Ecological controls on water-cycle response to climate variability in deserts.

The impact of climate variability on the water cycle in desert ecosystems is controlled by biospheric feedback at interannual to millennial timescales. This paper describes a unique field dataset from weighing lysimeters beneath nonvegetated and vegetated systems that unequivocally demonstrates the role of vegetation dynamics in controlling water cycle response to interannual climate variability related to El Nino southern oscillation in the Mojave Desert. Extreme El Nino winter precipitation (2.3-2.5 times normal) typical of the U.S. Southwest would be expected to increase groundwater recharge, which is critical for water resources in semiarid and arid regions. However, lysimeter data indicate that rapid increases in vegetation productivity in response to elevated winter precipitation reduced soil water storage to half of that in a nonvegetated lysimeter, thereby precluding deep drainage below the root zone that would otherwise result in groundwater recharge. Vegetation dynamics have been controlling the water cycle in interdrainage desert areas throughout the U.S. Southwest, maintaining dry soil conditions and upward soil water flow since the last glacial period (10,000-15,000 yr ago), as shown by soil water chloride accumulations. Although measurements are specific to the U.S. Southwest, correlations between satellite-based vegetation productivity and elevated precipitation related to El Nino southern oscillation indicate this model may be applicable to desert basins globally. Understanding the two-way coupling between vegetation dynamics and the water cycle is critical for predicting how climate variability influences hydrology and water resources in water-limited landscapes.

Comparison of volatile sulfur compound concentrations measured with a sulfide detector vs. gas chromatography.

The accuracy of the Halimeter, an inexpensive, simple instrument that measures total breath volatile sulfur compounds (VSCs), has not been adequately tested. We compared Halimeter measurements with those obtained with a specific and sensitive gas chromatographic (GC) technique. The Halimeter gave different, biexponential responses to a constant concentration of different VSCs: The relative response rate and sensitivity were hydrogen sulfide > methyl mercaptan > dimethylsulfide. The transient peak VSC concentration of oral samples was reached long before the sulfide detector fully responded. The GC measurement of initial total VSCs in breath samples was 2.7+/-0.48 times greater than the peak concentration of the Halimeter. However, the plateau phase measurement of the Halimeter was 25% greater than that of GC. While GC and Halimeter measurements positively correlated, appreciable differences were observed. In studies where relatively precise VSC measurements are required, GC is the preferable technique.

A new software routine that automates the fitting of protein X-ray crystallographic electron-density maps.

The classical approach to building the amino-acid residues into the initial electron-density map requires days to weeks of a skilled investigator's time. Automating this procedure should not only save time, but has the potential to provide a more accurate starting model for input to refinement programs. The new software routine MAID builds the protein structure into the electron-density map in a series of sequential steps. The first step is the fitting of the secondary alpha-helix and beta-sheet structures. These 'fits' are then used to determine the local amino-acid sequence assignment. These assigned fits are then extended through the loop regions and fused with the neighboring sheet or helix. The program was tested on the unaveraged 2.5 A selenomethionine multiple-wavelength anomalous dispersion (SMAD) electron-density map that was originally used to solve the structure of the 291-residue protein human heart short-chain L-3-hydroxyacyl-CoA dehydrogenase (SHAD). Inputting just the map density and the amino-acid sequence, MAID fitted 80% of the residues with an r.m.s.d. error of 0.43 A for the main-chain atoms and 1.0 A for all atoms without any user intervention. When tested on a higher quality 1.9 A SMAD map, MAID correctly fitted 100% (418) of the residues. A major advantage of the MAID fitting procedure is that it maintains ideal bond lengths and angles and constrains phi/psi angles to the appropriate Ramachandran regions. Recycling the output of this new routine through a partial structure-refinement program may have the potential to completely automate the fitting of electron-density maps.

Structural evidence for the evolution of pyrogenic toxin superantigens.

