A disulfide linked model of the complement protein C8γ complexed with C8α indel peptide

In a recent study C8γ (complement protein) with Cys40Ala substitution and a C8α derived peptide with Cys164Ala substitution were co-crystallized and their binding mode was revealed. Computer modeling and molecular dynamics simulations were performed in order to check the hypothesis that the residues Ala164 of C8α and Ala40 of C8γ occupied the right position if cysteine residues were in their place for disulfide bonding. Substitution of these two alanine residues with cysteine along with disulfide bond creation via molecular modeling and subsequent molecular dynamics simulation of the complex corroborated the hypothesis, which was also confirmed from recent crystallographic data. Average RMSD between backbone atoms of the indel peptide during the MD trajectory in comparison with the corresponding sequence of crystal structure of the C8α/γ complex was found only 0.085 nm. Figure Modeling the C*y/α comlexation. Ribbon representation of the C8y complexed with C8α indel peptide initial (green/cyan) X-ray structure and the final MD conformation (magenta/orange) after imposing the disulfide link. Average RMSD between backbone atoms of the indel peptide during MD trajectory in comparison with the corresponding sequence of crystal structure of the C8α/y complex was found only 0.085nm. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Conductometric and voltammetric studies on the bis(triphenyl phosphine) ruthenium(II) complex, cis-[RuCl2(L)(PPh3)2], where L: 2-(2′-pyridyl)quinoxaline

Conductometric investigation on the bis(triphenyl phosphine) ruthenium(II) complex, cis-[RuCl₂(L)(PPh₃)₂] (A) (where PPh₃: triphenyl phosphine and L: 2-(2′-pyridyl)quinoxaline, C₁₃N₃H₉), in dimethylsulfoxide (DMSO) was performed at temperatures ranging from 25 to 50 °C. In addition, cyclic voltammograms of A were recorded on platinum working electrode in dichloromethane (DCM) and dimethylsulfoxide (DMSO) using n-tetrabutylammonium hexafluorophosphate (NBu₄PF₆) as supporting electrolyte at 25 °C. The molar conductivities (Λ) demonstrate that A behaves as uni-univalent electrolyte in DMSO over the whole temperature range. This behavior can be explained in terms of the replacement upon dissolution of chlorine and PPh₃ ligands by DMSO molecules, and consequently, the formation of the ion-pair [RuCl(L)(PPh₃)(DMSO)₂]Cl [B⁺Cl⁻] which is dissociated in some extent. The Λ values were analyzed by means of the Lee-Wheaton conductivity equation in order to estimate the limiting molar conductivities (Λ^o) and the ion-pair association constants (K_A) of [B⁺Cl⁻]. The limiting ion conductivities for the B⁺ ion were evaluated using n-tetrabutylammonium chloride (NBu₄Cl) as “reference electrolyte”. The thermodynamic functions related with the ion association, such as Gibbs free energy , enthalpy , and entropy , were evaluated as well. The mobility of B⁺ was found to increase linearly with rising temperature and the consequent decrease of the viscosity (η) of DMSO. The K_A and values indicate that the association of [B⁺Cl⁻] increases to some extent with the rise of the temperature followed by the decrease of the dielectric constant (ε) of DMSO. The voltammetric experiments indicated that the couple Ru^3+/2+ is reversible and diffusion controlled in DCM and completely irreversible in DMSO.     

Spawning period of Mediterranean marine fishes

We collected all available information (i.e. international and local journals, conference proceedings, theses, technical reports) on the spawning season (n = 511 stocks, 168 species), gonadosomatic index (n = 237 stocks, 81 species) and sex ratio (n = 97 stocks, 68 species) of Mediterranean marine fish. The 511 stocks represented 20 orders (most were Perciformes, 283 stocks) and 65 families (most were Sparidae: 17 species and 63 stocks). Overall, 346 stocks (128 species) spawned between April and August, 139 stocks (60 species) between September and March, while the remaining 26 stocks (13 species) were all-year-round spawners. In addition, 174 stocks (34.1%) were characterised by an extended (>4 months) spawning season, but, for most stocks (332 stocks, 64.4%), spawning duration ranged from 2 to 4 months inclusive. Regardless of the onset and the duration of spawning, the spawning period of 284 and 287 stocks included June and July, respectively, indicating that most Mediterranean species are summer spawners. Female gonadosomatic index ranged between 0.06 and 37 (mean ± SE = 8.55 ± 0.647, n = 95) and was significantly higher (t-test: t = 5.58, P < 0.001) than the corresponding male one, which ranged between 0.06 and 30 (mean ± SE = 4.21 ± 0.431, n = 95). Congeneric species that occupied the same area and share the same requirements exhibited successive and non-overlapping spawning (e.g. Sparidae in the Adriatic Sea, Mugilidae in the Ionian Sea and Tunisian waters). The knowledge of the spawning period coupled with information on spawning and nursery grounds and detailed knowledge of mating systems, social interactions, maturity and fecundity may be very useful for fisheries management.     

