Molecular dynamics simulations of the ligand-induced chemical information transfer in the 5-HT(1A) receptor

Comparative molecular dynamics simulations of the 5-HT(1A) receptor in its empty as well as agonist- (i.e. active) and antagonist-bound (i.e. nonactive) forms have been carried out. The agonists 5-HT and (R)-8-OH-DPAT as well as the antagonist WAY100635 have been employed. The results of this study strengthen the hypothesis that the receptor portions close to the E/DRY/W motif, with prominence to the cytosolic extensions of helices 3 and 6, are particularly susceptible to undergo structural modification in response to agonist binding. Despite the differences in the structural/dynamics behavior of the two agonists when docked into the 5-HT(1A) receptor, they both exert a destabilization of the intrahelical and interhelical interactions found in the empty and antagonist-bound receptor forms between the arginine of the E/DRY sequence and both D133(3.49) and E340(6.30). For both agonists, the chemical information transfer from the extracellular to the cytosolic domains is mediated by a cluster of aromatic amino acids in helix 6, following the ligand interaction with selected amino acids in the extracellular half of the receptor, such as D116(3.32), S199(5.42), Y195(5.38), and F361(6.51). A significant reduction in the bend at P360(6.50), as compared to the empty and the antagonist-bound receptor forms, is one of the features of the agonist-bound forms that is related to the breakage of the interhelical salt bridge between the E/DRY arginine and E340(6.30). Another structural feature, shared by the agonist-bound receptor forms and not by the empty and antagonist-bound forms, is the detachment of helices 2 and 4, as marked by the movement of W161(4.50) away from helix 2, toward the membrane space.     

Mechanochemical preparation of hydrogen-bonded adducts between the diamine 1,4-diazabicyclo[2.2.2]octane and dicarboxylic acids of variable chain length: an X-ray diffraction and solid-state NMR study

Mechanical mixing of solid dicarboxylic acids of variable chain length HOOC(CH(2))(n)COOH (n = 1-7) with solid 1,4-diazabicyclo[2.2.2]octane generates the corresponding salts or co-crystals of the formula [N(CH(2)CH(2))(3)N]-H-[OOC(CH(2))(n)COOH] (n=1-7). Preparation of the same systems from solution has been instrumental for a full characterization of the mechanochemical products by means of single-crystal and powder-diffraction X-ray analyses, as well as by solid-state NMR. The acid-base adducts, whether involving proton transfer from the COOH group to the N-acceptor, that is having ((-))O...H-N((+)) interactions, or the formation of neutral O-H...N hydrogen bonds, show a melting point alternation phenomenon analogous to that shown by the neutral carboxylic acids. The carbon chemical shift tensors of the COOH group obtained from the sideband intensity of low speed spinning NMR spectra provide a reliable criterion for assigning the protonation state of the adducts.     

Rare fluctuations of native proteins sampled by equilibrium hydrogen exchange

We present a method for determining the ensembles of native protein structures that result from the large fluctuations of low probability revealed by hydrogen-exchange experiments. The measured protection factors are used to bias Monte Carlo simulations to sample the structures of the exchange competent species. The approach is illustrated by its application to the case of alpha-lactalbumin.     

"Oscillating" metallocene catalysts: what stops the oscillation?

The 150 MHz (13)C NMR microstructural analysis of polypropylene samples produced with two representative "oscillating" metallocene catalysts of largely different steric hindrance, namely [(2-(3,5-di-tert-butyl-4-methoxyphenyl)indenyl)(2)ZrP](+) and [(2-phenylindenyl)(2)ZrP](+) (P = polymeryl), and the implications on the origin of the stereocontrol are presented and discussed in detail. The original mechanistic proposal of an "oscillation" between a rac-like (isotactic-selective) and a meso-like (nonstereoselective) conformation cannot explain the observed polymer configuration. The isotactic-stereoblock nature of the polymers obtained with the former catalyst proves unambiguously that the active cation "oscillates" between the two enantiomorphous rac-like conformations at an average frequency that, even at high propene concentration, is only slightly lower than that of monomer insertion. The less-hindered [(2-phenylindenyl)(2)ZrP](+) gives instead a largely stereoirregular polypropylene, which is the logical consequence of a faster ligand rotation; however, depending on the use conditions (in particular, on the nature of the cocatalyst and the polarity of the solvent), the polymerization products may also contain appreciable amounts of a fairly isotactic fraction. The peculiar microstructure of this fraction, with isotactic blocks of the same relative configuration spanned by very short atactic ones, rules out the possibility that the latter are due to an active species in meso-like conformation and points rather to a conformationally "locked" rac-like species with restricted ring mobility. The hypothesis of a stereorigidity induced by the proximity to a counteranion, which would play the role of the interannular bridge in the rac-bis(indenyl) ansa-metallocenes, was tested by computer modeling on a [rac-(2-phenylindenyl)(2)ZrMe(C(3)H(6))][B(C(6)F(5))(4)] ion couple and found viable.     

