Development of 7TM receptor-ligand complex models using ligand-biased, semi-empirical helix-bundle repacking in torsion space: application to the agonist interaction of the human dopamine D2 receptor

Prediction of 3D structures of membrane proteins, and of G-protein coupled receptors (GPCRs) in particular, is motivated by their importance in biological systems and the difficulties associated with experimental structure determination. In the present study, a novel method for the prediction of 3D structures of the membrane-embedded region of helical membrane proteins is presented. A large pool of candidate models are produced by repacking of the helices of a homology model using Monte Carlo sampling in torsion space, followed by ranking based on their geometric and ligand-binding properties. The trajectory is directed by weak initial restraints to orient helices towards the original model to improve computation efficiency, and by a ligand to guide the receptor towards a chosen conformational state. The method was validated by construction of the β₁ adrenergic receptor model in complex with (S)-cyanopindolol using bovine rhodopsin as template. In addition, models of the dopamine D₂ receptor were produced with the selective and rigid agonist (R)-N-propylapomorphine ((R)-NPA) present. A second quality assessment was implemented by evaluating the results from docking of a library of 29 ligands with known activity, which further discriminated between receptor models. Agonist binding and recognition by the dopamine D₂ receptor is interpreted using the 3D structure model resulting from the approach. This method has a potential for modeling of all types of helical transmembrane proteins for which a structural template with sequence homology sufficient for homology modeling is not available or is in an incorrect conformational state, but for which sufficient empirical information is accessible.     

Water-based Synthesis and Properties of a Scandium 1,4-Naphthalenedicarboxylate

A new scandium naphthalenedicarboxylate with the framework composition [Sc₂(1,4-NDC)₃] (H₂-1,4-NDC = 1,4-naphthalenedicarboxylic acid) was obtained under hydrothermal synthesis conditions. A structure model could be developed by a combination of 3D electron diffraction measurements and computationally assisted structure determination, which was further validated by a good agreement with the experimental powder X-ray diffraction pattern. The structure consists of isolated ScO₆ octahedra interconnected by the carboxylate groups of linker molecules to form chains. These chains are connected by the naphthalene-moieties to form a three-dimensional framework with square-shaped pores and the organic group pointing into the pores. Although very similar synthesis conditions were chosen, [Sc₂(1,4-NDC)₃] is not isostructural to aluminum naphthalenedicarboxylate [Al(OH)(1,4-NDC)], which crystallizes in a MIL-53 type structure. This can be traced back to the different inorganic building units that are observed. The compound was thoroughly characterized by elemental analysis, IR spectroscopy, sorption measurements, thermogravimetric analysis and luminescence measurements. [Sc₂(1,4-NDC)₃] exhibits a high thermal stability and a ligand-based blue luminescence in the solid state at room temperature.     

How well does molecular simulation reproduce environment-specific conformations of the intrinsically disordered peptides PLP,TP2 and ONEG?

Understanding the conformational ensembles of intrinsically disordered proteins and peptides (IDPs) in their various biological environments is essential for understanding their mechanisms and functional roles in the proteome, leading to a greater knowledge of, and potential treatments for, a broad range of diseases. To determine whether molecular simulation is able to generate accurate conformational ensembles of IDPs, we explore the structural landscape of the PLP peptide (an intrinsically disordered region of the proteolipid membrane protein) in aqueous and membrane-mimicking solvents, using replica exchange with solute scaling (REST2), and examine the ability of four force fields (ff14SB, ff14IDPSFF, CHARMM36 and CHARMM36m) to reproduce literature circular dichroism (CD) data. Results from variable temperature (VT) ¹H and Rotating frame Overhauser Effect SpectroscopY (ROESY) nuclear magnetic resonance (NMR) experiments are also presented and are consistent with the structural observations obtained from the simulations and CD. We also apply the optimum simulation protocol to TP2 and ONEG (a cell-penetrating peptide (CPP) and a negative control peptide, respectively) to gain insight into the structural differences that may account for the observed difference in their membrane-penetrating abilities. Of the tested force fields, we find that CHARMM36 and CHARMM36m are best suited to the study of IDPs, and accurately predict a disordered to helical conformational transition of the PLP peptide accompanying the change from aqueous to membrane-mimicking solvents. We also identify an α-helical structure of TP2 in the membrane-mimicking solvents and provide a discussion of the mechanistic implications of this observation with reference to the previous literature on the peptide. From these results, we recommend the use of CHARMM36m with the REST2 protocol for the study of environment-specific IDP conformations. We believe that the simulation protocol will allow the study of a broad range of IDPs that undergo conformational transitions in different biological environments.

A protocol for simulating intrinsically disordered peptides in aqueous and hydrophobic solvents is proposed. Results from four force fields are compared with experiment. CHARMM36m performs the best for the simulated IDPs in all environments.     

Pulling rate, thermal and capillary conditions setting for rod growth

The purpose of this paper is to elaborate a procedure, based on a mathematical model, for the setting of the pulling rate, capillary and thermal conditions, in order to grow a cylindrical rod with prescribed radius and length, by edge-defined film-fed growth (EFG) method. First, in the case of an axisymmetric meniscus, we use simultaneously the catching and the angle fixation conditions in order to find a formula, which describes the fluctuation of the angle between the horizontal axis Or and the tangent line to the free surface of the meniscus at the three phase point. This angle appears in the system of differential equations which describes the evolution of the radius of the rod. During the growth this angle can fluctuate due to the fluctuations of the crystal radius, or crystallization front level, or pressure, respectively. In the second part of the paper it is shown in which kind this formula together with the energy balance equation at the crystallization front level can be used for setting the pulling rate, the thermal and capillary conditions to grow a cylindrical rod with prescribed radius and length. Numerical illustration and simulation are presented for rods having thermo-physical properties similar to NdYAG and InSb. This type of results can be useful for the experiment planning, since personal computer simulation is less expensive than experiment. With this aim the present study was undertaken.     

A kinetic study of the decomposition of HNO3 and its reaction with NO

The rate of reaction between NO and HNO₃ and the rate of thermal decomposition of HNO₃ have been measured by FTIR spectroscopy. The measurements were made in a teflon lined batch reactor having a surface to volume ratio of 14 m^?1. During the experiments, with initial HNO₃ concentrations between 2 and 12 ppm and NO concentrations between 2 and 30 ppm, a reactant stoichiometry of unity and a first order NO and HNO₃ dependence were confirmed. The observed rate constant for the reaction at 22°C and atmospheric pressure was determined to 1.1 (±0.3) 10^?5 ppm^?1 min^?1. At atmospheric pressure, HNO₃ decomposes into NO₂ and other products with a first order HNO₃ dependence and with a rate constant of 2.0 (±0.2) 10^?3 min^?1. The apparent activation energy for the decomposition is 13 (±4) kJ mol^?1.     

Evidence for nontermination of rotational bands in 74Kr

Three rotational bands in 74Kr were studied up to (in one case one transition short of) the maximum spin I(max) of their respective single-particle configurations. Their lifetimes have been determined using the Doppler-shift attenuation method. The deduced transition quadrupole moments reveal a modest decrease, but far from a complete loss of collectivity at the maximum spin I(max). This feature, together with the results of mean field calculations, indicates that the observed bands do not terminate at I = I(max).