ARL15, a GTPase implicated in rheumatoid arthritis, potentially repositions its truncated N-terminus as a function of guanine nucleotide binding

The ADP ribosylation factor like protein 15 (ARL15) gene encodes for an uncharacterized GTPase associated with rheumatoid arthritis (RA) and other metabolic disorders. Investigation of the structural and functional attributes of ARL15 is important to position the protein as a potential drug target. Using spectroscopy, we demonstrated that ARL15 exhibits properties inherent of GTPases. The Km and Vmax of the enzyme were calculated to be 100 μM and 1.47 μmole/min/μL, respectively. The equilibrium dissociation constant (Kd) of GTP binding with ARL15 was estimated to be about eight-fold higher than that of GDP. Small Angle X-ray Scattering (SAXS) data indicated that in solution, the apo state of monomeric ARL15 adopts a shape characterized by a globe of maximum linear dimension (Dmax) of 6.1 nm, and upon binding to GTP or GDP, the vector distribution profile changes to peak-n-tail shoulder with Dmax extended to 7.6 and 7.7 nm, respectively. Structure restoration using a sequence-based template and experimental SAXS data provided the first visual insight revealing that the folded N-terminal in the unbound state of the protein may toggle open upon binding to guanine nucleotides. The conformational dynamics observed in the N-terminal region offer a scope to develop drugs that target this unique GTPase, potentially providing treatments for a range of metabolic disorders.

Nucleotide Exchange on RAS Proteins Using Hydrolysable and Non-hydrolysable Nucleotides

Biochemical and biophysical assays using recombinant RAS require the protein to be in either the active or inactive state. Here we describe methods to exchange the nucleotide present in the purified RAS protein with either GDPβS, GppNHp, or GTP depending on the assay requirement. In addition, we also describe the HPLC method used to validate the exchange process and provide information on the efficiency of the nucleotide exchange.

Phosphorylation of RhoGDI1, a Rho GDP dissociation inhibitor, regulates root hair development in Arabidopsis under salt stress

To ensure optimal growth, plants actively regulate their growth and development based on environmental changes. Among these, salt stress significantly influences growth and yield. In this study, we demonstrate that the growth of root hairs of salt-stressed Arabidopsis thaliana seedlings is regulated by the SALT OVERLY SENSITIVE 2 (SOS2)-GUANOSINE NUCLEOTIDE DIPHOSPHATE DISSOCIATION INHIBITOR 1 (RhoGDI1)-Rho GTPASE OF PLANTS 2 (ROP2) module. We show here that the kinase SOS2 is activated by salt stress and subsequently phosphorylates RhoGDI1, a root hair regulator, thereby decreasing its stability. This change in RhoGDI1 abundance resulted in a fine-tuning of polar localization of ROP2 and root hair initiation followed by polar growth, demonstrating how SOS2-regulated root hair development is critical for plant growth under salt stress. Our results reveal how a tissue-specific response to salt stress balances the relationship of salt resistance and basic growth.

Protocols for Efficient Chemical Synthesis of N2 -Modified Guanosine Phosphate Derivatives: Versatile Probes for mRNA Labeling

A facile, reliable, and efficient method for the synthesis of N2 -modified guanosine nucleotides such as N2 -[benzyl-N-(propyl)carbamate]-guanosine-5'-O-monophosphate, N2 -[benzyl-N-(propyl)carbamate]-guanosine-5'-O-diphosphate, N2 -[benzyl-N-(propyl)carbamate]-guanosine-5'-O-triphosphate, and N2 -[benzyl-N-(propyl)carbamate]-N7 -methyl-guanosine-5'-O-diphosphate, starting from the corresponding nucleotide is described. The general process entails condensation between the exocyclic amine of guanosine nucleotide and 3-[(benzyloxycarbonyl)amino]propionaldehyde in aqueous methanol, followed by reduction using sodium cyanoborohydride to furnish the corresponding N2 -modified guanosine nucleotide in moderate yield with high purity (>99.5%). © 2023 Wiley Periodicals LLC. Basic Protocol: Synthesis of N2 -modified guanosine derivatives.

Synthesis, substitution kinetics, DNA/BSA binding and cytotoxicity of tridentate N^E^N (E = NH, O, S) pyrazolyl palladium(II) complexes

The pincer complexes, [Pd(L₁)Cl]BF₄ (PdL₁), [Pd(L₂)Cl]BF₄ (PdL₂), [Pd(L₃)Cl]BF₄ (PdL₃), [Pd(L₄)Cl]BF₄ (PdL₄) were prepared by reacting the corresponding ligands, 2,6-bis[(1H-pyrazol-1-yl)methyl]pyridine (L₁), bis[2-(1H-pyrazol-1-yl)ethyl]amine (L₂), bis[2-(1H-pyrazol-1-yl)ethyl]ether (L₃), and bis[2-(1H-prazol-1-yl)ethyl]sulphide (L₄) with [PdCl₂(NCMe)]₂ in the presence NaBF₄. The solid-state structures of complexes PdL₁-PdL₄ confirmed a tridentate coordination mode, with one chloro ligand completing the coordination sphere to afford square-planar complexes. Chemical behaviour of the complexes in solution confirms their stability in both aqueous and DMSO stock media. The electrochemical properties of the compounds showed irreversible two-electron reduction process. Kinetic reactivity of Pd complexes with the biological nucleophiles viz, thiourea (Tu), L-methionine (L-Met) and guanosine 5'-diphosphate disodium salt (5'-GMP) followed the order: PdL₂ < PdL₃ < PdL₄, and PdL₂ < PdL₁. The kinetic reactivity is subject to the electronic effects of the spectator ligand(s), and the trend was supported by the DFT computed results. The palladium complexes PdL₁-PdL₄ bind to calf thymus (CT-DNA) via intercalation mode. In addition, the bovine serum albumin (BSA) showed good binding affinity to the complexes. The mode of quenching mechanism of the intrinsic fluorescence of CT-DNA and BSA by the complexes was found to be static. The order of interactions of the complexes with DNA and BSA was in tandem with the rate of substitution kinetics. The complexes, however, displayed relatively low cytotoxicity (IC₅₀ > 100 µM) when tested against the human cervical adenocarcinoma (HeLa) cell line and the transformed human lung fibroblast cell line (MRC-5 SV2).

