Lipid exchange and transfer between biological lipid-protein structures

The dynamic state of membrane and lipoprotein lipids is all the more impressive when the complexity of lipoprotein and membrane structure is considered. For as long as such a ubiquitous and easily demonstrable process has been studied, the mechanism(s) of lipid exchange is still unknown. Is a direct contact between lipoproteins and membranes required for lipid exchange, or are molecules expelled from lipid-protein complexes to spend a transient existence in the aqueous environment before returning to their donor or being accomodated in another complex? Although recent studies suggest the certain proteins such as the phospholipid exchange proteins can exert some vectoral and selective control over exchange reactions, the exchange of lipids, as studied under most conditionsin vitro, seems to be a random occurrence and a purely physicochemical event. Ifin vitro studies are indeed reflective of the processesin vivo, the lipid exchange activity in a cell can likely be depicted as shown in Figure 18.     

Exchange of phospholipids between unilamellar vesicles of 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine and plasma very low density lipoproteins.

Purified phosphatidylcholine exchange protein from bovine liver was used to exchange [14C]dipalmitoyl phosphatidylcholine from sonicated vesicles to human plasma very low density lipoproteins (VLDL). The exchange of [14C]-dipalmitoyl phosphatidylcholine for VLDL phospholipids was temperature dependent and linear with respect to time and amount of exchange protein. In the absence of the exchange protein, less than 10% of the [14C]dipalmitoyl phosphatidylcholine was transferred. At an initial weight ratio of [14C]-dipalmitoyl phosphatidylcholine vesicles to VLDL phospholipid (1.2 mg) of 2.2, the exchange protein (14 microgram) replaced 55% of the VLDL phospholipids with [14C]dipalmitoyl phosphatidylcholine in 15 min; VLDL protein and cholesterol content were unaltered. From these studies we conclude that the exchange protein is a useful method to alter the phospholipid composition of VLDL under conditions such that there is minimal perturbation of the lipoprotein.     

A graphic analysis of respiratory heat exchange

A new graphic representation of respiratory heat exchange is proposed using the concept of equivalent temperatures directly related to enthalpy values. On such a diagram it is possible to 1) compute the value of the heat exchange (delta H) knowing the inspired temperature (TI) and the partial pressure of water vapor (PIH2O) [or the relative humidity (rhI)] of inspired gas; 2) estimate the variation in delta H following a given variation in TI and PIH2O or, inversely, to choose the variation in TI and PIH2O necessary to obtain a given variation in delta H; 3) dissociate inspiratory and expiratory exchanges and to evaluate the efficiency of the respiratory heat exchange process in different environmental situations; and 4) easily compare the results of different studies published on respiratory heat exchanges in humans or other animal species.     

Design and implementation of microarray gene expression markup language (MAGE-ML)

Background

Meaningful exchange of microarray data is currently difficult because it is rare that published data provide sufficient information depth or are even in the same format from one publication to another. Only when data can be easily exchanged will the entire biological community be able to derive the full benefit from such microarray studies.

Results

To this end we have developed three key ingredients towards standardizing the storage and exchange of microarray data. First, we have created a minimal information for the annotation of a microarray experiment (MIAME)-compliant conceptualization of microarray experiments modeled using the unified modeling language (UML) named MAGE-OM (microarray gene expression object model). Second, we have translated MAGE-OM into an XML-based data format, MAGE-ML, to facilitate the exchange of data. Third, some of us are now using MAGE (or its progenitors) in data production settings. Finally, we have developed a freely available software tool kit (MAGE-STK) that eases the integration of MAGE-ML into end users' systems.

Conclusions

MAGE will help microarray data producers and users to exchange information by providing a common platform for data exchange, and MAGE-STK will make the adoption of MAGE easier.     