Pathogenic bacteria have evolved a wide variety of toxins to invade and attack host organisms. In particular, strains of the bacteria Staphylococcus aureus and Streptococcus pyogenes produce a family of pyrogenic toxin superantigens (PTSAgs) that can cause illness, e.g., toxic shock syndrome, or synergize with a number of other immune system disorders. The PTSAgs are all similar in size and have a conserved two-domain tertiary fold despite minimal amino acid sequence identity. The tertiary structure of PTSAg domain 1 is similar to the immunoglobulin binding motif of streptococcal proteins G and L. PTSAg domain 2 resembles members of the oligosaccharide/oligonucleotide binding fold family that includes the B subunits of the AB(5) heat-labile enterotoxins, cholera toxin, pertussis toxin, and verotoxin. The strong structural homology between the pyrogenic toxins and other bacterial proteins suggests that the PTSAgs evolved through the recombination of two smaller beta-strand motifs.

Appropriate use and misuse of blood concentration measurements to quantitate first-pass metabolism.

First-pass metabolism commonly is determined from the difference in the area under the blood concentration time curve (AUC) that is observed with oral versus intravenous administration of a compound. It is not fully appreciated that this technique serves as an accurate indicator of first-pass metabolism only when the clearance of the compound under consideration is first order (unsaturated) throughout the range of blood concentrations observed in the study. For example, multiple publications continue to mistakenly use AUC measurements to assess the first-pass metabolism of ethanol, a compound cleared primarily via zero-order kinetics. This report briefly reviews the physiologic basis of measurements of first-pass metabolism, demonstrates the errors that result from application of this technique when clearance is not first order, and, using ethanol as an example, describes a technique that can be used to measure first-pass metabolism when clearance deviates from first order.

The structure of vitellogenin provides a molecular model for the assembly and secretion of atherogenic lipoproteins.

The assembly of atherogenic lipoproteins requires the formation in the endoplasmic reticulum of a complex between apolipoprotein (apo)B, a microsomal triglyceride transfer protein (MTP) and protein disulphide isomerase (PDI). Here we show by molecular modelling and mutagenesis that the globular amino-terminal regions of apoB and MTP are closely related in structure to the ancient egg yolk storage protein, vitellogenin (VTG). In the MTP complex, conserved structural motifs that form the reciprocal homodimerization interfaces in VTG are re-utilized by MTP to form a stable heterodimer with PDI, which anchors MTP at the site of apoB translocation, and to associate with apoB and initiate lipid transfer. The structural and functional evolution of the VTGs provides a unifying scheme for the invertebrate origins of the major vertebrate lipid transport system.

A common binding site on the microsomal triglyceride transfer protein for apolipoprotein B and protein disulfide isomerase.

The assembly of triglyceride-rich lipoproteins requires the formation in the endoplasmic reticulum of a complex between apolipoprotein B (apoB), a microsomal triglyceride transfer protein (MTP), and protein disulfide isomerase (PDI). In the MTP complex, the amino-terminal region of MTP (residues 22-303) interacts with the amino-terminal region of apoB (residues 1-264). Here, we report the identification and characterization of a site on apoB between residues 512 and 721, which interacts with residues 517-603 of MTP. PDI binds in close proximity to this apoB binding site on MTP. The proximity of these binding sites on MTP for PDI and amino acids 512-721 of apoB was evident from studies carried out in a yeast two-hybrid system and by co-immunoprecipitation. The expression of PDI with MTP and apoB16 (residues 1-721) in the baculovirus expression system reduced the amount of MTP co-immunoprecipitated with apoB by 73%. The interaction of residues 512-721 of apoB with MTP facilitates lipoprotein production. Mutations of apoB that markedly reduced this interaction also reduced the level of apoB-containing lipoprotein secretion.

Use of a two-compartment model to assess the pharmacokinetics of human ethanol metabolism.