Gas-Phase Internal Ribose Residue Loss from Mg-ATP and Mg-ADP Complexes: Experimental and Theoretical Evidence for Phosphate-Mg-Adenine Interaction

Gas-phase decompositions of magnesium complexes with adenosine-5'-triphosphate (ATP) and adenosine-5'-diphosphate (ADP) were studied by using electrospray ionization-collision-induced dissociation-tandem mass spectrometry, in the negative ion mode. The loss of internal ribose residue was observed and was found to occur directly from the [ADP-3H+Mg]^- ion. The occurrence of this process indicates the presence of a strong phosphate-Mg-adenine interaction. The performed quantum mechanics calculations confirmed the occurrence of this interaction in the [ADP-3H+Mg]^- ion, namely the presence of Mg-N7 bond and hydrogen bond between the phosphate oxygen atom and amino group. Although the finding concerns the gas phase, it indicates that phosphate-Mg-adenine interaction may be also of importance for biological processes. The loss of an internal ribose residue was also observed for calcium and zinc complexes with ATP/ADP as well as for magnesium complexes with guanosine-5'-triphosphate (GTP) or guanosine-5'-diphosphate (GDP). Therefore, it is reasonable to conclude that the presence of the phosphate-metal-nucleobase interaction is a feature of gas phase [NDP-3H+metal]^- ion (NDP, nucleoside-5'-diphosphate) and may also be important for biological processes.

Active and Inactive Cdc42 Differ in Their Insert Region Conformational Dynamics

Cell division control protein 42 homolog (Cdc42) protein, a Ras superfamily GTPase, regulates cellular activities, including cancer progression. Using all-atom molecular dynamics (MD) simulations and essential dynamic analysis, we investigated the structure and dynamics of the catalytic domains of GDP-bound (inactive) and GTP-bound (active) Cdc42 in solution. We discovered substantial differences in the dynamics of the inactive and active forms, particularly in the "insert region" (residues 122-135), which plays a role in Cdc42 activation and binding to effectors. The insert region has larger conformational flexibility in the GDP-bound Cdc42 than in the GTP-bound Cdc42. The G2 loop and switch I at the effector lobe of the catalytic domain exhibit large conformational changes in both the GDP- and the GTP-bound systems, but in the GTP-bound Cdc42, the switch I interactions with GTP are retained. Oncogenic mutations were identified in the Ras superfamily. In Cdc42, the G12V and Q61L mutations decrease the GTPase activity. We simulated these mutations in both GDP- and GTP-bound Cdc42. Although the overall structural organization is quite similar between the wild type and the mutants, there are small differences in the conformational dynamics, especially in the two switch regions. Taken together, the G12V and Q61L mutations may play a role similar to their K-Ras counterparts in nucleotide binding and activation. The conformational differences, which are mainly in the insert region and, to a lesser extent, in the switch regions flanking the nucleotide binding site, can shed light on binding and activation. We propose that the differences are due to a network of hydrogen bonds that gets disrupted when Cdc42 is bound to GDP, a disruption that does not exist in other Rho GTPases. The differences in the dynamics between the two Cdc42 states suggest that the inactive conformation has reduced ability to bind to effectors.

Spatiotemporal Trends of Malaria in Relation to Economic Development and Cross-Border Movement along the China-Myanmar Border in Yunnan Province

The heterogeneity and complexity of malaria involves political and natural environments, socioeconomic development, cross-border movement, and vector biology; factors that cannot be changed in a short time. This study aimed to assess the impact of economic growth and cross-border movement, toward elimination of malaria in Yunnan Province during its pre-elimination phase. Malaria data during 2011-2016 were extracted from 18 counties of Yunnan and from 7 villages, 11 displaced person camps of the Kachin Special Region II of Myanmar. Data of per-capita gross domestic product (GDP) were obtained from Yunnan Bureau of Statistics. Data were analyzed and mapped to determine spatiotemporal heterogeneity at county and village levels. There were a total 2,117 malaria cases with 85.2% imported cases; most imported cases came from Myanmar (78.5%). Along the demarcation line, malaria incidence rates in villages/camps in Myanmar were significantly higher than those of the neighboring villages in China. The spatial and temporal trends suggested that increasing per-capita GDP may have an indirect effect on the reduction of malaria cases when observed at macro level; however, malaria persists owing to complex, multi-faceted factors including poverty at individual level and cross-border movement of the workforce. In moving toward malaria elimination, despite economic growth, cooperative efforts with neighboring countries are critical to interrupt local transmission and prevent reintroduction of malaria via imported cases. Cross-border workers should be educated in preventive measures through effective behavior change communication, and investment is needed in active surveillance systems and novel diagnostic and treatment services during the elimination phase.

Microtubule Simulations Provide Insight into the Molecular Mechanism Underlying Dynamic Instability

The dynamic instability of microtubules (MTs), which refers to their ability to switch between polymerization and depolymerization states, is crucial for their function. It has been proposed that the growing MT ends are protected by a "GTP cap" that consists of GTP-bound tubulin dimers. When the speed of GTP hydrolysis is faster than dimer recruitment, the loss of this GTP cap will lead the MT to undergo rapid disassembly. However, the underlying atomistic mechanistic details of the dynamic instability remains unclear. In this study, we have performed long-time atomistic molecular dynamics simulations (1 μs for each system) for MT patches as well as a short segment of a closed MT in both GTP- and GDP-bound states. Our results confirmed that MTs in the GDP state generally have weaker lateral interactions between neighboring protofilaments (PFs) and less cooperative outward bending conformational change, where the difference between bending angles of neighboring PFs tends to be larger compared with GTP ones. As a result, when the GDP state tubulin dimer is exposed at the growing MT end, these factors will be more likely to cause the MT to undergo rapid disassembly. We also compared simulation results between the special MT seam region and the remaining material and found that the lateral interactions between MT PFs at the seam region were comparatively much weaker. This finding is consistent with the experimental suggestion that the seam region tends to separate during the disassembly process of an MT.

Early life environment and adult height: The case of Chile

In this paper, we analyze the relationship between adult height and early-life disease environment, proxied by the infant mortality rate (IMR) in the first year of life, using cohort-region level data for Chile for 1960-1989. IMRs show a remarkable reduction of 100 points per thousand over this thirty-year period, declining from 119.4 to 21.0 per thousand. We also document a 0.96 cm increase in height per decade.We find that the drop in IMRs observed among our cohorts explains almost all of the long-term trend in rising adult heights, and that per capita GDP does not appear to have any predictive power in this context. Results are robust in a variety of specifications, which include area and cohort dummies, an adjustment for internal migration, and urbanization rates. Our results point to the long-term effect of a public health policy.

