Pitfalls in metal-organic framework crystallography: towards more accurate crystal structures.

Single crystal X-ray diffraction (SC-XRD) is the principal method for determining the crystal structures of metal-organic frameworks (MOFs). This tutorial deals with the handling of MOF crystals and analysis of crystallographic data obtained from single-crystal X-ray diffraction, focusing on two features that are particularly important in MOF crystallography and have a large impact on the quality and reliability of the final crystal structures: (1) the treatment of pore-occupying entities (both in the physical crystals and in the crystallographic model) and (2) crystallographic twinning. Proper handling of samples and data will reduce the need for using solvent masking software (e.g. SQUEEZE) to obtain acceptable crystal structures. If SC-XRD is to retain its position as the definitive method of MOF structure determination, these issues must be addressed when a new MOF structure is determined and reported. The issues addressed in this review is also valid for other porous, crystalline solids such as porous organic cages, metal-organic polyhedra, covalent organic frameworks and zeotype materials.

A genome-wide association study of saturated, mono- and polyunsaturated red blood cell fatty acids in the Framingham Heart Offspring Study.

Most genome-wide association studies have explored relationships between genetic variants and plasma phospholipid fatty acid proportions, but few have examined apparent genetic influences on the membrane fatty acid profile of red blood cells (RBC). Using RBC fatty acid data from the Framingham Offspring Study, we analyzed over 2.5 million single nucleotide polymorphisms (SNPs) for association with 14 RBC fatty acids identifying 191 different SNPs associated with at least 1 fatty acid. Significant associations (p<1×10(-8)) were located within five distinct 1MB regions. Of particular interest were novel associations between (1) arachidonic acid and PCOLCE2 (regulates apoA-I maturation and modulates apoA-I levels), and (2) oleic and linoleic acid and LPCAT3 (mediates the transfer of fatty acids between glycerolipids). We also replicated previously identified strong associations between SNPs in the FADS (chromosome 11) and ELOVL (chromosome 6) regions. Multiple SNPs explained 8-14% of the variation in 3 high abundance (>11%) fatty acids, but only 1-3% in 4 low abundance (<3%) fatty acids, with the notable exception of dihomo-gamma linolenic acid with 53% of variance explained by SNPs. Further studies are needed to determine the extent to which variations in these genes influence tissue fatty acid content and pathways modulated by fatty acids.

Omega-3 fatty acids modulate collagen signaling in human platelets.

Dietary intake of the omega-3 fatty acids eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) results in cardioprotective benefits. However, the cellular and physiological bases for these benefits remain unclear. We hypothesized that EPA and DHA treatments would interfere with collagen-mediated platelet signaling. Thirty healthy volunteers received 28 days of 3.4 g/d EPA+DHA with and without a single dose of aspirin. Clinical hematologic parameters were then measured along with assays of collagen-stimulated platelet activation and protein phosphorylation. Omega-3 therapy led to a small but significant reduction in platelets (6.3%) and red blood cells (1.7%), but did not impair clinical time-to-closure assays. However, collagen-mediated platelet signaling events of integrin activation, α-granule secretion, and phosphatidylserine exposure were all reduced by roughly 50% after omega-3 incorporation, and collagen-induced tyrosine phosphorylation was significantly impaired. The diminished platelet response to collagen may account for some of the cardioprotective benefits provided by DHA and EPA.

The effects of EPA, DHA, and aspirin ingestion on plasma lysophospholipids and autotaxin.

Lysophophatidylcholine (LPC) and lysophosphatidic acid (LPA) are potent lysolipid mediators increasingly linked with atherosclerosis and inflammation. A current model proposing that plasma LPA is produced when LPC is hydrolyzed by the enzyme autotaxin has not been rigorously investigated in human subjects. We conducted a clinical trial of eicosapentaenoic acid/docosahexaenoic acid (EPA/DHA) and aspirin ingestion in normal volunteers. Fasting blood samples were drawn at baseline and after 4-week supplementation with EPA/DHA (3.4 g/d) with and without aspirin (650 mg). Plasma LPC and LPA species and autotaxin activity were measured. EPA-LPC and DHA-LPC concentrations increased significantly with EPA/DHA supplementation whereas EPA- and DHA-LPA did not. Autotaxin activity was unaffected by any treatment, and aspirin had no effect on any endpoint. Taken together, our data demonstrate that plasma LPC, but not LPA, species can be dynamically regulated by dietary supplementation, and argue against a simple model of LPA generation via LPC hydrolysis.

Endothelial bound lipoprotein lipase (LpL) depletion in hypoalbuminemia results from decreased endothelial binding, not decreased secretion.

