Molecular dynamics study of interactions of polymyxin B3 and its ALA-mutants with lipopolysaccharide

Introduction. Emergence of nosocomial bacterial pathogens (especially Gram-negative bacteria) with multiple resistance against almost all available antibiotics is a growing medical problem. No novel drugs targeting multidrug-resistant Gram-negative bacteria have been developed in recent years. In this context, there has been greatly renewed interest to cyclic lipodecapeptides polymyxins. Polymyxins exhibit rapid bactericidal activity, they are specific and highly potent against Gram-negative bacteria, but have potential nephrotoxic side effects. So polymyxins are attractive lead compounds to develop analogues with improved microbiological, pharmacological and toxicological properties. A detailed knowledge of the molecular mechanisms of polymyxin interactions with its cell targets is a prerequisite for the purposeful improvement of its therapeutic properties. The primary cell target of a polymyxin is a lipopolysaccharide (LPS)in the outer membrane of Gram-negative bacteria. The binding site of polymyxin on LPS has been supposed to be Kdo2-lipid A fragment. Methods.For all molecular modeling and molecular dynamics simulation experiments the YASARA suite of programs was used. Complex of antimicrobial peptide polymyxin В3 (PmB3) with Kdo2-lipid A portion of E. coli lipopolysaccharide was constructed by rigid docking with flexible side chains of the peptide. By alanine scanning of polymyxin В3 bound to LPS followed by simulated annealing minimization of the complexes in explicit water environment, the molecular aspects ofPmB3-LPS binding have beenstudied by 20 ns molecular dynamics simulations at 298 K and pH 7.0. The AMBER03 force field was used with a 1.05 nm force cutoff. To treat long range electrostatic interactions the Particle Mesh Ewald algorithm was used. Results. Ala-mutations of polymyxin’s residues Dab1, Dab3, Dab5, Dab8 and Dab9 in the PmB3-LPScomplex caused sustained structural changes resulting in the notable loss in stability of LPS complexes with Ala-mutants of PmB3. The mutations disturbed the characteristic hydrogen-bond network of PmB3-LPScomplex. Ala-mutations of Dab1, Dab8 and Dab9 amino acid residues of PmB3destabilized PmB3-LPS complex to a greater extent: the values of binding energy for these mutants showed increase and large-amplitude irregular fluctuations. Conclusions. Hydrogen bonding of polymyxin B with the lipopolysaccharide is an important factor of the stability of PmB3-LPScomplex. Detailed knowledge of the peculiarities of molecular interactions of polymyxins with its primary target on the outer membrane of Gram-negative bacteria is a prerequisite of a purposeful design of novel polymyxin-like lipopeptides

Bioenergy production on agricultural land in Slovakia

The potential of bioenergy accumulation and production of Slovakian agricultural soils was derived. Energetically most productive are the soil types like Chernozems (88.6 GJ.ha-1) and Mollic Fluvisols (76.14 GJ.ha-1). The least energy amount generate Gleys, Organosols, Solonetzes and Lithosols (31.63 GJ.ha-1). Energy accumulated in farmland exploita-bility by plants cropped is variable depending from soil representative and its properties. The lowest exploitability was found at Cambisol (0.7–1.8 %), the highest at Regosols (3.1–7.0 %). Рассчитан биоэнергетический потенциал накопления и продуктивности словацких сельскохозяйственных почв. Энергетически наиболее продуктивными являются такие типы почв, как Черноземы (88,6 ГДж/га-1) и Moллик Флювисоли (76,14 ГДж/га-1). Наименьшим энергетическим продуцированием обладают Глеесоли, Орга-носоли, Солонцы и Литосоли (31,63 ГДж/га-1). Энергия, которая накапливается в сельхозугодиях растениями, ва-рьируется в зависимости от представленной почвы и еѐ свойств. Самая низкая накопительная способность была найдена в Камбисолях (0.7-1.8%), а самая высокая в Регосолях (3.1-7.0%). Розрахований біоенергетичний потенціал нагромадження і продуктивності словацьких сільськогосподарсь-ких ґрунтів. Енергетично найбільш продуктивними є такі типи ґрунтів, як Чорноземи (88,6 ГДж/га-1) і Moллік Флювісолі (76,14 ГДж/га-1). Найменшим енергетичним продукуванням володіють Глеєсолі, Органосолі, Солонці і Літосолі (31,63 ГДж/га-1). Енергія, що накопичується в сільгоспугіддях рослинами варіюється в залежності від представленого ґрунту і його властивостей. Найнижча накопичувальна здатність була знайдена в Камбісолях (0.7-1.8%), а найвища в Регосолях (3.1-7.0%)

METHODOLOGY OF EXAMINATION OF THE HIGHER EDUCATION INSTITUTION FACULTY MEMBERS’ HEALTH AS WELL AS THE MEDICAL AID ORGANIZATION

The authors consider methodological approaches to the examination of health of the faculty members of Russian higher education institutions, as well as to the medical aid organization for this contingent

Somatoform disorders in the family doctor's practice.

