Elongation cutoff technique: low-order scaling SCF method

The elongation cutoff technique at restricted Hartree-Fock (HF) level of theory in conventional type of calculations, i.e., with two electron integrals (TEI) stored on a disc, is presented for two model systems. It is demonstrated that the number of TEI in the elongation cutoff calculations increases linearly with the system size thus, allowing to extend the conventional type of calculations to bigger systems. The step CPU (central processing unit) time in the elongation cutoff calculations is much lower than in the HF reference calculations. Such behavior reduces significantly the prefactor in the quadratic scaling relation. The total CPU time in the elongation calculation is about 40% lower than in the conventional HF calculations or comparable to direct type of calculations with the quantum fast multipoles method employed. It is shown that by introducing the interaction radius one can obtain linear scaling in the SCF calculations. Figure: The structure of density matrix and total CPU timings for polyglycine clusters in the elongation cutoff calculations. The structure of density matrix and total CPU timings for polyglycine clusters in the elongation cutoff calculations     

Protein Disulfide Isomerase Directly Interacts with β-Actin Cys374 and Regulates Cytoskeleton Reorganization

Recent studies support the role of cysteine oxidation in actin cytoskeleton reorganization during cell adhesion. The aim of this study was to explain whether protein disulfide isomerase (PDI) is responsible for the thiol-disulfide rearrangement in the β-actin molecule of adhering cells. First, we showed that PDI forms a disulfide-bonded complex with β-actin with a molecular mass of 110 kDa. Specific interaction of both proteins was demonstrated by a solid phase binding assay, surface plasmon resonance analysis, and immunoprecipitation experiments. Second, using confocal microscopy, we found that both proteins colocalized when spreading MEG-01 cells on fibronectin. Colocalization of PDI and β-actin could be abolished by the membrane-permeable sulfhydryl blocker, N-ethylmaleimide, by the RGD peptide, and by anti-αIIbβ3 antibodies. Consequently, down-regulation of PDI expression by antisense oligonucleotides impaired the spreading of cells and initiated reorganization of the cytoskeleton. Third, because of transfection experiments followed by immunoprecipitation and confocal analysis, we provided evidence that PDI binds to the β-actin Cys³⁷⁴ thiol. Formation of the β-actin-PDI complex was mediated by integrin-dependent signaling in response to the adhesion of cells to the extracellular matrix. Our data suggest that PDI is released from subcellular compartments to the cytosol and translocated toward the periphery of the cell, where it forms a disulfide bond with β-actin when MEG-01 cells adhere via the αIIbβ3 integrin to fibronectin. Thus, PDI appears to regulate cytoskeletal reorganization by the thiol-disulfide exchange in β-actin via a redox-dependent mechanism.     

3D-Hit: fast structural comparison of proteins

3D-Hit is a fast scanning method for detecting structural similarities between proteins. The algorithm is based on a hashing function, which decomposes proteins into segments of 13 residues. The scanning procedures start with assigning a set of similar segments from the database to each segment in the query protein. These initial hits are expanded by two iterations of structural superposition of larger segments of 99 and 299 residues. The method generates an alignment for the query protein by concatenating partial structural alignments.     

Fine structure and morphology of sterlet (Acipenser ruthenus L. 1758) spermatozoa and acrosin localization

Ultrastructure of sterlet Acipenser ruthenus L. 1758 sperm was examined by scanning and transmission electron microscopy, which allowed us to use various methods for visualizations of different parts of sterlet spermatozoa. Sperm cells possess a head with a distinct acrosome, a midpiece and a single flagellum surrounded by the flagellar plasma membrane. The average length of the head including the acrosome and the midpiece was estimated as 5.14+/-0.42 microm. Nine to 10 posterolateral projections were derived from the acrosome. Three inter-twining endonuclear canals bounded by membranes traversed the nucleus in its whole length from the acrosome to the implantation fossa. Acrosin was located in all the three parts (acrosome, endonuclear canals and implantation fossa). The proximal and distal centrioles located in the midpiece compacted of nine peripheral triplets of microtubules. One cut of the midpiece contained from two to six mitochondria with area of 215+/-85 nm(2) in average. The flagellum was 42.47+/-1.89 microm in length with typical eukaryotic organization of one central pair and nine peripheral pairs of microtubules. It passed through a cytoplasmic channel in the midpiece, which was formed by an invagination at the plasmalemma. The flagellum gradually developed two lateral extensions of its plasma membrane, so-called "fins". Detected morphological variation can be described by four principal component axes corresponding to groups of individual morphometric characters defined on the sperm structures. Correlations among the characters indicate that the sperms are variable in their shape rather than size. Significant variation among examined fish individuals was found only in flagellum and nucleus length. Comparison between the present and previous studies of morphology of sturgeon spermatozoa confirmed large inter- and/or intra-specific differences that could be of substantial taxonomic value.     