The Role of Policy and Institutions on Health Spending

This paper investigates the impact of policies and institutions on health expenditures for a large panel of Organisation for Economic Co-operation and Development countries for the period of 2000-2010. A set of 20 policy and institutional indicators developed by the Organisation for Economic Co-operation and Development are integrated into a theoretically motivated econometric framework, alongside control variables related to demographic (dependency ratio) and non-demographic (income, prices and technology) drivers of health expenditures per capita. Although a large share of cross-country differences in public health expenditures can be explained by demographic and economic factors (around 71%), cross-country variations in policies and institutions also have a significant influence, explaining most of the remaining difference in public health spending (23%). Copyright © 2016 John Wiley & Sons, Ltd.

Is prostate cancer incidence worldwide linked to artificial light at night exposures? Review of earlier findings and analysis of current trends

Widespread use of artificial light at night (ALAN) might contribute to the global burden of hormone-dependent cancers. Previous attempts to verify this association in population-level studies have been sparse. Using GLOBOCAN, US-DMSP, and World Bank 2010-2012 databases, we studied the association between ALAN and prostate cancer (PC) incidence in 180 countries worldwide, controlling for several country-level confounders. The PC-ALAN association emerged marginally significant when year-2012 PC age-standardized rate data were compared with ALAN levels (t = 1.886, p < .1); this association was more significant (t > 2.7; p < .01) when only 110 countries with well-maintained cancer registries were analyzed. Along with other variables, ALAN explains up to 79% of PC ASR variability. PC-ALAN association appears to vary regionally, with the greatest deviations in Central Africa, Small Island Developing States, Southeast Asia, and Gulf States.

Carbon emissions, logistics volume and GDP in China: empirical analysis based on panel data model

This paper studies the relationship among carbon emissions, GDP, and logistics by using a panel data model and a combination of statistics and econometrics theory. The model is based on the historical data of 10 typical provinces and cities in China during 2005-2014. The model in this paper adds the variability of logistics on the basis of previous studies, and this variable is replaced by the freight turnover of the provinces. Carbon emissions are calculated by using the annual consumption of coal, oil, and natural gas. GDP is the gross domestic product. The results showed that the amount of logistics and GDP have a contribution to carbon emissions and the long-term relationships are different between different cities in China, mainly influenced by the difference among development mode, economic structure, and level of logistic development. After the testing of panel model setting, this paper established a variable coefficient model of the panel. The influence of GDP and logistics on carbon emissions is obtained according to the influence factors among the variables. The paper concludes with main findings and provides recommendations toward rational planning of urban sustainable development and environmental protection for China.

Agricultural vulnerability over the Chinese Loess Plateau in response to climate change: Exposure, sensitivity, and adaptive capacity

Understanding how the vulnerability of agricultural production to climate change can differ spatially has practical significance to sustainable management of agricultural systems worldwide. Accordingly, this study developed a conceptual framework to assess the agricultural vulnerability of 243 rural counties on the Chinese Loess Plateau. Indicators representing the climate/agriculture interface were selected to describe exposure and sensitivity, while stocks of certain capitals were used to describe adaptive capacity. A vulnerability index for each county was calculated and the spatial distribution was mapped. Results showed that exposure, sensitivity, and adaptive capacity occur independently, with most contributing indicator values concentrated in a narrow range after normalization. Within the 49 most vulnerable counties, which together encompass 81 % of the vulnerability index range, 42 were characterized by high exposure and sensitivity but low adaptive capacity. The most vulnerable area was found to be located in the central northeast-southwest belt of Loess Plateau. Adaptation measures for both ecological restoration and economic development are needed and potential adaptation options need further investigation.

Unemployment and Suicide Mortality: Evidence from Regional Panel Data in Europe

This paper addresses the influence of economic activity on suicide mortality in Europe. To this end, it employs a new panel data set of 275 regions in 29 countries over the period 1999-2010. The results suggest that unemployment does have a significantly positive influence on suicides. In line with economic theory, this influence varies among gender and age groups. Men of working age are particularly sensitive, while old-age suicide mortality (older than 65 years old) hardly responds to unemployment. Moreover, real economic growth negatively affects the suicide rates of working-age men. The results withstand several robustness checks, such as sample variations, and after controlling for serial and spatial autocorrelation.

Tobacco Control Policies and Sudden Infant Death Syndrome in Developed Nations

This paper estimates the effects of higher cigarette prices and smoke-free policies on the prevalence of Sudden Infant Death Syndrome (SIDS). Using a panel of developed countries over a 20 year period, we find that higher cigarette prices are associated with reductions in the prevalence of SIDS. However, we find no evidence that smoke-free policies are associated with declines in SIDS.

Social capital and health: evidence that ancestral trust promotes health among children of immigrants

This paper presents evidence that generalized trust promotes health. Children of immigrants in a broad set of European countries with ancestry from across the world are studied. Individuals are examined within country of residence using variation in trust across countries of ancestry. The approach addresses reverse causality and concerns that the trust measure picks up institutional factors in the individual's contextual setting. There is a significant positive estimate of ancestral trust in explaining self-assessed health. The finding is robust to accounting for individual, parental, and extensive ancestral country characteristics. Individuals with higher ancestral trust are also less likely to be hampered by health problems in their daily life, providing evidence of trust influencing real life outcomes. Individuals with high trust feel and act healthier, enabling a more productive life.

The role of nutrition and genetics as key determinants of the positive height trend

The aim of this study was to identify the most important variables determining current differences in physical stature in Europe and some of its overseas offshoots such as Australia, New Zealand and USA. We collected data on the height of young men from 45 countries and compared them with long-term averages of food consumption from the FAOSTAT database, various development indicators compiled by the World Bank and the CIA World Factbook, and frequencies of several genetic markers. Our analysis demonstrates that the most important factor explaining current differences in stature among nations of European origin is the level of nutrition, especially the ratio between the intake of high-quality proteins from milk products, pork meat and fish, and low-quality proteins from wheat. Possible genetic factors such as the distribution of Y haplogroup I-M170, combined frequencies of Y haplogroups I-M170 and R1b-U106, or the phenotypic distribution of lactose tolerance emerge as comparably important, but the available data are more limited. Moderately significant positive correlations were also found with GDP per capita, health expenditure and partly with the level of urbanization that influences male stature in Western Europe. In contrast, male height correlated inversely with children's mortality and social inequality (Gini index). These results could inspire social and nutritional guidelines that would lead to the optimization of physical growth in children and maximization of the genetic potential, both at the individual and national level.

