Rapid acquisition of 1H and 19F NMR experiments for direct and competition ligand-based screening

Direct and competition ligand-based NMR experiments are often used in the screening of chemical fragment libraries against a protein target due to the high relative sensitivity of NMR for protein-binding events. A plethora of NMR methods has been proposed for this purpose. Two of these techniques are the (19)F T(2) filter and the (1)H selective T(2) filter experiments. Modifications of the pulse sequences of these experiments have resulted in a ～2-fold reduction in the experiment time thus allowing an increase in the screening throughput and making NMR an attractive technique for screening large compound collections.     

Trichogin GA IV: a versatile template for the synthesis of novel peptaibiotics

Trichogin GA IV, isolated from the fungus Trichoderma longibrachiatum, is the prototype of lipopeptaibols, the sub-class of short-length peptaibiotics exhibiting membrane-modifying properties. This peptaibol is predominantly folded in a mixed 3(10)-/α- helical conformation with a clear, albeit modest, amphiphilic character, which is likely to be responsible for its capability to perturb bacterial membranes and to induce cell death. In previous papers, we reported on the interesting biological properties of trichogin GA IV, namely its good activity against Gram positive bacteria, in particular methicillin-resistant S. aureus strains, its stability towards proteolytic degradation, and its low hemolytic activity. Aiming at broadening the antimicrobial activity spectrum by increasing the peptide helical amphiphilicity, in this work we synthesized, by solution and solid-phase methodologies, purified and fully characterized a set of trichogin GA IV analogs in which the four Gly residues at positions 2, 5, 6, 9, lying in the poorly hydrophilic face of the helical structure, are substituted by one (position 2, 5, 6 or 9), two (positions 5 and 6), three (positions 2, 5, and 9), and four (positions 2, 5, 6, and 9) Lys residues. The conformational preferences of the Lys-containing analogs were assessed by FT-IR absorption, CD and 2D-NMR techniques in aqueous, organic, and membrane-mimetic environments. Interestingly, it turns out that the presence of charged residues induces a transition of the helical conformation adopted by the peptaibols (from 3(10)- to α-helix) as a function of pH in a reversible process. The role played in the analogs by the markedly increased amphiphilicity was further tested by fluorescence leakage experiments in model membranes, protease resistance, antibacterial and antifungal activities, cytotoxicity, and hemolysis. Taken together, our biological results provide evidence that some of the least substituted among these analogs are good candidates for the development of new membrane-active antimicrobial agents.     

A solvent-dependent peptide spring unraveled by 2D-NMR

In this work, we introduce a 2D-NMR method to discriminate between the fully-extended and the 3₁₀-helical conformations for the C^α,α-diethylglycine homo-peptides in the solution phase. It is based on the observation of divergent cross-peak intensities in the NOESY spectra. In particular, any βCH₂(i-1)→NH(i) cross peak is more intense than the intraresidue βCH₂(i)→NH(i) cross peak when the peptide adopts the fully-extended conformation. In this 3D-structure a marked splitting of the chemical shifts of the two non-equivalent βCH₂ protons is also apparent. In contrast, an opposite trend of intensities of the same NOE cross-peaks indicates the occurrence of a 3₁₀-helical conformation. This 3D-structural shift is induced by a change in the nature of solvent.     

Computational studies of the metal-binding site of the wild-type and the H46R mutant of the copper, zinc superoxide dismutase

Impairment of the Zn(II)-binding site of the copper, zinc superoxide dismutase (CuZnSOD) protein is involved in a number of hypotheses and explanations for the still unknown toxic gain of function mutant varieties of CuZnSOD that are associated with familial forms of amyotrophic lateral sclerosis (ALS). In this work, computational chemistry methods have been used for studying models of the metal-binding site of the ALS-linked H46R mutant of CuZnSOD and of the wild-type variety of the enzyme. By comparing the energy and electronic structure of these models, a plausible explanation for the effect of the H46R mutation on the zinc site is obtained. The computational study clarifies the role of the D124 and D125 residues for keeping the structural integrity of the Zn(II)-binding site, which was known to exist but its mechanism has not been explained. Earlier results suggest that the explanation for the impairment of the Zn(II)-site proposed in this work may be useful for understanding the mechanism of action of the ALS-linked mutations in CuZnSOD in general.     

