Ferenc Bogár

Charge carrier mobility in quasi-one-dimensional systems: Application to a guanine stack

First the correct expression of charge mobilities in the one-dimensional (1-D) case in the deformation potential approximation are derived in detail. They differ substantially from the usual 3-D expressions. Starting from an ab initio HF band structure of a guanine stack, the effective masses, the deformation potentials, and the 1-D electron and hole mobilities, respectively, were calculated. The mobility values obtained seem to bee quite reasonable. No attempt was made to calculate from the mobilities the conductivities because of the lack of reliable experimental data (the activation energies of the electron and hole conductivities and dopant concentrations).

Functionalization of gold nanoparticles with amino acid, β-amyloid peptides and fragment

Gold nanoparticles (Au NPs) were functionalized by cysteine (Cys), beta-amyloid peptides (Cys(0)Abeta(1-28), Cys(0)Abeta(1-40), Abeta(1-42)) and a pentapeptide fragment (Leu-Pro-Phe-Phe-Asp-OH (LPFFD-OH)). Optical absorption spectra of these systems were recorded and the plasmon resonance maximum values (lambda(max)) of the UV-vis spectra together with the transmission electron microscopy (TEM) images were also analysed. Both TEM images and the appearance of a new absorption band between approximately 720 and 750 nm in the visible spectra of the Au-cysteine and Au-LPFFD-OH systems most probably indicate that upon addition of these molecules to Au NPs-containing aqueous dispersions formation of aggregates is occurred. The wavelength shift between the two observed absorption bands in cysteine- and pentapeptide-modified Au NPs systems are Deltalambda=185 and 193 nm, respectively. These results suggest that the monodisperse spherical gold nanoparticles were arranged to chained structure due to the effect of these molecules. For confirmation of the binding of citrate and cysteine onto the plasmonic metal surface (1)H NMR measurements were also performed. (1)H NMR results may suggest that the citrate layer on the metal surface is replaced by cysteine leading to a formation of organic double layer structure. In the presence of beta-amyloid peptides the aggregation was not observed, especially in the Au-Cys(0)Abeta(1-40) and Au-Abeta(1-42) systems, however compared to the cysteine or LPFFD-OH-containing gold dispersion with Cys(0)Abeta(1-28) measurable less aggregation were occurred. The spectral parameters clearly suggest that Abeta(1-42) can attach or bind to the surface of gold nanoparticles via both the apolar and the N-donors containing side-chains of amino acids and no aggregation in the colloidal gold dispersion was observed.

Correlation-corrected energy bands of polymers with large unit cell: poly(para-phenylene) and poly(peri-naphthalene)

Abstract The correlation-corrected band structures of quasi 1D poly(para-phenylene) (PPP) and poly(peri-naphthalene) (PPN) are presented, using the ab initio quasi-particle method based on the iterative solution of the inverse Dyson equation. A double zeta basis set is used with polarization functions for PPN and a double zeta basis is used for PPP.

Application of the many-body perturbation theory to normal saturated hydrocarbons in the localized representation

The second-order energy corrections are calculated for some normal saturated hydrocarbons by using the many body-perturbation theory (MBPT) based on localized orbitals. The correlation energies are expressed as the sum of contributions from virtual orbital pairs. We have found that these contributions are transferable and have interesting structural features: the trans-coplanar effects are relatively large. Partitioning the correlation energies according to the “order of neighbourhood” we have found that the zero order effects are the largest but the first and second neighbour contributions are also important.

On the hofmeister effect: Fluctuations at the protein-water interface and the surface tension

We performed molecular dynamics simulations on the tryptophane-cage miniprotein using a nonpolarizable force field, in order to model the effect of concentrated water solutions of neutral salts on protein conformation, which is a manifestation of Hofmeister effects. From the equilibrium values and the fluctuations of the solvent accessible surface area of the miniprotein, the salt-induced changes of the mean value of protein-water interfacial tension were determined. At 300 K, the chaotropic ClO4(-) and NO3(-) decreased the interfacial tension according to their position in the Hofmeister series (by approximately 5 and 2.7 mN/m, respectively), while the kosmotropic F(-) increased it (by 1 mN/m). These values were compared to those obtained from the Gibbs equation using the excess surface adsorption calculated from the probability distribution of the water molecules and ions around the miniprotein, and the two sets were found to be very close to each other. Our results present a direct evidence for the central role of interfacial tension and fluctuations at the protein-water interface in Hofmeister phenomena, and provide a computational method for the determination of the protein-water interfacial tension, establishing a link between the phenomenological and microscopic description of protein-water interfaces.

The electronic structure of the four nucleotide bases in DNA, of their stacks, and of their homopolynucleotides in the absence and presence of water.