The estrogen hypothesis of obesity

The explanation of obesity as a simple result of positive energy balance fails to account for the scope of variable responses to diets and lifestyles. It is postulated that individual physiological and anatomical variation may be responsible for developing obesity. Girls in poor families develop greater adiposity than their male siblings, a trend not present in richer environments. This indicates strong influence of estrogen on fat accumulation irrespective of poor socioeconomic conditions. Obesity rates in males and females of developed nations are similar, while in poorer nations obesity is much more prevalent in females. Female to male ratio of obesity correlates inversely with gross domestic product. Therefore, the parity of male and female obesity in developed countries may result from male exposure to environmental estrogen-like substances associated with affluence. These hormonally driven mechanisms may be equally active within both sexes in more developed areas, thereby increasing overall obesity.

Measuring the displacement and replacement of government health expenditure

Research assessing the relationship between government health expenditure and development assistance for health channeled to governments (DAHG) has not considered that this relationship may depend on whether DAHG is increasing or decreasing. We explore this issue using general method of moments estimation and a panel of financial flows data spanning 119 countries and 16 years. Our primary concern is how DAHG affects government health expenditure as source (GHES). We disaggregate the average effect of DAHG and separately identify the effects of increases versus decreases in DAHG. We find that a $1 year-over-year increase in DAHG leads to a $0.62 (90% confidence interval (CI): 0.15, 1.09) decrease in GHES, whereas a $1 year-over-year decrease in DAHG does not have an effect on GHES that is statistically different from zero (CI: -0.67, 1.17). Simulation shows that the displacement of GHES between 1995 and 2010 reduced total government health expenditure by $152.8 billion (CI: 46.9, 277.6). Moreover, the irregular disbursement of DAHG reduced total government expenditure by $96.9 billion (CI: 0.5, 212.4). Thus, this research shows that health aid is fungible and highlights the cost of displacement and erratic aid disbursement.

Structure of the GDP-bound G domain of the RGK protein Rem2

RGK proteins are atypical small GTP-binding proteins that are involved in the regulation of voltage-dependent calcium channels and actin cytoskeleton remodelling. The structure of the Rem2 G domain bound to GDP is reported here in a monoclinic crystal form at 2.66 Å resolution. It is very similar to the structure determined previously from an orthorhombic crystal form. However, differences in the crystal-packing environment revealed that the switch I and switch II regions are flexible and not ordered as previously reported. Comparison of the available RGK protein structures along with those of other small GTP-binding proteins highlights two structural features characteristic of this atypical family and suggests that the conserved tryptophan residue in the DXWEX motif may be a structural determinant of the nucleotide-binding affinity.

Vesicular stomatitis virus mRNA capping machinery requires specific cis-acting signals in the RNA

Many viruses of eukaryotes that use mRNA cap-dependent translation strategies have evolved alternate mechanisms to generate the mRNA cap compared to their hosts. The most divergent of these mechanisms are those used by nonsegmented negative-sense (NNS) RNA viruses, which evolved a capping enzyme that transfers RNA onto GDP, rather than GMP onto the 5' end of the RNA. Working with vesicular stomatitis virus (VSV), a prototype of the NNS RNA viruses, we show that mRNA cap formation is further distinct, requiring a specific cis-acting signal in the RNA. Using recombinant VSV, we determined the function of the eight conserved positions of the gene-start sequence in mRNA initiation and cap formation. Alterations to this sequence compromised mRNA initiation and separately formation of the GpppA cap structure. These studies provide genetic and biochemical evidence that the mRNA capping apparatus of VSV evolved an RNA capping machinery that functions in a sequence-specific manner.

The development of an europium-GTP assay to quantitate chemokine antagonist interactions for CXCR4 and CCR5

Chemokine receptors have been implicated in several disease processes such as acute and chronic inflammation, cancer, and allograft rejection and are therefore targets for drug development. The chemokine receptors CCR5 and CXCR4 are of particular interest as they serve as entry cofactors for human immunodeficiency virus. These receptors are members of the G protein-coupled receptor (GPCR) family. In this respect, assessing GPCR activation by GTP binding is an important tool to study the early stage of signal transduction. The assay normally utilizes the non-hydrolysable GTP analogue guanosine 5'-gamma-[35S]thiotriphosphate. In order to avoid the problems involved in working with radioactivity, a new non-radioactive version of the assay was developed using a europium-labeled GTP analogue in which europium-GTP binding can be assayed using time-resolved fluorescence. The assay was optimized for CXCR4 and CCR5 and validated for screening of chemokine antagonists using the small molecule CXCR4 antagonist AMD3100 and CCR5 antagonists.

Benefits of switching from a conventional to a low-GDP bicarbonate/lactate-buffered dialysis solution in a rat model

BACKGROUND

Long-term exposure to standard peritoneal dialysis fluid (PDF) results in alterations in peritoneal morphology and function. Studies investigating the long-term effects on the peritoneum of a low-glucose degradation product (GDP) bicarbonate/lactate-buffered PDF demonstrated its superior biocompatibility. We examined the potential of the low-GDP bicarbonate/lactate-buffered solution to reverse or reduce standard PDF-induced peritoneal alterations.

METHODS

Female Wistar rats received twice daily intraperitoneal infusions with either a lactate-buffered solution with 3.86% glucose at pH 5.5 (Dianeal, referred to as standard PDF), or a low-GDP bicarbonate/lactate-buffered solution with 3.86% glucose at physiologic pH (Physioneal, referred to as bicarbonate/lactate PDF) for different periods of time: (1) 12 weeks Dianeal (N= 9); (2) 12 weeks Physioneal (N= 9); (3) 20 weeks Dianeal (N= 11); (4) 20 weeks Physioneal (N= 10); (5) 12 weeks Dianeal followed by 8 weeks Physioneal (N= 10).

