How does a hydrocarbon staple affect peptide hydrophobicity?

Water is essential for the proper folding of proteins and the assembly of protein–protein/ligand complexes. How water regulates complex formation depends on the chemical and topological details of the interface. The dynamics of water in the interdomain region between an E3 ubiquitin ligase (MDM2) and three different peptides derived from the tumor suppressor protein p53 are studied using molecular dynamics. The peptides show bimodal distributions of interdomain water densities across a range of distances. The addition of a hydrocarbon chain to rigidify the peptides (in a process known as stapling) results in an increase in average hydrophobicity of the peptide–protein interface. Additionally, the hydrophobic staple shields a network of water molecules, kinetically stabilizing a water chain hydrogen‐bonded between the peptide and MDM2. These properties could result in a decrease in the energy barrier associated with dehydrating the peptide–protein interface, thereby regulating the kinetics of peptide binding. © 2015 Wiley Periodicals, Inc.     

Potential of prodendronic polyamines with modulated segmental charge density as novel coating for fast and efficient analysis of peptides and basic proteins by CE and CE‐MS

In this work, the suitability of a new polymer family has been investigated as capillary coatings for the analysis of peptides and basic proteins by CE. This polymer family has been designed to minimize or completely prevent protein–capillary wall interactions and to modify the EOF. These coating materials are linear polymeric chains bearing as side cationizable moiety a dentronic triamine derived from N,N,N’,N’‐tetraethyldiethylenetriamine (TEDETA), which is linked to the backbone through a spacer (unit labeled as TEDETAMA). Four different polymers have been prepared and evaluated: a homopolymer which comprised only of those cationizable repetitive units of TEDETAMA, and three copolymers that randomly incorporate TEDETAMA together with neutral hydrosoluble units of N‐(2‐hydroxypropyl) methacrylamide (HPMA) at different molar percentages (25:75, 50:50 and 75:25). It has been demonstrated that the composition of the copolymers influences the EOF and therefore the separation of the investigated biopolymers. Among the novel polymers studied, poly‐(TEDETAMA‐co‐HPMA) 50:50 copolymer was successfully applied as coating material of the inner capillary surface in CE‐UV and CE‐MS, providing EOF reversing together with fast and efficient baseline separation of peptides and basic proteins. Finally, the feasibility of the polymer‐coated capillary was shown through the analysis of lysozyme in a cheese sample.     

Enhanced Photocatalytic Activity of MIL‐125 by Post‐Synthetic Modification with CrIII and Ag Nanoparticles

NH₂‐MIL‐125, [Ti₈O₈(OH)₄(bdc‐NH₂)₆] (bdc^2?=1,4‐benzene dicarboxylate) is a highly porous metal–organic framework (MOF) that has a band gap lying within the ultraviolet region at about 2.6 eV. The band gap may be reduced by a suitable post‐synthetic modification of the nanochannels using conventional organic chemistry methods. Here, it is shown that the photocatalytic activity of NH₂‐MIL‐125 in the degradation of methylene blue under visible light is remarkably augmented by post‐synthetic modification with acetylacetone followed by Cr^III complexation. The latter metal ion extends the absorption from the ultraviolet to the visible light region (band gap 2.21 eV). The photogenerated holes migrate from the MOF’s valence band to the Cr^III valence band, promoting the separation of holes and electrons and increasing the recombination time. Moreover, it is shown that the MOF’s photocatalytic activity is also much improved by doping with Ag nanoparticles, formed in situ by the reduction of Ag⁺ with the acetylacetonate pendant groups (the resulting MOF band gap is 2.09 eV). Presumably, the Ag nanoparticles are able to accept the MOF’s photogenerated electrons, thus avoiding electron–hole recombination. Both, the Cr‐ and Ag‐bearing materials are stable under photocatalytic conditions. These findings open new avenues for improving the photocatalytic activity of MOFs.     

Existence results for degenerate <Emphasis Type="Italic">p</Emphasis>(<Emphasis Type="Italic">x</Emphasis>)-Laplace equations with Leray-Lions type operators

We show the existence and multiplicity of solutions to degenerate p(x)-Laplace equations with Leray-Lions type operators using direct methods and critical point theories in Calculus of Variations and prove the uniqueness and nonnegativeness of solutions when the principal operator is monotone and the nonlinearity is nonincreasing. Our operator is of the most general form containing all previous ones and we also weaken assumptions on the operator and the nonlinearity to get the above results. Moreover, we do not impose the restricted condition on p(x) and the uniform monotonicity of the operator to show the existence of three distinct solutions.     

A note on fractional $${\varvec{}}$$-Lalacian roblems with singular weights

We study a class of fractional p-Laplacian problems with weights which are possibly singular on the boundary of the domain. We provide existence and multiplicity results as well as characterizations of critical groups and related applications.     

