Gauge invariance,charge conservation,and variational principles

We present new results on the correspondence between symmetries, conservation laws and variational principles for field equations in general non-abelian gauge theories. Our main result states that second order field equations possessing translational and gauge symmetries and the corresponding conservation laws are always derivable from a variational principle. We also show by the way of examples that the above result fails in general for third order field equations.     

NMR studies of the Zn2+ interactions with rat and human beta-amyloid (1-28) peptides in water-micelle environment

Alzheimer's disease is a fatal neurodegenerative disorder involving the abnormal accumulation and deposition of peptides (amyloid-beta, Abeta) derived from the amyloid precursor protein. Here, we present the structure and the Zn2+ binding sites of human and rat Abeta(1-28) fragments in water/sodium dodecyl sulfate (SDS) micelles by using 1H NMR spectroscopy. The chemical shift variations measured after Zn2+ addition at T>310 K allowed us to assign the binding donor atoms in both rat and human zinc complexes. The Asp-1 amine, His-6 Ndelta, Glu-11 COO-, and His-13 Nepsilon of rat Abeta28 all enter the metal coordination sphere, while His-6 Ndelta, His-13, His-14 Nepsilon, Asp-1 amine, and/or Glu-11 COO- are all bound to Zn2+ in the case of human Abeta28. Finally, a comparison between the rat and human binding abilities was discussed.     

MMM-QSAR recognition of ribonucleases without alignment: comparison with an HMM model and isolation from Schizosaccharomyces pombe, prediction, and experimental assay of a new sequence

The study of type III RNases constitutes an important area in molecular biology. It is known that the pac1+ gene encodes a particular RNase III that shares low amino acid similarity with other genes despite having a double-stranded ribonuclease activity. Bioinformatics methods based on sequence alignment may fail when there is a low amino acidic identity percentage between a query sequence and others with similar functions (remote homologues) or a similar sequence is not recorded in the database. Quantitative structure-activity relationships (QSAR) applied to protein sequences may allow an alignment-independent prediction of protein function. These sequences of QSAR-like methods often use 1D sequence numerical parameters as the input to seek sequence-function relationships. However, previous 2D representation of sequences may uncover useful higher-order information. In the work described here we calculated for the first time the spectral moments of a Markov matrix (MMM) associated with a 2D-HP-map of a protein sequence. We used MMMs values to characterize numerically 81 sequences of type III RNases and 133 proteins of a control group. We subsequently developed one MMM-QSAR and one classic hidden Markov model (HMM) based on the same data. The MMM-QSAR showed a discrimination power of RNAses from other proteins of 97.35% without using alignment, which is a result as good as for the known HMM techniques. We also report for the first time the isolation of a new Pac1 protein (DQ647826) from Schizosaccharomyces pombe strain 428-4-1. The MMM-QSAR model predicts the new RNase III with the same accuracy as other classical alignment methods. Experimental assay of this protein confirms the predicted activity. The present results suggest that MMM-QSAR models may be used for protein function annotation avoiding sequence alignment with the same accuracy of classic HMM models.     

Structural features of the Cu(II) complex with the rat Abeta(1-28) fragment

The interaction between Cu(II) and the rat amyloid beta (1-28) fragment in micellar solutions at pH 7.5 was investigated by CD and NMR spectroscopy; the proton-copper distances were used in restrained molecular dynamics simulations to obtain a structural model of the Cu(II) complex.     

CuII binding sites located at His-96 and His-111 of the human prion protein: thermodynamic and spectroscopic studies on model peptides

The prion protein (PrP) is a Cu(2+)-binding cell-surface glycoprotein. Using PrP peptide fragments, by means of potentiometric, spectroscopic and thermodynamic techniques, we have shown that Cu(2+) ions bind to the region comprising His-96, His-111 and the octarepeat domain within residues 60-91. Cu(2+) may bind in different modes, which strongly depend both on His position within the peptide sequence and on the adjacent residues. We have used a series of protected oligopeptides having His at the C- or the N-terminus, inducing different binding modes to amide nitrogens around the His residue, either towards the N- or C-terminus. His imidazole acts as an anchoring site for Cu(2+) and then binding to ionized amide nitrogens follows. When it is directed towards the C-terminus the formation of a less stable seven-membered chelate ring with a {N(im), N(-)} binding mode occurs. When coordination goes towards the N-terminus the thermodynamically more stable six-membered chelate ring is formed. NMR data suggest that both the coordination modes are possible for the model peptides; however, the thermodynamic measurements show that they only slightly differ in energy and the influence of the adjacent amino acid residues can address the coordination toward the C- or the N-terminus.     