RESULTS

Chronic standard PDF exposure resulted in loss of ultrafiltration capacity, increased VEGF expression and vascular density, higher advanced glycation end product (AGE) accumulation, up-regulation of TGF-beta expression, and development of fibrosis compared to low-GDP bicarbonate/lactate-buffered PDF. The PDF-induced alterations were time-dependent. Crossover from standard PDF to low-GDP bicarbonate/lactate PDF resulted in a less impaired ultrafiltration (UF), less pronounced VEGF expression and neoangiogenesis, and less severe AGE accumulation, TGF-beta expression, and fibrosis compared to continuous standard PDF exposure for 20 weeks.

CONCLUSION

Low-GDP bicarbonate/lactate-buffered PDF has the potential to slow down standard PDF-induced peritoneal membrane damage.

Conformational states of the switch I region of Ha-ras-p21 in hinge residue mutants studied by fluorescence lifetime and fluorescence anisotropy measurements

The hinge residues (Val29 and Ile36) of the switch I region (also known as the effector loop) of the Ha-ras-p21 protein have been mutated to glycines to accelerate the conformational changes typical for the effector loop. In this work, we have studied the influence of the combined mutations on the steady-state structure of the switch I region of the protein in both the inactive GDP-bound conformation as in the active GTP-bound conformation. Here, we use the fluorescence properties of the single tryptophan residue in the Y32W mutant of Ha-ras-p21. This mutant has already been used extensively as a reference form of the protein. Reducing the size of the side chains of the hinge residues not only accelerates the conformational changes but also affects the steady-state structures of the effector loop as indicated by the changes in the fluorescence properties. A thorough analysis of the fluorescence changes (quantum yield, lifetimes, etc.) proves that these changes are from a reshuffling between the rotamer populations of Trp. The population reshuffling is caused by the overall structural rearrangement along the switch I region. The effects are clearly more pronounced in the inactive GDP-bound conformation than in the active GTP-bound conformation. The effect of both mutations seems to be additive in the GDP-bound state, but cooperative in the GTP-bound state.

M1 muscarinic receptor signaling in mouse hippocampus and cortex

The five subtypes (M1-M5) of muscarinic acetylcholine receptors signal through G(alpha)(q) or G(alpha)(i)/G(alpha)(o). M1, M3 and M5 receptors couple through G(alpha)(q) and function predominantly as postsynaptic receptors in the central nervous system. M1 and M3 receptors are localized to brain regions involved in cognition, such as hippocampus and cortex, but their relative contribution to function has been difficult to ascertain due to the lack of subtype specific ligands. A functional and genetic approach was used to identify the predominant muscarinic receptor subtype(s) mediating responses in mouse hippocampus and cortex, as well as the relative degree of spare muscarinic receptors in hippocampus. The nonselective muscarinic agonist oxotremorine-M stimulated G(alpha)(q)/11-specific GTP-gamma-35S binding in a concentration dependent manner with a Hill slope near unity in wild type mouse hippocampus and cortex. Muscarinic receptor stimulated G(alpha)(q)/11-specific GTP-gamma-35S binding was virtually abolished in both the hippocampus and cortex of M1 receptor knockout (KO) mice. In contrast, there was no loss of signaling in M3 receptor KO mice in either brain region. Muscarinic receptor reserve in wildtype mouse hippocampus was measured by Furchgott analysis after partial receptor alkylation with propylbenzylcholine mustard. Occupation of just 15% of the M1 receptors in mouse hippocampus was required for maximal efficacy of oxotremorine-M-stimulated GTP-gamma-35S binding indicating a substantial level of spare receptors. These findings support a role for the M1 receptor subtype as the primary G(alpha)(q)/11-coupled muscarinic receptor in mouse hippocampus and cortex.

Effects of cold exposure in vivo and uncouplers and recouplers in vitro on potato tuber mitochondria

Effects of cold exposure in vivo and treatment with laurate, carboxyatractylate, atractylate, nucleotides, and BSA in vitro on potato tuber mitochondria have been studied. Cold exposure of tubers for 48-96 h resulted in some uncoupling that could be reversed completely by BSA and partially by ADP, ATP, UDP, carboxyatractylate, and atractylate. UDP was less effective than ADP and ATP, and atractylate was less effective than carboxyatractylate. The recoupling effects of nucleotides were absent when the nucleotides were added after carboxyatractylate. GDP, UDP, and CDP did not recouple mitochondria from either the control or the cold-exposed tubers. This indicates that the cold-induced fatty acid-mediated uncoupling in potato tuber mitochondria is partially due to the operation of the ATP/ADP antiporter. As to the plant uncoupling protein, its contribution to the uncoupling in tuber is negligible or, under the conditions used, somehow desensitized to nucleotides.

Stress-induced membrane association of the Streptococcus mutans GTP-binding protein, an essential G protein, and investigation of its physiological role by utilizing an antisense RNA strategy

SGP (for Streptococcus GTP-binding protein) is a Streptococcus mutans essential GTPase which has significant sequence identity to the previously identified Escherichia coli Era protein and to numerous other prokaryotic GTPase proteins of unknown function. Recent studies in our laboratory have addressed the possible role of SGP in the stress response of the oral pathogen S. mutans. Here we report that during growth in the early stationary phase, and in response to elevated temperatures or acidic pH, the distribution of SGP between the cytoplasm and the membranes of S. mutans cells varies. Immunoblot analysis of soluble and membrane protein fractions collected from the mid-log and early stationary growth phases of bacterial populations grown at normal temperature (37 degrees C) and at the elevated temperature of 43 degrees C, or at acidic pH, demonstrated that the total amount of SGP increased with the age of the bacterial culture, elevated temperature, or acidic pH. Furthermore, it was established that a substantial amount of SGP is associated with the membrane fraction under stress conditions. In order to investigate the physiological role of SGP, we constructed an S. mutans strain capable of chromosomal sgp antisense RNA expression, which interferes with the normal information processing of the sgp gene. Utilizing this strain, we determined conditions whereby the streptococcal cells can be depleted of SGP, thus avoiding the problem of constructing a conditional lethal system. From the results of measurements of the nucleotide pools extracted from the antisense strain and its isogenic counterpart, we propose that one of the physiological roles of SGP is regulation and modulation of the GTP/GDP ratio under different growth conditions. Moreover, we observed that in SGP-depleted cells the levels of glucan-binding protein A (GbpA) substantially increased, suggesting that GbpA may have stress response-related physiological functions. Finally, the potential applications of the antisense RNA approach that we employed are discussed.

