Different responses of rat cerebral mitochondrial 2-oxoglutarate dehydrogenase activity to ammonia and hepatic encephalopathy in synaptic and nonsynaptic mitochondria

The effects of in vitro treatment with ammonium chloride and acute hepatic encephalopathy (HE) induced by thioacetamide treatment (TAA), on the 2-oxoglutarate dehydrogenase (OGDH) activity in synaptic and nonsynaptic mitochondria from rat brain were examined. In control conditions, V_max and K_m for 2-oxoglutaric acid (2-OG) were higher in the synaptic than in nonsynaptic mitochondria by about 45 and 55%, respectively. A particularly high sensitivity of OGDH to ammonium ions in vitro was observed in nonsynaptic mitochondria, as manifested by a 30% decrease of V_max and a 60% decrease of K_m for 2-OG. Synaptic mitochondria showed a slight response to HE which was manifested by a 12% increase of V_max. In nonsynaptic mitochondria a 19% decrease of K_m for 2-OG was observed, but V_max was unaffected. Nonsynaptic mitochondria from HE rats reacted to the addition of ammonium ions in vitro with a 30% inhibition of V_max but with no alteration of K_m for 2-OG. In synaptic mitochondria from HE rats there was a slight inhibition of V_max, but an about 15% decrease of K_m for 2-OG. Based on these results, the different responses of OGDH in two mitochondrial populations to HE and ammonium ions in vitro would appear to be due to intrinsic differences between the properties of the enzyme in the synaptic and nonsynaptic brain compartments.     

Lattice simulations of protein crystal formation

A new algorithm is presented for the lattice simulation of protein crystal growth. The algorithm allows the calculation of the size distribution of microcrystals in the volume and timescale of experiments and within the framework of the previously-published microscopic model [A.M. Kierzek, W.M. Wolf, P. Zielenkiewicz, Biophys. J. 73 (1997) 571-580]. Simulations for the tetragonal lysozyme crystal show that there are two critical sizes in the development of ordered phase. The first one corresponds to the size of the smallest stable complex which, in the case of the tetragonal lysozyme crystal, is the particular tetramer. In a volume of 5 mul the tetramer appears in the millisecond timescale. The second critical radius of approximately 100 monomers is only reached by a few of all the smallest stable complexes formed in the solution. The model predicts that out of 10(7) tetramers which appear in solution, only eight reach the size of 100 monomers within 8 h. After exceeding the second critical radius the microcrystals grow to the size of 10(4) monomers in the minute timescale and are thus assumed to quickly lead to macroscopic crystals. The predicted number of crystals formed during 8 h of nucleation is in qualitative agreement with arrested nucleation experiments.     

Optimal and suboptimal protocols for a class of mathematical models of tumor anti-angiogenesis

Tumor anti-angiogenesis is a cancer treatment approach that aims at preventing the primary tumor from developing its own vascular network needed for further growth. In this paper the problem of how to schedule an a priori given amount of angiogenic inhibitors in order to minimize the tumor volume is considered for three related mathematical formulations of a biologically validated model developed by Hahnfeldt et al. [1999. Tumor development under angiogenic signalling: a dynamical theory of tumor growth, treatment response, and postvascular dormancy. Cancer Res. 59, 4770-4775]. Easily implementable piecewise constant protocols are compared with the mathematically optimal solutions. It is shown that a constant dosage protocol with rate given by the averaged optimal control is an excellent suboptimal protocol for the original model that achieves tumor values that lie within 1% of the theoretically optimal values. It is also observed that the averaged optimal dose is decreasing as a function of the initial tumor volume.     

Theoretical model of thalassemic erythrocyte shape transformation

Our earlier model of reticulocyte shape transformation [Pawlowski, P.H., Burzynska, B., Zielenkiewicz, P., 2006. Theoretical model of reticulocyte to erythrocyte shape transformation. J. Theor. Biol. 243, 24-38] was applied to explain the morphological properties of thalassemic erythrocytes. Modification of the standard set of parameters of the model, describing minimal cell volume, membrane bending rigidity, and membrane tension, allowed for simulation of development of α- and β-thalassemic cells from splenectomized and nonsplenectomized individuals. This resulted in observation of thin rim discocytes, tailed erythrocytes and oval forms, as well as in differentiation of time of the cell shape metamorphosis. A comparative analysis of the susceptibility of thalassemic and normal erythrocytes to undergo deformation as well of their stability was performed.     

