Two Clusters of Fluoroquinolone and Clindamycin-Resistant Clostridium difficile PCR Ribotype 001 Strain Recognized by Capillary Electrophoresis Ribotyping and Multilocus Variable Tandem Repeat Analysis.

Aim: To perform a retrospective analysis of the high occurrence of Clostridium difficile infection in the surgical department of a Czech tertiary care hospital and to identify weaknesses in C. difficile infection (CDI) prevention and control policies.

Methods: Clinical and epidemiological data on eleven CDI cases were collected.

Engineering the Pseudomonas aeruginosa II lectin: designing mutants with changed affinity and specificity.

This article focuses on designing mutations of the PA-IIL lectin from Pseudomonas aeruginosa that lead to change in specificity. Following the previous results revealing the importance of the amino acid triad 22-23-24 (so-called specificity-binding loop), saturation in silico mutagenesis was performed, with the intent of finding mutations that increase the lectin's affinity and modify its specificity. For that purpose, a combination of docking, molecular dynamics and binding free energy calculation was used.

How ionic strength affects the conformational behavior of human and rat beta amyloids--a computational study.

Progressive cerebral deposition of amyloid beta occurs in Alzheimers disease and during the aging of certain mammals (human, monkey, dog, bear, cow, cat) but not others (rat, mouse). It is possibly due to different amino acid sequences at positions 5, 10 and 13. To address this issue, we performed series of 100 ns long trajectories (each trajectory was run twice with different initial velocity distribution) on amyloid beta (1-42) with the human and rat amino acid sequence in three different environments: water with only counter ions, water with NaCl at a concentration of 0.

New PAH derivatives functionalized by cyclic nitrone framework: synthetic design, anti-proliferative activity and interaction with DNA.

Novel approach to functionalized polycyclic aromatic hydrocarbons (PAHs) is presented. Incorporation of cyclic nitrone framework into the structure of PAHs was studied with respect to their anti-proliferative activities and interaction with double stranded DNA. Theoretical docking studies and UV titration methods were used for preliminary evaluation of binding of new PAH derivatives to DNA structure.

Influence of the O-phosphorylation of serine, threonine and tyrosine in proteins on the amidic ¹⁵N chemical shielding anisotropy tensors.

Density functional theory was employed to study the influence of O-phosphorylation of serine, threonine, and tyrosine on the amidic (15)N chemical shielding anisotropy (CSA) tensor in the context of the complex chemical environments of protein structures. Our results indicate that the amidic (15)N CSA tensor has sensitive responses to the introduction of the phosphate group and the phosphorylation-promoted rearrangement of solvent molecules and hydrogen bonding networks in the vicinity of the phosphorylated site. Yet, the calculated (15)N CSA tensors in phosphorylated model peptides were in range of values experimentally observed for non-phosphorylated proteins.

Analysis of the Nse3/MAGE-binding domain of the Nse4/EID family proteins.

Background: The Nse1, Nse3 and Nse4 proteins form a tight sub-complex of the large SMC5-6 protein complex. hNSE3/MAGEG1, the mammalian ortholog of Nse3, is the founding member of the MAGE (melanoma-associated antigen) protein family and the Nse4 kleisin subunit is related to the EID (E1A-like inhibitor of differentiation) family of proteins. We have recently shown that human MAGE proteins can interact with NSE4/EID proteins through their characteristic conserved hydrophobic pocket.

Interactions of amyloid β peptide 1-40 and cerebrosterol.

Amyloid β peptides appear to play a role in physiological processes; however, they are also involved in the pathogenesis of Alzheimer disease. Their actions under normal conditions are probably mediated by soluble monomeric L-isoforms at low concentrations, perhaps via highly specific interactions. On the contrary, toxic effects of aggregated natural L-isoforms/synthetic D-isoforms on membranes are very similar, but synthetic reverse/random L: -isoforms without pronounced aggregation properties are not toxic.

Photoremovable chiral auxiliary.

A new concept of a photoremovable chiral auxiliary (PCA), based on the chiral benzoin chromophore, is introduced. This moiety can control the asymmetric formation of a Diels-Alder adduct, and then be removed in a subsequent photochemical step in high chemical and quantum yields. Selective formation of the products at up to 96% ee was observed in the presence of a Lewis acid catalyst in the case of a 2-methoxybenzoinyl chiral auxiliary.

Influence of the acetylcholinesterase active site protonation on omega loop and active site dynamics.

Existence of alternative entrances in acetylcholinesterase (AChE) could explain the contrast between the very high AChE catalytic efficiency and the narrow and long access path to the active site revealed by X-ray crystallography. Alternative entrances could facilitate diffusion of the reaction products or at least water and ions from the active site. Previous molecular dynamics simulations identified side door and back door as the most probable alternative entrances.

Recognition of selected monosaccharides by Pseudomonas aeruginosa Lectin II analyzed by molecular dynamics and free energy calculations.

In this study, interactions of selected monosaccharides with the Pseudomonas aeruginosa Lectin II (PA-IIL) are analyzed in detail. An interesting feature of the PA-IIL binding is that the monosaccharide is interacting via two calcium ions and the binding is unusually strong for protein-saccharide interaction. We have used Molecular Mechanics Poisson-Boltzmann Surface Area (MM/PBSA) and normal mode analysis to calculate the free energy of binding.

Why acetylcholinesterase reactivators do not work in butyrylcholinesterase.

The pyridinium oxime therapy for treatment of organophosphate poisoning is a well established, but not sufficient method. Recent trends also focus on prophylaxis as a way of preventing even the entrance of organophosphates into the nervous system. One of the possible prophylactic methods is increasing the concentration of butyrylcholinesterase in the blood with the simultaneous administration of butyrylcholinesterase reactivators, when the enzyme is continuously reactivated by oxime.