Structural mobility in human manganese superoxide dismutase

Human manganese superoxide dismutase (MnSOD) is a homotetramer of 22 kDa subunits, a dimer of dimers containing dimeric and tetrameric interfaces. We have investigated conformational mobility at these interfaces by measuring amide hydrogen/deuterium (H/D) exchange kinetics and 19F NMR spectra, both being excellent methods for analyzing local environments. Human MnSOD was prepared in which all nine tyrosine residues in each subunit are replaced with 3-fluorotyrosine. The 19F NMR spectrum of this enzyme showed five sharp resonances that have been assigned by site-specific mutagenesis by replacing each 3-fluorotyrosine with phenylalanine; four 19F resonances not observed are near the paramagnetic manganese and extensively broadened. The temperature dependence of the line widths and chemical shifts of the 19F resonances were used to estimate conformational mobility. 3-Fluorotyrosine 169 at the dimeric interface showed little conformational mobility and 3-fluorotyrosine 45 at the tetrameric interface showed much greater mobility by these measures. In complementary studies, H/D exchange mass spectrometry was used to measure backbone dynamics in human MnSOD. Using this approach, amide hydrogen exchange kinetics were measured for regions comprising 78% of the MnSOD backbone. Peptides containing Tyr45 at the tetrameric interface displayed rapid exchange of hydrogen with deuterium while peptides containing Tyr169 in the dimeric interface only displayed moderate exchange. Taken together, these studies show that residues at the dimeric interface, such as Tyr169, have significantly less conformational freedom or mobility than do residues at the tetrameric interface, such as Tyr45. This is discussed in terms of the role in catalysis of residues at the dimeric interface.     

Character compatibility of molecular markers to distinguish asexual and sexual reproduction

Particularly in polyploids, the potential of the high variability of dominant markers such as random amplified polymorphic DNA fragments (RAPDs) and amplified fragment length polymorphisms (AFLPs) in population genetic studies and analysis of breeding systems is reduced due to their dominant nature. In contrast, the criterion of character compatibility is hindered neither by dominance nor by polyploidy as allelic interpretation is not necessary. Character compatibility, which can be used to detect events of genetic exchange (or recombination), is particularly informative if these events are expected to be rare such as in taxa with extensive vegetative reproduction or apomixis. Binary unordered characters such as presence and absence of anonymous DNA markers are incompatible if all four pairwise combinations of character states are present among the individuals studied. Because incompatible character state distributions defy any progenitor–derivative relationship among individuals, they provide strong evidence for genetic exchange. Both the absolute number of incompatible character combinations and the probability of compatibility can be used as a measure of incompatibility. Although these measures may not directly relate to the frequency of genetic exchange, they provide a useful tool to heuristically explore data sets. The most commonly used input for multivariate analyses and analysis of molecular variance in population genetic studies of (dis)similarity of marker distributions are amalgamates of mutation and recombination. Character compatibility can be used to complement these traditional methods of analysis. Advantages and disadvantages of character incompatibility relative to multilocus analysis of modes of reproduction and population genetics are demonstrated with data from RAPDs, isozymes, and restriction fragment length polymorphisms (RFLPs) of the nuclear ribosomal and chloroplast genome.     

Native and recombinant Slc26a3 (downregulated in adenoma, Dra) do not exhibit properties of 2Cl-/1HCO3- exchange

The recent proposal that Dra/Slc26a3 mediates electrogenic 2Cl(-)/1HCO(3)(-) exchange suggests a required revision of classical concepts of electroneutral Cl(-) transport across epithelia such as the intestine. We investigated 1) the effect of endogenous Dra Cl(-)/HCO(3)(-) activity on apical membrane potential (V(a)) of the cecal surface epithelium using wild-type (WT) and knockout (KO) mice; and 2) the electrical properties of Cl(-)/(OH(-))HCO(3)(-) exchange by mouse and human orthologs of Dra expressed in Xenopus oocytes. Ex vivo (36)Cl(-) fluxes and microfluorometry revealed that cecal Cl(-)/HCO(3)(-) exchange was abolished in the Dra KO without concordant changes in short-circuit current. In microelectrode studies, baseline V(a) of Dra KO surface epithelium was slightly hyperpolarized relative to WT but depolarized to the same extent as WT during luminal Cl(-) substitution. Subsequent studies indicated that Cl(-)-dependent V(a) depolarization requires the anion channel Cftr. Oocyte studies demonstrated that Dra-mediated exchange of intracellular Cl(-) for extracellular HCO(3)(-) is accompanied by slow hyperpolarization and a modest outward current, but that the steady-state current-voltage relationship is unaffected by Cl(-) removal or pharmacological blockade. Further, Dra-dependent (36)Cl(-) efflux was voltage-insensitive in oocytes coexpressing the cation channels ENaC or ROMK. We conclude that 1) endogenous Dra and recombinant human/mouse Dra orthologs do not exhibit electrogenic 2Cl(-)/1HCO(3)(-) exchange; and 2) acute induction of Dra Cl(-)/HCO(3)(-) exchange is associated with secondary membrane potential changes representing homeostatic responses. Thus, participation of Dra in coupled NaCl absorption and in uncoupled HCO(3)(-) secretion remains compatible with electroneutrality of these processes, and with the utility of electroneutral transport models for predicting epithelial responses in health and disease.     