Synthesis and complete assignment of the 1H and 13C NMR signals of some oxopyrancoumarin and oxofuropyrancoumarin derivatives

The synthesis of four pyranocoumarins starting from phloroglucinol and the complete (1)H and (13)C NMR assignment of seven pyranocoumarins has been performed using 1D and 2D NMR techniques including COSY, HMQC and HMBC experiments.     

Asymptotic decay under nonlinear and noncoercive dissipative effects for electrical conduction in biological tissues

We consider a nonlinear model for electrical conduction in biological tissues. The nonlinearity appears in the interface condition prescribed on the cell membrane. The purpose of this paper is proving asymptotic convergence for large times to a periodic solution when time-periodic boundary data are assigned. The novelty here is that we allow the nonlinearity to be noncoercive. We consider both the homogenized and the non-homogenized version of the problem.     

Free volume from molecular dynamics simulations and its relationships to the positron annihilation lifetime spectroscopy

The free volume micro-structural properties of propylene glycol obtained by means of molecular dynamics simulations have been investigated and compared with the experimental data from positron annihilation lifetime spectroscopy (PALS). The results are also compared to those recently obtained on glycerol. The bulk microstructures of the samples have been analyzed in the temperature range 100–350 K with a probe-based procedure for exploring the free volume cavities of the microstructures. The basic free volume property, i.e., mean cavity volume, is compared with the hole volume data from PALS. A comparison between calculated and experimental data suggests the existence of a threshold volume for the smallest cavity detectable by PALS, which may be ascribed to fast local motions of the matrix constituents. At high temperatures the cavity analysis reveals the formation of an infinite cavity, i.e., percolation phenomenon. The onset temperatures of the percolation process in propylene glycol and glycerol are found to be close to the characteristic PALS temperature \(T^{\rm L}_{\rm b2}\) , where a pronounced change in the PALS response occurs, as well as to the characteristic dynamic Schönhals temperature \(T^{\rm SCH}_{\rm B}\) , and Stickel’s temperature \(T^{\rm ST}_{\rm B}\) , marking a dramatic change in the primary α properties.     

Full-fledged proteomic analysis of bioactive wheat amylase inhibitors by a 3-D analytical technique: Identification of new heterodimeric aggregation states

Wheat proteinaceous alpha-amylase inhibitors (alpha-AIs) are increasingly investigated for their agronomical role as natural defence molecules of plants against the attack of insects and pests, but also for their effects on human health. The wheat genomes code for several bioactive alpha-AIs that share sequence homology, but differ in their specificity against alpha-amylases from different species and for their aggregation states. Wheat alpha-AIs are traditionally classified as belonging to the three classes of tetrameric, homodimeric and monomeric forms, each class being constituted by a number of polypeptides that display different electrophoretic mobilities. Here we describe a proteomic approach for the identification of bioactive alpha-AIs from wheat and, in particular, a 3-D technique that allows to best identify and characterize the dimeric fraction. The technique takes advantage of the thermal resistance of alpha-AIs (resistant to T > 70 degrees C) and consists in the separation of protein mixtures by 2-D polyacrylamide/starch electrophoresis under nondissociating PAGE (ND-PAGE, first dimension) and dissociating (urea-PAGE or U-PAGE second dimension) conditions, followed by in-gel spontaneous reaggregation of protein complexes and identification of the alpha-amylase inhibitory activity (antizymogram, third dimension) using enzymes from human salivary glands and from the larvae of Tenebrio molitor coleopter (yellow mealworm). Dimeric alpha-AIs from Triticum aestivum (bread wheat) were observed to exist as heterodimers. The formation of heterodimeric complexes was also confirmed by in vitro reaggregation assays carried out on RP-HPLC purified wheat dimeric alpha-AIs, and their bioactivity assayed by antizymogram analysis. The present 3-D analytical technique can be exploited for fast, full-fledged identification and characterization of wheat alpha-AIs.