Determination of Conformational Equilibria in Proteins Using Residual Dipolar Couplings

In order to carry out their functions, proteins often undergo significant conformational fluctuations that enable them to interact with their partners. The accurate characterization of these motions is key in order to understand the mechanisms by which macromolecular recognition events take place. Nuclear magnetic resonance spectroscopy offers a variety of powerful methods to achieve this result. We discuss a method of using residual dipolar couplings as replica-averaged restraints in molecular dynamics simulations to determine large amplitude motions of proteins, including those involved in the conformational equilibria that are established through interconversions between different states. By applying this method to ribonuclease A, we show that it enables one to characterize the ample fluctuations in interdomain orientations expected to play an important functional role.     

Dealing with Crystal Forms (The Kingdom of Serendip?)

The variety of crystal forms that may be associated with one specific molecule of interest can be extremely large: in addition to polymorphs, all sorts of crystalline solids can be obtained, from molecular and ionic co‐crystals to hydrates/solvates, to, needless to say, polymorphs of all these new crystal forms. Lack of predictability of crystallization experiments, far from representing a failure or a nuisance, should encourage in the crystal maker the same attitude shown by the three princes of Serendip (who were making unexpected discoveries by virtue of their “sagacity and readiness of mind”) to be ready to pick new avenues as the crystal experiments will yield something unplanned for.     

Chemical composition and antimicrobial activities of the essential oils from Ocimum selloi and Hesperozygis myrtoides

Ocimum selloi, a traditional medicinal plant from Brazil, is sold in open-air markets at Rio de Janeiro State. Hesperozygis myrtoides is a very aromatic small bush found in the State of Minas Gerais, Brazil, growing at an altitude of 1800m. The chemical composition of both essential oils was analyzed as well as their antimicrobial activity against fungi and bacteria. For all specimens of Ocimum selloi obtained at open-air markets, methylchavicol was major compound found (93.6% to 97.6%) in their essential oils. The major compounds identified in the oil of H. myrtoides were pulegone (44.4%), isomenthone (32.7%), and limonene (3.5%). Both oils displayed antimicrobial activity against all tested microorganisms but Candida albicans was the most susceptible one. Combinations of the two oils in different proportions were tested to verify their antimicrobial effect against C. albicans, which, however, was not modified in any of the concentrations tested. The minimum inhibitory concentration (MIC) was determined to confirm the antimicrobial activity against C. albicans as well as other clinical isolates (C. glabrata, C. krusei, C. parapsilosis and C. tropicalis).     

Monte Carlo computer simulations and electron microscopy of colloidal cluster formation via emulsion droplet evaporation

We consider a theoretical model for a binary mixture of colloidal particles and spherical emulsion droplets. The hard sphere colloids interact via additional short-ranged attraction and long-ranged repulsion. The droplet-colloid interaction is an attractive well at the droplet surface, which induces the Pickering effect. The droplet-droplet interaction is a hard-core interaction. The droplets shrink in time, which models the evaporation of the dispersed (oil) phase, and we use Monte Carlo simulations for the dynamics. In the experiments, polystyrene particles were assembled using toluene droplets as templates. The arrangement of the particles on the surface of the droplets was analyzed with cryogenic field emission scanning electron microscopy. Before evaporation of the oil, the particle distribution on the droplet surface was found to be disordered in experiments, and the simulations reproduce this effect. After complete evaporation, ordered colloidal clusters are formed that are stable against thermal fluctuations. Both in the simulations and with field emission scanning electron microscopy, we find stable packings that range from doublets, triplets, and tetrahedra to complex polyhedra of colloids. The simulated cluster structures and size distribution agree well with the experimental results. We also simulate hierarchical assembly in a mixture of tetrahedral clusters and droplets, and find supercluster structures with morphologies that are more complex than those of clusters of single particles.     

Studies on the reactivity of 3-methyl-4-nitro-5-styrylisoxazoles with S-nucleophiles

We have investigated the reactivity of 3-methyl-4-nitro-5-styrylisoxazoles with S-nucleophiles. This study revealed that the title compounds were optimal Michael acceptors toward thiols. A procedure was also established to prepare isoxazole-containing sulfides in one-pot and without the use of chromatography. Isoxazole-containing sulfides were converted into the corresponding sulfones in high yield.     

Towards a mesoscopic model of water-like fluids with hydrodynamic interactions

We present a mesoscopic lattice model for non-ideal fluid flows with directional interactions, mimicking the effects of hydrogen bonds in water. The model supports a rich and complex structural dynamics of the orientational order parameter, and exhibits the formation of disordered domains whose size and shape depend on the relative strength of directional order and thermal diffusivity. By letting the directional forces carry an inverse density dependence, the model is able to display a correlation between ordered domains and low density regions, reflecting the idea of water as a denser liquid in the disordered state than in the ordered one.     

