Biomedical subjects

E J Fernandez

Publications and source records attributed to E J Fernandez.

At least 19 recordsLinked to original sources

PubMed2001

Protein unfolding during reversed-phase chromatography: I. Effect of surface properties and duration of adsorption.

Residue-level features of bovine pancreatic trypsin inhibitor (BPTI) unfolding on reversed-phase chromatography (RPC) surfaces were investigated using hydrogen-deuterium exchange labeling and NMR. A set of silica-based RPC surfaces was used to examine the influence of alkyl chain length and media pore size on adsorbed BPTI conformation. In all cases there was substantial unfolding in the adsorbed state; however, residual protection from exchange was consistently observed. Particle pore size did not influence conformation substantially for C4-alkyl modified silica; however, 120 A pore C18 media produced more hydrogen exchange than any other surface examined. In this case, the radius of curvature inside the pore approaches the size of the BPTI molecule. Generally, the pattern of hydrogen exchange protection was uniform; however, the beta-sheet region was selectively protected on the large-pore C18 media. The beta-sheet region forms a hydrophobic core that forms early when BPTI folds in solution. This suggests that partially unfolded states possessing a native-like structure play an important role in adsorption and elution in RPC. Finally, increased contact time with the surface before elution fostered unfolding and altered chromatographic behavior considerably.

Adsorption↗

PubMed2001

Protein unfolding during reversed-phase chromatography: II. Role of salt type and ionic strength.

While reversed-phase chromatography (RPC) may be a powerful method for purification of proteins at the analytical scale, both preparative and analytical applications have been hindered by the complex chromatographic behavior of proteins compared to small molecules. Further, preparative applications have been limited because of poor yields caused by the denaturing conditions involved. One means for modulating both the stability and chromatographic behavior of proteins is through the use of added salt. In this investigation, we show how salt type and ionic strength affect protein conformation on RPC surfaces. Exposure of amide groups of adsorbed BPTI was monitored using nuclear magnetic resonance (NMR) spectroscopy and hydrogen-deuterium isotope exchange. Sodium chloride, sodium acetate, and ammonium sulfate were studied at ionic strengths up to I = 0.375, with adsorption hold times being 5 min and 2 h. We found that increasing ionic strength decreased exposure of the exchange reporter groups in essentially all cases. However, even at the same ionic strength the level and distribution of residue protection varied with salt type and hold time. NaCl does not protect certain reporter groups at all, while those that it does protect to some degree at short hold times can exchange slightly more at longer times. The pattern and level of protection for NaAc at short times is similar to that for NaCl, but at longer times more uniform protection is seen as the reporter groups completely exposed at short times become more protected. For (NH(4))(2)SO(4) the pattern of protection at short hold time is similar to those of the other salts, although it protects all groups much more. This would be expected from the Hofmeister series. However, at longer times the level of protection with (NH(4))(2)SO(4) decreases below that of the other salts, while it uniquely protects all groups to nearly the same level. Such subtle variations in the protein structure would not have been detected without the measurements and analysis used here. Chromatographic retention times and peak shapes were obtained for the above systems. Variations of behavior were seen that could not be correlated with any of the above protection patterns and levels or even with heuristics such as the Hofmeister series. This suggests further conformational changes upon elution may be critical to the retention process. However, an excellent correlation was found between peak width at half-height and the average degree of unfolding, as indicated by the average level of isotopic exchange. Thus, while further studies are needed to definitively determine the connection between protein unfolding and retention, use of this correlation may improve designing and screening for chromatographic conditions that minimize protein unfolding.

Adsorption↗

PubMed2001

Structural studies of chemokines that inhibit HIV-1 entry.

The chemokine receptors CCR5 and CXCR4 have emerged as essential mediators of HIV-1 pathophysiology, functioning as co-receptors for viral entry into cells. The physiological agonists of these receptors inhibit HIV-1 infection in vitro. The discovery of small molecules that disrupt the interactions between HIV-1 and chemokine receptors is one strategy to limit the spread of the virus. These compounds will complement already existing therapies that include HIV-1 reverse transcriptase and protease inhibitors. The complete structural elucidation of a chemokine ligand-receptor complex would be valuable for rational drug design, but has yet to be achieved. Structural studies of chemokine agonists and antagonists can also be useful in understanding interactions that may be important for drug optimization. This review examines the surface properties of the chemokine ligands human SDF-1alpha and HHV-8 vMIP-II, with a goal of determining receptor-interacting sites. In combination with site-directed mutagenesis of the chemokines and structure-activity relationships of chemokine-based peptides, this approach will lead to a better understanding of the interactions in the chemokine ligand-receptor system.

Chemokines↗

PubMed2000

Comparison of the structure of vMIP-II with eotaxin-1, RANTES, and MCP-3 suggests a unique mechanism for CCR3 activation.

