Amino Acid Solvation in Aqueous Kosmotrope Solutions: Temperature Dependence of the L-Histidine-Glycerol Interaction

We have studied thermodynamics of interaction between the aromatic amino acid l-histidine and glycerol, which is one of the most important stabilizing agents for proteins in water. The pair and triplet interaction parameters have been extracted from enthalpy and solubility data using standard thermodynamic manipulations in a wide temperature range. Our results indicate for the first time that the l-histidine–glycerol pair and triplet interactions are characterized by rather small enthalpy and entropy changes, which do not depend on temperature in either cold or hot water. These temperature-independent enthalpies and entropies of interaction lead to zero heat capacity changes during the amino acid transfer from water to both dilute and rather concentrated aqueous glycerol solutions. We attribute this behavior to a delicate balance between contributions from hydrophobic and hydrophilic fragments in the solute molecules. This unique feature appears to be the major reason that thermodynamics of pair and triplet interactions are nearly identical at standard and physiological temperatures

Electrophoretic mobility shift assays with GFP-tagged proteins (GFP-EMSA)

The electrophoretic mobility shift assay (EMSA) is commonly used for the study of nucleic acid-binding proteins. The technique can be used to demonstrate that a protein is binding to RNA or DNA through visualization of a shift in electrophoretic mobility of the nucleic acid band. A major disadvantage of the EMSA is that it does not always provide an absolute certitude that the band shift is due to the protein under scrutiny, as contaminants in the sample could also cause the band shift. Here we describe a variation of the standard EMSA allowing to visualize with added certitude, the co-localized band shifts of a GFP-tagged protein binding to its cognate nucleic acid target sequence stained with an intercalator, such as GelRed. Herein, we present an illustrative protocol of this useful technique called GFP-EMSA along with specific notes on its advantages and limitations

High-throughput differential scanning fluorimetry of GFP-tagged proteins

Differential scanning fluorimetry is useful for a wide variety of applications including characterization of protein function, structure–activity relationships, drug screening, and optimization of buffer conditions for protein purification, enzyme activity, and crystallization. A limitation of classic differential scanning fluorimetry is its reliance on highly purified protein samples. This limitation is overcome through differential scanning fluorimetry of GFP-tagged proteins (DSF-GTP). DSF-GTP specifically measures the unfolding and aggregation of a target protein fused to GFP through its proximal perturbation effects on GFP fluorescence. As a result of this unique principle, DSF-GTP can specifically measure the thermal stability of a target protein in the presence of other proteins. Additionally, the GFP provides a unique in-assay quality control measure. Here, we describe the workflow, steps, and important considerations for executing a DSF-GTP experiment in a 96-well plate format

Disulfide driven folding for a conditionally disordered protein

Abstract Conditionally disordered proteins are either ordered or disordered depending on the environmental context. The substrates of the mitochondrial intermembrane space (IMS) oxidoreductase Mia40 are synthesized on cytosolic ribosomes and diffuse as intrinsically disordered proteins to the IMS, where they fold into their functional conformations; behaving thus as conditionally disordered proteins. It is not clear how the sequences of these polypeptides encode at the same time for their ability to adopt a folded structure and to remain unfolded. Here we characterize the disorder-to-order transition of a Mia40 substrate, the human small copper chaperone Cox17. Using an integrated real-time approach, including chromatography, fluorescence, CD, FTIR, SAXS, NMR, and MS analysis, we demonstrate that in this mitochondrial protein, the conformational switch between disordered and folded states is controlled by the formation of a single disulfide bond, both in the presence and in the absence of Mia40. We provide molecular details on how the folding of a conditionally disordered protein is tightly regulated in time and space, in such a way that the same sequence is competent for protein translocation and activity