Functional coupling between TRPC3 and RyR1 regulates the expressions of key triadic proteins

We have shown that TRPC3 (transient receptor potential channel canonical type 3) is sharply up-regulated during the early part of myotube differentiation and remains elevated in mature myotubes compared with myoblasts. To examine its functional roles in muscle, TRPC3 was "knocked down" in mouse primary skeletal myoblasts using retroviral-delivered small interference RNAs and single cell cloning. TRPC3 knockdown myoblasts (97.6 +/- 1.9% reduction in mRNA) were differentiated into myotubes (TRPC3 KD) and subjected to functional and biochemical assays. By measuring rates of Mn(2+) influx with Fura-2 and Ca(2+) transients with Fluo-4, we found that neither excitation-coupled Ca(2+) entry nor thapsigargin-induced store-operated Ca(2+) entry was significantly altered in TRPC3 KD, indicating that expression of TRPC3 is not required for engaging either Ca(2+) entry mechanism. In Ca(2+) imaging experiments, the gain of excitation-contraction coupling and the amplitude of the Ca(2+) release seen after direct RyR1 activation with caffeine was significantly reduced in TRPC3 KD. The decreased gain appears to be due to a decrease in RyR1 Ca(2+) release channel activity, because sarcoplasmic reticulum (SR) Ca(2+) content was not different between TRPC3 KD and wild-type myotubes. Immunoblot analysis demonstrated that TRPC1, calsequestrin, triadin, and junctophilin 1 were up-regulated (1.46 +/- 1.91-, 1.42 +/- 0.08-, 2.99 +/- 0.32-, and 1.91 +/- 0.26-fold, respectively) in TRPC3 KD. Based on these data, we conclude that expression of TRPC3 is tightly regulated during muscle cell differentiation and propose that functional interaction between TRPC3 and RyR1 may regulate the gain of SR Ca(2+) release independent of SR Ca(2+) load.     

A Genome-Scale Metabolic Reconstruction of Mycoplasma genitalium,iPS189

With a genome size of ∼580 kb and approximately 480 protein coding regions, Mycoplasma genitalium is one of the smallest known self-replicating organisms and, additionally, has extremely fastidious nutrient requirements. The reduced genomic content of M. genitalium has led researchers to suggest that the molecular assembly contained in this organism may be a close approximation to the minimal set of genes required for bacterial growth. Here, we introduce a systematic approach for the construction and curation of a genome-scale in silico metabolic model for M. genitalium. Key challenges included estimation of biomass composition, handling of enzymes with broad specificities, and the lack of a defined medium. Computational tools were subsequently employed to identify and resolve connectivity gaps in the model as well as growth prediction inconsistencies with gene essentiality experimental data. The curated model, M. genitalium iPS189 (262 reactions, 274 metabolites), is 87% accurate in recapitulating in vivo gene essentiality results for M. genitalium. Approaches and tools described herein provide a roadmap for the automated construction of in silico metabolic models of other organisms.     

The open state gating mechanism of gramicidin a requires relative opposed monomer rotation and simultaneous lateral displacement

The gating mechanism of the open state of the gramicidin A (gA) channel is studied by using a new Monte Carlo Normal Mode Following (MC-NMF) technique, one applicable even without a target structure. The results demonstrate that the lowest-frequency normal mode (NM) at approximately 6.5 cm(-1) is the crucial mode that initiates dissociation. Perturbing the gA dimer in either direction along this NM leads to opposed, nearly rigid-body rotations of the gA monomers around the central pore axis. Tracking this NM by using the eigenvector-following technique reveals the channel's gating mechanism: dissociation via relative opposed monomer rotation and simultaneous lateral displacement. System evolution along the lowest-frequency eigenvector shows that the large-amplitude motions required for gating (dissociation) are not simple relative rigid-body motions of the monomers. Gating involves coupling intermonomer hydrogen bond breaking, backbone realignment, and relative monomer tilt with complex side chain reorganization at the intermonomer junction.     

Boosting Autofermentation Rates and Product Yields with Sodium Stress Cycling: Application to Production of Renewable Fuels by Cyanobacteria

