Molecular Dynamics simulations with a Molecular Mechanics force field and a quite complete exploration of the QM/MM potential energy surfaces have been performed to study the D-glutamate --> L-glutamate reaction catalyzed by Bacillus subtilis glutamate racemase. The results show that the whole process involves four successive proton transfers that occur in three different steps. The Michaelis complex is already prepared to make the first proton transfer (from Cys74 to Asp10) possible. The second step involves two proton transfers (from the alpha-carbon to Cys74, and from Cys185 to the alpha-carbon), which occurs in a concerted way, although highly asynchronic. Finally, in the third step, the nascent deprotonated Cys185 is protonated by His187. The positively charged ammonium group of the substrate plays a very important key role in the reaction. It accompanies each proton transfer in a concerted and coupled way, but moving itself in the opposite direction from Asp10 to His187. Thus, the catalytic action of Bacillus subtilis glutamate racemase is driven by its own substrate of the reaction, D-glutamate.

The structural simplicity of native cyclodextrins (CDs) contrasts with their complex behavior in the bulk of aqueous solutions, mainly when they are combined with other cosolutes. Many scientific and industrial applications based on these molecules are supported only by empirical information. The lack of fundamental knowledge, which would allow one to rationally optimize many of these applications, is notable mainly at the solution/air interface. Basic information on phenomena such as the spontaneous adsorption of native CDs or on the structure of CD aggregates in the bulk solution is really scarce. In order to fill these gaps, a detailed computational study on the adsorption and aggregation of α- and β-CDs as a function of temperature is presented here. Our simulations reproduce, at atomic resolution, the experimentally observed much higher ability of β-CD to aggregate compared to that of α-CD at 298 K, as well as their dependence on temperature. The adsorption of both individual CDs and small CD aggregates (up to 20 molecules) to the solution/air interface is found to be negligible. 0.8 μs long trajectories of single CD molecules in aqueous solution reveal that the main differences in the behavior of both CDs are their flexibility, higher for β-CD, and the occupancy of individual intramolecular hydrogen bonds that is significantly longer for the same cyclodextrin. The aggregation pattern of α- and β-CDs is followed at the hundreds of ns time scale, allowing both the spontaneous self-assembly of cyclodextrins and their redistribution along the aggregates to be observed. This is the first attempt to study the adsorption and aggregation of native cyclodextrins by atomistic molecular dynamics simulations.

Adjuvants are a diverse family of substances whose main objective is to increase the strength, quality, and duration of the immune response caused by vaccines. The most commonly used adjuvants are aluminum-based, oil-water emulsion, and bacterial-origin adjuvants. In this paper, we will discuss how the election of adjuvants is important for the adjuvant-mediated induction of immunity for different types of vaccines. Aluminum-based adjuvants are the most commonly used, the safest, and have the best efficacy, due to the triggering of a strong humoral response, albeit generating a weak induction of cell-mediated immune response. Freund’s adjuvant is the most widely used oil-water emulsion adjuvant in animal trials; it stimulates inflammation and causes aggregation and precipitation of soluble protein antigens that facilitate the uptake by antigen-presenting cells (APCs). Adjuvants of bacterial origin, such as flagellin, E. coli membranes, and monophosphoryl lipid A (MLA), are known to potentiate immune responses, but their safety and risks are the main concern of their clinical use. This minireview summarizes the mechanisms that classic and novel adjuvants produce to stimulate immune responses.

The database is freely available under http://cyclo-lib.mduse.com/ CONTACT: Angel.Pineiro@usc.es.