Correction of optical distortions in dry depth profiling with confocal Raman microspectroscopy

We present a generalized approach to obtain improved Raman intensity profiles from in‐depth studies performed by confocal Raman microspectroscopy (CRM) with dry objectives. The approach is based on regularized deconvolution of the as‐measured confocal profile, through a kernel that simulates optical distortions due to diffraction, refraction and collection efficiency on the depth response. No specific shape or restrictions for the recovered profile are imposed. The strategy was tested by probing, under different instrumental conditions, a series of model planar interfaces, generated by the contact of polymeric films of well‐defined thickness with a substrate. Because of the aforementioned optical distortions, the as‐measured confocal response of the films appeared highly distorted and featureless. The signal computed after deconvolution recovers all the films features, matching very closely with the response expected. Copyright © 2011 John Wiley & Sons, Ltd.     

FT-infrared band analysis and temperature programmed dessorption for the Y,L and ferrierite zeolites

With the aim to qualifying and quantifying the acidity of the Y, L and ferrierite zeolites, an infrared band analysis of pyridine adsorption and programmed temperature dessorption measurements were carried out to a set of nine samples of the Y, L and ferrierite zeolites. The infrared spectra before and after the pyridine adsorption process had revealed that the ferrierite zeolite shows, almost in the totality, Br?nsted acid sites. The Y and L zeolites present, also, significative concentrations of Br?nsted and Lewis acid sites. These facts allow to conclude that zeolite ferrierite is the strongest acid zeolite among these three types.     

The Social Climbing Game

The structure of societies depends, to some extent, on the incentives of the individuals they are composed of. We study a stylized model of this interplay, that suggests that the more individuals aim at climbing the social hierarchy, the more society’s hierarchy gets strong. Such a dependence is sharp, in the sense that a persistent hierarchical order emerges abruptly when the preference for social status gets larger than a threshold. This phase transition has its origin in the fact that the presence of a well defined hierarchy allows agents to climb it, thus reinforcing it, whereas in a “disordered” society it is harder for agents to find out whom they should connect to in order to become more central. Interestingly, a social order emerges when agents strive harder to climb society and it results in a state of reduced social mobility, as a consequence of ergodicity breaking, where climbing is more difficult.     

Application of a He3Ne infrared laser source for detection of geometrical dimensions of cracks and scratches on finished surfaces of metals

In this study, the authors addressed a new method of measurement for microscratches and cracks on finished metallic surfaces. The technology proposed here can be used in aviation, automobile, machine-tools, bearings, electrical and thermal devices (detection of electrical and thermal contact resistance), and many other industrial fields where finished surfaces have to be inspected for quality before use. The technology is based on the application of He3Ne laser optics. This measurement method allows for the inspection of geometrical parameters such as depth and width of scratches and cracks and consists of a low-energy He3Ne red laser beam (wavelength 633 nm) with a cross-section of 0.48 mm, beam expander with special designed slit, multi-axis stage with sample holder and CCD (charge-coupled device) visual detection system. Using experimental data, a mathematical algorithm was created in order to calculate the depths and widths of the scratches and cracks where the method of center of gravity (centroid) of the imaged area was used. The results showed a good correlation between the experimental and calculated values of the dimensions of the scratches. Future work will deal with the determination of the geometrical dimensions of microcracks.     

A phase-field model for quasi-incompressible solid–liquid transitions

According to a unified thermodynamic scheme, we derive the general kinetic equation ruling the phase-field evolution in a binary quasi-incompressible mixture for both transition and separation phenomena. When diffusion effects are negligible in comparison with source and production terms, a solid–liquid phase transition induced by temperature and pressure variations is obtained. In particular, we recover the explicit expression of the liquid–pressure curve separating the solid from the liquid stability regions in the pressure–temperature plane. Consistently with physical evidence, its slope is positive (negative) for substances which compress (expand) during the freezing process.     

On the Null Cone for Quiver Representations Under Reflection Functors

Let d be a prehomogeneous dimension vector for a connected quiver Q with the property that c ^? d has a negative entry for some ? ∈ ? where c is the Coxeter transformation corresponding to an admissible numbering of the vertices Q ₀ of Q. Denote by rep(Q, d) the variety of d-dimensional representations of Q and by Sl(d) the product of the special linear groups at all vertices Q ₀. We show how to find the irreducible components of the null cone of the algebraic quotient rep(Q, d)//Sl(d).