The Parametrically Forced Pendulum: A Case Study in 1 1/2 Degree of Freedom

This paper is concerned with the global coherent (i.e., non-chaotic) dynamics of the parametrically forced pendulum. The system is studied in a === degree of freedom Hamiltonian setting with two parameters, where a spatio-temporal symmetry is taken into account. Our explorations are restricted to large regions of coherent dynamics in phase space and parameter plane. At any given parameter point we restrict to a bounded subset of phase space, using KAM theory to exclude an infinitely large region with rather trivial dynamics. In the absence of forcing the system is integrable. Analytical and numerical methods are used to study the dynamics in a parameter region away from integrability, where the analytic results of a perturbation analysis of the nearly integrable case are used as a starting point. We organize the dynamics by dividing the parameter plane in fundamental domains, guided by the linearized system at the upper and lower equilibria. Away from integrability some features of the nearly integrable coherent dynamics persist, while new bifurcations arise. On the other hand, the chaotic region increases.2000 Mathematical Subject Classification: 37J20, 37J40, 37M20, 70H08.Dedicated to Professor Shui-Nee Chow on the occasion of his 60th birthday.     

Facile preparation of recyclable biocatalyst-decorated magnetic nanobeads in aqueous media

A facile process was developed to manufacture biocatalyst-conjugated magnetic nanobeads, which afford no loss of the intrinsic activity and enantioselectivity of biocatalysts. Up to 90% of their activities remained after six-time recycling in aqueous media.     

Analysis of chiral amino acids in cerebrospinal fluid samples linked to different stages of Alzheimer disease

Chiral micellar electrokinetic chromatography with laser-induced fluorescence detection (chiral-MEKC-LIF) was used to investigate D- and L-amino acid contents in cerebrospinal fluid (CSF) samples related to different Alzheimer disease (AD) stages. CSF samples were taken from (i) control subjects (S1 pool), (ii) subjects showing a mild cognitive impairment who remained stable (S2 pool), (iii) subjects showing an mild cognitive impairment that progressed to AD (S3 pool) and (iv) subjects diagnosed with AD (S4 pool). The optimized procedure only needed 10 μL of CSF and it included sample cleaning, derivatization with FITC and chiral-MEKC-LIF separation. Eighteen standard amino acids were baseline separated with efficiencies up to 703,000 plates/m, high sensitivity (LODs in the nM range) and good resolution (values ranging from 2.6 to 9.5). Using this method, L-Arg, L-Leu, L-Gln, γ-aminobutyric acid, L-Ser, D-Ser, L-Ala, Gly, L-Lys, L-Glu and L-Asp were detected in all the CSF samples. S3 and S4 samples (i.e. AD subjects) showed significant lower amounts of L-Arg L-Lys, L-Glu and L-Asp compared to the non-AD S1 and S2 samples, showing in the S4 group the lowest amounts of L-Arg L-Lys, L-Glu and L-Asp. Moreover, γ-aminobutyric acid was significantly higher in AD subjects with the highest amount also found for S4. No significant differences were observed for the rest of amino acids including D-Ser. Based on the obtained chiral-MEKC-LIF data, it was possible to correctly classify all the samples into the four groups. These results demonstrate that the use of enantioselective procedures as the one developed in this work can provide some new light on the investigations of AD, including the discovery of new biomarkers related to different stages of AD.     

High-performance liquid chromatography-diode array detection-electrospray ionization multi-stage mass spectrometric screening of an insect/plant system: the case of Spodoptera littoralis/Lycopersicon esculentum phenolics and alkaloids

High-performance liquid chromatography-diode array detection-electrospray ionization multi-stage mass spectrometry (HPLC-DAD-ESI-MS(n)) is considered to be a very valuable tool for the characterization of compounds found in trace amounts in natural matrices, as their previous isolation and clean-up steps can be avoided. Micro-scale separation increases the potential of this analytical technique, allowing the determination of compounds in reduced samples. Spodoptera littoralis represents a major challenge to Solanaceae plants, as it is one of the most deleterious pests. The S. littoralis/Lycopersicon esculentum system was studied for the first time concerning glycoalkaloids and phenolics. Using HPLC-DAD-ESI-MS(n) we were able to characterize 15 phenolic compounds in L. esculentum leaves. Nine of them are reported for the first time. Some differences were found between leaves of cerasiforme and 'Bull's heart' varieties. However, in the materials of S. littoralis (larvae, adults, exuviae and excrements) reared in both L. esculentum leaves no phenolics were identified. α-Tomatine was the main glycoalkaloid in the host plant. The glycoalkaloid composition of the different S. littoralis materials was distinct, with α-tomatine and dehydrotomatine being the main detected compounds in larvae and excrements. These results add knowledge to the ecological interaction in this insect/plant duo, for which it is hard to obtain considerable sample amounts.