In silico mutagenesis and docking studies of Pseudomonas aeruginosa PA-IIL lectin predicting binding modes and energies.

This article is focused on the application of two types of docking software, AutoDock and DOCK. It is aimed at studying the interactions of a calcium-dependent bacterial lectin PA-IIL (from Pseudomonas aeruginosa) and its in silico mutants with saccharide ligands. The effect of different partial charges assigned to the calcium ions was tested and evaluated in terms of the best agreement with the crystal structure.

TRITON: a graphical tool for ligand-binding protein engineering.

Unlabelled: The new version of the TRITON program provides user-friendly graphical tools for modeling protein mutants using the external program MODELLER and for docking ligands into the mutants using the external program AutoDock. TRITON can now be used to design ligand-binding proteins, to study protein-ligand binding mechanisms or simply to dock any ligand to a protein.

Availability: Executable files of TRITON are available free of charge for academic users at http://ncbr.

Acetylcholinesterases--the structural similarities and differences.

Acetylcholinesterase (AChE) is a widely spread enzyme playing a very important role in nerve signal transmission. As AChE controls key processes, its inhibition leads to the very fast death of an organism, including humans. However, when this feature is to be used for killing of unwanted organisms (i.

Different mechanisms of CDK5 and CDK2 activation as revealed by CDK5/p25 and CDK2/cyclin A dynamics.

A detailed analysis is presented of the dynamics of human CDK5 in complexes with the protein activator p25 and the purine-like inhibitor roscovitine. These and other findings related to the activation of CDK5 are critically reviewed from a molecular perspective. In addition, the results obtained on the behavior of CDK5 are compared with data on CDK2 to assess the differences and similarities between the two kinases in terms of (i) roscovitine binding, (ii) regulatory subunit association, (iii) conformational changes in the T-loop following CDK/regulatory subunit complex formation, and (iv) specificity in CDK/regulatory subunit recognition.

The mechanism of inhibition of the cyclin-dependent kinase-2 as revealed by the molecular dynamics study on the complex CDK2 with the peptide substrate HHASPRK.

Molecular dynamics (MD) simulations were used to explain structural details of cyclin-dependent kinase-2 (CDK2) inhibition by phosphorylation at T14 and/or Y15 located in the glycine-rich loop (G-loop). Ten-nanosecond-long simulations of fully active CDK2 in a complex with a short peptide (HHASPRK) substrate and of CDK2 inhibited by phosphorylation of T14 and/or Y15 were produced. The inhibitory phosphorylations at T14 and/or Y15 show namely an ATP misalignment and a G-loop shift (~5 A) causing the opening of the substrate binding box.

Activation and inhibition of cyclin-dependent kinase-2 by phosphorylation; a molecular dynamics study reveals the functional importance of the glycine-rich loop.

Nanoseconds long molecular dynamics (MD) trajectories of differently active complexes of human cyclin-dependent kinase 2 (inactive CDK2/ATP, semiactive CDK2/Cyclin A/ATP, fully active pT160-CDK2/Cyclin A/ATP, inhibited pT14-; pY15-; and pT14,pY15,pT160-CDK2/Cyclin A/ATP) were compared. The MD simulations results of CDK2 inhibition by phosphorylation at T14 and/or Y15 sites provide insight into the structural aspects of CDK2 deactivation. The inhibitory sites are localized in the glycine-rich loop (G-loop) positioned opposite the activation T-loop.

Analysis of CDK2 active-site hydration: a method to design new inhibitors.

The interactions between the protein and the solvent were analyzed, and protein regions with a high density of water molecules, as well as structural water molecules, were determined by using molecular dynamics (MD) simulations. A number of water molecules that were in contact with the protein for the whole trajectory were determined. Their interaction energies and hydrogen bonds with protein residues were analyzed.

Enantioselective chromatography and molecular modeling of novel aryloxyaminopropan-2-ols with the alkyl carbamate function.

A series of different racemic aryloxyaminopropan-2-ol derivatives 1a-d-3a-d with potential beta-adrenergic blocking effects related to propanolol 4 and atenolol 5 was resolved by HPLC using Chiralcel OD-H and Chiralpak AD as chiral stationary phases. Mobile phases consisted of a hexane/alcohol (propan-2-ol or ethanol) mixture doped with a modifier (DEA or TFA). The retention behavior of the compounds depended on the position of the carbamate attached to the aryloxy moiety and on the length of the alkyl residue in the carbamate.

Investigation of the complexation of (+)-catechin by beta-cyclodextrin by a combination of NMR, microcalorimetry and molecular modeling techniques.

(+)-Catechin is a polyphenolic compound of natural origin that presents anti-oxidant properties of interest for therapeutics or cosmetics uses. Preliminary studies on inclusion into cyclodextrin cavities yielded contradictory results both for the quantitative (affinity constant) and qualitative description of the interaction. By a combination of several experimental and theoretical methods, the present study resolved the previous ambiguities about the interaction between (+)-catechin and beta-cyclodextrin.

Dynamics and binding modes of free cdk2 and its two complexes with inhibitors studied by computer simulations.

This article presents a molecular dynamics (MD) study of the cdk2 enzyme and its two complexes with the inhibitors isopentenyladenine and roscovitine using the Cornell et al. force field from the AMBER software package. The results show that inserting an inhibitor into the enzyme active site does not considerably change enzyme structure but it seemingly changes the distribution of internal motions.