Malate exchange between the cytosol and mitochondria

1. By comparing the relative isotopic yields in glucose and CO(2) from precursors of mitochondrial and cytosolic malate, it is evident that the rate of isotopic exchange between these compartments is rapid. 2. A variety of potential inhibitors of malate exchange were tested, but no specific and effective inhibitor of the isotopic exchange has been found. 3. Compounds such as n-butylmalonate and p-iodobenzylmalonate, which have been used as inhibitors of the malate-phosphate transport system in isolated mitochondria, do not appear to be sufficiently specific to be useful in studies with intact cells.     

Glycodynamers: dynamic analogs of arabinofuranoside oligosaccharides

Dynamic analogs of alpha-(1-->5)-D-oligoarabinofuranosides were prepared by oxime polycondensation. These equilibrium polymers were characterized by (1)H NMR studies, NMR DOSY, and MALDI mass spectrometry. Their reversibility under mild acidic conditions was demonstrated by component exchange reaction followed by (1)H NMR studies. Their size and composition can be tuned by component exchange emphasizing their constitutionally dynamic character. They represent dynamic versions of biopolymers, biodynamers.     

Mechanism of Inhibition of the Human Sirtuin Enzyme SIRT3 by Nicotinamide: Computational and Experimental Studies

Sirtuins are key regulators of many cellular functions including cell growth, apoptosis, metabolism, and genetic control of age-related diseases. Sirtuins are themselves regulated by their cofactor nicotinamide adenine dinucleotide (NAD⁺) as well as their reaction product nicotinamide (NAM), the physiological concentrations of which vary during the process of aging. Nicotinamide inhibits sirtuins through the so-called base exchange pathway, wherein rebinding of the reaction product to the enzyme accelerates the reverse reaction. We investigated the mechanism of nicotinamide inhibition of human SIRT3, the major mitochondrial sirtuin deacetylase, in vitro and in silico using experimental kinetic analysis and Molecular Mechanics-Poisson Boltzmann/Generalized Born Surface Area (MM-PB(GB)SA) binding affinity calculations with molecular dynamics sampling. Through experimental kinetic studies, we demonstrate that NAM inhibition of SIRT3 involves apparent competition between the inhibitor and the enzyme cofactor NAD⁺, contrary to the traditional characterization of base exchange as noncompetitive inhibition. We report a model for base exchange inhibition that relates such kinetic properties to physicochemical properties, including the free energies of enzyme-ligand binding, and estimate the latter through the first reported computational binding affinity calculations for SIRT3:NAD⁺, SIRT3:NAM, and analogous complexes for Sir2. The computational results support our kinetic model, establishing foundations for quantitative modeling of NAD⁺/NAM regulation of mammalian sirtuins during aging and the computational design of sirtuin activators that operate through alleviation of base exchange inhibition.     

Identification and metabolism of polyphosphoinositides in isolated islets of Langerhans.

