Ion-induced alterations of the local hydration environment elucidate Hofmeister effect in a simple classical model of Trp-cage miniprotein.

Protein stability is known to be influenced by the presence of Hofmeister active ions in the solution. In addition to direct ion-protein interactions, this influence manifests through the local alterations of the interfacial water structure induced by the anions and cations present in this region. In our earlier works it was pointed out that the effects of Hofmeister active salts on the stability of Trp-cage miniprotein can be modeled qualitatively using non-polarizable force fields. These simulations reproduced the structure-stabilization and structure-destabilization effects of selected kosmotropic and chaotropic salts, respectively. In the present study we use the same model system to elucidate atomic processes behind the chaotropic destabilization and kosmotropic stabilization of the miniprotein. We focus on changes of the local hydration environment of the miniprotein upon addition of NaClO4 and NaF salts to the solution. The process is separated into two parts. In the first, 'promotion' phase, the protein structure is fixed, and the local hydration properties induced by the simultaneous presence of protein and ions are investigated, with a special focus on the interaction of Hofmeister active anions with the charged and polar sites. In the second, 'rearrangement' phase we follow changes of the hydration of ions and the protein, accompanying the conformational relaxation of the protein. We identify significant factors of an enthalpic and entropic nature behind the ion-induced free energy changes of the protein-water system, and also propose a possible atomic mechanism consistent with the Collins's rule, for the chaotropic destabilization and kosmotropic stabilization of protein conformation.

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.

Functionalization of gold nanoparticles with amino acid, beta-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.

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.

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.

Density functional study of infinite polyserine chains.

Two different helical conformations (alpha and 3-10 helices) of polyserine are studied using density functional theory. The infinite system characterized by exact translational-rotational symmetry is examined in vacuum using the BLYP exchange-correlation functional. Geometry analysis in terms of hydrogen bond strength and total energies of the different conformers are presented. The structural changes due to the presence of the serine side chain are identified comparing the polyserine and polyglycine chains. The rotational energy curves of the side chain are presented for both investigated helices. Band structures of polyserine and polyglycine conformers are also compared.