The product of the cph oncogene is a truncated, nucleotide-binding protein that enhances cellular survival to stress

Cph was isolated from neoplastic Syrian hamster embryo fibroblasts initiated by 3-methylcholanthrene (MCA), and was shown to be a single copy gene in the hamster genome, conserved from yeast to human cells, expressed in fetal cells and most adult tissues, and acting synergistically with H-ras in the transformation of murine NIH3T3 fibroblasts. We have now isolated Syrian hamster full-length cDNAs for the cph oncogene and proto-oncogene. Nucleotide sequence analysis revealed that cph was activated in MCA-treated cells by a point-mutational deletion at codon 214, which caused a shift in the normal open reading frame (ORF) and brought a translation termination codon 33 amino acids downstream. While proto-cph encodes a protein (pcph) of 469 amino acids, cph encodes a truncated protein (cph) of 246 amino acids with a new, hydrophobic C-terminus. Similar mechanisms activated cph in other MCA-treated Syrian hamster cells. The cph and proto-cph proteins have partial sequence homology with two protein families: GDP/GTP exchange factors and nucleotide phosphohydrolases. In vitro translated, gel-purified cph proteins did not catalyze nucleotide exchange for H-ras, but were able to bind nucleotide phosphates, in particular ribonucleotide diphosphates such as UDP and GDP. Steady-state levels of cph mRNA increased 6.7-fold in hamster neoplastic cells, relative to a 2.2-fold increase in normal cells, when they were subjected to a nutritional stress such as serum deprivation. Moreover, cph-transformed NIH3T3 cells showed increased survival to various forms of stress (serum starvation, hyperthermia, ionizing radiation), strongly suggesting that cph participates in cellular mechanisms of response to stress.

Rab11 is required for trans-golgi network-to-plasma membrane transport and a preferential target for GDP dissociation inhibitor

The rab11 GTPase has been localized to both the Golgi and recycling endosomes; however, its Golgi-associated function has remained obscure. In this study, rab11 function in exocytic transport was analyzed by using two independent means to perturb its activity. First, expression of the dominant interfering rab11S25N mutant protein led to a significant inhibition of the cell surface transport of vesicular stomatitis virus (VSV) G protein and caused VSV G protein to accumulate in the Golgi. On the other hand, the expression of wild-type rab11 or the activating rab11Q70L mutant had no adverse effect on VSV G transport. Next, the membrane association of rab11, which is crucial for its function, was perturbed by modest increases in GDP dissociation inhibitor (GDI) levels. This led to selective inhibition of the trans-Golgi network to cell surface delivery, whereas endoplasmic reticulum-to-Golgi and intra-Golgi transport were largely unaffected. The transport inhibition was reversed specifically by coexpression of wild-type rab11 with GDI. Under the same conditions two other exocytic rab proteins, rab2 and rab8, remained membrane bound, and the transport steps regulated by these rab proteins were unaffected. Neither mutant rab11S25N nor GDI overexpression had any impact on the cell surface delivery of influenza hemagglutinin. These data show that functional rab11 is critical for the export of a basolateral marker but not an apical marker from the trans-Golgi network and pinpoint rab11 as a sensitive target for inhibition by excess GDI.

Wiskott-Aldrich syndrome protein, a novel effector for the GTPase CDC42Hs, is implicated in actin polymerization

The Rho family of GTPases control diverse biological processes, including cell morphology and mitogenesis. We have identified WASP, the protein that is defective in Wiskott-Aldrich syndrome (WAS), as a novel effector for CDC42Hs, but not for the other Rho family members, Rac and Rho. This interaction is dependent on the presence of the G protein-binding domain. Cellular expression of epitope-tagged WASP produces clusters of WASP that are highly enriched in polymerized actin. This clustering is not observed with a C-terminally deleted WASP and is inhibited by coexpression with dominant negative CDC42Hs-N17, but not with dominant negative forms of Rac or Rho. Thus, WASP provides a novel link between CDC42Hs and the actin cytoskeleton, which suggests a molecular mechanism for many of the cellular abnormalities in WAS. The WASP sequence contains two novel domains that are homologous to other proteins involved in action organization.

Studies of crystallization conditions for native and subtilisin-cleaved pig brain tubulin

A survey of crystallization conditions for pig brain tubulin, using standard vapor diffusion techniques in sitting drops or capillaries, has resulted in irregular, fragile needles or plates with a largest dimension of 0.5 mm. These occurred in 2.5% PEG (MW 3350), 0.1 M Pipes, pH 6.2 and 6.4, 2-16 mM MgSO4, 10-15 mM DTE, and 0.1 mM GDP at 8 degrees C. When GTP replaced GDP these aggregates did not form under any of the conditions surveyed (temperature: 8-10 degrees C; MgSO4: 2-16 mM; pH 6-7; PEG, MW 3350: 1.25-12.5%). EM observations demonstrated that sheets of rings appear in crystal solutions in the presence of GDP or GTP. These results are consistent with the results of Howard and Timasheff (1986, Biochemistry 25, 8292-8300) that tubulin rings form in the presence of GDP or GTP but more readily in GDP. Tubulin crystallization experiments are hampered by tubulin's high degree of heterogeneity. Much of the variability lies in the carboxyl terminal region. Conditions for limited digestion of the heterodimer by subtilisin, removing only the carboxyl terminus, were determined. Reduction of heterogeneity was demonstrated by isoelectric focusing. The solubilities of native and subtilisin-cleaved tubulin in MgSO4, (NH4)2SO4, PEG (MW 1450, 3350, 10,000), DMSO, and MPD were compared. Subtilisin-cleaved tubulin precipitated more readily than native tubulin under all conditions surveyed, consistent with the removal of the highly acidic carboxyl terminus. Vapor diffusion experiments using subtilisin-cleaved tubulin under conditions where native tubulin forms needles or plates resulted in similar aggregates.

Regulation of polyphosphoinositide-specific phospholipase C activity by purified Gq

The hydrolysis of phosphatidylinositol 4,5-bisphosphate (PIP2) by phospholipase C yields the second messengers inositol 1,4,5-trisphosphate (InsP3) and 1,2-diacylglycerol. This activity is regulated by a variety of hormones through G protein pathways. However, the specific G protein or proteins involved has not been identified. The alpha subunit of a newly discovered pertussis toxin-insensitive G protein (Gq) has recently been isolated and is now shown to stimulate the activity of polyphosphoinositide-specific phospholipase C (PI-PLC) from bovine brain. Both the maximal activity and the affinity of PI-PLC for calcium ion were affected. These results identify Gq as a G protein that regulates PI-PLC.