The effect of pH variation on the exchangeability with deuterium of protons strongly coupled to Mo(V) in the active and desulpho forms of xanthine oxidase was studied by e.p.r. and rapid freezing, in extension of the work of Gutteridge, Tanner & Bray [Biochem. J. (1978) 175, 887-897]. Above neutrality, exchange rates increased with increasing pH. Detailed studies were made on the desulpho enzyme under a variety of conditions, and exchange rate constants at 22 degrees C ranged from 0.16s -1 at pH 6.6 to 1.6s -1 at pH 11.3. The mechanism of proton exchange in the enzyme is discussed. The interpretation by the above workers that the strongly coupled proton of the active enzyme is on sulphur and that of the desulpho enzyme is on oxygen remains valid (and is in agreement with other work), as do their proposals for the structures of the protonated and deprotonated species. However, pK values cannot be calculated from the exchange data. It is likely that the relatively low rates of exchange observed are due to the difference of structure between the protonated and the deprotonated forms. In the case of the desulpho enzyme, an exchange mechanism, which involves the proton exchanging both as such and along with oxygen in the form of a hydroxyl ion, is discussed.     

No evidence of short-term exchange of meat for sex among chimpanzees

The meat-for-sex hypothesis posits that male chimpanzees (Pan troglodytes) trade meat with estrous females in exchange for short-term mating access. This notion is widely cited in the anthropological literature and has been used to construct scenarios about human evolution. Here we review the theoretical and empirical basis for the meat-for-sex hypothesis. We argue that chimpanzee behavioral ecology does not favor the evolution of such exchanges because 1) female chimpanzees show low mate selectivity and require little or no material incentive to mate, violating existing models of commodity exchange; and 2) meat-for-sex exchanges are unlikely to provide reproductive benefits to either partner. We also present new analyses of 28 years of data from two East African chimpanzee study sites (Gombe National Park, Tanzania; Kanyawara, Kibale National Park, Uganda) and discuss the results of previously published studies. In at least three chimpanzee communities, 1) the presence of sexually receptive females did not increase hunting probability, 2) males did not share preferentially with sexually receptive females, and 3) sharing with females did not increase a male's short-term mating success. We acknowledge that systematic meat sharing by male chimpanzees in expectation of, or in return for, immediate copulations might be discovered in future studies. However, current data indicate that such exchanges are so rare, and so different in nature from exchanges among humans, that with respect to chimpanzees, sexual bartering in humans should be regarded as a derived trait with no known antecedents in the behavior of wild chimpanzees.     

Simulating Daily and Half-Hourly Fluxes of Forest Carbon Dioxide and Water Vapor Exchange with a Simple Model of Light and Water Use

For the large-scale application of simple, aggregated models, it is important to be able to link the values of model parameters to easily measurable ecosystem characteristics. However, the aggregation of model inputs and outputs over time and space can hamper this linkage. In this paper, two temporal versions of the same simple carbon dioxide (CO₂) and water exchange model, based on the concepts of water- and light-use efficiencies, were used to simulate the half-hourly and daily CO₂ and water exchange of a Douglas fir forest (Pseudotsuga menziesii (Mirb.) Franco) in the Netherlands for 2 years, before and after a thinning. We tested the performance of the models and the interpretability of changes in optimized parameter values, due to the thinning, in terms of ecosystem functioning. The performance of the half-hourly model was satisfactory, whereas the performance of the daily model was high for water exchange but clearly lower for CO₂ exchange. A comparison of the model parameters before and after the thinning showed that the coefficients of the half-hourly model could be separated into more physiologically determined and stand-determined characteristics, but this separation was not clear for the daily model. These results show that if the temporal resolution of the model is high enough, the effects of a major ecosystem manipulation, such as thinning, can be detected and interpreted using eddy flux data and a very simple biophysical model. The model parameters have an unambiguous interpretation and can be inferred from basic ecosystem observables, such as leaf area index (LAI) and aboveground biomass. A sensitivity analysis found strong correlations between parameter sets with similar model performance. For any comparison of the parameter values of different studies, ranges of parameter values and their correlations should be presented rather than one optimized value. Received 2 May 2001; accepted 15 February 2002.     

