Exploitation of proteomics strategies in protein structure-function studies

Mass spectrometry plays a central role in structural proteomics, particularly in highly intensive structural genomics projects. This review paper reports some examples taken from recent work from the authors' laboratory and is aimed at showing that modem proteomics strategies are instrumental in the integration of structural genomic projects in fields such as: (i) protein-protein interactions, (ii) protein-DNA interactions, (iii) protein-ligand interactions, and (iv) protein-folding intermediates

On a Dirichlet problem with (p,q)(p,q)-Laplacian and parametric concave-convex nonlinearity

A homogeneous Dirichlet problem with $(p,q)$-Laplace differential operator and reaction given by a parametric $p$-convex term plus a $q$-concave one is investigated. A bifurcation-type result, describing changes in the set of positive solutions as the parameter $\lambda>0$ varies, is proven. Since for every admissible $\lambda$ the problem has a smallest positive solution $\bar u_{\lambda}$, both monotonicity and continuity of the map $\lambda \mapsto \bar u_{\lambda}$ are studied.Comment: 12 pages, comments are welcom

Moser iteration applied to elliptic equations with critical growth on the boundary

This paper deals with boundedness results for weak solutions of an elliptic equation where the functions are Carath\'eodory functions satisfying certain $p$-structure conditions that have critical growth even on the boundary. Based on a modified version of the Moser iteration we are able to prove that every weak solution of our problem is bounded up to the boundary. Under some additional assumptions this leads directly to $C^{1,\alpha}$-regularity for weak solutions of the problem.Comment: 17 pages; comments are welcom

Deamidation at Asparagine and Glutamine As a Major Modification upon Deterioration/Aging of Proteinaceous Binders in MuralPaintings

Proteomic strategies are herein proved to be a complementary approach to the well established amino acid composition analysis for the characterization of the aging and deterioration phenomena occurring to proteinaceous materials in works-of-art. Amino acid analyses on several samples demonstrated that proteins in the frescoes from the Camposanto Monumentale in Pisa are deteriorated as revealed by the decrease in Met, Lys, and Tyr content and by the presence in all the samples of amino malonic acid as a result of Ser, Phe, and Cys oxidation. Proteomic analysis identified deamidation at Asn and Gln as a further major event occurred. This work paves the way to the exploitation of proteomic strategies for the investigation of the molecular effects of aging and deterioration in historical objects. Results show that proteomic searches for deamidation by liquid chromatography-tandem mass spectrometry (LC-MS/MS) could constitute a routine analysis for paintings or any artistic and historic objects where proteins are present. Peptides that can be used as molecular markers when casein is present were identified

Structural characterization of the M* partly folded intermediate of wild-type and P138A EcAspAT

A combination of spectroscopic techniques, hydrogen/deuterium exchange, and limited proteolysis experiments coupled to mass spectrometry analysis was used to depict the topology of the monomeric M*partly folded intermediate of aspartate aminotransferase from Escherichia coli in wild type (WT) as well as in a mutant form in which the highly conserved cis-proline at position 138 was replaced by a trans-alanine (P138A). Fluorescence analysis indicates that, although M* is an off-pathway intermediate in the folding of WT aspartate aminotransferase from E. coli, it seems to coincide with an on-pathway folding intermediate for the P138A mutant. Spectroscopic data, hydrogen/deuterium exchange, and limited proteolysis experiments demonstrated the occurrence of conformational differences between the two M*intermediates, with P138A-M* being conceivably more compact than WT-M*. Limited proteolysis data suggested that these conformational differences might be related to a different relative orientation of the small and large domains of the protein induced by the presence of the cis-proline residue at position 138. These differences between the two M* species indicated that in WT-M* Pro138 is in the cis conformation at this stage of the folding process. Moreover, hydrogen/deuterium exchange results showed the occurrence of few differences in the native N2 forms of WT and P138A, the spectroscopic features and crystallographic structures of which are almost superimposabl

New supersymmetric Wilson loops in ABJ(M) theories

We present two new families of Wilson loop operators in N= 6 supersymmetric Chern-Simons theory. The first one is defined for an arbitrary contour on the three dimensional space and it resembles the Zarembo's construction in N=4 SYM. The second one involves arbitrary curves on the two dimensional sphere. In both cases one can add certain scalar and fermionic couplings to the Wilson loop so it preserves at least two supercharges. Some previously known loops, notably the 1/2 BPS circle, belong to this class, but we point out more special cases which were not known before. They could provide further tests of the gauge/gravity correspondence in the ABJ(M) case and interesting observables, exactly computable by localizationComment: 9 pages, no figure. arXiv admin note: text overlap with arXiv:0912.3006 by other author

Least energy sign-changing solution for degenerate Kirchhoff double phase problems

In this paper we study the following nonlocal Dirichlet equation of double phase type \begin{align*} -\psi \left [ \int_\Omega \left ( \frac{|\nabla u |^p}{p} + \mu(x) \frac{|\nabla u|^q}{q}\right)\,\mathrm{d} x\right] \mathcal{G}(u) = f(x,u)\quad \text{in } \Omega, \quad u = 0\quad \text{on } \partial\Omega, \end{align*} where $\mathcal{G}$ is the double phase operator given by \begin{align*} \mathcal{G}(u)=\operatorname{div} \left(|\nabla u|^{p-2}\nabla u + \mu(x) |\nabla u|^{q-2}\nabla u \right)\quad u\in W^{1,\mathcal{H}}_0(\Omega), \end{align*} $\Omega\subseteq \mathbb{R}^N$, $N\geq 2$, is a bounded domain with Lipschitz boundary $\partial\Omega$, $1<p<N$, $p<q<p^*=\frac{Np}{N-p}$, $0 \leq \mu(\cdot)\in L^\infty(\Omega)$, $\psi(s) = a_0 + b_0 s^{\vartheta-1}$ for $s\in\mathbb{R}$, with $a_0 \geq 0$, $b_0>0$ and $\vartheta \geq 1$, and $f\colon\Omega\times\mathbb{R}\to\mathbb{R}$ is a Carath\'{e}odory function that grows superlinearly and subcritically. We prove the existence of two constant sign solutions (one is positive, the other one negative) and of a sign-changing solution which has exactly two nodal domains and which turns out to be a least energy sign-changing solution of the problem above. Our proofs are based on variational tools in combination with the quantitative deformation lemma and the Poincar\'{e}-Miranda existence theorem