Hypertriglyceridemia in nephrotic (NS) and Nagase analbuminemic rats (Analb) results from reduced triglyceride clearance. NS and Analb have reduced or absent albumin, reduced plasma oncotic pressure (pi), but Analb lack proteinuria. The heparin releasable lipoprotein lipase (LpL) pool in both models is greatly reduced, suggesting reduced LpL is related to low albumin or pi and not proteinuria. To determine the cause of endothelial LpL reduction, we studied effectors of endothelial LpL (eLpL) levels from gene expression, to delivery and endothelial binding. eLpL was measured as heparin releasable activity. eLpL and secretion rate was measured in isolated hearts perfused with heparin. mRNA levels were measured in rat hearts by kinetic RT-PCR. Finally, binding of (125)I-LpL by competition assays rat endothelial cells measured serum-induced changes in affinity. eLpL in vivo was reduced in nephrotic and Analb rats. While the eLpL pool was reduced in isolated perfused hearts, neither LpL secretion by isolated hearts nor myocardial mRNA was reduced in NS or Analb. Binding of LpL to RAEC preincubated with serum from either NS or Analb was reduced compared to control. LpL mRNA levels and release rate was not altered in hearts from NS rats, while eLpL is depleted, suggesting that reduced eLpL in NS is not the result of reduced delivery. The finding that NS serum alters LpL binding to RAEC suggests LpL depletion results from decreased binding rather than defective delivery. This in turn is a consequence of reduced serum albumin or pi but does not require proteinuria.

Endothelial chylomicron binding is altered by interaction with high-density lipoprotein in Heymann's nephritis.

Very-low-density lipoprotein (VLDL) catabolism is impaired in the nephrotic syndrome, partly as a result of structural changes that impair endothelial binding in the presence of lipoprotein lipase. Previous results suggested that postsynthetic modification of VLDL by high-density lipoprotein (HDL) in nephrotic syndrome rats causes their failure to bind endothelia normally. It is unknown (1) whether the structure of secreted lipoproteins is normal before exposure to nephrotic syndrome serum and (2) whether the same structural or functional defects are imparted to chylomicrons (CMs) through their interaction with HDL from nephrotic syndrome rats. CMs were isolated from thoracic duct lymph from rats with passive Heymann's nephritis (HN) and normal controls. CMs from control rats were incubated with HDL from either HN or control rats and reisolated, and apolipoprotein E (apo E) content and endothelial binding were determined. We found that CMs secreted by HN and control rats had similar apo E/B-48 ratios. HDL from HN rats had significantly lower apo E/A-I ratios than controls. Incubation of nascent control CMs with control HDL resulted in a 4-fold increase in CM apo E content, but binding was unaffected. Incubation with HDL from HN resulted in only a 50% increase in CM apo E content but reduced binding of these treated CMs by 50% compared either with nascent control CMs or with CMs incubated with control HDL. HDL from rats with HN alters CM binding to lipoprotein lipase by a mechanism that does not involve reducing the content of apo E already present on CMs at the time of secretion.

Lipoprotein-stimulated mesangial cell proliferation and gene expression are regulated by lipoprotein lipase.

BACKGROUND: Hyperlipidemia accelerates the progression of glomerular disease, and lipoproteins bind glomerular mesangial cells (MC) and induce proliferation and cytokine expression. In the vessel wall, the binding of lipoproteins to endothelial cells is markedly enhanced by lipoprotein lipase (LpL), synthesized by the underlying smooth muscle cells. While it is known that LpL is localized to the glomerulus, it is not known if and how it modulates the lipoprotein-mesangial interaction. METHODS: Very low-density lipoprotein (VLDL) was isolated from rats and was used to treat cultured primary rat MCs. Binding studies were done with and without LpL and with/without pretreatment with heparanase, which degrades cell surface heparan sulfate proteoglycan (HSPG), known to modulate the LpL-lipoprotein interaction in blood vessels. VLDL/LpL was also used to assess MC proliferation and gene expression of the cytokine platelet-derived growth factor (PDGF). RESULTS: LpL enhanced VLDL binding to MCs by as much as 200-fold, and most of this effect was blocked by pretreatment with heparanase. LpL amplified VLDL-driven MC proliferation and increased VLDL-induced PDGF expression. Heparanase pretreatment of cells eliminated both of these amplifications. LpL alone increased MC proliferation and PDGF gene expression. DISCUSSION: As in the vessel wall, LpL enhances VLDL binding to MCs. MCs respond to LpL binding by proliferating and expressing cytokines such as PDGF. LpL may be a crucial paracrine mediator of the glomerular response to circulating lipoproteins, amplifying a response that includes cytokine elaboration, influx of circulating monocytes, and eventual sclerosis.

Proteinuria and plasma compositional changes contribute to defective lipoprotein catabolism in the nephrotic syndrome by separate mechanisms.