Sodium concentration cycling was examined as a new strategy for redistributing carbon storage products and increasing autofermentative product yields following photosynthetic carbon fixation in the cyanobacterium Arthrospira (Spirulina) maxima. The salt-tolerant hypercarbonate strain CS-328 was grown in a medium containing 0.24 to 1.24 M sodium, resulting in increased biosynthesis of soluble carbohydrates to up to 50% of the dry weight at 1.24 M sodium. Hypoionic stress during dark anaerobic metabolism (autofermentation) was induced by resuspending filaments in low-sodium (bi)carbonate buffer (0.21 M), which resulted in accelerated autofermentation rates. For cells grown in 1.24 M NaCl, the fermentative yields of acetate, ethanol, and formate increase substantially to 1.56, 0.75, and 1.54 mmol/(g [dry weight] of cells·day), respectively (36-, 121-, and 6-fold increases in rates relative to cells grown in 0.24 M NaCl). Catabolism of endogenous carbohydrate increased by approximately 2-fold upon hypoionic stress. For cultures grown at all salt concentrations, hydrogen was produced, but its yield did not correlate with increased catabolism of soluble carbohydrates. Instead, ethanol excretion becomes a preferred route for fermentative NADH reoxidation, together with intracellular accumulation of reduced products of acetyl coenzyme A (acetyl-CoA) formation when cells are hypoionically stressed. In the absence of hypoionic stress, hydrogen production is a major beneficial pathway for NAD⁺ regeneration without wasting carbon intermediates such as ethanol derived from acetyl-CoA. This switch presumably improves the overall cellular economy by retaining carbon within the cell until aerobic conditions return and the acetyl unit can be used for biosynthesis or oxidized via respiration for a much greater energy return.Growth of aquatic microbial oxygenic phototrophs (AMOPs) such as cyanobacteria, algae, and diatoms as renewable feedstocks for energy production has been proposed as an advantageous alternative to growing land-based crops for biofuels (9, 11, 14). These organisms can be grown efficiently on water, sunlight, carbon dioxide, and minimal nutrients on nonarable land or at coastal marine sites. They produce easily digested biopolymers that can be more readily converted to fuels than recalcitrant cellulosic feedstocks. Nevertheless, efficient strategies for converting accumulated biomass from AMOPs into useful fuels are still needed.One strategy for converting cyanobacterial biomass to liquid and gaseous fuels is to allow these cells to rely on their own fermentative pathways—a process termed “autofermentation.” With autofermentation, cells anaerobically catabolize their internally stored carbohydrate molecules (glycogen and soluble sugars), producing CO₂, reductants, and energy as ion gradients and phosphorylation to regenerate ATP. The reducing equivalents in the form of NAD(P)H may be reused by the cell or excreted from the cell as reduced carbon products, typically organic acids and alcohols. The identities of these products are determined by the physiological conditions and by which fermentative enzymes are active. The genomes of cyanobacteria differ in terms of which genes of fermentative enzymes are present and functional, leading to a range of possible fermentative product yields and rates. A major limitation to the technological use of autofermentation for fuel production from biomass is the slow time scale of the conversion in relation to the light/dark cycle of growth.Two fermentation products useful as fuels that are excreted by some cyanobacteria are ethanol and hydrogen. Ethanol production via autofermentation occurs naturally in some cyanobacteria (22). Genetic engineering has been applied successfully to establish autofermentative ethanol production in the cyanobacterium Synechococcus sp. PCC 7942, which does not produce detectable amounts of ethanol in the wild type (10). This strain was created by insertion of the genes for pyruvate decarboxylase and alcohol dehyrogenase from Zymomonas mobilis. Genetic engineering has also been successfully applied to stimulate fermentative hydrogen production in Synechococcus sp. PCC 7002 by increasing the level of the limiting cellular reductant NADH via disruption of the lactate dehydrogenase gene (19).For biotechnological applications, the following two goals have been identified for increasing production of autofermentation products and hydrogen by AMOPs (1): (i) increase photoautotrophic accumulation of stored carbohydrates and (ii) increase the catabolic rate of carbohydrates under dark anaerobic conditions. Here we have continued our work with Arthrospira (Spirulina) maxima with efforts to achieve these two goals.Different approaches for increasing carbohydrate content for cyanobacteria exist. One is nutrient deprivation. Many cyanobacteria, including Arthrospira species, do not have nitrogenase (nif) genes and therefore require a nitrogen source (such as nitrate, ammonia, or urea) for protein synthesis. Deprivation of a nitrogen source is a well-documented strategy for increasing the glycogen content (stored as insoluble carbohydrate granules) in many nondiazotrophic cyanobacteria (3, 13, 23, 26). Sulfur deprivation has also been shown to increase the glycogen content in at least two cyanobacteria when incubated in the presence of methane (2). Recently, it was demonstrated that sulfur and nitrogen limitation, rather than complete deprivation, provides optimal autofermentative hydrogen yields in the cyanobacterium Synechocystis sp. PCC 6803 (5).A different approach, which increases soluble sugars in cyanobacteria, involves adaptation of cells to media with high concentrations of sodium salts. Many cyanobacteria accumulate organic molecules such as glucosyl-glycerol and/or trehalose to osmotically balance their cytosols with the extracellular medium (6, 17, 20). In addition to glycogen, these molecules can serve as substrates for fermentation in cyanobacteria (22). Both glucosyl-glycerol and trehalose are present in Arthrospira platensis (29) and A. maxima CS-328 (8). It was shown that a 4-fold increase in carbohydrate content can be achieved by growing A. platensis in media supplemented with additional 1 M NaCl relative to no additional NaCl (28).Acceleration of carbohydrate autofermentation in cyanobacteria by application of selective physiological stresses has been previously proposed (1). Here we report a new strategy that combines the established method for increasing carbohydrate content in Arthrospira by adapting filaments to highly saline growth media (28) with hypoionic stress to accelerate autofermentation. The entire process can be described as “sodium stress cycling,” which relies on hyperionic conditions (high salt) during growth to accumulate sugars, followed by hypoionic stress (low salt) to force catabolism during autofermentation. By resuspending filaments grown in media containing excess NaCl into buffer containing only sufficient solute to prevent lysis at the start of autofermentation, we achieve a large increase in total fermentative product yields relative to cells that were not adapted to high salt. However, this strategy did not lead to higher hydrogen yields, demonstrating that other fermentative routes (primarily ethanol production) are used for NADH recycling in A. maxima under hypoionic conditions.     

