The alternate ligand Jagged enhances the robustness of Notch signaling patterns.

The Notch pathway, an example of juxtacrine signaling, is an evolutionary conserved cell-cell communication mechanism. It governs emergent spatiotemporal patterning in tissues during development, wound healing and tumorigenesis. Communication occurs when Notch receptors of one cell bind to either of its ligands, Delta/Jagged of the neighboring cell. In general, Delta-mediated signaling drives neighboring cells to have an opposite fate (lateral inhibition) whereas Jagged-mediated signaling drives cells to maintain similar fates (lateral induction). Here, by deriving and solving a reduced set of 12 coupled ordinary differential equations for the Notch-Delta-Jagged system on a hexagonal grid of cells, we determine the allowed states across different parameter sets. We also show that Jagged (at low dose) acts synergistically with Delta to enable more robust pattern formation by making the neighboring cell states more distinct from each other, despite its lateral induction property. Our findings extend our understanding of the possible synergistic role of Jagged with Delta which had been previously proposed through experiments and models in the context of chick inner ear development. Finally, we show how Jagged can help to expand the bistable (both uniform and hexagon phases are stable) region, where a local perturbation can spread over time in an ordered manner to create a biologically relevant, perfectly ordered lateral inhibition pattern.

Infiltration of tumor spheroids by activated immune cells.

Recent years have seen a tremendous growth of interest in understanding the role that the adaptive immune system could play in interdicting tumor progression. In this context, it has been shown that the density of adaptive immune cells inside a solid tumor serves as a favorable prognostic marker across different types of cancer. The exact mechanisms underlying the degree of immune cell infiltration is largely unknown. Here, we quantify the temporal dynamics of the density profile of activated immune cells around a solid tumor spheroid. We propose a computational model incorporating immune cells with active, persistent movement and a proliferation rate that depends on the presence of cancer cells, and show that the model able to reproduce semi-quantitatively the experimentally measured infiltration profile. Studying the density distribution of immune cells inside a solid tumor can help us better understand immune trafficking in the tumor micro-environment, hopefully leading towards novel immunotherapeutic strategies.

Three-dimensional cancer cell migration directed by dual mechanochemical guidance.

Directed cell migration guided by external cues plays a central role in many physiological and pathophysiological processes. The microenvironment of cells often simultaneously contains various cues and the motility response of cells to multiplexed guidance is poorly understood. Here we combine experiments and mathematical models to study the three-dimensional migration of breast cancer cells in the presence of both contact guidance and a chemoattractant gradient. We find that the chemotaxis of cells is complicated by the presence of contact guidance as the microstructure of extracellular matrix (ECM) vary spatially. In the presence of dual guidance, the impact of ECM alignment is determined externally by the coherence of ECM fibers and internally by cell mechanosensing Rho/Rock pathways. When contact guidance is parallel to the chemical gradient, coherent ECM fibers significantly increase the efficiency of chemotaxis. When contact guidance is perpendicular to the chemical gradient, cells exploit the ECM disorder to locate paths for chemotaxis. Our results underscore the importance of fully characterizing the cancer cell microenvironment in order to better understand invasion and metastasis.

Cluster size distribution of cells disseminating from a primary tumor.

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, [Formula: see text], where µmin increases with increase in Γ. For Γ ≤ 0, [Formula: see text], 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.

Bottom-Up View of the Mechanism of Action of Protein-Stabilizing Osmolytes.

The molecular mechanism of osmolytes on the stabilization of native states of protein is still controversial irrespective of extensive studies over several decades. Recent investigations in terms of experiments and molecular dynamics simulations challenge the popular osmophobic model explaining the mechanistic action of protein-stabilizing osmolytes. The current Perspective presents an updated view on the mechanistic action of osmolytes in light of resurgence of interesting experiments and computer simulations over the past few years in this direction. In this regard, the Perspective adopts a bottom-up approach starting from hydrophobic interactions and eventually adds complexity in the system, going toward the protein, in a complex topology of hydrophobic and electrostatic interactions. Finally, the Perspective unifies osmolyte-induced protein conformational equilibria in terms of preferential interaction theory, irrespective of individual preferential binding or exclusion of osmolytes depending on different osmolytes and protein surfaces. The Perspective also identifies future research directions that can potentially shape this interesting area.

Unifying the Contrasting Mechanisms of Protein-Stabilizing Osmolytes.

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.

Osmolyte-Induced Macromolecular Aggregation Is Length-Scale Dependent.

Cells survive in extreme environmental conditions by accumulating small organic molecules called osmolytes. While we have reached a consensus on the role of osmolytes toward macromolecular conformational stability at a single-macromolecule level, there is a lack of clarity on how osmolytes might influence macromolecular aggregation, an important feature to maintain cellular homeostasis. In this regard, here, we explore how a popular osmolyte trimethyl amine N-oxide (TMAO) individually dictates the self-assembling propensity of hydrophobic and charged macromolecules. Our computer simulation-based results reveal that the TMAO-induced self-aggregation of hydrophobic macromolecules, relative to that in neat water, is strongly dependent on the macromolecular length scale. Specifically, a free energy-based analysis indicates that the self-aggregation propensity of hydrophobic macromolecules in aqueous TMAO relative to neat water follows a nonmonotonic trend. When compared with neat water, TMAO promotes hydrophobic self-assembly at a shorter length scale while discourages hydrophobic self-assembly at a larger length scale. The overall nonmonotonic trend is found to be entropy driven. A molecular-level analysis suggests that length-scale-dependent preferential exclusion/binding of osmolytes (relative to water) from/to macromolecules in the process of aggregation holds the key to the nonmonotonic behavior. The overall result is found to be robust, even in the presence of the charge distributions on the macromolecules.

Osmolyte-Induced Collapse of a Charged Macromolecule.

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.

Role of α and ß relaxations in collapsing dynamics of a polymer chain in supercooled glass-forming liquid.

Understanding the effect of glassy dynamics on the stability of bio-macromolecules and investigating the underlying relaxation processes governing degradation processes of these macromolecules are of immense importance in the context of bio-preservation. In this work, we have studied the stability of a model polymer chain in a supercooled glass-forming liquid at different amounts of supercooling in order to understand how dynamics of supercooled liquids influence the collapse behavior of the polymer. Our systematic computer simulation studies find that, apart from long time relaxation processes (α relaxation), short time dynamics of the supercooled liquid, known as ß relaxation, is also correlated with the stability of the model polymer. We also show that anti-plasticizing effect found in this context can be rationalized using the ß-relaxation process and how it is modified due to changes in the specific interactions between the biomolecules and the solvent molecules or changes in the local packing around the biomolecules. Our results corroborate with other recent results which suggest that it is important to take in to account both the α and ß relaxation times while choosing appropriate bio-preservatives. We believe that our results will have implications in understanding the primary factors in protein stabilization in the context of bio-preservation.

Heterogeneous Impacts of Protein-Stabilizing Osmolytes on Hydrophobic Interaction.

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.

Growth-mediated autochemotactic pattern formation in self-propelling bacteria.

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.