Synthesis of N2, N2, 7-trimethylguanosine cap derivatives

Several derivatives of N2,N2-7-trimethylguanosine (m3(2,2,7G)-cap, which was found at the 5' ends of small nuclear RNAs, were synthesized by use of S-phenyl N2,N2,7-trimethylguanosine 5'-phosphorothioate (PhSpm3(2,2,7)G) as a key intermediate. This compound was activated by iodine in the presence of phosphoric acid and diphosphoric acid to give N2,N2,7-trimethylguanosine-5'-diphosphate (ppm3(2,2,7)G) and 5'-triphosphate (ppm3(2,2,7)G), respectively. Similar reactions of PhSpm3(2,2,7)G with ADP and GDP gave capped dinucleoside triphosphates, m3(2,2,7)G5'pppA and m3(2,2,7)G5'pppG, respectively.

Cold depolymerization of microtubules to double rings: geometric stabilization of assemblies

The kinetic pathway of microtubule depolymerization at 0 degrees C has been examined. Microtubules made of MAP-containing and MAP-free tubulins were depolymerized at 0 degree C in the presence of [3H]GDP or [3H]GTP or of trace amounts of 125I dimeric tubulin. The products of depolymerization were separated on a column, their structures were identified by electron microscopy, and the time course of incorporation of 3H or 125I labels in the different components of the system was determined. Two predominant assembly states of tubulin found in the nonmicrotubule state were alpha-beta dimers and double rings. Kinetic data indicate that ring formation from disassembling microtubules does not occur by direct coiling of protofilaments as previously thought, but disassembling GDP subunits are in very rapid equilibrium with curved oligomers that are kinetic intermediates in the isodesmic assembly of GDP-tubulin. The formation of oligomers and rings from dimers, at concentrations as low as 10 microM, is much faster than nucleotide exchange on alpha-beta-tubulin. Disassembly of double rings, in contrast, is slower than nucleotide exchange on alpha-beta-tubulin, by 1 order of magnitude in the absence of MAPs and 2 orders of magnitude in the presence of MAPs. These results support the model proposed previously to explain spontaneous oscillations in microtubule assembly. They are consistent with the existence of an equilibrium between two conformations of tubulin, "straight", i.e., microtubule forming, and "curved", i.e., ring forming, under the allosteric control of bound nucleotide. The straight conformation requires the presence of two ionizable hydroxyls on the gamma-phosphate in GTP or GDP-Pi.

Brown adipose tissue metabolism in ob/ob mice: effects of a high-fat diet and adrenalectomy

Adrenalectomy prevents development of obesity in ob/ob mice fed high-carbohydrate stock diets partly by stimulating the low thermogenic capacity of their brown adipose tissue (BAT). Adrenalectomy, however, fails to prevent development of obesity in ob/ob mice fed a high-fat diet. Effects of adrenalectomy on BAT metabolism in ob/ob mice fed a high-fat diet were thus examined. ob/ob mice fed the high-fat diet developed gross obesity despite normal BAT metabolism, as assessed by rates of norepinephrine turnover in BAT, GDP binding to BAT mitochondria, and GDP-inhibitable, chloride-induced mitochondrial swelling. Adrenalectomy failed to arrest the development of obesity or to influence BAT metabolism in ob/ob mice fed the high-fat diet. Development of obesity in ob/ob mice fed a high-fat diet is not associated with low thermogenic capacity of BAT or with adrenal secretions, as it is in ob/ob mice fed high-carbohydrate stock diets.

A study of the kinetic mechanism of elongation factor Ts

Elongation factor Ts (EF-Ts) catalyzes the reaction EF-Tu X GDP + nucleotide diphosphate (NDP) reversible EF-Tu X NDP + GDP where NDP is GDP, IDP, GTP, or GMP X PCP. The EF-Ts-catalyzed exchange rates were measured at a series of concentrations of EF-Tu X [3H] GDP and free nucleotide. Plotting the rate data according to the Hanes method produced a series of lines intersecting on the ordinate, a characteristic of substituted enzyme mechanisms. GDP is a competitive inhibitor of IDP exchange, a result predicted for the substituted enzyme mechanism but inconsistent with ternary complex mechanisms that involve an intermediate complex containing EF-Ts and both substrates. The exchange of both GTP and the GTP analog GMP X PCP also follow the substituted enzyme mechanism. The maximal rates of exchange of GDP and GTP are the same, which indicates that the rates of dissociation of EF-Ts from EF-Tu X GDP and EF-Tu X GTP are the same. The steady-state maximal exchange rate is slower by a factor of 20 than the previously reported rate of dissociation of GDP from EF-Ts X EF-Tu. This is interpreted to mean that the rate-determining step in the exchange reaction is the dissociation of EF-Ts from EF-Tu X GDP.

Euglena gracilis chloroplast elongation factor Tu. Interaction with guanine nucleotides and aminoacyl-tRNA

The interaction of the chloroplast elongation factor Tu (EF-Tuchl) from Euglena gracilis with guanine nucleotides and aminoacyl-tRNA has been investigated. The apparent dissociation constant at 37 degrees C for the EF-Tuchl X GDP complex is about 3 X 10(-7) M and for the EF-Tuchl X GTP complex, it is about 1 order of magnitude higher. The sulfhydryl modifying reagent N-ethylmaleimide severely inhibits the polymerization activity of Euglena EF-Tuchl. In the presence of N-ethylmaleimide, the dissociation constant for the modified EF-Tuchl X GDP complex is increased by an order of magnitude. Conversely, both GDP and GTP protect EF-Tuchl from the modification. The polymerization activity of EF-Tuchl is also sensitive to the antibiotic kirromycin. In the presence of kirromycin, the apparent dissociation constant for the EF-Tuchl X GTP complex is lowered 10-fold. The interaction of aminoacyl-tRNA with EF-Tuchl was investigated by examining the ability of EF-Tuchl to prevent the spontaneous hydrolysis of Phe-tRNA and by gel filtration chromatography. The binding of aminoacyl-tRNA to EF-Tuchl occurs only in the presence of GTP indicating the formation of the ternary complex EF-Tuchl X GTP X Phe-tRNA. The effect of kirromycin on the interaction was also investigated. In the presence of kirromycin, no interaction between EF-Tuchl and Phe-tRNA is observed, even in the presence of GTP.

