Recent progress in protein 3D structure comparison

Quantitation of protein 3-D structure similarity is crucial in such fields as evolutionary studies, structural modeling and prediction of biological function. There are various approaches, many of which are tailored to specific problems. This review summarizes the recent developments in this field with particular interest in two main areas: i) improvements to and statistical interpretation of the root-man-square distance between equivalent atoms, rmsd; and ii) methods of protein structural classification based on geometrical features. Special attention is given to fast methods capable of analyzing large structural databases.     

Rheology of a lyotropic mesophase through a stress-relaxation experiment

We report on the first rheological study of the structural relaxations in a nematic liquid crystalline phase. Linear dynamic and transient shear experiments were applied to a polydomain nematic phase of the CTAB/water system: a liquid crystalline mixture composed of 28 wt% CTAB at 35 degrees C. The decay of the shear modulus, G(t), was analyzed using the CONTIN inverse Laplace transform to obtain a distribution of relaxation times which were compared with ones from the usual fitting procedure based on a generalized Maxwell model. The behavior of the nematic lyotropic structure of the CTAB/water system is characterized by the presence of both slow and fast relaxation times. These were interpreted as being due to a progressive loss of the lyotropic domain orientation and to the breaking/reforming process of the cylindrical aggregates, respectively.     

A biofunctional polymeric coating for microcantilever molecular recognition

An innovative route to activate silicon microcantilevers (MCs) for label free molecular recognition is presented. The method consists in coating the underivatized MCs with a functional ter-polymer based on N,N-dimethylacrylamide (DMA) bearing N-acryloyloxysuccinimide (NAS) and 3-(trimethoxysilyl)propyl-methacrylate (MAPS), two functional monomers that confer to the polymer the ability to react with nucleophilic species on biomolecules and with glass silanols, respectively. The polymer was deposited onto MCs by dip coating. Polymer coated MCs were tested in both static and dynamic modes of actuation, featuring detection of DNA hybridization as well as protein/protein interaction. In the dynamic experiments, focused on protein detection, the MCs showed an average mass responsivity of 0.4 Hz/pg for the first resonant mode and of 2.5 Hz/pg for the second resonant mode. The results of the static experiments, dedicated to DNA hybridization detection, allowed for direct estimation of the DNA duplex formation energetics, which resulted fully consistent with the nominal expected values. These results, together with easiness and cheapness, high versatility, and excellent stability of the recognition signal, make the presented route a reliable alternative to standard SAM functionalization (for microcantilevers (MCs) and for micro-electro-mechanical systems (MEMS) in general).     

A solid-phase approach to the synthesis of N-1-alkyl analogues of cyclic inosine-diphosphate-ribose (cIDPR)

We report here an efficient solid-phase synthesis of N-1-alkyl-substituted analogues of cyclic inosine-diphosphate-ribose (cIDPR), a mimic of cyclic ADP-ribose (cADPR). Our synthetic strategy makes use of a polystyrene support to which inosine was bonded through a 2′,3′-acetal linkage. Insertion of a ω-hydroxy-polymethylene chain of variable length on N-1, followed by conversion into N-1-alkylinosine-bis-phosphate derivatives and cyclization, allowed to obtain analogues of cIDPR of various ring size. The cyclization step was carried out both in solid-phase and in solution by pyrophosphate bond formation. The effect of the N-1-polymethylene chain length on the cyclization yields as well as the reaction conditions, which led to the solid-phase pyrophosphate bond formation, were thoroughly investigated.     

Experimental evidence of non-standard bifurcations in non-smooth oscillator dynamics

Analytical and experimental investigations are performed in order to characterize the dynamic behaviour of a non-smooth rotational oscillator, which exhibits multiple discontinuity boundaries in the phase space. The physical system consists of a rotating body subjected to an elastic restoring force and in contact with one or two rough discs rotating with constant driving velocities. The presence of multiple discontinuity boundaries caused by frictional contacts leads to non-standard bifurcations that are studied by means of a simple mechanical model.A test set-up has then been built to investigate the correctness of modelling of the friction force and the validity of the proposed model for technical applications: the experimental measurements qualitatively and quantitatively capture the basic scenarios anticipated by the model while a strong robustness of the phenomena pointed out by the theoretical analyses has been revealed in the experiments.     

Testing the suitability of different high-performance liquid chromatographic methods to determine aflatoxin M1 in a soft fresh Italian cheese

Aflatoxin M1 (AFM1) is a toxic undesirable compound in milk. AFM1 affinity for caseins causes a concentration effect during milk process for dairy transformation. In spite of this, no official method of analysis, nor maximum tolerance level for aflatoxin M1 in cheese have been established. Thus, the aim of this work was to test the suitability of different HPLC methods for the AFM1 quantification in soft cheese samples at three different contamination levels (low, medium and high, at respectively nearly 30, 100 and 250 ng/kg). Nine participants were selected among Italian laboratories accredited by the Italian accreditation body (ACCREDIA) for HPLC toxin analysis. They were asked to analyze samples applying the method routinely used. The different applied methods were compared, and precision and accuracy parameters were evaluated. The main differences among HPLC procedures were registered at the level of extraction step. The use of an enzymatic digestion for the extraction of the toxin from cheese seemed to be particularly advantageous and the use of immunoaffinity columns seemed to be determinant for the improvement of sensitivity at low contamination levels. In general, the applied methods well discriminated the 3 levels of contamination, even though they performed better at the medium and high concentration levels (100 and 250 ng/kg) than at the low one (30 ng/kg). In fact relative standard deviation for reproducibility at low level was higher (60.1%) than the same value at medium and high levels (22.8% and 28.9%, respectively).     

Experimental evidence of bifurcating nonlinear normal modes in piecewise linear systems

A system with piecewise linear restoring forces, typical of damaged beams with a breathing crack, exhibits bifurcations characterized by the onset of superabundant modes in internal resonance with a significantly different shape than that of modes on a fundamental branch. A 2-DOF frame with piecewise linear stiffness is analyzed by means of an experimental investigation; the frame is forced by an harmonic base excitation and the operative modal shapes as well as the response amplitude are directly measured; the results are compared with numerical outcomes for different damping values. This study shows that the shapes and the frequencies of certain nonlinear normal modes (NNMs) of the related autonomous system strongly affect the forced response, in both the numerical and the experimental environments. Therefore, it is possible to match the NNM with the forced response of the system, leading to the prospect of identifying the severity and position of the damage from experimental tests.     

A cryogenic underground observatory for rare events: CUORE, an update

CUORE is a proposed tightly packed array of 1000 TeO₂ bolometers, each being a cube 5 cm on a side with a mass of 750 g. The array consists of 25 vertical towers, arranged in a square of 5 towers by 5 towers, each containing ten layers of four crystals. The design of the detector is optimized for ultralow-background searches for neutrinoless double beta decay of ¹³⁰Te (33.8% abundance), cold dark matter, solar axions, and rare nuclear decays. A preliminary experiment involving 20 crystals of various sizes (MIBETA) has been completed, and a single CUORE tower is being constructed as a smaller scale experiment called CUORICINO. The expected performance and sensitivity, based on Monte Carlo simulations and extrapolations of present results, are reported.