The use of spin desalting columns in DMSO‐quenched H/D‐exchange NMR experiments

Dimethylsulfoxide (DMSO)‐quenched hydrogen/deuterium (H/D)‐exchange is a powerful method to characterize the H/D‐exchange behaviors of proteins and protein assemblies, and it is potentially useful for investigating non‐protected fast‐exchanging amide protons in the unfolded state. However, the method has not been used for studies on fully unfolded proteins in a concentrated denaturant or protein solutions at high salt concentrations. In all of the current DMSO‐quenched H/D‐exchange studies of proteins so far reported, lyophilization was used to remove D₂O from the protein solution, and the lyophilized protein was dissolved in the DMSO solution to quench the H/D exchange reactions and to measure the amide proton signals by two‐dimensional nuclear magnetic resonance (2D NMR) spectra. The denaturants or salts remaining after lyophilization thus prevent the measurement of good NMR spectra. In this article, we report that the use of spin desalting columns is a very effective alternative to lyophilization for the medium exchange from the D₂O buffer to the DMSO solution. We show that the medium exchange by a spin desalting column takes only about 10 min in contrast to an overnight length of time required for lyophilization, and that the use of spin desalting columns has made it possible to monitor the H/D‐exchange behavior of a fully unfolded protein in a concentrated denaturant. We report the results of unfolded ubiquitin in 6.0M guanidinium chloride.     

Influence of ionic strength on sodium-calcium exchange of two temperate climate soils

Salt-affected soils have been studied extensively with respect to their Na–Ca exchange properties. These studies have focused on soil environments of the arid West. However, because of irrigation and oil well brine discharges in the temperate region of the U.S. there is need to understand sodicity behavior of such soils. In this study, two Kentucky soils (Pembroke and Uniontown) at the 0–10 cm depth were studied to evaluate the influence of ionic strength (I) and sodium adsorption ratio (SAR) on cation selectivity coefficients. The data showed that both soils exhibit at least two classes of exchange sites and in general the apparent affinity for Na⁺ increased when solution ionic strength increased. Furthermore, both soils under all three ionic strengths tested showed greater affinity for Na⁺ than the average agricultural saline soil of the arid West. The data suggested the need for establishing critical salt dispersion thresholds for temperate climate soils and developing effective brine management approaches.     

Temperature and Microtopography Interact to Control Carbon Cycling in a High Arctic Fen

High arctic wetlands hold large stores of soil carbon (C). The fate of these C stores in a changing climate is uncertain, as rising air temperatures may differentially affect photosynthesis and ecosystem respiration (ER). In this study, open-top warming chambers were used to increase air and soil temperatures in contrasting microtopographic positions of a high arctic fen in NW Greenland. CO₂ exchange between the ecosystem and the atmosphere was measured on 28 dates over a 3-year period. Measurements of the normalized difference vegetation index, leaf and stem growth, leaf-level gas exchange, leaf nitrogen, leaf δ¹³C, and fine root production were made to investigate the mechanisms and consequences of observed changes in CO₂ exchange. Gross ecosystem photosynthesis (GEP) increased with chamber warming in hollows, which are characterized by standing water, and in hummocks, which extend above the water table. ER, however, increased only in hummocks, such that net ecosystem exchange (NEE) increased in hollows, but did not change in hummocks with chamber warming. Complementary measurements of plant growth revealed that increases in GEP corresponded with increases in C allocation to aboveground biomass in hummocks and belowground biomass in hollows. Our results and those of several recent studies clearly demonstrate that effects of climate change on the C balance of northern wetlands will depend upon microtopography which, in turn, may be sensitive to climate change.     

Modifications to the C‐Terminus of Arf1 Alter Cell Functions and Protein Interactions

Arf family proteins are ≈21‐kDa GTP‐binding proteins that are critical regulators of membrane traffic and the actin cytoskeleton. Studies examining the complex signaling pathways underlying Arf action have relied on recombinant proteins comprised of Arf fused to epitope tags or proteins, such as glutathione S‐transferase or green fluorescent protein, for both cell‐based mammalian cell studies and bacterially expressed recombinant proteins for biochemical assays. However, the effects of such protein fusions on the biochemical properties relevant to the cellular function have been only incompletely studied at best. Here, we have characterized the effect of C‐terminal tagging of Arf1 on (i) function in Saccharomyces cerevisiae, (ii) in vitro nucleotide exchange and (iii) interaction with guanine nucleotide exchange factors and GTPase‐activating proteins. We found that the tagged Arfs were substantially impaired or altered in each assay, compared with the wild‐type protein, and these changes are certain to alter actions in cells. We discuss the results related to the interpretation of experiments using these reagents and we propose that authors and editors consistently adopt a few simple rules for describing and discussing results obtained with Arf family members that can be readily applied to other proteins.     

