Determination of the conformational states of strychnine in solution using NMR residual dipolar couplings in a tensor-free approach.

Small molecules with rotatable bonds can occupy different conformational states in solution as a consequence of their thermal fluctuations. The accurate determination of the structures of such states, as well as of their statistical weights, has been challenging because of the technical difficulties in extracting information from experimental measurements, which are normally averaged over the conformational space available. Here, to achieve this objective, we present an approach based on a recently proposed tensor-free method for incorporating NMR residual dipolar couplings as structural restraints in replica-averaged molecular dynamics simulations. This approach enables the information provided by the experimental data to be used in the spirit of the maximum entropy principle to determine the structural ensembles of small molecules. Furthermore, in order to enhance the sampling of the conformational space we incorporated the metadynamics method in the simulations. We illustrate the method in the case of strychnine, determining the three major conformational states of this small molecule and their associated occupation probabilities.

ADP ribosylation adapts an ER chaperone response to short-term fluctuations in unfolded protein load.

Gene expression programs that regulate the abundance of the chaperone BiP adapt the endoplasmic reticulum (ER) to unfolded protein load. However, such programs are slow compared with physiological fluctuations in secreted protein synthesis. While searching for mechanisms that fill this temporal gap in coping with ER stress, we found elevated levels of adenosine diphosphate (ADP)-ribosylated BiP in the inactive pancreas of fasted mice and a rapid decline in this modification in the active fed state. ADP ribosylation mapped to Arg470 and Arg492 in the substrate-binding domain of hamster BiP. Mutations that mimic the negative charge of ADP-ribose destabilized substrate binding and interfered with interdomain allosteric coupling, marking ADP ribosylation as a rapid posttranslational mechanism for reversible inactivation of BiP. A kinetic model showed that buffering fluctuations in unfolded protein load with a recruitable pool of inactive chaperone is an efficient strategy to minimize both aggregation and costly degradation of unfolded proteins.

Adsorption and reduction of glutathione disulfide on α-Al2O3 nanoparticles: experiments and modeling.

Glutathione disulfide (GSSG; γ-GluCysGly disulfide) was used as a physiologically relevant model molecule to investigate the fundamental adsorption mechanisms of polypeptides onto α-alumina nanoparticles. Its adsorption/desorption behavior was studied by enzymatic quantification of the bound GSSG combined with zeta potential measurements of the particles. The adsorption of GSSG to alumina nanoparticles was rapid, was prevented by alkaline pH, was reversed by increasing ionic strength, and followed a nearly ideal Langmuir isotherm with a standard Gibbs adsorption energy of -34.7 kJ/mol. Molecular dynamics simulations suggest that only one of the two glutathionyl moieties contained in GSSG binds stably to the nanoparticle surface. This was confirmed experimentally by the release of GSH from the bound GSSG upon reducing its disulfide bond with dithiothreitol. Our data indicate that electrostatic interactions via the carboxylate groups of one of the two glutathionyl moieties of GSSG are predominantly responsible for the binding of GSSG to the alumina surface. The results and conclusions presented here can provide a base for further experimental and modeling studies on the interactions of biomolecules with ceramic materials.

Supramolecular self-assembly driven by electrostatic repulsion: The 1D aggregation of rubrene pentagons on Au111.

At present, organic molecules are among the best candidate "building blocks" for the construction of self-assembling nanoscale devices based on metal substrates. Control of the formation of specific patterns in the submonolayer regime is usually achieved by appropriate choice and/or functionalization of the adsorbates. The effect of this intervention, though, is limited by the typically short-range character of the bonding. We present here a theoretical study on the system rubrene/gold to show that substrate-induced molecular charging can instead determine the assembly on larger scales. DFT calculations and electrostatic considerations are used to discuss the charge transfer at the metal/organic interface. This allows rationalization of previous puzzling experimental results and, in particular, of the unusual molecular gap broadening upon adsorption observed in STS spectra. The self-assembly process is further studied by means of classical molecular dynamics simulations. The charged adsorbates are modeled as mutually repulsive standing dipoles, with van der Waals interactions intervening at short distances. The striking resemblance between the experimental STM images and the results of our MD simulations shows that this simple model is able to capture the key effects driving the assembly in this system. The competition between long-range repulsive interactions and short-range attractive forces leads to characteristic and easily recognizable 1D patterns. We suggest that experimental evidence of the presence of similar patterns in other metal/organic systems can provide crucial information on the electronic level alignment at the interface, that is, on the occurrence of charge-transfer processes between metal and organic adsorbates.

Structure and energetics of diphenylalanine self-assembling on Cu(110).

We investigate the dynamical features of the adsorption of diphenylalanine molecules on the Cu(110) surface and of their assembling into supramolecular structures by a combination of quantum and classical atomistic modeling with dynamic scanning tunneling microscopy and spectroscopic experiments. Our results reveal a self-assembling mechanism in which isolated adsorbed molecules change their conformation and adsorption mode as a consequence of their mutual interactions. In particular, the formation of zwitterions after proton transfer between initially neutral molecules is found to be the key event of the assembling process, which stabilizes the supramolecular structures. Because of the constraints on the intermolecular bonds exerted by the surface-molecule interactions, the assembly process is strictly stereoselective, and may suggest a general model for patterning and functionalization of bare metal surfaces with short chiral peptides.