Polymorphic Self-Organization of Lauroyl Peptide in Response to pH and Concentration.

Amphipathic peptides are attractive building blocks for the preparation of self-assembling, bio-inspired, and stimuli responsive nanomaterials with pharmaceutical interest. The bioavailability of these materials can be improved with the insertion of d amino acid residues to avoid fast proteolysis in vivo. With this knowledge, a new lauroyl peptide consisting of a sequence of glycine, glycine, d-serine, and d-lysine was designed.

Switchable length nanotubes from a self-assembling pH and thermosensitive linear l,d-peptide-polymer conjugate.

Preparation and characterization of a pH and thermosensitive linear l,d-octapeptide-poly(dimethylamino ethyl methacrylate) ((l-Val-d-Val)-PDMAEMA) conjugate is reported. The hydrophobic uncharged linear (l-Val-d-Val) octapeptide was designed to self-assemble in nanotubes by exploiting the tubular self-assembling properties of linear peptides with regularly alternating enantiomeric sequences. pH and thermosensitive PDMAEMA was obtained by atom transfer radical polymerization (ATRP).

Oxidized Buckypaper for Stir-Disc Solid Phase Extraction: Evaluation of Several Classes of Environmental Pollutants Recovered from Surface Water Samples.

This paper describes, for the first time, the use of oxidized buckypaper (BP) as a sorbent membrane of a stir-disc solid phase extraction module. The original device, consisting of a BP disc ( d = 34 mm) enveloped in a polypropylene mesh pouch, was designed to extract organic micropollutants (OMPs) from environmental water samples in dynamic mode. High-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) was used to analyze the extracts.

Liquid chromatography/mass spectrometry identification of intermediates and vulcanization products by using squalene as vulcanization model compound.

Rationale: Sulfur-vulcanized rubber is a three-dimensional polymer network, insoluble in all organic solvents. For this reason, vulcanization products are difficult to study and identify by conventional analytical techniques. To simplify this task, low molecular weight olefins have been used as model compounds (MCs) in place of rubber in vulcanization experiments.

Geometrical, conformational and topological restraints in regular nucleosome compaction in chromatin.

The folding of the nucleosome array into a chromatin fiber modulates DNA accessibility and is therefore an important factor for the control of gene expression. The statistical analysis of the nucleosome repeat length in chromatin fibers reveals the presence of a ten-fold periodicity suggesting the existence of orientational constraints of the nucleosome units that provide the geometrical conditions of helical conformations. Recently, the elucidation of the x-ray crystal structure of a nucleosome tetramer array and the interpretation of electron microscopy images of reconstituted nucleosome arrays suggested two different architectures of the chromatin fiber.

Prediction of nucleosome positioning in genomes: limits and perspectives of physical and bioinformatic approaches.

Nucleosomes, the fundamental repeating subunits of all eukaryotic chromatin, are responsible for packaging DNA into chromosomes inside the cell nucleus and controlling gene expression. While it has been well established that nucleosomes exhibit higher affinity for select DNA sequences, until recently it was unclear whether such preferences exerted a significant, genome-wide effect on nucleosome positioning in vivo. For this reason, an increasing interest is arising on a wide-ranging series of experimental and computational analyses capable of predicting the nucleosome positioning along genomes.

A statistical thermodynamic approach for predicting the sequence-dependent nucleosome positioning along genomes.

Nucleosomes are the fundamental repeating unit of chromatin and constitute the structural building blocks of the eukaryotic genome. The distribution of nucleosomes along the genome is a significant aspect of chromatin structure and influences gene regulation through modulation of DNA accessibility. For this reason, an increasing interest is arising in models capable of predicting the nucleosome positioning along genomes.

Peptides with regular enantiomeric sequences: a wide class of modular self-assembling architectures.

Organic trans-annular assemblies constitute an expanding class of structures with promising applications for the design of nanotechnological devices. Among the strategies developed for the engineering of organic nanotubes, those characterized by regular alternating enantiomeric amino acid sequences have been proven particularly useful. In fact, cyclic peptides with an even number of regularly alternating D- and L-amino acids have the tendency to adopt local beta-conformation that are capable of forming trans-annular self-assembling architectures, hydrogen bond directed.

A statistical approach for analyzing structural and regulative information in prokaryotic genomes.

Although DNA is iconized as a straight double helix, it does not exist in this canonical form in biological systems. Instead, it is characterized by sequence dependent structural and dynamic deviations from the monotonous regularity of the canonical B-DNA. Despite the complexity of the system, we showed that DNA structural and dynamics large-scale properties can be predicted starting from the simple knowledge of nucleotide sequence by adopting a statistical approach.

A simple procedure to weight empirical potentials in a fitness function so as to optimize its performance in ab initio protein-folding problem.

In an approach to the protein folding problem by a Genetic Algorithm, the fitness function plays a critical role. Empirical potentials are generally used to build the fitness function, and they must be weighted to obtain a valuable one. The weights are generally found by the comparison with a set of misfolded structures (decoys), but a dependence of the obtained fitness generally arises on the used decoys.