MITOCHONDRIAL VDAC AND BACTERIAL PORA/C1: ION PERMEATION AND SELECTIVITY

VDAC and PorA/C1 are large diameter channels with properties reminiscent of those found in narrow channels. VDAC, located in the mitochondrial outer membrane, shows high selectivity for ATP over comparably sized ions. VDAC is characterized by a single open state with anionic selectivity and multiple cation-selective closed states. PorA/C1 from Neisseria meningitidis achieves high cationic selectivity and large conductance. VDAC has multiple functions in cellular processes and the most important one is the regulation of metabolite flow across the outer membrane. A variety of functions could be achieved by the existence of different isoforms. In this thesis I summarized the electrophysiological properties of VDAC-like proteins from Drosophila Melanogaster encoded by genes CG17137, CG17139 and CG17140. The ability of these proteins to form channels was tested on planar membranes and liposomes. Channel activity was observed with varying degrees of similarity to VDAC. Two of these proteins (CG17137, CG17140) produced channels with anionic selectivity in the open state. Sometimes channels exhibited closure and voltage gating, but for CG17140 this occurred at much higher voltages than is typical for VDAC. CG17139 did not form channels. The special selectivity of VDAC for large anions was explored using the mutant of the mouse isoform 2. Inserted into planar membranes, mutant channels lack voltage gating, have a lower conductance, demonstrate cationic selectivity and, surprisingly, are still permeable to ATP. The estimated ATP flux through the mutant is comparable to that for the wildtype. Also we determined that the intact outer membrane containing the mutant is permeable to NADH and ADP/ATP. Both experiments support the counterintuitive conclusion that converting a channel from anion to cation preference does not substantially influence the flux of negatively charged metabolites. However, this finding supports the previous proposal that ATP translocation through VDAC is facilitated by a set of specific interactions between ATP and the channel wall. The third part of my thesis represents experimental data supporting the theoretical model for the PorA/C1 structure. This model explains the almost ideal cationic selectivity of the channel and high level of rectification. These properties are proposed to arise from a high density of charges in the channel that results in both high selectivity and high ionic flux

Processing of experimental data describing internal deflagration explosions

This article is devoted to issues related to experimental studies of internal deflagration explosions or emergency explosions occurring inside buildings and premises. In internal emergency explosions, the main role in reducing the explosive pressure to a safe level is played by discharge openings blocked by safety structures (SS). As discharge openings, windows are often used, covered with glazed window blocks, or opened explosion venting structures (EVS). The article deals with processing experimental data obtained in the study of deflagration explosions occurring inside buildings and premises. The main features and difficulties that arise while analyzing experimental materials are described. The article considers the general methodology for processing experimental data to study deflagration explosions inside buildings and premises. Examples of processing materials from experiments performed in chambers equipped with a transparent edge allow high-speed filming of the explosive combustion process inside the chamber. The article presents a technique that allows, based on data processing on the overpressure in the explosion chamber, to obtain complete characteristics of the loads that occur in the experimental chamber during an internal deflagration explosion. The proposed technique makes it possible to abandon the transparent edge of the explosion chamber and obtain data on the explosion process based on the numerical processing of the excess pressure created in the explosion chamber. An example of processing a full-scale experiment to determine the effectiveness of a real explosion venting structure (EVS) is given

Geovisualization of forest simulation modelling results: A case study of carbon sequestration and biodiversity

Sustainable forest management requires new tools to analyze spatial and temporal forest dynamics and to examine those forest parameters that are related to sustainability. We built a prototype system for data analysis and decision-making at forest enterprise level by integrating a forest ecosystem model EFIMOD-PRO (long-term prediction of forest growth and soil development) with an interactive visualization system CommonGIS for analysis of spatially and temporally related data. Using the prototype, a case study in Central European Russia simulated four silvicultural regimes over 200 years: natural development, selective forestry, legal forestry according to the Russian forestry legislation, and illegal forest practice. Exploratory analysis of the simulation results demonstrated that (1) natural stand development is the best alternative for carbon sequestration; (2) legal forest management is the best regime for timber production; (3) selective forestry combines the advantages of two previous strategies, and can be the best strategy for implementing sustainable forest management; and (4) illegal forest practices lead to a fast decrease in forest productivity and decreasing biodiversity. Interactive and dynamic visualizations with maps and statistical graphics played a crucial role in data cleaning, model validation, and analysis of simulation results. The case study demonstrated the potential of integrating forest ecosystem models with exploratory data visualization for the analysis and expert evaluation at the local level. The prototype can be used to present ecological and silvicultural consequences of various management practices to stakeholders and differing social groups, thus stimulating effective decision-making for sustainable forestry

Oxidation Of Adenosine And Inosine: The Chemistry Of 8-oxo-7,8-dihydropurines, Purine Iminoquinones, And Purine Quinones As Observed By Ultrafast Spectroscopy

Oxidative damage to purine nucleic acid bases proceeds through quinoidal intermediates derived from their corresponding 8-oxo-7,8-dihydropurine bases. Oxidation studies of 8-oxo-7,8-dihyroadenosine and 8-oxo-7,8-dihydroinosine indicate that these quinoidal species can produce stable cross links with a wide variety of nucleophiles in the 2-positions of the purines. An azide precursor for the adenosine iminoquinone has been synthesized and applied in ultrafast transient absorption spectroscopic studies. Thus, the adenosine iminoquinone can be observed directly, and its susceptibility to nudeophilic attack with various nucleophiles as well as the stability of the resulting cross linked species have been evaluated Finally, these observations indicate that this azide might be a very useful photoaffurity labeling agent, because the reactive intermediate, adenosine iminoquinone, is such a good mimic for the universal purine base adenosine

Diarylethene-Based Photoswitchable Inhibitors of Serine Proteases

A bicyclic peptide scaffold was chemically adapted to generate diarylethene-based photoswitchable inhibitors of serine protease Bos taurus trypsin 1 (T1). Starting from a prototype molecule—sunflower trypsin inhibitor-1 (SFTI-1)—we obtained light-controllable inhibitors of T1 with Ki in the low nanomolar range, whose activity could be modulated over 20-fold by irradiation. The inhibitory potency as well as resistance to proteolytic degradation were systematically studied on a series of 17 SFTI-1 analogues. The hydrogen bond network that stabilizes the structure of inhibitors and possibly the enzyme–inhibitor binding dynamics were affected by isomerization of the photoswitch. The feasibility of manipulating enzyme activity in time and space was demonstrated by controlled digestion of gelatin-based hydrogel and an antimicrobial peptide BP100-RW. Finally, our design principles of diarylethene photoswitches are shown to apply also for the development of other serine protease inhibitor