The mechanism of protein stabilization by zwitterionic osmolytes has remained a long-standing puzzle. While osmolytes are prevalently hypothesized to stabilize proteins by preferentially excluding themselves from the protein surface, emerging experimental and theoretical lines of evidence of preferential binding of the popular osmolyte trimethyl amine N-oxide (TMAO) to some protein surfaces are contradicting this view. Here, we address these contrasting perspectives by investigating the folding mechanism of a set of mini proteins in aqueous solutions of two different osmolytes glycine and TMAO via free energy simulations. Our results demonstrate that, while both osmolytes are found to stabilize the folded conformation of the mini proteins, their mechanisms of action can be mutually opposite: Specifically, glycine always depletes from the surface of all mini proteins, thereby conforming to the osmophobic model, but TMAO is found to display ambivalent signatures of protein-specific preferential binding to and exclusion from the protein surface. At the molecular level, the presence of an extended hydrophobic patch in protein topology is found to be a recurrent motif in proteins leading to favorable binding with TMAO. Finally, an analysis combining the preferential interaction theory and folding free energetics reveals that irrespective of preferential binding vs exclusion of osmolytes, it is the relative preferential depletion of osmolytes on transition from folded to unfolded conformations of proteins, which drives the overall conformational equilibrium toward the folded state in the presence of osmolytes. Taken together, moving beyond the model system and hypothesis, this work brings out contrasting mechanisms of stabilizing osmolytes on proteins and provides a unifying justification.

In the recent surge of investigations on osmolyte-induced conformational landscape of hydrophobic macromolecules notwithstanding, there is a lack of understanding of how the presence of Coulombic charges in the macromolecule dictates its own conformational preference in aqueous media of osmolyte. Toward this end, in this work, we have computationally simulated the trimethyl amine N-oxide (TMAO)-induced collapse behavior of a charge-neutral polymer by varying the number of oppositely charged monomeric beads of a given charge density. From our free-energy-based analysis, at low charge density, there emerges a nonmonotonic trend in the extent of osmolyte-induced protection of collapsed conformation of the charge-neutral polymer as a function of the number of periodically distributed charged monomers: specifically, we observe that, at low charge density, with incremental introduction of oppositely charged monomers in the charge-neutral polymer, the process of osmolyte-induced polymer collapse first gets free-energetically destabilized relative to that in uncharged polymer. However, with further increase in the number of charged monomers of low charge density, there is a recurrence of osmolyte-induced stabilization of polymer collapse. On the contrary, the nonmonotonic trend in osmolyte-induced polymer collapse across the number of charged monomer beads diminishes with an increase in charge density: the aqueous TMAO solution becomes a denaturant of the polymer collapse at higher charge distribution in charge-neutral polymer with higher charge density. A molecular-level analysis of the polymer−osmolyte interaction reveals that the differential interaction of nitrogen and oxygen atoms of TMAO with the charged polymer beads, together with the competing effect of polymer−TMAO dispersion interaction and electrostatic interaction, holds the key in dictating the trend in the osmolyte-induced protection of the polymer collapse across various charge densities and charge distributions.

Osmolytes' mechanism of protecting proteins against denaturation is a longstanding puzzle, further complicated by complex diversities inherent in protein sequences. An emergent approach in understanding the osmolytes' mechanism of action toward biopolymer has been to investigate osmolytes' interplay with hydrophobic interaction, the major driving force of protein folding. However, the crucial question is whether all of these protein-stabilizing osmolytes display a single unified mechanism toward hydrophobic interactions. By simulating the hydrophobic collapse of a macromolecule in aqueous solutions of two such osmoprotectants, glycine and trimethyl N-oxide (TMAO), both of which are known to stabilize protein's folded conformation, we here demonstrate that these two osmolytes can impart mutually contrasting effects toward hydrophobic interaction. Although TMAO preserves its protectant nature across diverse range of polymer-osmolyte interactions, glycine is found to display an interesting crossover from being a protectant at weaker polymer-osmolyte interactions to being a denaturant of hydrophobicity at stronger polymer-osmolyte interactions. A preferential-interaction analysis reveals that a subtle balance of conformation-dependent exclusion/binding of osmolyte molecules from/to the macromolecule holds the key to overall heterogenous behavior. Specifically, TMAOs' consistent stabilization of collapsed configuration of macromolecule is found to be a result of TMAOs' preferential binding to polymers via hydrophobic methyl groups. However, polar glycine's crossover from being a protectant to denaturant across polymer-osmolyte interaction is rooted in its switch from preferential exclusion to preferential binding to the polymer with increasing interaction. Overall, by highlighting the complex interplay of osmolytes with hydrophobic interaction, this work puts forward the necessity of quantitative categorization of osmolytes' action in protein.

Bacteria, while developing a multicellular colony or biofilm, can undergo pattern formation by diverse intricate mechanisms. One such route is directional movement or chemotaxis toward or away from self-secreted or externally employed chemicals. In some bacteria, the self-produced signaling chemicals or autoinducers themselves act as chemoattractants or chemorepellents and thereby regulate the directional movements of the cells in the colony. In addition, bacteria follow a certain growth kinetics which is integrated in the process of colony development. Here, we study the interplay of bacterial growth dynamics, cell motility, and autochemotactic motion with respect to the self-secreted diffusive signaling chemicals in spatial pattern formation. Using a continuum model of motile bacteria, we show growth can act as a crucial tuning parameter in determining the spatiotemporal dynamics of a colony. In action of growth dynamics, while chemoattraction toward autoinducers creates arrested phase separation, pattern transitions and suppression can occur for a fixed chemorepulsive strength.

The first stage of the metastatic cascade often involves motile cells emerging from a primary tumor either as single cells or as clusters. These cells enter the circulation, transit to other parts of the body and finally are responsible for growth of secondary tumors in distant organs. The mode of dissemination is believed to depend on the EMT nature (epithelial, hybrid or mesenchymal) of the cells. Here, we calculate the cluster size distribution of these migrating cells, using a mechanistic computational model, in presence of different degree of EMT-ness of the cells; EMT is treated as given rise to changes in their active motile forces (μ) and cell-medium surface tension (Γ). We find that, for (μ > μmin, Γ > 1), when the cells are hybrid in nature, the mean cluster size, N ¯ ∼ Γ 2 . 0 / μ 2 . 8, where μmin increases with increase in Γ. For Γ ≤ 0, N ¯ = 1, the cells behave as completely mesenchymal. In presence of spectrum of hybrid states with different degree of EMT-ness (motility) in primary tumor, the cells which are relatively more mesenchymal (higher μ) in nature, form larger clusters, whereas the smaller clusters are relatively more epithelial (lower μ). Moreover, the heterogeneity in μ is comparatively higher for smaller clusters with respect to that for larger clusters. We also observe that more extended cell shapes promote the formation of smaller clusters. Overall, this study establishes a framework which connects the nature and size of migrating clusters disseminating from a primary tumor with the phenotypic composition of the tumor, and can lead to the better understanding of metastasis.