Corvids avoid odd evaluation by following simple rules in a risky exchange task

In their natural environment, animals often make decisions crucial for survival, such as choosing the best patch or food, or the best partner to cooperate. The choice can be compared to a gamble with an outcome that is predictable but not certain, such as rolling a dice. In economics, such a situation is called a risky context. Several models show that although individuals can generally evaluate the odds of each potential outcome, they can be subject to errors of judgment or choose according to decision-making heuristics (simple decision rules). In non-human primates, similar errors of judgment have been reported and we have recently shown that they also use a decisional heuristics when confronted with a risky choice in an exchange task. This suggests a common evolutionary origin to the mechanisms underlying decision-making under risk in primates. However, whether the same mechanisms are also present in more distantly related taxa needs to be further investigated. Other social species, like corvids, are renowned for their advanced cognitive skills and may show similar responses. Here, we analyse data on corvids (carrion crows, hooded crows, common ravens and rooks) tested in a risky exchange task comparable to the one used in non-human primates. We investigated whether corvids could exchange according to the odds of success or, alternatively, whether they used a heuristic similar to the one used by non-human primates. Instead, most corvids chose a course of action (either a low or high exchange rate) that remained constant throughout the study. In general, corvids’ mean exchange rates were lower compared to non-human primates, indicating that they were either risk-adverse or that they do not possess the cognitive capabilities to evaluate odds. Further studies are required to evaluate the flexibility in exchange abilities of these birds in exchange abilities of these birds.     

A mechanistic investigation of the thiol-disulfide exchange step in the reductive dehalogenation catalyzed by tetrachlorohydroquinone dehalogenase

Tetrachlorohydroquinone dehalogenase catalyzes the reductive dehalogenation of tetrachloro- and trichlorohydroquinone to give 2,6-dichlorohydroquinone in the pathway for degradation of pentachlorophenol by Sphingobium chlorophenolicum. Previous work has suggested that this enzyme may have originated from a glutathione-dependent double bond isomerase such as maleylacetoacetate isomerase or maleylpyruvate isomerase. While some of the elementary steps in these two reactions may be similar, the final step in the dehalogenation reaction, a thiol-disulfide exchange reaction that removes glutathione covalently bound to Cys13, certainly has no counterpart in the isomerization reaction. The thiol-disulfide exchange reaction does not appear to have been evolutionarily optimized. There is little specificity for the thiol; many thiols react at high rates. TCHQ dehalogenase binds the glutathione involved in the thiol-disulfide exchange reaction very poorly and does not alter its pK(a) in order to improve its nucleophilicity. Remarkably, single-turnover kinetic studies show that the enzyme catalyzes this step by approximately 10000-fold. This high reactivity requires an as yet unidentified protonated group in the active site.     

RasGRP Ras guanine nucleotide exchange factors in cancer

RasGRP proteins are activators of Ras and other related small GTPases by the virtue of functioning as guanine nucleotide exchange factors （GEFs）. In vertebrates, four RasGRP family members have been described. RasGRP-1 through -4 share many structural domains but there are also subtle differences between each of the different family members. Whereas SOS RasGEFs are ubiquitously expressed, RasGRP proteins are expressed in distinct patterns, such as in different cells of the hematopoietic system and in the brain. Most studies have concentrated on the role of RasGRP proteins in the development and function of immune cell types because of the predominant RasGRP expression profiles in these cells and the immune phenotypes of mice deficient for Rasgrp genes. However, more recent studies demonstrate that RasGRPs also play an important role in tumorigenesis. Examples are skin- and hematological- cancers but also solid malignancies such as melanoma or prostate cancer. These novel studies bring up many new and unanswered questions related to the molecular mechanism of RasGRP-driven oncogenesis, such as new receptor systems that RasGRP appears to respond to as well as regulatory mechanisms for RasGRP expression that appear to be perturbed in these cancers. Here we will review some of the known aspects of RasGRP biology in lymphocytes and will discuss the exciting new notion that RasGRP Ras exchange factors play a role in oncogenesis downstream of various growth factor receptors.