Enantioselective biocatalytic synthesis of (S)-monastrol

The first enantioselective biocatalytic synthesis of (S)-monastrol has been developed via an unexpected and unusual enzymatic pathway as suitable route. Whereas attempts for a direct hydrolysis of racemic monastrol were not successful, formation of racemic O-butanoyl monastrol and subsequent enantioselective hydrolysis furnished O-butanoyl (S)-monastrol with 97% ee. Cleavage of the O-butanoyl moiety then gave the desired (S)-monastrol with 96% ee.     

Novel insights into the calcium action in cherry fruit development revealed by high-throughput mapping

Plant Molecular Biology - This work provides the first system-wide datasets concerning metabolic changes in calcium-treated fruits, which reveal that exogenously applied calcium may specifically...     

Quantitative structure activity relationships (QSAR) of substituded (S)-phenylpiperidines as preferential dopamine autoreceptor antagonists

A QSAR analysis for substituted (S)-phenylpiperidines as dopamine (DA) antagonists is described. The studied derivatives differ at the nitrogen substitutent (R) and at the substitutents (X) of the phenyl-ring. The analysis was done using the C-QSAR suite program (Biobyte) through the Internet. Clog P, CMR, M_Vol, B₁ and L (the Verloop's sterimol parameters for the substitutents) were used as parameters. In all the three studied cases clog P plays a significant part in the QSAR of DA antagonists, followed by the steric factors. In one case the electronic effect contributes significantly.     

Synthesis of 13C-labeled and functionalized Hyaluronan derivatives for biophysical studies and surface modifications

A convergent synthesis of a tetrasaccharide partial sequence of ¹³C-labeled Hyaluronan is presented. This tetrasaccharide can be used for biophysical studies as well as for surface modifications. Furthermore, tetrasaccharide 7 can be employed for the synthesis of additionally labeled higher oligomers of Hyaluronan on the basis of the presented methodology.     

Cis-trans isomerization of the Epstein-Barr virus determinant peptide EENLLDFVRF after the DM1 TCR recognition of the HLA-B*4405/peptide complex

The Epstein–Barr virus determinant peptide EENLLDFVRF shows high immunogenicity when presented by HLA-B*4405 allotype. This fact is accompanied by a cis–trans isomerization of the Leu5-Asp6 peptide bond upon TCR binding of the pMHC complex. Molecular dynamics simulations of pMHC/TCR structures, with the EENLLDFVRF peptide in cis and trans conformations have been employed in order to examine the structure and dynamics of the pMHC complex with such an unusual conformation. The results, based on MM-PBSA free energy computations as well as buried surface area analysis and interactions at the pMHC/TCR interface, indicate that the TCR binds preferably the pMHC complex with the Leu5-Asp6 peptide bond in cis conformation. It is the first time that this notable conformational feature of T-cell epitope is investigated.     

Nck1 and Grb2 localization patterns can distinguish invadopodia from podosomes

Invadopodia are matrix-degrading ventral cell surface structures formed in invasive carcinoma cells. Podosomes are matrix-degrading structures formed in normal cell types including macrophages, endothelial cells, and smooth muscle cells that are believed to be related to invadopodia in function. Both invadopodia and podosomes are enriched in proteins that regulate actin polymerization including proteins involved in N-WASp/WASp-dependent Arp2/3-complex activation. However, it is unclear whether invadopodia and podosomes use distinct mediators for N-WASp/WASp-dependent Arp2/3-complex activation. We investigated the localization patterns of the upstream N-WASp/WASp activators Nck1 and Grb2 in invadopodia of metastatic mammary carcinoma cells, podosomes formed in macrophages, and degradative structures formed in Src-transformed fibroblasts and PMA-stimulated endothelial cells. We provide evidence that Nck1 specifically localizes to invadopodia, but not to podosomes formed in macrophages or degradative structures formed in Src-transformed fibroblasts and PMA-stimulated endothelial cells. In contrast, Grb2 specifically localizes to degradative structures formed in Src-transformed fibroblasts and PMA-stimulated endothelial cells, but not invadopodia or podosomes formed in macrophages. These findings suggest that distinct upstream activators are responsible for N-WASp/WASp activation in invadopodia and podosomes, and that all these ventral cell surface degradative structures have distinguishing molecular as well as structural characteristics. These patterns of Nck1 and Grb2 localization, identified in our study, can be used to sub-classify ventral cell surface degradative structures.