The Peptides Mimicking the Third Intracellular Loop of 5-Hydroxytryptamine Receptors of the Types 1B and 6 Selectively Activate G Proteins and Receptor-Specifically Inhibit Serotonin Signaling via the Adenylyl Cyclase System

The third intracellular loop (ICL3) of G protein-coupled receptors has, as a rule, a key role in their interaction with heterotrimeric G proteins. We synthesized peptides corresponding to the C-terminal region of the ICL3 (C-ICL3) of 5-hydroxytryptamine receptors of the type 1B (5-HT_1BR) and 6 (5-HT₆R) and studied their influence on the functional activity of adenylyl cyclase signaling system (ACSS) in synaptosomal membranes isolated from the rat brain. The 5-HT_1BR-peptide ARERKATKTL^307–316K-amide mimicking agonist-activated 5-HT_1BR reduced forskolin-stimulated adenylyl cyclase (AC) activity and activated pertussis toxin-sensitive G proteins. It lowered inhibitory effects of serotonin and 5-HT_1BR-agonists on forskolin-stimulated AC activity and their stimulating effects on GTP binding. This was not the case in the presence of 5-HT_1BR-antagonists. The 5-HT₆R-peptides mimicking 5-HT₆R activated both the basal AC activity and GTP binding of cholera toxin-sensitive G proteins. They lowered the stimulating effect of serotonin and 5-HT₆R-agonists on AC and G_s proteins, but in the presence of 5-HT₆R-antagonists their action was blocked. Of all the 5-HT₆R-peptides with linear and dimeric structure we studied the palmitoylated peptide KHSRKALKASL^258–268K(Pal)A-amide had a most pronounced effect both on the basal and 5-HT₆R-agonist-stimulated ACSS. The data was obtained indicating that the peptides corresponding to C-ICL3 of 5-HT_1BR and 5-HT₆R selectively activate G_i and G_s proteins, respectively, and in a receptor-specific manner reduce signal transduction via serotonin-sensitive ACSS in the rat brain. The results of the study give strong evidence in favor of active participation of C-ICL3 of these 5-HTRs in their coupling with the G proteins.     

Imprint of evolutionary conservation and protein structure variation on the binding function of protein tyrosine kinases

MOTIVATION: According to the models of divergent molecular evolution, the evolvability of new protein function may depend on the induction of new phenotypic traits by a small number of mutations of the binding site residues. Evolutionary relationships between protein kinases are often employed to infer inhibitor binding profiles from sequence analysis. However, protein kinases binding profiles may display inhibitor selectivity within a given kinase subfamily, while exhibiting cross-activity between kinases that are phylogenetically remote from the prime target. The emerging insights into kinase function and evolution combined with a rapidly growing number of publically available crystal structures of protein kinases complexes have motivated structural bioinformatics analysis of sequence-structure relationships in determining the binding function of protein tyrosine kinases. RESULTS: In silico profiling of Imatinib mesylate and PD-173955 kinase inhibitors with protein tyrosine kinases is conducted on kinome scale by using evolutionary analysis and fingerprinting inhibitor-protein interactions with the panel of all publically available protein tyrosine kinases crystal structures. We have found that sequence plasticity of the binding site residues alone may not be sufficient to enable protein tyrosine kinases to readily evolve novel binding activities with inhibitors. While evolutionary signal derived solely from the tyrosine kinase sequence conservation can not be readily translated into the ligand binding phenotype, the proposed structural bioinformatics analysis can discriminate a functionally relevant kinase binding signal from a simple phylogenetic relationship. The results of this work reveal that protein conformational diversity is intimately linked with sequence plasticity of the binding site residues in achieving functional adaptability of protein kinases towards specific drug binding. This study offers a plausible molecular rationale to the experimental binding profiles of the studied kinase inhibitors and provides a theoretical basis for constructing functionally relevant kinase binding trees.     