Opioid receptor binding and in vivo antinociceptive activity of position 3-substituted morphiceptin analogs

Analogs of morphiceptin (Tyr-Pro-Phe-Pro-NH2), a mu-selective opioid receptor ligand, with position 3-modifications, including altered size, lipophilicity, and electronic character, while maintaining aromaticity were synthesized. The activity of the new analogs in in vitro assays and in in vivo hot-plate test of analgesia was compared and the results were consistent. [D-1-Nal3]Morphiceptin was the most potent analog of this series with a 26-fold increase in mu-opioid receptor affinity, a 15-fold potency increase in the GPI assay, and a significant potency increase in the hot-plate analgesic test, as compared with morphiceptin. [d-Qal3]Morphiceptin was found to be a weak antagonist in the GPI assay.     

Lead toxicity through the leadzyme

Lead is one of the most dangerous toxic agents for all living organisms. In humans, elevated levels of lead have been linked to a number of disorders for which various molecular mechanisms have been proposed. However, none of them has been fully understood. It has also been known for several years that at micromolar concentrations lead can bind a unique RNA motif and catalyze a site-specific hydrolysis of the polyribonucleotide chain. This motif, called leadzyme, may be one of the major targets for lead within the cell, and it can cleave various cellular RNAs. A search of GenBank revealed the sequences that can potentially fold into the structure containing the leadzyme motif and that they are rather common in eukaryotic genomes. We found that the domain occurs with a high frequency in human mRNA sequences. Thus, the leadzyme nucleolytic properties should be considered as a possible mechanism for destruction of RNA within a cell. In particular, targeting of the RNA scaffold of ribosomes or spliceosomes may explain lead-mediated toxicity leading to cell death.     

Impact of glafenine hydrochloride on human endothelial cells and human vascular smooth muscle cells: a substance reducing proliferation, migration and extracellular matrix synthesis

The aim of this study was to examine the effects of glafenine hydrochloride (a nonsteroidal anti-inflammatory drug) on proliferation, clonogenic activity, cell-cycle, migration, and the extracellular matrix protein tenascin of human aortic smooth muscle cells (haSMCs) and human endothelial cells (ECs) in vitro.HaSMCs and ECs were seeded in tissue culture flasks. The cells were treated for 4 days with glafenine hydrochloride (10 microM, 50 microM, 100 microM). Half of the treated groups were incubated again with glafenine hydrochloride, the other half received medium free of glafenine hydrochloride every 4 days until day 20. The growth kinetics and clonogenic activity were assessed. Cell cycle distribution was investigated by FACS, migratory ability was evaluated, and effects on extracellular matrix synthesis were assessed by immunofluorescence.Glafenine hydrochloride inhibited the proliferation and clonogenic activity of haSMCs and ECs in a dose-dependent manner. A block in the G2/M phase and a reduction in the G1 phase occurred. The migratory ability of haSMCs was impaired in a dose-dependent manner and the extracellular matrix protein tenascin was reduced. As glafenine hydrochloride has the ability to fully inhibit proliferation and to partially inhibit migration in haSMCs, it could be an interesting substance for further research in the field of restenosis therapy.     

ORFeus: Detection of distant homology using sequence profiles and predicted secondary structure

ORFeus is a fully automated, sensitive protein sequence similarity search server available to the academic community via the Structure Prediction Meta Server (http://BioInfo.PL/Meta/). The goal of the development of ORFeus was to increase the sensitivity of the detection of distantly related protein families. Predicted secondary structure information was added to the information about sequence conservation and variability, a technique known from hybrid threading approaches. The accuracy of the meta profiles created this way is compared with profiles containing only sequence information and with the standard approach of aligning a single sequence with a profile. Additionally, the alignment of meta profiles is more sensitive in detecting remote homology between protein families than if aligning two sequence-only profiles or if aligning a profile with a sequence. The specificity of the alignment score is improved in the lower specificity range compared with the robust sequence-only profiles.