A critical concentration of N-terminal pyroglutamylated amyloid beta drives the misfolding of Ab1-42 into more toxic aggregates.

A wide consensus based on robust experimental evidence indicates pyroglutamylated amyloid-β isoform (AβpE3-42) as one of the most neurotoxic peptides involved in the onset of Alzheimer's disease. Furthermore, AβpE3-42 co-oligomerized with excess of Aβ1-42, produces oligomers and aggregates that are structurally distinct and far more cytotoxic than those made from Aβ1-42 alone. Here, we investigate quantitatively the influence of AβpE3-42 on biophysical properties and biological activity of Aβ1-42.

Electrostatic theory of the assembly of PAMAM dendrimers and DNA.

The electrostatic interactions mediated by counterions between a cationic PAMAM dendrimer, modelized as a sphere of radius and cationic surface charge highly increasing with generation, and a DNA, modelized as an anionic elastic line, are analytically calculated in the framework of condensation theory. Under these interactions the DNA is wrapped around the sphere. For excess phosphates relative to dendrimer primary amines, the free energy of the DNA-dendrimer complex displays an absolute minimum when the complex is weakly negatively overcharged.

Lamellar cationic lipid-DNA complexes from lipids with a strong preference for planar geometry: A Minimal Electrostatic Model.

We formulate and analyze a minimal model, based on condensation theory, of the lamellar cationic lipid (CL)-DNA complex of alternately charged lipid bilayers and DNA monolayers in a salt solution. Each lipid bilayer, composed by a random mixture of cationic and neutral lipids, is assumed to be a rigid uniformly charged plane. Each DNA monolayer, located between two lipid bilayers, is formed by the same number of parallel DNAs with a uniform separation distance.

Differential toxicity, conformation and morphology of typical initial aggregation states of Aβ1-42 and Aβpy3-42 beta-amyloids.

Among the different species of water-soluble β-peptides (Aβ1-42, Aβ1-40 and N-terminal truncated Aβ-peptides), Aβpy3-42 is thought to play a relevant role in Alzheimer's pathogenesis due to its abundance, resistance to proteolysis, fast aggregation kinetics, dynamic structure and high neurotoxicity. To evaluate the specific structural characteristics and neurotoxicity of Aβpy3-42, we separated different aggregation states of Aβ1-42 and Aβpy3-42 using fast protein liquid chromatography, isolating in both cases three peaks that corresponded to sa (small), ma (medium) and la (large) aggregates. Conformational analysis, by circular dichroism showed a prevailing random coil conformation for sa and ma, and typical β-sheet conformation for la.

Clusters in strong polyelectrolyte solutions in the condensation theory approach.

The interaction free energy of parallel clusters of like-charged rod polyelectrolytes in solution is calculated in the framework of the extended condensation theory. For sufficiently high linear charge density of the polyelectrolyte, clustering takes place. The greater is the number of polyelectrolytes participating to the cluster, the smaller is the equilibrium interpolyelectrolyte distance, and the deeper is the corresponding free energy minimum.

Wrapped-around models for the lac operon complex.

The protein-DNA complex, involved in the lac operon of enteric bacteria, is paradigmatic in understanding the extent of DNA bending and plasticity due to interactions with protein assemblies acting as DNA regulators. For the lac operon, two classes of structures have been proposed: 1), with the protein tetramer lying away from the DNA loop (wrapped-away model); and 2), with the protein tetramer lying inside the DNA loop (wrapped-around model). A recently developed electrostatic analytical model shows that the size and net charge of the Lac protein tetramer allow the bending of DNA, which is consistent with another wrapped-around model from the literature.

N-terminal truncated pyroglutamyl beta amyloid peptide Abetapy3-42 shows a faster aggregation kinetics than the full-length Abeta1-42.

We tested directly the differences in the aggregation kinetics of three important beta amyloid peptides, the full-length Abeta1-42, and the two N-terminal truncated and pyroglutamil modified Abetapy3-42 and Abetapy11-42 found in different relative concentrations in the brains in normal aging and in Alzheimer disease. By following the circular dichroism signal and the ThT fluorescence of the solution in phosphate buffer, we found substantially faster aggregation kinetics for Abetapy3-42. This behavior is due to the particular sequence of this peptide, which is also responsible for the specific oligomeric aggregation states, found by TEM, during the fibrillization process, which are very different from those of Abeta1-42, more prone to fibril formation.