Using the ab initio Hartree-Fock crystal orbital method in its linear combination of atomic orbital form, the energy band structure of the four homo-DNA-base stacks and those of poly(adenilic acid), polythymidine, and polycytidine were calculated both in the absence and presence of their surrounding water molecules. For these computations Clementis double zeta basis set was applied. To facilitate the interpretation of the results, the calculations were supplemented by the calculations of the six narrow bands above the conduction band of poly(guanilic acid) with water. Further, the sugar-phosphate chain as well as the water structures around poly(adenilic acid) and polythymidine, respectively, were computed. Three important features have emerged from these calculations. (1) The nonbase-type or water-type bands in the fundamental gap are all close to the corresponding conduction bands. (2) The very broad conduction band (1.70 eV) of the guanine stack is split off to seven narrow bands in the case of poly(guanilic acid) (both without and with water) showing that in the energy range of the originally guanine-stack-type conduction band, states belonging to the sugar, to PO(4)(-), to Na(+), and to water mix with the guanine-type states. (3) It is apparent that at the homopolynucleotides with water in three cases the valence bands are very similar (polycytidine, because it has a very narrow valence band, does not fall into this category). We have supplemented these calculations by the computation of correlation effects on the band structures of the base stacks by solving the inverse Dyson equation in its diagonal approximation taken for the self-energy the MP2 many body perturbation theory expression. In all cases the too large fundamental gap decreased by 2-3 eV. In most cases the widths of the valence and conduction bands, respectively, decreased (but not in all cases). This unusual behavior is most probably due to the rather large complexity of the systems. From all this emerges the following picture for the charge transport in DNA: There is a possibility in short segments of the DNA helix of a Bloch-type conduction of holes through the nucleotide base stacks of DNA combined with hopping (and in a lesser degree with tunneling). The motivation of this large scale computation was that recently in Zurich (ETH) they have performed high resolution x-ray diffraction experiments on the structure of the nucleosomes. The 8 nucleohistones in them are wrapped around by a DNA superhelix of 147 base pairs in the DNA B form. The most recent investigations have shown that between the DNA superhelix (mostly from its PO(4) (-) groups) there is a charge transfer to the positively charged side chains (first of all arginines and lysines) of the histones at 120 sites of the superhelix. This would cause a hole conduction in DNA and an electronic one in the proteins.

Calculation of the band structure of polyguanilic acid in the presence of water and Na+ ions

Using the Hartree-Fock crystal orbital method with a combined symmetry (helix) operation, the band structure of polyguanilic acid was calculated in the presence of water and Na(+) ions. The water structure was optimized with the help of molecular mechanics. The obtained band structure shows that both the valence and conduction bands are purely guanine type. The three impurity bands in the 10.66 eV large gap are close to the conduction band and therefore cannot play any role in the assumed hole conduction of the system. Namely, according to detailed x-ray diffraction investigations of the nucleosomes in chromatin, there are possibilities of charge transfer from the negative sites of DNA to the positive ones in histones. Therefore most probably there is a hole conduction in DNA and an electronic one in the histone proteins.

β-Amyloid and the Pathomechanisms of Alzheimer’s Disease: A Comprehensive View

Protein dyshomeostasis is the common mechanism of neurodegenerative diseases such as Alzheimer’s disease (AD). Aging is the key risk factor, as the capacity of the proteostasis network declines during aging. Different cellular stress conditions result in the up-regulation of the neurotrophic, neuroprotective amyloid precursor protein (APP). Enzymatic processing of APP may result in formation of toxic Aβ aggregates (β-amyloids). Protein folding is the basis of life and death. Intracellular Aβ affects the function of subcellular organelles by disturbing the endoplasmic reticulum-mitochondria cross-talk and causing severe Ca2+-dysregulation and lipid dyshomeostasis. The extensive and complex network of proteostasis declines during aging and is not able to maintain the balance between production and disposal of proteins. The effectivity of cellular pathways that safeguard cells against proteotoxic stress (molecular chaperones, aggresomes, the ubiquitin-proteasome system, autophagy) declines with age. Chronic cerebral hypoperfusion causes dysfunction of the blood-brain barrier (BBB), and thus the Aβ-clearance from brain-to-blood decreases. Microglia-mediated clearance of Aβ also declines, Aβ accumulates in the brain and causes neuroinflammation. Recognition of the above mentioned complex pathogenesis pathway resulted in novel drug targets in AD research.

Calculation of the charge-carrier mobility of polyguanylic acid: The simultaneous effect of stretching and twisting

Charge-carrier (electron and hole) mobilities of polyguanylic acid have been computed using the deformation-potential approximation from ab initio Hartree-Fock band structure. Mobilities resulting from electron scattering on torsional acoustic phonons are calculated and compared to those obtained from a previous calculation [F. B. Beleznay et al., J. Chem. Phys. 119, 5690 (2003)] considering interaction with compressional phonons. The simultaneous effect of the two independent scatterings is also calculated.

Determination of binding capacity and adsorption enthalpy between Human Glutamate Receptor (GluR1) peptide fragments and kynurenic acid by surface plasmon resonance experiments. Part 2: Interaction of GluR1270–300 with KYNA

In the course of our previous work, the interactions of two peptide fragments (GluR1201-230 and GluR1231-259) of human glutamate receptor (GluR1201-300) polypeptide with kynurenic acid (KYNA) were investigated by surface plasmon resonance (SPR) spectroscopy. Besides quantitation of the interactions, the enthalpies of binding of KYNA on certain peptide fragment-modified gold surfaces were also reported. In the present work, a third peptide fragment (GluR1270-300) of the glutamate receptor was synthesized and its interaction with KYNA was investigated by an SPR technique. This 31-membered peptide was chemically bonded onto a gold-coated SPR chip via a cysteine residue. The peptide-functionalized biosensor chip was analyzed by atomic force microscopy (AFM) and theoretical calculations were performed on the structure and dimensions of the peptide on the gold surface. In order to determine the isosteric heat of adsorption of the binding of KYNA on the peptide-functionalized gold thin film, SPR experiments were carried out between +10°C and +40°C. The results on the GluR1270-300-KYNA system were compared with the previously published binding parameters of the interactions of GluR1201-230 and GluR1231-259 with KYNA. The binding abilities of KYNA with all three peptide fragments immobilized on the gold surface were estimated by a molecular docking procedure and the binding free energies of these AMPA receptor subunits with KYNA were determined.