The relationship between blood ethanol concentration and hepatic ethanol metabolism commonly is calculated using the Michaelis-Menten equation and a one-compartment model that assumes equality of blood and hepatic ethanol concentrations. However, at low blood concentrations, most of the ethanol arriving at the liver is metabolized, and hepatic ethanol concentrations may fall far below that of the entering blood. We have developed a two-compartment model of ethanol metabolism that accounts for the fall in ethanol concentration that may occur as blood traverses the liver and used this model to make predictions concerning ethanol metabolism at various blood ethanol concentrations. The two-compartment model predicts that near-complete saturation will occur more abruptly and at a lower blood concentration (approximately 3 mM) than is the case with the one-compartment model. Thus, the two-compartment model predicts a near-constant ethanol elimination rate for blood ethanol concentrations above 3 mM (as commonly observed in human subjects), whereas the one-compartment model predicts an increasing elimination rate over the range of concentrations observed in experimental studies. In agreement with observed data, the two-compartment model predicts that first-pass metabolism should be extremely sensitive to the rate of ethanol absorption. Application of this model to previously published data indicated that, when absorption was slowed via concomitant food ingestion, first-pass metabolism accounts for approximately 50% and 10% of ethanol dosages of 0.15 g/kg and 0.3 g/kg, respectively. When ingested without food, there is negligible first-pass metabolism of even very small ethanol dosages (0.15 g/kg). These findings suggest that first-pass metabolism is an unimportant determinant of the blood ethanol response to ingestion of potentially inebriating doses of ethanol.

The structural basis of lipid interactions in lipovitellin, a soluble lipoprotein.

BACKGROUND: The conformation and assembly of lipoproteins, protein containing large amounts of noncovalently bound lipid, is poorly understood. Lipoproteins present an unusual challenge as they often contain varying loads of lipid and are not readily crystallized. Lipovitellin is a large crystallizable oocyte protein of approximately 1300 residues that contains about 16% w/w lipid. Lipovitellin contains two large domains that appear to be conserved in both microsomal triglyceride transfer protein and apolipoprotein B-100. To gain insight into the conformation of a lipoprotein and the potential modes of binding of both neutral and phospholipid, the crystal structure of lamprey lipovitellin has been determined. RESULTS: We report here the refined crystal structure of lipovitellin at 2.8 A resolution. The structure contains 1129 amino acid residues located on five peptide chains, one 40-atom phosphatidylcholine, and one 13-atom hydrocarbon chain. The protein contains a funnel-shaped cavity formed primarily by two beta sheets and lined predominantly by hydrophobic residues. CONCLUSIONS: Using the crystal structure as a template, a model for the bound lipid is proposed. The lipid-binding cavity is formed primarily by a single-thickness beta-sheet structure which is stabilized by bound lipid. This cavity appears to be flexible, allowing lipid to be loaded or unloaded.

Use of measurements of ethanol absorption from stomach and intestine to assess human ethanol metabolism.

Controversy exists concerning the site (stomach vs. liver) and magnitude of first-pass metabolism of ethanol. We quantitated gastric and total ethanol absorption rates in five male subjects and utilized these measurements to evaluate first-pass metabolism. Gastric emptying of ethanol (0.15 g/kg) was determined via a gamma camera and gastric absorption from the ratio of gastric ethanol to [14C]polyethylene glycol. Gastric absorption accounted for 30% and 10% of ethanol administered with food and water, respectively. With food, estimated gastric mucosal ethanol concentrations fell from 19 to 5 mM over 2 h. Calculations using these concentrations and kinetic data for gastric alcohol dehydrogenase showed <2% of the dose underwent gastric metabolism. Application of observed ethanol absorption rates to a model of human hepatic ethanol metabolism indicated that only 30% and 4% of the dose underwent first-pass metabolism when administered with food and water, respectively. We conclude that virtually all first-pass ethanol metabolism occurs in the liver and first-pass metabolism accounts for only a small fraction of total clearance.

Crystal structure of a trapped phosphoenzyme during a catalytic reaction.

The crystal structure of the fructose-2,6-bisphosphatase domain trapped during the reaction reveal a phosphorylated His 258, and a water molecule immobilized by the product, fructose-6-phosphate. The geometry suggests that the dephosphorylation step requires prior removal of the product for an 'associative in-line' phosphoryl transfer to the catalytic water.

