Identifying Ligand Binding Conformations of the β2-Adrenergic Receptor by Using Its Agonists as Computational Probes

Recently available G-protein coupled receptor (GPCR) structures and biophysical studies suggest that the difference between the effects of various agonists and antagonists cannot be explained by single structures alone, but rather that the conformational ensembles of the proteins need to be considered. Here we use an elastic network model-guided molecular dynamics simulation protocol to generate an ensemble of conformers of a prototypical GPCR, β2-adrenergic receptor (β2AR). The resulting conformers are clustered into groups based on the conformations of the ligand binding site, and distinct conformers from each group are assessed for their binding to known agonists of β2AR. We show that the select ligands bind preferentially to different predicted conformers of β2AR, and identify a role of β2AR extracellular region as an allosteric binding site for larger drugs such as salmeterol. Thus, drugs and ligands can be used as "computational probes" to systematically identify protein conformers with likely biological significance. © 2012 Isin et al

Passive and Active Oxidation of Si(100) by Atomic Oxygen: A Theoretical Study of Possible Reaction Mechanisms

Reaction mechanisms for oxidation of the Si(100) surface by atomic oxygen were studied with high-level quantum mechanical methods in combination with a hybrid QM/MM (Quantum mechanics/Molecular Mechanics) method. Consistent with previous experimental and theoretical results, three structures, “back-bond”, “on-dimer”, and “dimer-bridge”, are found to be the most stable initial surface products for O adsorption (and in the formation of SiO2 films, i.e., passive oxidation). All of these structures have significant diradical character. In particular, the “dimer-bridge” is a singlet diradical. Although the ground state of the separated reactants, O+Si(100), is a triplet, once the O atom makes a chemical bond with the surface, the singlet potential energy surface is the ground state. With mild activation energy, these three surface products can be interconverted, illustrating the possibility of the thermal redistribution among the initial surface products. Two channels for SiO desorption (leading to etching, i.e., active oxidation) have been found, both of which start from the back-bond structure. These are referred to as the silicon-first (SF) and oxygen-first (OF) mechanisms. Both mechanisms require an 89.8 kcal/mol desorption barrier, in good agreement with the experimental estimates of 80−90 kcal/mol. “Secondary etching” channels occurring after initial etching may account for other lower experimental desorption barriers. The calculated 52.2 kcal/mol desorption barrier for one such secondary etching channel suggests that the great variation in reported experimental barriers for active oxidation may be due to these different active oxidation channels

Noise Properties of NbN-MgO-NbN SQUIDs

DC-SQUIDs made of refractive materials NbN-MgO-NbN were prepared using thin film preparation techniques. The noise properties of these SQUIDs were investigated. The white energy sensitivity of typical devices is 600h (8mF0/ÃHz). The measured values are compared with theoretical predictions and the standard optimization rules. The low frequency noise was measured directly and using different modulation schemes. The SQUIDs show a relatively high 1/f noise onset in the range of 100Hz. The main contribution comes from out-of-phase critical current fluctuations and can be effectively suppressed by bias modulation