The role of water in reactions catalysed by hydrolases under conditions of molecular crowding

The biophysics of water in cell biology: perspectives on a keystone for both marine sciences and cancer research

The biophysics of water, has been debated over more than a century. Although its importance is still underestimated, significant breakthroughs occurred in recent years. The influence of protein condensation on water availability control was documented, new findings on water-transport proteins emerged, and the way water molecules rearrange to minimize free energy at interfaces was deciphered, influencing membrane thermodynamics. The state of knowledge continued to progress in the field of deep-sea marine biology, highlighting unknown effects of high hydrostatic pressure and/or temperature on interactions between proteins and ligands in extreme environments, and membrane structure adaptations. The role of osmolytes in protein stability control under stress is also discussed here in relation to fish egg hydration/buoyancy. The complexity of water movements within the cell is updated, all these findings leading to a better view of their impact on many cellular processes. The way water flow and osmotic gradients generated by ion transport work together to produce the driving force behind cell migration is also relevant to both marine biology and cancer research. Additional common points concern water dynamic changes during the neoplastic transformation of cells and tissues, or embryo development. This could improve imaging techniques, early cancer diagnosis, and understanding of the molecular and physiological basis of buoyancy for many marine species.

Self-Assembling Polypeptides in Complex Coacervation

Intracellular compartmentalization plays a pivotal role in cellular function, with membrane-bound organelles and membrane-less biomolecular "condensates" playing key roles. These condensates, formed through liquid-liquid phase separation (LLPS), enable selective compartmentalization without the barrier of a lipid bilayer, thereby facilitating rapid formation and dissolution in response to stimuli. Intrinsically disordered proteins (IDPs) or proteins with intrinsically disordered regions (IDRs), which are often rich in charged and polar amino acid sequences, scaffold many condensates, often in conjunction with RNA.Comprehending the impact of IDP/IDR sequences on phase separation poses a challenge due to the extensive chemical diversity resulting from the myriad amino acids and post-translational modifications. To tackle this hurdle, one approach has been to investigate LLPS in simplified polypeptide systems, which offer a narrower scope within the chemical space for exploration. This strategy is supported by studies that have demonstrated how IDP function can largely be understood based on general chemical features, such as clusters or patterns of charged amino acids, rather than residue-level effects, and the ways in which these kinds of motifs give rise to an ensemble of conformations.Our laboratory has utilized complex coacervates assembled from oppositely charged polypeptides as a simplified material analogue to the complexity of liquid-liquid phase separated biological condensates. Complex coacervation is an associative LLPS that occurs due to the electrostatic complexation of oppositely charged macro-ions. This process is believed to be driven by the entropic gains resulting from the release of bound counterions and the reorganization of water upon complex formation. Apart from their direct applicability to IDPs, polypeptides also serve as excellent model polymers for investigating molecular interactions due to the wide range of available side-chain functionalities and the capacity to finely regulate their sequence, thus enabling precise control over interactions with guest molecules.Here, we discuss fundamental studies examining how charge patterning, hydrophobicity, chirality, and architecture affect the phase separation of polypeptide-based complex coacervates. These efforts have leveraged a combination of experimental and computational approaches that provide insight into molecular level interactions. We also examine how these parameters affect the ability of complex coacervates to incorporate globular proteins and viruses. These efforts couple directly with our fundamental studies into coacervate formation, as such "guest" molecules should not be considered as experiencing simple encapsulation and are instead active participants in the electrostatic assembly of coacervate materials. Interestingly, we observed trends in the incorporation of proteins and viruses into coacervates formed using different chain length polypeptides that are not well explained by simple electrostatic arguments and may be the result of more complex interactions between globular and polymeric species. Additionally, we describe experimental evidence supporting the potential for complex coacervates to improve the thermal stability of embedded biomolecules, such as viral vaccines.Ultimately, peptide-based coacervates have the potential to help unravel the physics behind biological condensates, while paving the way for innovative methods in compartmentalization, purification, and biomolecule stabilization. These advancements could have implications spanning medicine to biocatalysis.

A life off the beaten track in biomechanics: Imperfect elasticity, cytoskeletal glassiness, and epithelial unjamming

Textbook descriptions of elasticity, viscosity, and viscoelasticity fail to account for certain mechanical behaviors that typify soft living matter. Here, we consider three examples. First, strong empirical evidence suggests that within lung parenchymal tissues, the frictional stresses expressed at the microscale are fundamentally not of viscous origin. Second, the cytoskeleton (CSK) of the airway smooth muscle cell, as well as that of all eukaryotic cells, is more solid-like than fluid-like, yet its elastic modulus is softer than the softest of soft rubbers by a factor of 104-105. Moreover, the eukaryotic CSK expresses power law rheology, innate malleability, and fluidization when sheared. For these reasons, taken together, the CSK of the living eukaryotic cell is reminiscent of the class of materials called soft glasses, thus likening it to inert materials such as clays, pastes slurries, emulsions, and foams. Third, the cellular collective comprising a confluent epithelial layer can become solid-like and jammed, fluid-like and unjammed, or something in between. Esoteric though each may seem, these discoveries are consequential insofar as they impact our understanding of bronchospasm and wound healing as well as cancer cell invasion and embryonic development. Moreover, there are reasons to suspect that certain of these phenomena first arose in the early protist as a result of evolutionary pressures exerted by the primordial microenvironment. We have hypothesized, further, that each then became passed down virtually unchanged to the present day as a conserved core process. These topics are addressed here not only because they are interesting but also because they track the journey of one laboratory along a path less traveled by.