No Arabic abstract
The implementation of natural and artificial proteins with designer properties and functionalities offers unparalleled opportunity for functional nanoarchitectures formed through self-assembly. However, to exploit the opportunities offered we require the ability to control protein assembly into the desired architecture while avoiding denaturation and therefore retaining protein functionality. Here we address this challenge with a model system of fluorescent proteins. Using techniques of self-assembly manipulation inspired by soft matter where interactions between components are controlled to yield the desired structure, we show that it is possible to assemble networks of proteins of one species which we can decorate with another, whose coverage we can tune. Consequently, the interfaces between domains of each component can also be tuned, with applications for example in energy transfer. Our model system of fluorescent proteins eGFP and mCherry retain their fluorescence throughout the assembly process, thus demonstrating that functionality is preserved.
We present a computational study on the folding and aggregation of proteins in aqueous environment, as function of its concentration. We show how the increase of the concentration of individual protein species can induce a partial unfolding of the native conformation without the occurrence of aggregates. A further increment of the protein concentration results in the complete loss of the folded structures and induces the formation of protein aggregates. We discuss the effect of the protein interface on the water fluctuations in the protein hydration shell and their relevance in the protein-protein interaction.
Dynamin is a ubiquitous GTPase that tubulates lipid bilayers and is implicated in many membrane severing processes in eukaryotic cells. Setting the grounds for a better understanding of this biological function, we develop a generalized hydrodynamics description of the conformational change of large dynamin-membrane tubes taking into account GTP consumption as a free energy source. On observable time scales, dissipation is dominated by an effective dynamin/membrane friction and the deformation field of the tube has a simple diffusive behavior, which could be tested experimentally. A more involved, semi-microscopic model yields complete predictions for the dynamics of the tube and possibly accounts for contradictory experimental results concerning its change of conformation as well as for plectonemic supercoiling.
Protein aggregation in the form of amyloid fibrils has important biological and technological implications. Although the self-assembly process is highly efficient, aggregates not in the fibrillar form would also occur and it is important to include these disordered species when discussing the thermodynamic equilibrium behavior of the system. Here, we initiate such a task by considering a mixture of monomeric proteins and the corresponding aggregates in the disordered form (micelles) and in the fibrillar form (amyloid fibrils). Starting with a model on the respective binding free energies for these species, we calculate their concentrations at thermal equilibrium. We then discuss how the incorporation of the disordered structure furthers our understanding on the various amyloid promoting factors observed empirically, and on the kinetics of fibrilization.
The hydrophobic effect stabilizes the native structure of proteins by minimizing the unfavourable interactions between hydrophobic residues and water through the formation of a hydrophobic core. Here we include the entropic and enthalpic contributions of the hydrophobic effect explicitly in an implicit solvent model. This allows us to capture two important effects: a length-scale dependence and a temperature dependence for the solvation of a hydrophobic particle. This consistent treatment of the hydrophobic effect explains cold denaturation and heat capacity measurements of solvated proteins.
We study the liquid-liquid phase separation (LLPS) of a cell-free transcription-translation (TXTL) system. When the TXTL reaction, composed of a large amount of proteins, is concentrated, the uniformly mixed state becomes unstable and membrane-less droplets form spontaneously. This LLPS droplet formation can be induced when the TXTL reaction is enclosed in water-in-oil emulsion droplets in which water evaporates (dehydration) from the surface. As the emulsion droplets shrink, smaller LLPS droplets appear inside the emulsion droplets and coalesce into phase-separated domains that partition the location of proteins. We show that the LLPS in the emulsion droplets can be accelerated by interfacial drift in the outer oil phase. This further provides an experimental platform for studying the interplay between biological reactions and intracellular phase separation.