated IDRs, revealing an additional layer of modulation at the multi-domain protein level. Applying the molecular grammar to the with-no-lysine (WNK) kinase crowding-sensing system, we find that regions within the disordered C-terminal domain - the domain necessary for crowding-induced phase separation and cell volume recovery - are predicted as hypersensitive, a property that is conserved across distant WNK homologues despite sequence divergence, and that is shared by heterologous IDRs capable of functionally replacing it. Together, our results establish environmental ensemble sensitivity as a sequence-encoded, context-dependent, and quantitatively tunable property of IDRs, provide a framework for understanding how physicochemical changes can be transduced in cells without dedicated receptor architectures as exemplified by the WNK crowding-sensing system, and offer design principles for engineering synthetic protein-based environmental sensors.

biophysics↗

bioRxiv2025

Functional diversity of Arabidopsis late embryogenesis abundant proteins in response to changes in the physicochemical environment

Some desiccation-tolerant organisms accumulate intrinsically disordered proteins (IDPs), such as Late Embryogenesis Abundant (LEA) proteins, which help protect other proteins from inactivation and/or aggregation during desiccation. Like other IDPs, LEA proteins adopt ensembles of extended conformations that shift in response to environmental changes. Desiccation causes dramatic changes in the cellular environment, but it is unclear how the structural malleability of LEAs is related to their protective function. In this work, we measured the in vitro protective function and structural sensitivity to changes in the environment of four Arabidopsis thaliana LEA proteins from different families. We found that all LEAs showed different protection efficiencies of the labile enzyme lactate dehydrogenase under desiccation in vitro. In line with this, we identified distinct ensemble structural changes when these LEA proteins were exposed to different physicochemical environments. Specifically, AtEM1, AtLEA7, and AtLEA4-5 showed compaction when the solution was crowded with polymers, whereas AtLEA6-2.2 showed larger structural changes when salt concentrations were increased. Furthermore, the ensembles of AtEM1, AtLEA7, and AtLEA4-5 gained helicity under desiccated conditions, while that of AtLEA6-2.2 remained largely disordered. Our results highlight how ensemble properties of LEA proteins contribute to their distinct functional activities in vitro. This work advances our understanding of the molecular features that contribute to functional diversity in desiccation-related IDPs.

biophysics↗

bioRxiv2021

Intrinsically disordered protein biosensor tracks the physical-chemical effects of osmotic stress on cells

Cell homeostasis is perturbed when dramatic shifts in the external environment cause the physical-chemical properties inside the cell to change. Methods that dynamically monitor these intracellular effects are currently lacking. Here, we leveraged the environmental sensitivity and structural plasticity of intrinsically disordered regions (IDRs) to develop a FRET biosensor capable of monitoring rapid intracellular changes caused by osmotic stress. The biosensor, named SED1, utilizes the Arabidopsis intrinsically disordered AtLEA4-5 protein expressed in plants under water deficit. Computational modeling and in vitro studies reveal that SED1 is highly sensitive to macromolecular crowding. SED1 exhibits large and near-linear osmolarity-dependent changes in FRET inside living bacteria, yeast, plant, and human cells, demonstrating the broad utility of this tool for studying water-associated stress. This study demonstrates the remarkable ability of IDRs to sense the cellular environment across the tree of life and provides a blueprint for their use in environmentally-responsive molecular tools.

cell biology↗