Microwave-assisted acylation of 7-amino-5-aryl-6-cyanopyrido[2,3-d]pyrimidines

A microwave-assisted method is described for monoacylating 7-amino-5-aryl-6-cyanopyrido[2,3-d]pyrimidines using excess acid chlorides in pyridine. A diacylated intermediate is effectively deacylated to the product amide by a macroporous-Tris resin. A small library of 17 amides was prepared to validate the method. The integration of commercial microwave technology into the ArQule chemistry platform is also discussed.     

Sol-Gel Nanosized Semiconducting Titania-Based Powders for Thick-Film Gas Sensors

Pure, 5 at%, and 10 at% Ta- or Nb-doped TiO₂ nanosized powders were prepared by the sol-gel method. The powders heated to 400°C have the crystalline anatase structure. While the pure TiO₂ powder heated to 850°C has the rutile structure, the addition of Ta and Nb inhibited the anatase-to-rutile phase transformation at this temperature. Ta was soluble in the titania lattice up to the concentration of 10 at%, while the solubility of Nb was 5 at%. Thick films were fabricated with these powders by screen printing technology and then fired at 650°C and 850°C for 1 h. SEM observations showed that the anatase-to-rutile phase transformation induces a grain growth of about one order of magnitude for pure TiO₂. The addition of Ta and Nb is effective to keep the TiO₂ grain size at the nanometric level even at 850°C. Conductance measurements showed that a good gas response is observed only for the nanostructured titania-based films. The CO response of these materials is only slightly affected by humidity.     

Patient-specific finite element analysis of popliteal stenting

Nitinol self-expanding stents are used for the endovascular management of peripheral artery diseases of the popliteal artery, which is located behind the knee joint. Unfortunately, the complex kinematics of the artery during the leg flexion leads to severe loading conditions, favouring the mechanical failure of the stent, calling for a specific biomechanical analysis. For this reason, in the present study we reconstruct by medical image analysis the patient-specific popliteal kinematics during leg flexion, which is subsequently exploited to compute the mechanical response of a stent model, virtually implanted in the artery by structural finite element analysis (FEA). The medical image analysis indicates a non-uniform configuration change of the artery during the leg flexion, leading to an increase of the vessel curvature above the knee. The computed mechanical response of the stent reflects the non-uniform configuration change of the artery as after the flexion the average stress is higher in the part of the stent located above the knee. Although the proposed analysis is limited to a case-study, it shows the capability of patient-specific FEA simulations to compute the mechanical response of a stent model subjected to the complex and severe loading conditions of the popliteal artery during leg flexion.     

Stochastic PAC models for vacancy motions with trapping and detrapping

In order to explain PAC data for tetragonal zirconia at temperatures between 900 and 1300oC, we have developed a four-state stochastic model. The model simulates vacancies which trap and detrap at a PAC probe nucleus. While trapped, the vacancies hop around the probe in equivalent sites. The four states in this Winkler–Gerdau stochastic theory are three trapped states with equivalent electric field gradients (EFGs) of different orientations and a detrapped state with a weaker EFG whose axis of symmetry is oriented along the diagonal between the three trapped EFGs. There are three hopping rates in this model: w, the rate a trapped vacancy hops around the probe, w_D, the detrapping rate, and w_t, the trapping rate. We report results of calculations for values of these hopping rates implied by our tetragonal zirconia data, and we report heuristic fitting functions which summarize the computer results and can be used to fit data efficiently for a wide range of parameters. This revised version was published online in August 2006 with corrections to the Cover Date.