The supramolecular association of polyelectrolytes to complementary charged surfactants and protein assemblies.

Cohesion matters! The correlation between the conformational rigidity of the polyelectrolyte and the size and stability of the globular assembly is discussed in this review article. Some examples of models for the association of polyelectrolytes to globular assemblies are shown here.Supramolecular complexes of strong polyelectrolytes and oppositely charged ionic micelles or protein assemblies derive their main stabilization from electrostatic interactions that include the counterion condensation/release mechanism and from hydrophobic interactions distributed along apolar sections of the components.

Attraction between like-charged polyelectrolytes in the extended condensation theory.

The interaction free energy of like-charged polyelectrolytes in solution is calculated in the framework of the extended counterion condensation theory, recently given by Schurr and Fujimoto, Biophys. Chem. 2002, 101-102, 425-445.

Intracellular accumulation of a mild-denatured monomer of the human PrP fragment 90-231, as possible mechanism of its neurotoxic effects.

Because of high tendency of the prion protein (PrP) to aggregate, the exact PrP isoform responsible for prion diseases as well as the pathological mechanism that it activates remains still controversial. In this study, we show that a pre-fibrillar, monomeric or small oligomeric conformation of the human PrP fragment 90-231 (hPrP90-231), rather than soluble or fibrillar large aggregates, represents the neurotoxic species. In particular, we demonstrate that monomeric mild-denatured hPrP90-231 (incubated for 1 h at 53 degrees C) induces SH-SY5Y neuroblastoma cell death, while, when structured in large aggregates, it is ineffective.

Generalized electrostatic model of the wrapping of DNA around oppositely charged proteins.

Histonelike proteins in prokaryotes and histone octamers in eukaryotes carry large positive charges, which are responsible of strong electrostatic interactions with DNA. As a result, DNA wraps around proteins and genetic information is condensed. We describe a generalized model of these electrostatic interactions mediated by salt that explains the wrapping of DNA around the nucleosome octamer, around remodeling factors in eukaryotes and around histonelike proteins in prokaryotes.

Modeling H3 histone N-terminal tail and linker DNA interactions.

Molecular dynamics computer simulations were performed for the 25-residue N-terminal tail of the H3 histone protein in the proximity of a DNA segment of 10 base pairs (bp), representing a model for the linker DNA in chromatin. Several least biased configurations were used as initial configurations. The secondary structure content of the protein was increased by the presence of DNA close to it, but the locations of the secondary motifs were different for different initial orientations of the DNA grooves with respect to the protein.

Electrostatic interactions with histone tails may bend linker DNA in chromatin.

Is linker DNA bent in the 30-nm chromatin fiber at physiological conditions? We show here that electrostatic interactions between linker DNA and histone tails including salt condensation and release may bend linker DNA, thus affecting the higher order organization of chromatin.

Hyaluronan chain conformation and dynamics.

An overview of the present state of research in the field of hyaluronan chain conformational aspects is presented. The relationship between structure and dynamics are illustrated for a series of hyaluronan oligomers. Conformational characteristics of hyaluronan chains are discussed, together with the dynamic chain patterns, evaluated by using a theoretical approach to diffusive polymer dynamics.

Designing generalized statistical ensembles for numerical simulations of biopolymers.

Conformational properties of polymers, such as average dihedral angles or molecular alpha-helicity, display a rather weak dependence on the detailed arrangement of the elementary constituents (atoms). We propose a computer simulation method to explore the polymer phase space using a variant of the standard multicanonical method, in which the density of states associated to suitably chosen configurational variables is considered in place of the standard energy density of states. This configurational density of states is used in the Metropolis acceptance/rejection test when configurations are generated with the help of a hybrid Monte Carlo algorithm.

Modeling the backbone dynamics of reduced and oxidized solvated rat microsomal cytochrome b5.

In this article, a description of the statistics and dynamics of cytochrome b(5) in both reduced and oxidized forms is given. Results of molecular dynamics computer simulations in the explicit solvent have been combined with mode-coupling diffusion models including and neglecting the molecule-solvent correlations. R(1) and R(1 rho) nuclear magnetic relaxation parameters of (15)N in the protein backbone have been calculated and compared with experiments.