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.

Metal chelates anchored to poly-L-peptides and linear D,L-α-peptides with promising nanotechnological applications.

Regular configurationally alternating amino acid sequences generate cyclic and linear helical peptides with a local β-conformation able to self-assemble in nanowires and nanoscaffolds directed and stabilized by hydrogen bonds. The possibility of modulating the chemical profile of the various amino acid residues containing reactive side chains means that peptides could be flexible templates for creating various building blocks. A method for the design of molecules with potential spintronic properties is described.

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.

Discrete Haar transform and protein structure.

The discrete Haar transform of the sequence of the backbone dihedral angles (phi and psi) was performed over a set of X-ray protein structures of high resolution from the Brookhaven Protein Data Bank. Afterwards, the new dihedral angles were calculated by the inverse transform, using a growing number of Haar functions, from the lower to the higher degree. New structures were obtained using these dihedral angles, with standard values for bond lengths and angles, and with omega = 0 degree.

A graph-topological approach to recognition of pattern and similarity in RNA secondary structures.

Secondary and tertiary RNA structures play an important role in many biological processes. Therefore the necessity arises to find similar higher-order structures for different but functionally homologous RNA sequences. We propose here a graph-topological approach to the problem, which shows two main features: simplified graph representation which allows the recognition of similarity of RNA secondary structures with the same branching look despite minor differences.

A genetic algorithm to search for optimal and suboptimal RNA secondary structures.

Genetic algorithms are a search method used in solving problems by selection, recombination and mutation of tentative solutions, until the better ones are achieved. They are very efficient when the 'building block' hypothesis is effective for the solutions, which means that a better solution can be obtained by assembling short 'motifs' or 'schemata' that can be retrieved in some other worse solutions. The additive nature of the secondary structure free energy rules suggests the validity of this hypothesis, and therefore the likely power of a genetic algorithm approach to search for RNA secondary structures.

Recognition of the folding consensus in RNA secondary structures by the topological-filtering method.

Functionally homologous RNA sequences can substantially diverge in their primary sequences but it can be reasonably assumed that they are related in their higher-degree structures. The problem to find such structures and simultaneously satisfy as far as possible the free-energy-minimization criterion, is considered here in two aspects. Firstly a quantitative measure of the folding consensus among secondary structures is defined, translating each structure into a linear representation and using the correlation theorem to compare them.

Three-dimensional folding of Tetrahymena thermophila rRNA IVS sequence: a proposal.

We studied the Tetrahymena thermophila rRNA IVS sequence with the aim of obtaining a model of the structure characterized by the bases proximity of the self-reactions sites. The considered sequence kept up those fragments essential for its catalytic activity as demonstrated by deletion mutants. The first step was the theoretical analysis with a computer method previously proposed, to find optimal free energy secondary structures with the required features, under the suitable constrains.

Secondary structures of Tetrahymena thermophila rRNA IVS sequence involved in its self-splicing reactions: a new computer analysis.

The secondary structures of Tetrahymena thermophila rRNA IVS sequence involved in the self-splicing reactions, are theoretically investigated with a refined computer method previously proposed, able to select a set of the deepest free energy RNA secondary structures under constraints of model hypotheses and experimental evidences. The secondary structures obtained are characterized by the close proximity of self-reactions sites and account for double mutations experiments, and differential digestion data.

A new method to find a set of energetically optimal RNA secondary structures.

We present a computer method to determine nucleic acid secondary structures. It is based on three steps: 1) the search for all possible helical regions relied on a mathematical approach derived from the convolution theorem; it uses a tetradimensional complex vector representation of the bases along the sequence; 2) a 'tree' search for a set of minimum free energy structures, by the aid of an approximate energy evaluation to reduce the computer time requirements; 3) the exact calculation and refinement of the energies. A method to introduce the experimental data and reach an arrangement between them and the free energy minimization criterion is shown.

Specific interactions between DNA left-handed supercoils and actinomycin D.

The interactions between the natural cyclopentapeptide antibiotic actinomycin D (ACT) and circular pBR322 DNA have been studied by freezing the topological state of the DNA in the complex by topoisomerase I reaction. Both supercoiled and relaxed DNAs, in the complexes at low antibiotic/DNA base-pair ratios, showed a dramatic decrease in linking number that cannot be explained by taking into account only the generally accepted unwinding of 28 degrees for each ACT molecule bound. Recent results derived from the crystallographic analysis of the complex between GpC and ACT suggest that ACT could mediate non-covalent cross-links between distant sections of DNA.

DNA topology in a chromatin model system.

The synthetic copolypeptide (Lys33, Leu67)100-Orn20, modeled on some general features of the histone sequences, has been found to supercoil the DNA double helix, wrapping it into a micelle, as a result of cohesive interactions between the polypeptide hydrophobic moieties. X-ray low-angle diffraction of complexes between the polypeptide and DNA is characterized by maxima at 50, 32, and 23 A, reminiscent of the chromatin pattern. The existence of a nucleosome-like structure along the DNA is suggested by gel electrophoresis analysis of DNA fragments after micrococcal nuclease digestion, showing the presence of a fragment of about 100 basepairs (bp) long.