Biology subjects

To, P.

Publications and source records attributed to To, P..

4 recordsLinked to original sources

bioRxiv2026

Locus coeruleus activation transforms cortical taste representations

Norepinephrine neurons in the locus coeruleus (LC) shape sensory responses across the brain, yet how LC activity reorganizes population representations of behaviorally relevant sensory attributes remains unclear. We addressed this question in the primary gustatory cortex (GC), a system largely unexplored in neuromodulation research and well-suited for linking sensory coding to affective value. Using miniscope calcium imaging in awake mice combined with optogenetic LC activation, we tested how phasic and tonic LC activity modulate GC encoding of three taste attributes: palatability, mixture ratio, and intensity. Phasic LC activation enhanced correlations between neuronal responses and tastant palatability and expanded the dynamic range of taste representations along a palatability-relevant axis. This expansion was driven primarily by an aversive shift in the representation of all tastants except sucrose, the most palatable stimulus. For mixture ratio and concentration, LC activation induced both stretching and rotation of attribute axes, potentially reflecting dependencies between these attributes and palatability. Analysis of LC-induced changes in neuronal tuning revealed that these population-level transformations likely arise from a combination of multiplicative gain modulation and flexible, tastant-specific changes in tuning. In contrast, tonic LC activation engaged fewer GC neurons and did not produce stretching along any attribute axis, demonstrating that LC effects on population coding depend on activation pattern. Together, these findings provide causal evidence that phasic LC activation reshapes GC population geometry to preferentially enhance palatability encoding, establishing a framework for understanding how neuromodulation may bias taste representations relevant to feeding behavior.

neuroscience↗

bioRxiv2023

Intrinsically Disordered Regions Promote Protein Refoldability and Facilitate Retrieval from Biomolecular Condensates

Many eukaryotic proteins contain intrinsically disordered regions (IDRs) that intersperse globular folded domains, in contrast with bacterial proteins which are typically highly globular1, 2. Recent years have seen great progress in identifying biological functions associated with these elusive protein sequence: in specific cases, they mediate liquid liquid phase separation3, perform molecular recognition4, or act as sensors to changes in the environment5. Nevertheless, only a small number of IDRs have annotated functions6 despite their presence in 64% of yeast proteins,7 stimulating some to question what general purpose they may serve8, 9. Here, by interrogating the refoldability of two fungal proteomes (Saccharomyces cerevisiae and Neurosporra crassa), we show that IDRs render their host proteins more refoldable from the denatured state, allowing them to cohere more closely to Anfinsens thermodynamic hypothesis10, 11. The data provide an exceptionally clear picture of which biophysical and topological characteristics enable refoldability. Moreover, we find that almost all yeast proteins that partition into stress granules during heat shock are refoldable, a finding that holds for other condensates such as P-bodies and the nucleolus. Finally, we find that the Hsp104 unfoldase12 is the principal actor in mediating disassembly of heat stress granules and that the efficiency with which condensed proteins are returned to the soluble phase is also well explained by refoldability. Hence, these studies establish spontaneous refoldability as an adaptive trait that endows proteins with the capacity to reform their native soluble structures following their extraction from condensates. Altogether, our results provide an intuitive model for the function of IDRs in many multidomain proteins and clarifies their relationship to the phenomenon of biomolecular condensation.

biochemistry↗

bioRxiv2021

Systematic Interrogation of Protein Refolding Under Cellular-Like Conditions

The journey by which proteins navigate their energy landscapes to their native structures is complex, involving (and sometimes requiring) many cellular factors and processes operating in partnership with a given polypeptide chains intrinsic energy landscape. The cytosolic environment and its complement of chaperones play critical roles in granting proteins safe passage to their native states; however, the complexity of this medium has generally precluded biophysical techniques from interrogating protein folding under cellular-like conditions for single proteins, let alone entire proteomes. Here, we develop a limited-proteolysis mass spectrometry approach paired with an isotope-labeling strategy to globally monitor the structures of refolding E. coli proteins in the cytosolic medium and with the chaperones, GroEL/ES (Hsp60) and DnaK/DnaJ/GrpE (Hsp70/40). GroEL can refold the majority (85%) of the E. coli proteins for which we have data, and is particularly important for restoring acidic proteins and proteins with three to five domains, trends that come to light because our assay measures the structural outcome of the refolding process itself, rather than indirect measures like binding or aggregation. For the most part, DnaK and GroEL refold a similar set of proteins, supporting the view that despite their vastly different structures, these two chaperones both unfold misfolded states, as one mechanism in common. Finally, we identify a cohort of proteins that are intransigent to being refolded with either chaperone. The data support a model in which chaperone-nonrefolders have evolved to fold efficiently once and only once, co-translationally, and remain kinetically trapped in their native conformations.

biophysics↗

bioRxiv2020

Non-Refoldability is Pervasive Across the E. coli Proteome

The foundational paradigm of protein folding is that the primary sequence of a protein contains all the information needed for it to adopt a specific native structure1,2. This remarkable property is explained by Anfinsens thermodynamic hypothesis3,4, which asserts that because native states minimize the Gibbs free energy of a protein molecule under physiological conditions, proteins can reliably navigate to their native structures and remain in those states by ergodically sampling their free energy landscapes5. Most experiments of protein folding - conducted on purified, small, single-domain soluble proteins - follow the proportion of protein molecules that are folded as a function of time, temperature, denaturant concentration, or sequence6-8, and have yielded immense insight into the molecular determinants that underpin stable globular folds9,10. However, our reliance on the thermodynamic hypothesis as a ground truth to interpret these experiments has limited our ability to study the folding of complex proteins or to consider alternative non-thermodynamic scenarios11,12. Here, we introduce an experimental approach to probe protein refolding for whole proteomes. We accomplish this by first unfolding and refolding E. coli lysates, and then interrogating the resulting protein structures using a permissive protease that preferentially cleaves at flexible regions. Using mass spectrometry, we analyze the digestion patterns to globally assess structural differences between native and refolded proteins. These studies reveal that following denaturation, many proteins are incapable of navigating back to their native structures. Our results signal a pervasive role for co-translational folding in shaping protein biogenesis, and suggest that the apparent stability of many native states derive from kinetic persistence rather than thermodynamic stability.

biophysics↗