Structure-function relationship in Escherichia coli initiation factors. Biochemical and biophysical characterization of the interaction between IF-2 and guanosine nucleotides

Equilibrium dialysis and protection from heat inactivation and proteolysis show that initiation factor 2 (IF-2) interacts not only with GTP but also with GDP and that its conformation is changed upon binding of either nucleotide. The apparent Ka (at 25 degrees C) for the IF-2 X GDP and IF-2 X GTP complexes was 8.0 X 10(4) and 7.0 X 10(3) M(-1), respectively. The lower affinity for GTP is associated with a more negative delta S0. The interaction, monitored by 1HNMR spectroscopy, is characterized by fast exchange and results in line broadening and downfield shift of the purine C-8 and ribose C-1' protons of GTP as well as of the beta, gamma-methylene protons of (beta-gamma-methylene)guanosine 5'-triphosphate. The interaction of guanosine nucleotides with IF-2 requires an H bond donor (or acceptor) group at position C-2 of the purine and involves the beta- and/or gamma-phosphate of the nucleotide while the ribose 2'-OH group or the integrity of the furan ring are less critical. IF-2 binds to ribosomal particles with decreasing affinity: 30 S greater than 70 S greater than 50 S. GTP and GDP have no effect on the binding to 70 S. GTP stimulates the binding to the 30 S and depresses somewhat the binding to the 50 S subunits; GDP has the opposite effect. These results seem to rule out that the release of IF 2 from 70 S is due to a "GDP-conformation" of the factor incompatible with its permanence on the ribosome. The rate and the extent of 30 S initiation complex formation are approximately 2-fold higher with IF-2 X GTP than with IF-2 alone. At low concentrations of IF-2 and 30 S subunits, GDP inhibits this reaction, acting as a strong competitive inhibitor of GTP (Ki = 1.25 X 10(-5)m) and preventing IF-2 from binding to the ribosomal subunit.

The structure of the EF-Tu . GDP . Me2+ complex

The structure of the MgGDP complex at the active site of elongation factor (EF-Tu) has been investigated by using phosphorothioate analogs of GDP in the absence and presence of various metal ions, electron paramagnetic resonance (EPR) and nuclear magnetic resonance (NMR) measurements. The high stereoselectivity of EF-Tu for the diastereomers of guanosine 5'-O-(1-thiodiphosphate) (GDP[alpha S]) is independent of the nature of the metal ion and is caused by the interaction of the protein with the alpha-phosphate of GDP. By using GDP analogs where the oxygens at either the alpha-phosphate or the beta-phosphate have been selectively labelled with 17O and measuring their effect on the EPR spectrum of EF-Tu-bound manganese we are able to show that only the beta-phosphate of GDP is coordinated to the metal ion in the EF-Tu . Me2+ . GDP complex. 31P-NMR studies on GDP and guanosine 5'-O-(2-thiodiphosphate) (GDP[beta S]) bound to EF-Tu indicate that in the EF-Tu . Me2+ . GDP complex Mg2+ interacts more strongly with the beta-phosphate than with the alpha-phosphate. Together with binding studies using GDP[beta S] our NMR results also indicate that the protein is complexed to the beta-phosphorous of GDP via two oxygens.

Primary structure of the polypeptide chain elongation factor Tu from E. coli. I. Amino acid sequence of fragment B

The complete amino acid sequence of Fragment B obtained by the limited tryptic digestion of E. coli polypeptide chain elongation factor Tu (EF-Tu) was determined. Seven peptides formed from Fragment B by cleavage with cyanogen bromide (designated as CB1 to CB7 according to their order of alignment from N- to C-termini of Fragment B) were purified, and six of them were completely sequenced by the manual method of sequential Edman degradation with direct identification of the phenylthiohydantoin-amino acids. The remaining one cyanogen bromide peptide (CB6) containing 109 amino acid residues was further digested with trypsin. Twelve tryptic peptides (designated as T1 to T12 according to their order of alignment from N- to C-termini of CB6) were isolated, and their amino acid sequences were analyzed. The alignment of CB peptides was based on the results of the automated sequence analysis of Fragment B from its N-terminal, and the sequence analysis of the overlapping peptides containing sulfhydryl groups obtained by the complete tryptic digestion of Fragment B. The alignment of peptides T1 to T12 on CB6 was based on the result of the automated sequence analysis of CB6, and the sequence of the overlapping peptide obtained by the chemical cleavage of CB6 at the tryptophan residue using cyanogen bromide in heptafluorobutyric acid. The nucleotide sequence of the tuf A gene was also utilized for the alignment of these peptides. Fragment B comprises amino acid residues 59 to 263 of E. coli EF-Tu, which consists of 393 amino acids. It contains two functional (SH1 and SH2) and one non-functional (SH3) sulfhydryl groups of EF-Tu. All of the five histidine residues in Fragment B were distributed within the first N-terminal quarter, and three of them were found to be clustered around SH2. Although E. coli EF-Tu consists of two gene products (tuf A and tuf B), no microheterogeneity was found in the amino acid sequence of Fragment B.

Isolation of eukaryotic initiation factor 2 from yeast Saccharomyces cerevisiae

Protein synthesis initiation factor eIF-2 has been isolated from the high speed supernatant fraction of the yeast Saccharomyces cerevisiae. This purification steps include ammonium sulfate fractionation, column chromatography on Sephacryl 300 and hydroxyapatite, and glycerol gradient sedimentation. Electrophoresis of the purified factor on sodium dodecyl sulfate polyacrylamide gels reveals three polypeptides with a total Mr of 127,000. The molecular weights of the subunits are 31,000, 46,500, and 49,600. The pI of each of these subunits is 4.5, 7.3, and 8.6, respectively. The stoichiometry of the subunits varies from 1:1:1 to 1:0.25:1 suggesting that the active factor may be composed of only two subunits with total Mr of 80,000. The factor is part of a high molecular weight complex during the first steps of the purification. Prior to chromatography on Sephacryl, this complex is broken up in high salt. The activity of the factor is stabilized by inclusion of GDP in all buffers during the preparation and is stimulated by magnesium ion.