Triglyceride (TG)-rich lipoproteins are primarily increased in the nephrotic syndrome (NS) as a result of decreased catabolism. Lipoprotein lipase (LpL) is the rate limiting enzyme for lipolysis of TG. The biologically active endothelial bound LpL pool is reduced in NS providing one mechanism for decreased clearance of very low density lipoprotein (VLDL). LpL, however, is also reduced in the Nagase Analbuminemic Rat (NAR) to the same extent as in NS, suggesting that other factors contribute to decreased VLDL clearance. Hyperlipidemia worsens with the onset of proteinuria and is reduced when proteinuria abates. We established that while VLDL from NS rats bind poorly to bovine aortic endothelial cells (BAEC) in the presence of saturating LpL while, VLDL from NAR bind more avidly than control. We then established that rat aortic endothelial cells (RAEC) incubated with serum from NAR or from NS rats bind significantly less exogenous LpL. Thus decreased clearance of VLDL in NS results from: 1) reduced endothelial bound LpL; an effect of serum from animals with reduced oncotic pressure (pi) that makes cells unable to bind LpL; and 2) an alteration in VLDL binding to endothelial bound LpL. The former has no relationship to proteinuria while the latter occurs as a consequence of proteinuria. These effects combine to suppress VLDL clearance.

Hypoalbuminemia and proteinuria contribute separately to reduced lipoprotein catabolism in the nephrotic syndrome.

BACKGROUND: Hypertriglyceridemia is a result of reduced triglyceride (TG)-rich lipoprotein (TRL) catabolism and occurs in rats with nephrotic syndrome (NS) and in Nagase analbuminemic rats (NARs). While the heparin-releasable lipoprotein lipase (LpL) pool in NAR and in NS is similar, TG levels are significantly greater in NS, suggesting that factors other than reduced LpL alone act in NS but not in NARs. Furthermore, clearance of chylomicrons (CM) and very low-density lipoprotein (VLDL) is normal in vivo in NAR despite low LpL levels. We tested the hypotheses that impaired binding of VLDL and impaired VLDL-high density lipoprotein (HDL) interactions contribute to hyperlipidemia in NS. METHODS: TG and apoB secretion was measured using Triton WR 1339. Clearance of CMs by perfused hearts from NS and NAR was determined. Binding of VLDL from control, NS and NAR to rat aortic endothelial cells (RAECs) was measured prior to and following incubation with HDL from NS, NARs, and control. ApoE, protein, and TG content was determined. RESULTS: TG levels were greatest in NS (516 +/- 95 mg/dL), intermediate in NAR (193 +/- 20), and least in control (97 +/- 16, P = 0.05), while in contrast, TG secretion was least in NS (178 +/- 33 mg/dL/hour) versus 212 +/- 17 in NAR and 294 +/- 15 in control (P < 0.001 vs. NS). Clearance of CMs by NS and NAR hearts was the same and significantly reduced versus control (P < 0.005). Binding of NS-VLDL to endothelial cells was reduced, while NAR-VLDL binding was increased versus control (P < 0.001). Incubation of NS-VLDL with control or NAR HDL increased VLDL binding compared with binding following incubation with NS HDL (P < 0.001). CONCLUSION: Increased TG levels in both NS and NAR are the result of decreased TRL clearance. TG levels are greater in NS because of the presence of a combined defect: (1) a decrease in endothelial-bound LpL that occurs as a consequence of reduced serum albumin concentration, and (2) a defect in VLDL binding to endothelial-bound LpL. This latter defect occurs only in the presence of proteinuria and is conferred by HDL.

Estrogen effects on triglyceride metabolism in analbuminemic rats.

BACKGROUND: Triglyceride (TG) levels are normally lower in female rats, while the opposite is the case in the Nagase analbuminemic rats (NAR). Increased TG levels in normal males are caused by a testosterone-mediated decrease in postheparin (PH) lipoprotein lipase (LpL). Castration of males reduces TG, while castration of females is without effect. TG levels are reduced by castration of the female NAR, suggesting that estrogen rather than testosterone causes hypertriglyceridemia in this strain. The mechanism for this increase is unknown. METHODS: We measured secretion of very-low density lipoprotein (VLDL) TG using Triton WR 1339 clearance as the disappearance from blood of 3H-trioleate and 14C-cholesterol-labeled chylomicrons (CM), and the activity of the PH lipases: LpL and hepatic lipase (HL). All were determined in Sprague-Dawley (SD) and NAR female, male, and ovariectomized (OVX) rats. RESULTS: TG levels were significantly greater in female NAR in comparison to all other groups. Ovariectomy of NAR significantly ameliorated hypertriglyceridemia. VLDL TG secretion was significantly greater in intact female NAR compared with all other groups. There were no other differences in VLDL TG secretion among the other groups. The clearance of CM was greatest in female SD rats, and OVX had no effect. NAR cleared CM less well than did SD rats (P < 0.001), but among NAR, clearance was greatest in OVX NAR and male NAR (P < 0. 002). Both PH LpL activity and HL activity were lowest in female NAR (P < 0.05). Ovariectomy partially corrected the defect in HL (P < 0. 05). CONCLUSION: TG levels in female NAR are in part a result of increased VLDL-TG secretion, an effect mediated by estrogen. The presence of an estrogen-mediated catabolic defect that was alleviated by OVX was also observed. This catabolic defect is likely a result of an estrogen-mediated decrease both in LpL and HL expressed only in the presence of analbuminemia.