Crystal structure of Aplysia ADP ribosyl cyclase, a homologue of the bifunctional ectozyme CD38.

ADP ribosyl cyclase synthesizes the novel secondary messenger cyclic ADP ribose (cADPR) utilizing NAD as a substrate. The enzyme shares extensive sequence similarity with two lymphocyte antigens, CD38 and BST-1, which hydrolyse as well as synthesize cADPR. The crystal structure provides a model for these cell surface enzymes. Cyclase contains two spatially separated pockets composed of sequence conserved residues, suggesting that the cyclization reaction may entail use of distinct sites. The enzyme dimer encloses a cavity which may entrap the intermediate, ADP ribose.

Use of maltose hydrolysis measurements to characterize the interaction between the aqueous diffusion barrier and the epithelium in the rat jejunum.

Rates of intestinal absorption and surface hydrolysis are determined by the interaction of two barriers: poorly stirred fluid adjacent to the mucosa, and the epithelial cell. These two barriers commonly are modeled as a fixed, flat layer of epithelium covered by a fixed thickness of unstirred fluid. To more accurately simulate these barriers in a villous mucosa, maltase activity (measured in vitro) was distributed over an anatomically correct model of rat jejunal villi. We then determined what interaction of the aqueous and epithelial barriers best predicted in vivo maltose hydrolysis rates measured over a broad range of infusate concentrations. Hydrolysis was accurately predicted by a model in which unstirred fluid extended from 20 microm over the villous tips throughout the intervillous space. In this model, the depth of diffusion into the intervillous space is inversely proportional to the efficiency of epithelial handling of the solute. As a result, both the aqueous barrier and the functional surface area are variables rather than constants. Some implications of our findings (relative to the conventional model) include: higher predicted Vmax, efficient handling of low concentrations of a solute at the villous tips while high concentrations must penetrate thick aqueous barriers, and sensitive regulation of transport rates via ease of access to the intervillous space.

Crystal structure of the rat liver fructose-2,6-bisphosphatase based on selenomethionine multiwavelength anomalous dispersion phases.

The crystal structure of the recombinant fructose-2,6-bisphosphatase domain, which covers the residues between 251 and 440 of the rat liver bifunctional enzyme, 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, was determined by multiwavelength anomalous dispersion phasing and refined at 2.5 A resolution. The selenomethionine-substituted protein was induced in the methionine auxotroph, Escherichia coli DL41DE3, purified, and crystallized in a manner similar to that of the native protein. Phase information was calculated using the multiwavelength anomalous dispersion data collected at the X-ray wavelengths near the absorption edge of the K-shell alpha electrons of selenium. The fructose-2,6-bisphosphatase domain has a core alpha/beta structure which consists of six stacked beta-strands, four parallel and two antiparallel. The core beta-sheet is surrounded by nine alpha-helices. The catalytic site, as defined by a bound phosphate ion, is positioned near the C-terminal end of the beta-sheet and close to the N-terminal end of an alpha-helix. The active site pocket is funnel-shaped. The narrow opening of the funnel is wide enough for a water molecule to pass. The key catalytic residues, including His7, His141, and Glu76, are near each other at the active site and probably function as general acids and/or bases during a catalytic cycle. The inorganic phosphate molecule is bound to an anion trap formed by Arg6, His7, Arg56, and His141. The core structure of the Fru-2,6-P2ase is similar to that of the yeast phosphoglycerate mutase and the rat prostatic acid phosphatase. However, the structure of one of the loops near the active site is completely different from the other family members, perhaps reflecting functional differences and the nanomolar range affinity of Fru-2,6-P2ase for its substrate. The imidazole rings of the two key catalytic residues, His7 and His141, are not parallel as in the yeast phosphoglycerate mutase. The crystal structure is used to interpret the existing chemical data already available for the bisphosphatase domain. In addition, the crystal structure is compared with two other proteins that belong to the histidine phosphatase family.

