Compaction of Ribosomal Protein S6 by Sucrose Occurs Only Under Native Conditions

Differential effect of polyol and sugar osmolytes on the refolding of homologous alpha amylases: A comparative study

Polyol and sugar osmolytes are known to enhance the stability of proteins, however, their role in assisting protein folding is not well understood. We asked whether these osmolytes have the same effect during refolding of a pair of thermophilic and mesophilic proteins. Herein, we have chosen α-amylases from Bacillus licheniformis (BLA) and Bacillus amyloliquefaciens (BAA) as thermophilic like and mesophilic counterparts respectively, having similar structures but differing thermostability. The effect of a series of polyols with varying number of -OH groups from 2 to 6 (Ethylene glycol, glycerol, erythritol, xylitol and sorbitol) and sugars (trehalose and sucrose) has been studied on the refolding of BLA and BAA. Our study demonstrates that glycerol, sorbitol and trehalose are the efficient cosolvents for BAA refolding, while comparatively less effective for BLA. Urea induced destabilization of BLA and BAA is differently compensated by polyol and sugar osmolytes during refolding. This suggests that the early species formed during BLA and BAA refolding are differently susceptible towards urea, indicating differential nature of their refolding pathways. Addition of trehalose at different times during refolding showed that the presence of trehalose is essential at the early stages of refolding. It is one of the first systematic study wherein the comparative effect of polyol and sugar assisted refolding of thermophilic and mesophilic protein has been carried out. The study highlights the differential effect of protein-osmolyte interactions during refolding of thermophilic and mesophilic proteins which may have implications in protein formulations, refolding and inhibition of aggregation.

Structural characterisation of the natively unfolded enterocin EJ97

Bacteriocins belong to the wide variety of antimicrobial ribosomal peptides synthesised by bacteria. Enterococci are Gram-positive, catalase-negative bacteria that produce lactic acid as the major end product of glucose fermentation. Many enterococcal strains produce bacteriocins, named enterocins. We describe in this work, the structural characterisation of the 44 residues-long enterocin EJ97, produced by Enterococcus faecalis EJ97. To this end, we have used a combined theoretical and experimental approach. First, we have characterised experimentally the conformational properties of EJ97 in solution under different conditions by using a number of spectroscopic techniques, namely fluorescence, CD, FTIR and NMR. Then, we have used several bioinformatic tools as an aid to complement the experimental information about the conformational properties of EJ97. We have shown that EJ97 is monomeric in aqueous solution and that it appears to be chiefly unfolded, save some flickering helical- or turn-like structures, probably stabilised by hydrophobic clustering. Accordingly, EJ97 does not show a cooperative sigmoidal transition when heated or upon addition of GdmCl. These conformational features are essentially pH-independent, as shown by NMR assignments at pHs 5.9 and 7.0. The computational results were puzzling, since some algorithms revealed the natively unfolded character of EJ97 (FoldIndex, the mean scaled hydropathy), whereas some others suggested the presence of ordered structure in its central region (PONDR, RONN and IUPRED). A future challenge is to produce much more experimental results to aid the development of accurate software tools for predicting disorder in proteins.

Osmolyte perturbation reveals conformational equilibria in spin-labeled proteins

Recent evidence suggests that proteins at equilibrium can exist in a manifold of conformational substates, and that these substates play important roles in protein function. Therefore, there is great interest in identifying regions in proteins that are in conformational exchange. Electron paramagnetic resonance spectra of spin-labeled proteins containing the nitroxide side chain (R1) often consist of two (or more) components that may arise from slow exchange between conformational substates (lifetimes > 100 ns). However, crystal structures of proteins containing R1 have shown that multicomponent spectra can also arise from equilibria between rotamers of the side chain itself. In this report, it is shown that these scenarios can be distinguished by the response of the system to solvent perturbation with stabilizing osmolytes such as sucrose. Thus, site-directed spin labeling (SDSL) emerges as a new tool to explore slow conformational exchange in proteins of arbitrary size, including membrane proteins in a native-like environment. Moreover, equilibrium between substates with even modest differences in conformation is revealed, and the simplicity of the method makes it suitable for facile screening of multiple proteins. Together with previously developed strategies for monitoring picosecond to millisecond backbone dynamics, the results presented here expand the timescale over which SDSL can be used to explore protein flexibility.

Trehalose-mediated thermal stabilization of glucose oxidase from Aspergillus niger

Thermal inactivation and enzyme kinetics of glucose oxidase (a FAD dependent enzyme) were studied in the absence and presence of trehalose. The inactivation rate constant decreased by up to 50% at temperatures between 50 and 70 degrees C in the presence of 0.6M trehalose; as a consequence the glucose oxidase half-life increased. Intrinsic fluorescence spectra showed a maximum center of spectral mass (CSM) red shift of 6.5nm. Therefore, major structural changes seem to be related to glucose oxidase thermal inactivation. Trehalose decreased the rate constant for unfolding as monitored by CSM red shift kinetics indicating that this disaccharide favors the most compact folded state. The E(a) for unfolding was increased from 204 to 221kJ mol(-1). It is proposed that FAD dissociation is preceded by the exposition of hydrophobic regions, while the presence of trehalose was able to hinder the release of FAD. Enzyme kinetics analysis showed that trehalose does not affect V(max) but instead decreases K(m); as a result enzyme efficiency was increased. The stabilizing effect of trehalose in a cofactor-dependent enzyme has not been tested to date. In addition, glucose oxidase has an enormous commercial importance and therefore, the use of trehalose to stabilize glucose oxidase in its multiple applications seems to be promising.

Thermodynamics and mechanism of cutinase stabilization by trehalose

Trehalose has been widely used to stabilize cellular structures such as membranes and proteins. The effect of trehalose on the stability of the enzyme cutinase was studied. Thermal unfolding of cutinase reveals that trehalose delays thermal unfolding, thus increasing the temperature at the midpoint of unfolding by 7.2 degrees . Despite this stabilizing effect, trehalose also favors pathways that lead to irreversible denaturation. Stopped-flow kinetics of cutinase folding and unfolding was measured and temperature was introduced as experimental variable to assess the mechanism and thermodynamics of protein stabilization by trehalose. The main stabilizing effect of trehalose was to delay the rate constant of the unfolding of an intermediate. A full thermodynamic analysis of this step has revealed that trehalose induces the phenomenon of entropy-enthalpy compensation, but the enthalpic contribution increases more significantly leading to a net stabilizing effect that slows down unfolding of the intermediate. Regarding the molecular mechanism of stabilization, trehalose increases the compactness of the unfolded state. The conformational space accessible to the unfolded state decreases in the presence of trehalose when the unfolded state acquires residual native interactions that channel the folding of the protein. This residual structure results into less hydrophobic groups being newly exposed upon unfolding, as less water molecules are immobilized upon unfolding.