Mechanisms of hypoalbuminemia in hemodialysis patients.

Hypoalbuminemia is the most powerful predictor of mortality in end-stage renal disease. Since protein-calorie malnutrition can decrease albumin synthesis it is assumed that hypoalbuminemia results principally from malnutrition in these patients, but albumin synthesis may also be decreased as part of the acute-phase response, and hypoalbuminemia can also result from redistribution of albumin pools or from albumin losses. We measured albumin synthesis, fractional catabolic rate, and distribution from the turnover of [125I] human albumin in six hemodialysis patients with plasma albumin less than 35 mg/ml and in six patients with plasma albumin greater than 40 mg/ml. Patients with liver disease, HIV, or other infection were excluded. Both groups were maintained with high-flux polysulfone dialyzers for more than three months. Kt/Vurea and PCR were measured during each dialysis (N = 12 to 18/patient). A four-day calorie and protein intake was determined by dietary history and long-term nutritional status was determined anthropometrically. Measured variables included serum urea, creatinine, transferrin, and the positive acute-phase proteins alpha 2- macroglobulin, C-reactive protein, ferritin, and IGF-1. Albumin synthesis was significantly reduced in the low albumin group. There were no differences in dietary intake, body composition, PCR, BUN, creatinine, or Kt/Vurea. Plasma albumin concentration correlated negatively with ferritin, C-reactive protein and alpha 2-macroglobulin. Albumin synthesis rate correlated negatively with both alpha 2-macroglobulin and Kt/Vurea. Both plasma albumin concentration and synthesis rate correlated positively with IGF-1, and both were independent of PCR and all other nutrition-related variables.(ABSTRACT TRUNCATED AT 250 WORDS)

Nucleotide Availability in Maize (Zea mays L.) Root Tips (Estimation of Free and Protein-Bound Nucleotides Using 31P-Nuclear Magnetic Resonance and a Novel Protein-Ligand-Binding Assay).

Sequestration of nucleotides in cells through protein binding could influence the availability of nucleotides and free energy for metabolic reactions and, therefore, affect rates of physiological processes. We have estimated the proportion of nucleotides bound to proteins in maize (Zea mays L.) root tips. Binding of nucleoside mono- and diphosphates to total root-tip protein was studied in vitro using high-performance liquid chromatography and a new ligand-binding technique. We estimate that approximately 40% of the ADP, 65% of the GDP, 50% of the AMP, and virtually all the GMP in aerobic cells are bound to proteins. In hypoxic cells, free concentrations of these nucleotides increase proportionately much more than total intracellular concentrations. Little or no binding of CDP, UDP, CMP, and UMP was observed in vitro. Binding of nucleoside triphosphate (NTP) to protein was estimated from in vivo 31P-nuclear magnetic resonance relaxation measurements. In aerobic root tips most (approximately 70%) of the NTP is free, whereas under hypoxia NTP appears predominantly bound to protein. Our results indicate that binding of nucleotides to proteins in plant cells will significantly influence levels of free purine nucleotides available to drive and regulate respiration, protein synthesis, ion transport, and other physiological processes.

Comparison of binding by concentrated peritoneal dialysate and serum.

Major advances in dialysis therapy have occurred over the last decade, yet various abnormalities persist in end-stage renal disease (ESRD) patients. The etiology of these residual defects remains largely unknown. We are currently testing the hypothesis that some of these abnormalities are due to retention of small molecular weight, protein bound toxins, which are poorly dialyzable. We sought an alternative to blood as a source of bound toxins. Spent peritoneal dialysate (PD) was tested as a source. With use of a series of filtration devices, PD albumin content was increased about 35-fold. Evidence of bound ligands was shown by two methods. Salicylate binding by patients' sera and concentrated PD (n = 8) were markedly reduced, unbound salicylate being 14.9 +/- 5.1% (SD) and 15.8 +/- 4.9% at albumin concentrations of 3.30 +/- 1.04 and 3.23 +/- 0.84 g/dl. Serum from eight normal subjects, diluted to 2.95 g/dl albumin, had 7.4 +/- 1.1% unbound salicylate. HPLC analysis of deproteinized concentrated dialysate was compared to ultrafiltrates of the same fluid. Numerous bound peaks were seen, particularly in the late eluting peaks. Spent PD is a rich source of protein bound ligands for further study.