Characterization of a large conductance, cation-selective channel from sea urchin eggs that is sensitive to sulfhydryl reducing agents.

Vesicles containing large conductance cation selective channels were isolated from sea urchin (Strongylocentrotus purpuratus) eggs. Addition of the vesicles to one side of lipid bilayer led to the rapid appearance of 200 or more identical channels. These channels would then inactivate within 2 to 10 min. The inactivation could be prevented by the addition of sulfhydryl reducing agents (e.g., dithiothreitol or glutathione) to the cis side of the membrane. Only one channel type is present. The channel is cation selective, with a conductance of 572 ps in symmetrical 0.5 M KCl. The relative cation selectivity is K (1.0) > Cs (0.53) approximately < Na (0.52) > Li (0.2). The permeability ratio (Px/Pk) is 1.37 (Li) > 1.27 (Na) > 0.57 (Cs). Most organic cations (choline, tetraethylamine, tetrabutylamine, gallamine, lysine, histidine, arginine, etc.) and multivalent cations (La+3, alkali earth family, Zn+2, Eu+3, etc.) produced a significant channel block. The highest observed affinity was for La+3 which produced a 50% decrease in conductance in 500 mM KCl at a concentration of 8 microM. The biophysical properties of this channel are similar to those of a non-selective channel found in ascidian egg plasma membrane (Dale & DeFelice, 1984). A soluble extract of the egg supernatant can also prevent the inactivation of the channels. Using deactivated channels reconstituted into a planar lipid bilayer as an assay, this factor was partially purified. It is heat and acetone stable with a molecular weight of between 10 and 20 K. One of the major bands remaining in the purest fraction cross reacted with antibodies raised against E. coli thioredoxin.

Crystallization of ADP-ribosyl cyclase from Aplysia californica.

ADP-ribosyl cyclase synthesizes the secondary messenger cyclic ADP-ribose from NAD+. Diffraction quality crystals of the enzyme from ovotestes of Aplysia californica have been obtained. Crystallographic analysis of this enzyme will yield insight into the mode of binding of the novel cyclic nucleotide and the mechanism by which NAD+ is cyclized.

The multisubunit active site of fumarase C from Escherichia coli.

The crystal structure of the tetrameric enzyme, fumarase C from Escherichia coli, has been determined to a resolution of 2.0 A. A tungstate derivative used in the X-ray analysis is a competitive inhibitor and places the active site of fumarase in a region which includes atoms from three of the four subunits. The polypeptide conformation is similar to that of delta-crystallin and is comprised of three domains. The central domain, D2, is a unique five-helix bundle. The association of the D2 domains results in a tetramer which has a core of 20 alpha-helices. The other two domains, D1 and D3, cap the helical bundle on opposite ends giving both the single subunit and the tetramer a dumbbell-like appearance. Fumarase C has sequence homology to the eukaryotic fumarases, aspartase, arginosuccinate lyase, adenylosuccinate lyase and delta-crystallin.

Diurnal rhythm of heme turnover assessed by breath carbon monoxide concentration measurements.

Measurements of pulmonary carbon monoxide (CO) excretion can be used as a quantitative indicator of heme turnover. We determined whether a diurnal variation of heme turnover occurs by using a recently described technique that estimates breath CO excretion from measurements of alveolar CO concentration corrected for environmental CO to yield an endogenous PCO. This simple technique, unlike the previously employed rebreathing method, makes it possible to repeatedly measure CO excretion throughout a 24-hour period. Nine studies in seven healthy adult subjects demonstrated a diurnal rhythm of CO excretion with a peak excretion rate at about noon that was 26% greater than the nadir, which occurred at about midnight. The rhythm of CO production underlying the observed breath CO excretion was calculated to have an amplitude of about twice that of CO excretion and a phase shift relative to excretion of about 4 hours. We conclude that a diurnal variation in the rate of heme turnover occurs, and when CO determinations are used to assess minor alterations in heme turnover, consideration must be given to the time of day at which the measurements are obtained.