Development of a New 3D Hybrid Model for Epithelia Morphogenesis.

Many epithelial developmental processes like cell migration and spreading, cell sorting, or T1 transitions can be described as planar deformations. As such, they can be studied using two-dimensional tools and vertex models that can properly predict collective dynamics. However, many other epithelial shape changes are characterized by out-of-plane mechanics and three-dimensional effects, such as bending, cell extrusion, delamination, or invagination. Furthermore, during planar cell dynamics or tissue repair in monolayers, spatial intercalation between the apical and basal sides has even been detected. Motivated by this lack of symmetry with respect to the midsurface, we here present a 3D hybrid model that allows us to model differential contractility at the apical, basal or lateral sides. We use the model to study the effects on wound closure of solely apical or lateral contractile contributions and show that an apical purse-string can be sufficient for full closure when it is accompanied by volume preservation.

Helix formation by alanine-based peptides in pure water and electrolyte solutions: insights from molecular dynamics simulations.

Specific ion effects on oligopeptide conformations in solution are attracting strong research attention, because of their impact on the protein-folding problem and on several important biological-biotechnological applications. In this work, we have addressed specific effects of electrolytes on the tendency of oligopeptides toward formation and propagation of helical segments. We have used replica-exchange molecular dynamics (REMD) simulations to study the conformations of two short hydrophobic peptides [Ace-(AAQAA)3-Nme (AQ), and Ace-A8-Nme (A8)] in pure water and in aqueous solutions of sodium chloride (NaCl) and sodium iodide (NaI) with concentrations of 1 and 3 M. The average helicities of the AQ peptide have been analyzed to yield Lifson-Roig (LR) parameters for helix nucleation and helix propagation. The salt dependence of these parameters suggests that electrolytes tend to stabilize the helical conformations of short peptides by enhancing the helix nucleation parameter. The helical conformations of longer oligopeptides are destabilized in the presence of salts, however, because the helix propagation parameters are reduced by electrolytes. On top of this general trend, we observe a significant specific salt effect in these simulations. The hydrophobic iodide ion in NaI solutions has a high affinity for the peptide backbone, which reflects itself in an enhanced helix nucleation and a reduced helix propagation parameter with respect to pure water or NaCl solutions. The present work thus explains the computational evidence that electrolytes tend to stabilize the compact conformations of short peptides and destabilize them for longer peptides, and it also sheds additional light on the specific salt effects on compact peptide conformations.

Specific interactions of sodium salts with alanine dipeptide and tetrapeptide in water: insights from molecular dynamics.

We examine computationally the dipeptide and tetrapeptide of alanine in pure water and solutions of sodium chloride (NaCl) and iodide (NaI), with salt concentrations up to 3 M. Enhanced sampling of the configuration space is achieved by the replica exchange method. In agreement with other works, we observe preferential sodium interactions with the peptide carbonyl groups, which are enhanced in the NaI solutions due to the increased affinity of the less hydrophilic iodide anion for the peptide methyl side-chains and terminal blocking groups. These interactions have been associated with a decrease in the helicities of more complex peptides. In our simulations, both salts have a small effect on the dipeptide, but consistently stabilize the intramolecular hydrogen-bonding interactions and "α-helical" conformations of the tetrapeptide. This behavior, and an analysis of the intermolecular interaction energies show that ion-peptide interactions, or changes in the peptide hydration due to salts, are not sufficient determining factors of the peptide conformational preferences. Additional simulations suggest that the observed stabilizing effect is not due to the employed force-field, and that it is maintained in short peptides but is reversed in longer peptides. Thus, the peptide conformational preferences are determined by an interplay of energetic and entropic factors, arising from the peptide sequence and length and the composition of the solution.