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Register a new userProteins at air-water and oil-water interfaces in an all-atom model
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We study the behavior of five proteins at the air-water and oil-water interfaces by all-atom molecular dynamics. The proteins are found to get distorted when pinned to the interface. This behavior is consistent with the phenomenological way of introducing the interfaces in a coarse-grained model through a force that depends on the hydropathy indices of the residues. Proteins couple to the oil-water interface stronger than to the air- water one. They diffuse slower at the oil-water interface but do not depin from it, whereas depinning events are observed at the other interface. The reduction of the disulfide bonds slows the diffusion down.
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The formation of smart emulsions or foams whose stability can be controlled on-demand by switching external parameters is of great interest for basic research and applications. An emerging group of smart stabilizers are microgels, which are nano- and micro-sized, three-dimensional polymer networks that are swollen by a good solvent. In the last decades, the influence of various external stimuli on the two-dimensional phase behavior of microgels at air- and oil-water interfaces has been studied. However, the impact of the top-phase itself has been barely considered. Here, we present data that directly address the influence of the top-phase on the microgel properties at interfaces. The dimensions of pNIPAM microgels are measured after deposition from two interfaces, i.e., air- and decane-water. While the total in-plane size of the microgel increases with increasing interfacial tension, the portions or fractions of the microgels situated in the aqueous phase are not affected. We correlate the area microgels occupy to the surface tensions of the interfaces, which allows to estimate an elastic modulus. In comparison to nanoindentation measurements, we observe a larger elastic modulus for the microgels. By combining compression, deposition, and visualization, we show that the two-dimensional phase behavior of the microgel monolayers is not altered, although the microgels have a larger total in-plane size at higher interfacial tension. A peer reviewed and extended version of this preprint and the electronic supplementary information can be found under S.~Bochenek, A.~Scotti, W.~Richtering, textit{Soft Matter}, 2020, DOI: 10.1039/d0sm01774d.
We use a coarse-grained model to study the conformational changes in two barley proteins, LTP1 and its ligand adduct isoform LTP1b, that result from their adsorption to the air-water interface. The model introduces the interface through hydropathy indices. We justify the model by all-atom simulations. The choice of the proteins is motivated by making attempts to understand formation and stability of foam in beer. We demonstrate that both proteins flatten out at the interface and can make a continuous stabilizing and denser film. We show that the degree of the flattening depends on the protein -- the layers of LTP1b should be denser than those of LTP1 -- and on the presence of glycation. It also depends on the number ($le 4$) of the disulfide bonds in the proteins. The geometry of the proteins is sensitive to the specificity of the absent bonds. We provide estimates of the volume of cavities of the proteins when away from the interface.
Problems of search and recognition appear over different scales in biological systems. In this review we focus on the challenges posed by interactions between proteins, in particular transcription factors, and DNA and possible mechanisms which allow for a fast and selective target location. Initially we argue that DNA-binding proteins can be classified, broadly, into three distinct classes which we illustrate using experimental data. Each class calls for a different search process and we discuss the possible application of different search mechanisms proposed over the years to each class. The main thrust of this review is a new mechanism which is based on barrier discrimination. We introduce the model and analyze in detail its consequences. It is shown that this mechanism applies to all classes of transcription factors and can lead to a fast and specific search. Moreover, it is shown that the mechanism has interesting transient features which allow for stability at the target despite rapid binding and unbinding of the transcription factor from the target.
Using concepts from perturbation and local molecular field theories of liquids we divide the potential of the SPC/E water model into short and long ranged parts. The short ranged parts define a minimal reference network model that captures very well the structure of the local hydrogen bond network in bulk water while ignoring effects of the remaining long ranged interactions. This deconstruction can provide insight into the different roles that the local hydrogen bond network, dispersion forces, and long ranged dipolar interactions play in determining a variety of properties of SPC/E and related classical models of water. Here we focus on the anomalous behavior of the internal pressure and the temperature dependence of the density of bulk water. We further utilize these short ranged models along with local molecular field theory to quantify the influence of these interactions on the structure of hydrophobic interfaces and the crossover from small to large scale hydration behavior. The implications of our findings for theories of hydrophobicity and possible refinements of classical water models are also discussed.
Experiments indicate that unbinding rates of proteins from DNA can depend on the concentration of proteins in nearby solution. Here we present a theory of multi-step replacement of DNA-bound proteins by solution-phase proteins. For four different kinetic scenarios we calculate the depen- dence of protein unbinding and replacement rates on solution protein concentration. We find (1) strong effects of progressive rezipping of the solution-phase protein onto DNA sites liberated by unzipping of the originally bound protein; (2) that a model in which solution-phase proteins bind non-specifically to DNA can describe experiments on exchanges between the non specific DNA- binding proteins Fis-Fis and Fis-HU; (3) that a binding specific model describes experiments on the exchange of CueR proteins on specific binding sites.
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