Journal of Molecular Biology最新文献

Allosteric proteins and membrane-less biomolecular condensates are physics-governed pivotal functional components. Allosteric regulation is an inherent physical property of dynamic proteins, and dynamic proteins are allosteric. Thus, in biomolecular condensates (like everywhere else in the cell), allostery is at play, and often missing in condensate descriptions is that the cooperative transitions can involve allosteric effects. The condensate environment can be especially conducive to allostery. Condensed settings can increase the chance of protein interaction and allosteric encounters in function-specific condensates. Specific protein-protein interactions provide the structural framework for signals to transmit cooperatively and dynamically, ultimately modulating cell activity. Their interfaces are commonly enriched in nonpolar (hydrophobic) surface. With abundant functionally specific proteins, and surfaces accommodating multiple hydrophobic patches, interconnected multivalent molecular networks are expected. Lacking hydrophobic cores, disordered proteins' folding-upon-binding scenarios often form strong hydrophobic interfaces, and cooperative (partially disordered) multimers are also common. Repelling water is a major force in condensate formation, albeit not the sole. Here we emphasize dilution as functional and allosteric determinant. Extremely high dilution in rapidly growing proliferating cells can stimulate senescence; lower dilution increases concentration, thus, higher probability of increased proximity and reduced separation, driving protein-protein interactions, and allostery. Is there then effective allostery in condensates? We believe that it depends on the cell state. Under normal physiological conditions, with condensates water content around 40% of total cell mass-yes; over 70% could be too diluted. If too low-it can become function-poor aggregate-like. Effective allostery and signaling require specific interactions, extending from clustered receptors to the cytoskeleton.

Halophilic organisms have adapted to survive in environments with extremely high salinity, such as saline lakes. To achieve this, they modify their proteome to withstand salt concentrations that inactivate non-adapted mesophilic proteins. The surfaces of halophilic proteins feature a very characteristic amino acid composition, favoring short, polar, and acidic amino acids-such as aspartate, glutamate, and threonine-while disfavoring bulky, hydrophobic amino acids-such as lysine, methionine, and leucine. In this work, we review our understanding of the molecular basis of haloadaptation. We critically examine the role of electrostatic interactions in stabilizing halophilic proteins, while underlining the importance of other contributions from hydrophobic solvation and preferential ion exclusion. Finally, we describe the mechanistic link by which the halophilic amino acid composition optimizes function in hypersaline environments, balancing the trade-off between stability, solubility, and catalytic function.

Understanding how proteins have evolved to adapt their stability and function to changing temperatures remains a central question in molecular biology. While structural analyses, site-directed mutagenesis, and directed evolution have yielded valuable insights, ancestral sequence reconstruction (ASR) has recently emerged as a powerful tool for addressing the drivers behind protein evolution. Specifically, by enabling the inference and experimental characterization of reconstructed ancient proteins, ASR provides unique perspectives on the molecular mechanisms underlying both thermostability and low-temperature-adaptation. This review outlines the historical development of research on protein temperature adaptation and highlights the role of ASR in advancing the field. Selected case studies illustrate how ASR has uncovered structural and dynamic features associated with extreme thermostability or enhanced activity at low temperatures. Common sources of uncertainty in ASR and how they can be addressed are also discussed. Finally, the broader potential of ASR is described, both for elucidating early evolutionary processes and for guiding the design of enzymes useful for industrial applications.