B lymphocyte activation by coinfection prevents immune control of friend virus infection

Although the adaptive immune response almost invariably fails to completely eliminate retroviral infections, it can exert significant protection from disease and long-term control of viral replication. Friend virus (FV), a mouse retrovirus, causes persistent infection in all strains of mice and erythroleukaemia in susceptible strains, the course of which can be strongly influenced by both genetic and extrinsic factors. In this study we examine the impact of coinfection on the requirements for immune control of FV infection. We show that congenic C57BL/6 mice, in which the introduction of an allele of the Friend virus susceptibility 2 gene provides the potential for FV-induced leukemia development, effectively resist FV infection, and both T cell- and Ab-dependent mechanisms contribute to their resistance. However, we further demonstrate that coinfection with lactate dehydrogenase-elevating virus (LDV) renders these otherwise immunocompetent mice highly susceptible to FV infection and subsequent disease. The presence of LDV delays induction of FV-specific neutralizing Abs and counteracts the protective contribution of adaptive immunity. Importantly, the disease-enhancing effect of LDV coinfection requires the presence of a polyclonal B cell repertoire and is reproduced by direct polyclonal B cell activation. Thus, immune activation by coinfecting pathogens or their products can contribute to the pathogenicity of retroviral infection.     

Use of Long-Range Repetitive Element Polymorphism-PCR To Differentiate Bacillus anthracis Strains

The genome of Bacillus anthracis is extremely monomorphic, and thus individual strains have often proven to be recalcitrant to differentiation at the molecular level. Long-range repetitive element polymorphism-PCR (LR REP-PCR) was used to differentiate various B. anthracis strains. A single PCR primer derived from a repetitive DNA element was able to amplify variable segments of a bacterial genome as large as 10 kb. We were able to characterize five genetically distinct groups by examining 105 B. anthracis strains of diverse geographical origins. All B. anthracis strains produced fingerprints comprising seven to eight bands, referred to as “skeleton” bands, while one to three “diagnostic” bands differentiated between B. anthracis strains. LR REP-PCR fingerprints of B. anthracis strains showed very little in common with those of other closely related species such as B. cereus, B. thuringiensis, and B. mycoides, suggesting relative heterogeneity among the non-B. anthracis strains. Fingerprints from transitional non-B. anthracis strains, which possessed the B. anthracis chromosomal marker Ba813, scarcely resembled those observed for any of the five distinct B. anthracis groups that we have identified. The LR REP-PCR method described in this report provides a simple means of differentiating B. anthracis strains.     

B. subtilis ykuD protein at 2.0 A resolution: insights into the structure and function of a novel, ubiquitous family of bacterial enzymes

The crystal structure of the product of the Bacillus subtilis ykuD gene was solved by the multiwavelength anomalous dispersion (MAD) method and refined using data to 2.0 A resolution. The ykuD protein is a representative of a distinctly prokaryotic and ubiquitous family found among both pathogenic and nonpathogenic Gram-positive and Gram-negative bacteria. The deduced amino acid sequence reveals the presence of an N-terminal LysM domain, which occurs among enzymes involved in cell wall metabolism, and a novel, putative catalytic domain with a highly conserved His/Cys-containing motif of hitherto unknown structure. As the wild-type protein did not crystallize, a double mutant was designed (Lys117Ala/Gln118Ala) to reduce excess surface conformational entropy. As expected, the structure of the LysM domain is similar to the NMR structure reported for an analogous domain from Escherichia coli murein transglycosylase MltD. The molecular model also shows that the 112-residue-long C-terminal domain has a novel tertiary fold consisting of a beta-sandwich with two mixed sheets, one containing five strands and the other, six strands. The two beta-sheets form a cradle capped by an alpha-helix. This domain contains a putative catalytic site with a tetrad of invariant His123, Gly124, Cys139, and Arg141. The stereochemistry of this active site shows similarities to peptidotransferases and sortases, and suggests that the enzymes of the ykuD family may play an important role in cell wall biology.     

The DC-module of doublecortin: dynamics, domain boundaries, and functional implications

The doublecortin-like (DC) domains, which usually occur in tandem, constitute novel microtubule-binding modules. They were first identified in doublecortin (DCX), a protein expressed in migrating neurons, and in the doublecortin-like kinase (DCLK). They are also found in other proteins, including the RP1 gene product which-when mutated-causes a form of inherited blindness. We previously reported an X-ray structure of the N-terminal DC domain of DCLK (N-DCLK), and a solution structure of an analogous module of human doublecortin (N-DCX). These studies showed that the DC domain has a tertiary fold closely reminiscent of ubiquitin and similar to several GTPase-binding domains. We now report an X-ray structure of a mutant of N-DCX, in which the C-terminal fragment (residues 139-147) unexpectedly shows an altered, "open" conformation. However, heteronuclear NMR data show that this C-terminal fragment is only transiently open in solution, and assumes a predominantly "closed" conformation. While the "open" conformation may be artificially stabilized by crystal packing interactions, the observed switching between the "open" and "closed" conformations, which shortens the linker between the two DC-domains by approximately 20 A, is likely to be of functional importance in the control of tubulin polymerization and microtubule bundling by doublecortin.