Modelling the dynamics of LCMV infection in mice: II. Compartmental structure and immunopathology

In this study, we develop a mathematical model for analysis of the compartmental aspects and immunopathology of lymphocytic choriomeningitis virus (LCMV) infection in mice. We used sets of original and published data on systemic (extrasplenic) virus distribution to estimate the parameters of virus growth and elimination for spleen and other anatomical compartments, such as the liver, kidney, thymus and lung as well as transfer rates between blood and the above organs. A mathematical model quantitatively integrating the virus distribution kinetics in the host, the specific cytotoxic T lymphocyte (CTL) response in spleen and the re-circulation of effector CTL between spleen, blood and liver is advanced to describe the CTL-mediated immunopathology (hepatitis) in mice infected with LCMV. For intravenous and "peripheral" routes of infection we examine the severity of the liver disease, as a function of the virus dose and the host's immune status characterized by the numbers of precursor and/or cytolytic effector CTL. The model is used to predict the efficacy of protection against virus persistence and disease in a localized viral infection as a function of the composition of CTL population. The modelling analysis suggests quantitative demands to CTL memory for maximal protection against a wide range of doses of infection with a primarily peripheral site of virus replication without the risk of favoring immunopathology. It specifies objectives for CTL vaccination to ensure virus elimination with minimal immunopathology vs. vaccination for disease.     

Detailed kinetic analysis of a family 52 glycoside hydrolase: a beta-xylosidase from Geobacillus stearothermophilus

Geobacillus stearothermophilus T-6 encodes for a beta-xylosidase (XynB2) from family 52 of glycoside hydrolases that was previously shown to hydrolyze its substrate with net retention of the anomeric configuration. XynB2 significantly prefers substrates with xylose as the glycone moiety and exhibits a typical bell-shaped pH dependence curve. Binding properties of xylobiose and xylotriose to the active site were measured using isothermal titration calorimetry (ITC). Binding reactions were enthalpy driven with xylobiose binding more tightly than xylotriose to the active site. The kinetic constants of XynB2 were measured for the hydrolysis of a variety of aryl beta-D-xylopyranoside substrates bearing different leaving groups. The Br?nsted plot of log k(cat) versus the pK(a) value of the aglycon leaving group reveals a biphasic relationship, consistent with a double-displacement mechanism as expected for retaining glycoside hydrolases. Hydrolysis rates for substrates with poor leaving groups (pK(a) > 8) vary widely with the aglycon reactivity, indicating that, for these substrates, the bond cleavage is rate limiting. However, no such dependence is observed for more reactive substrates (pK(a) < 8), indicating that in this case hydrolysis of the xylosyl-enzyme intermediate is rate limiting. Secondary kinetic isotope effects suggest that the intermediate breakdown proceeds with modest oxocarbenium ion character at the transition state, and bond cleavage proceeds with even lower oxocarbenium ion character. Inhibition studies with several gluco analogue inhibitors could be measured since XynB2 has low, yet sufficient, activity toward 4-nitrophenyl beta-D-glucopyranose. As expected, inhibitors mimicking the proposed transition state structure, such as 1-deoxynojirimycin, bind with much higher affinity to XynB2 than ground state inhibitors.     

Genetic aberrations in Chernobyl-related thyroid cancers: implications for possible future nuclear accidents or nuclear attacks

Cases of thyroid cancer among children in Belarus represent a unique model system in which the cause of the cancer is known--radiation. Although other sources of radiation-induced cancers are diminishing (survivors of Hiroshima and Nagasaki, and individuals exposed to diagnostic or therapeutic radiation) fears of radiation exposure from accidents and terrorism are increasing. Our analysis of current data reveals that Chernobyl-related cancer cases might have a specific pattern of genetic aberrations. These data strongly confirm the hypothesis that radiation-induced cancers might arise as a result of specific gene aberrations that are distinct from those in sporadic cancers, suggesting that methods of prevention and treatment of radiation-induced cancers might require a different approach. Understanding of the molecular mechanisms of Chernobyl-related papillary thyroid carcinomas will help to identify mechanisms by which radiation causes aberrations and oncogenic cell transformation. Thus, in turn, it will be important in the development of new treatments or technologies to minimize the effects of radiation damage from nuclear accidents or nuclear attacks.