Somatoform disorders – psycho­genic diseases are characterized by pathological physical symptoms that resemble somatic illness. Thus, any organic manifestations, which can be attributed to known diseases are not detected, but there are non-specific functional impairments. Somatoform disorders include somatization disorder, undifferentiated somatoform disorder, hypocho­n­driacal disorder, somatoform dysfunction of the autonomic nervous system and stable somatoform pain disorder. The first part of the article reviewes features of the clinical manifestations of somatization disorder and undifferentiated somatoform disorder. Role of non-benzodiazepine tranquilizers (ADAPTOL) and metabolic drugs (VASONAT) in the treatment of patients with somatoform disorders is discussed. In review article data of neurologists and cardiologists on the effectiveness of anxiolytic drug ADAPTOL and metabolic drug VASONAT in different clinical groups of patients (coronary artery disease, chronic ischemia of the brain), which can significantly improve quality of life, increase exercise tolerance, improve cognitive function and correct mental and emotional disorders are presented

Homology modeling and molecular dynamics study of Mycobacterium tuberculosis urease

Introduction. M. tuberculosis urease (MTU) is an attractive target for chemotherapeutic intervention in tuberculosis by designing new safe and efficient enzyme inhibitors. A prerequisite for designing such inhibitors is an understanding of urease's three-dimensional (3D) structure organization. 3D structure of M. tuberculosis urease is unknown. When experimental three-dimensional structure of a protein is not known, homology modeling, the most commonly used computational structure prediction method, is the technique of choice. This paper aimed to build a 3D-structure of M. tuberculosis urease by homology modeling and to study its stability by molecular dynamics simulations. Materials and methods. To build MTU model, five high-resolution X-ray structures of bacterial ureases with three-subunit composition (2KAU, 5G4H, 4UBP, 4СEU, and 4EPB) have been selected as templates. For each template five stochastic alignments were created and for each alignment, a three-dimensional model was built. Then, each model was energy minimized and the models were ranked by quality Z-score. The MTU model with highest quality estimation amongst 25 potential models was selected. To further improve structure quality the model was refined by short molecular dynamics simulation that resulted in 20 snapshots which were rated according to their energy and the quality Z-score. The best scoring model having minimum energy was chosen as a final homology model of 3D structure for M. tuberculosis. The final model of MTU was also validated by using PDBsum and QMEAN servers. These checks confirmed good quality of MTU homology model. Results and discussion. Homology model of MTU is a nonamer (homotrimer of heterotrimers, (αβγ)3) consisting of 2349 residues. In MTU heterotrimer, sub-units α, β, and γ tightly interact with each other at a surface of approximately 3000 Å2. Sub-unit α contains the enzyme active site with two Ni atoms coordinated by amino acid residues His347, His349, carbamylated Lys430*, His459, His485, Asp 573, Gly490. Helix-turn-helix motif (residues 524-545) forms a mobile flap that covers the active site and is in closed conformation impeding access to the enzyme active site. The structural stability of MTU model was checked by molecular dynamics simulation in explicit water at 300 К and рН 7,4. During the simulation, root mean square deviations of Сα atoms (RMSD Сα) and root mean square fluctuations (RMSF) of amino acid residues of MTU were monitored for 60 ns. Also, the distance between the loop that covers the active site and the dinickel center was monitored. Analysis of MD trajectory indicate that the enzyme global structure is stable and the flap covering the active center remains in closed state during the simulation time. Conclusion. Predicted three-dimensional structure of M. tuberculosis urease can be used in the studies of structure-function relationships of the enzyme, in designing new safe and efficient enzyme inhibitors aimed to struggle with infectious diseases promoted by urease activity