Vectors for Glucose-Dependent Protein Expression in <Emphasis Type="Italic">Saccharomyces cerevisiae</Emphasis>

Based on the p426 series of expression vectors developed by Mumberg et al. (Gene 156, 119–122, 1995), we have generated a set of plasmids that allow the glucose-dependent expression of target genes in the yeast, Saccharomyces cerevisiae. The ADH1 promoter in plasmid p426-ADH1 was replaced by the 1-kb 5′-region from either of the following genes: HXK1, YGR243, HXT4 and HXT7. Expression mediated by the respective 5′-regions was monitored with EGFP, yEGFP3-CLN2pest and TurboGFP as marker genes. Fluorescence is induced 2.7-fold using the HXK1, 2.3-fold using the YGR243-, 5-fold using the HXT7- and 12.6-fold using the HXT4 5′-regions upon depletion of glucose to a concentration of <0.5 g/l.     

The effect of hydrothermal treatment on column performance for monolithic silica capillary columns

Monolithic silica capillary columns with i.d. 100 μm and monolithic silica rods were prepared with tetramethoxysilane (TMOS) or a mixture of TMOS and metyltrimethoxysilane (MTMS) using different hydrothermal treatments at T=80 °C or 120 °C. Nitrogen physisorption was applied for the pore characterization of the rods and inverse size exclusion chromatography (ISEC) for that of the capillary columns. Using nitrogen physisorption, it was shown change of pore size and surface area corresponds to that of hydrothermal treatment and silica precursor. The results from ISEC agreed well with those from nitrogen physisorption regarding the pore size distribution (PSD). In addition, the retention factors for hexylbenzene with the ODS-modified capillary columns in methanol/water=80/20 at T=30 °C could also support the results from nitrogen physisorption. Furthermore, column efficiency for the columns was evaluated with alkylbenzenes and three kinds of peptides, leucine-enkephalin, angiotensin II, and insulin. Column efficiency for alkylbenzenes was similar independently of the hydrothermal treatment at T=120 °C. Even for TMOS columns, there was no significant difference in column efficiency for the peptides despite the difference in hydrothermal treatment. In contrast, for hybrid columns, it was possible to confirm the effect on hydrothermal treatment at T=120 °C resulting in a different column efficiency, especially for insulin. This difference supports the results from both nitrogen physisorption and ISEC, showing the presence of more small pores of ca. 3-6 nm for a hybrid silica without hydrothermal treatment at T=120 °C. Consequently, the results suggest that hydrothermal treatment for a hybrid column with higher temperature or longer time is necessary, compared to that for a TMOS column, to provide higher column efficiency with increase in molecular size of solute.     

Immobilized trypsin on epoxy organic monoliths with modulated hydrophilicity: novel bioreactors useful for protein analysis by liquid chromatography coupled to tandem mass spectrometry

The development of epoxy organic monoliths with modulated hydrophilicity for the preparation of novel trypsin-based microreactors is reported. Porous polymer monoliths have been prepared using methacrylate chemistry triggered by γ-ray irradiation. In situ polymerization has been optimized and extended to medium and high polymer densities using glycidyl methacrylate (GMA) as reactive monomer as well as to the hydrophilic nature of the co-monomers (glyceryl monomethacrylate, GlyMA and acrylamide, AMD). Enzyme immobilization was smoothly achieved by passing a buffered trypsin solution through the columns kept at room temperature. The activities of the immobilized enzyme were characterized by the apparent Michaelis constant (K(m)) and the apparent maximum velocity (V(max)) of the reaction using a non chromogenic, low-molecular mass substrate N-α-benzoyl-l-arginine ethyl ester (BAEE). For the kinetic constants determination a new off-line chromatographic procedure was developed on purpose. The most efficient IMERs were obtained by immobilizing trypsin on monolithic skeleton prepared with hydrophilic monomers (GlyMA and AMD). One of the most promising bioreactor was applied to the digestion of model proteins with different molecular weight and complexity such as human serum albumin (HSA), β-casein and ribonuclease B (RNase B), and the produced peptides were analyzed by liquid chromatography-mass spectrometry. Using a digestion time of only 25 min the proteins were recognized by the database with satisfactory sequence coverage, which was 78.22, 49.76 and 80.68% for HSA, β-casein and RNase B, respectively.     

Description of sounds recorded from Longman's beaked whale, Indopacetus pacificus

Sounds from Longman's beaked whale, Indopacetus pacificus, were recorded during shipboard surveys of cetaceans surrounding the Hawaiian Islands archipelago; this represents the first known recording of this species. Sounds included echolocation clicks and burst pulses. Echolocation clicks were grouped into three categories, a 15 kHz click (n?=?106), a 25 kHz click (n?=?136), and a 25 kHz pulse with a frequency-modulated upsweep (n?=?70). The 15 and 25 kHz clicks were relatively short (181 and 144 ms, respectively); the longer 25 kHz upswept pulse was 288 ms. Burst pulses were long (0.5 s) click trains with approximately 240 clicks/s.