Re-determination of the Pseudobinary System Li2O-MoO3

The quasi-binary phase diagram lithium oxide - molybdenum(VI) oxide was investigated by differential scanning calorimetry and X-ray diffraction. The four intermediate phases Li4MoO5, Li2MoO4, Li4Mo5O17, and Li2Mo4O13 show incongruent melting. The system has one eutectic point at 50.5 mol% MoO3 and 49.5 mol% LiO0.5 with a eutectic temperature of 524.6 deg C. At this point the melt is in equilibrium with Li2MoO4 and Li4Mo5O17.Comment: excerpt from a published article, with 3 figures and 1 tabl

Account of diffusion in local thermodynamic equilibrium and two-temperature plasma models

A self-consistent account of the effect of diffusion on charge transport in local thermodynamic equilibrium (LTE) and two-temperature (2T) ionization-equilibrium plasmas amounts to introducing into Ohm’s law, in addition to the conventional term proportional to the electric field (conduction current) and thermal-diffusion terms, also terms describing the diffusion due to plasma composition variations, which are proportional to the temperature gradient (or, in the case of 2T plasmas, to ∇Te and ∇Th) and to the plasma pressure gradient. These terms are calculated, with the use of the Stefan–Maxwell equations, for the particular case of 2T ionization-equilibrium atomic plasmas with singly charged ions. Also proposed is a simple way of approximate evaluation of reactive thermal conductivity in such plasmas. An online tool performing evaluation of the relevant coefficients for 2T argon, xenon, and mercury plasmas has been deployed on the internet. Representative modelling results show that the new form of Ohm’s law, when introduced into standard LTE or 2T models, may describe the electric field reversal in front of arc anodes, an effect that has been simulated previously only by means of (more complex) models taking into account deviations from ionization equilibrium.info:eu-repo/semantics/publishedVersio

Numerical modelling of high-pressure arc discharges: matching the LTE arc core with the electrodes

A widely used approach to simulation of high-pressure arc discharges is based on the system of magneto-hydrodynamic equations written in the approximation of local thermodynamic equilibrium (LTE). In this work, boundary conditions on the surface of the electrodes are formulated with the use of equations of balance of energy in the non-equilibrium near electrode layers that separate the LTE bulk plasma and the electrodes. As an example, numerical simulations of a free-burning arc in atmospheric-pressure argon plasma in the current range from 20 to 200 A are reported. Simulation results are in reasonably good agreement with those given by more sophisticated models and with the experiment. Simulations performed for cathodes of slightly different geometries have predicted a strong effect produced by details of the cathode geometry over the distribution of the current density along the cathode surface and therefore over the plasma temperature, an interesting and potentially important result that is worth further numerical investigation and experimental verification.info:eu-repo/semantics/publishedVersio

Chronobiological approaches to antiangiogenic photodynamic therapy of tumors: the first experimental evaluatIon

In research of the last decade, rhythmic (circadian) variations of vascular endothelial growth factor (VEGF) production by tumors were discovered. The present paper authors have earlier synthesized and characterized a new derivative photosensitizer — an immunoconjugate of hematoporphyrin with antiVEGF antibodies. Aim: To elaborate and to test a novel modification of the photodynamic therapy of tumors (PDT) method, founding upon a timed introduction of the immunoconjugated photosensitizer to tumor-bearing animals, so that this coincides with a maximum content of VEGF in tumor tissues. Methods: Circadian variations of VEGF contents in murine transplanted tumors, Lewis lung carcinoma and sarcoma 180, were determined by ELISA method. Immunoconjugated photosensitizer concentrations in tumors were estimated by spectrofluorometry. Photoirradiation of the tumors was carried out with a red light (wavelength of 635 nm) from a semiconductor laser. Light doses were chosen, calculating on a partial inhibition of tumor growth, in order that a dependence of PDT efficiency on a daily time-moment (circadian rhythm phase) of the treatment could be observed distinctly. Results: Circadian variations of the VEGF levels in Lewis lung carcinoma and sarcoma 180 were demonstrated with the maximum at 14:00 h and the minimum at 02:00 h. Intra-abdominal introduction into tumor-bearing mice of the immunoconjugated photosensitizer resulted in a greater accumulation of the immunoconjugate in tumors at 14:00 h than at 02:00 h. Laser irradiation of carcinomas and sarcomas at 14:00 h or 02:00 h after introduction of the immunoconjugated photosensitizer to mice the day before at the same time points, induced a significantly enhanced inhibition of tumor growth in animals treated at day-time versus those treated at night-time. Conclusion: The obtained results justify further attempts to transfer principles of tumor chronochemotherapy onto photodynamic therapy