Herpesvirus-8 macrophage inflammatory protein-II (vMIP-II) binds a uniquely wide spectrum of chemokine receptors. We report the X-ray structure of vMIP-II determined to 2.1 A resolution. Like RANTES, vMIP-II crystallizes as a dimer and displays the conventional chemokine tertiary fold. We have compared the surface topology and electrostatic potential of vMIP-II to those of eotaxin-1, RANTES, and MCP-3, three CCR3 physiological agonists with known three-dimensional structures. Surface epitopes identified on RANTES to be involved in binding to CCR3 are mimicked on the eotaxin-1 and MCP-3 surface. However, the surface topology of vMIP-II in these regions is markedly different. The results presented here indicate that the structural basis for interaction with the chemokine receptor CCR3 by vMIP-II is different from that for the physiological agonists eotaxin-1, RANTES, and MCP-3. These differences on vMIP-II may be a consequence of its broad-range receptor recognition capabilities.

Amino Acid Sequence↗

PubMed2000

Inhibition of human platelet aggregation by gangliosides.

The content and composition of gangliosides is modified upon platelet stimulation, suggesting that these lipids may play functional roles in platelet physiology. Therefore, the effect of exogenously added gangliosides on human platelet aggregation was evaluated. The pretreatment of platelets with a mixture of total gangliosides from bovine brain and a series of purified mono-, di- and tri-sialogangliosides partially inhibit the collagen-induced aggregation process and ATP release and completely block the generation of the second aggregation wave when ADP is used as agonist. The inhibition was exerted at around 100 microM by G(TOT) as well as purified G(M1), G(M3), G(D1a), and G(T1b) gangliosides, whereas asialoG(M1) and sulphatide did not show a significant influence on platelet aggregation. Thrombin, Ca(2+) ionophores (A23187 and Ionomycin), arachidonic acid, and U46619 were unable to bypass the inhibitory effect exerted by gangliosides, suggesting that gangliosides inhibit platelet aggregation by inhibiting the synthesis or action of prostaglandins. Gangliosides inhibited U46619-induced aggregation, thus suggesting that they block the action of thromboxane A(2). Epinephrine induces a partial aggregation on gangliosides-treated platelets, similar to fluoroaluminate and phorbol myristate acetate, indicating that these platelets are still functional. To summarize, these results indicate that the major pathway(s), but not all, driving to the aggregation process following the interaction of ligand-receptor may be blocked by pretreatment of human platelets with gangliosides.

15-Hydroxy-11 alpha,9 alpha-(epoxymethano)prosta-5↗

PubMed2000

Crystal structure of Lysbeta(1)82-Lysbeta(2)82 crosslinked hemoglobin: a possible allosteric intermediate.

The crystal structure of human hemoglobin crosslinked between the Lysbeta82 residues has been determined at 2.30 A resolution. The crosslinking reaction was performed under oxy conditions using bis(3, 5-dibromosalicyl) fumarate; the modified hemoglobin has increased oxygen affinity and lacks cooperativity. Since the crystallization occurred under deoxy conditions, the resulting structure displays conformational characteristics of both the (oxy) R and the (deoxy) T-states. beta82XLHbA does not fully reach its T-state conformation due to the presence of the crosslink. The R-state-like characteristics of deoxy beta82XLHbA include the position of the distal Hisbeta63 (E7) residue, indicating a possible reason for the high oxygen affinity of this derivative. Other areas of the molecule, particularly those thought to be important in the allosteric transition, such as Tyrbeta145 (HC2) and the switch region involving Proalpha(1)44 (CD2), Thralpha(1)41 (C6) and Hisbeta(2)97 (FG4), are in intermediate positions between the R and T-states. Thus, the structure may represent a stabilized intermediate in the allosteric transition of hemoglobin.

Allosteric Regulation↗

PubMed1999

Distribution of lupus anticoagulant and anticardiolipin antibody isotypes in a population with antiphospholipid syndrome.

OBJECTIVE: To analyze the distribution of lupus anticoagulant (LAC) and anticardiolipin antibody (aCL) isotypes in a population with antiphospholipid syndrome and to explore whether there is an association with the site of thrombotic episodes and the number of recurrent spontaneous abortions. METHODS: Ninety-two patients (73 female, 19 male) with positive LAC and/or aCL were included as 2 groups: (1) 20 patients with secondary antiphospholipid syndrome (APS) (16 had thrombotic episodes and 4 thrombocytopenia); (2) 72 patients with primary APS (31 presented thrombotic episodes and 41 had recurrent spontaneous abortion). RESULTS: In Group 1 seven of 20 (35%) patients with secondary APS had IgG aCL, 9 (45%) had both IgG/IgM aCL, and 2 (10%) had IgM aCL; the remaining patients had combinations of aCL isotypes. In Group 2 patients with primary APS, IgG aCL was positive in 41%, IgG/IgM mixture in 21%, and 15% of patients had combinations of the 3 isotypes. Sixteen of 20 (80%) patients with secondary disease and 37 of 72 (51%) with primary disease tested positive for LAC. CONCLUSION: The presence of one or any mixture of isotype of aCL with or without LAC is not associated with the site of thrombosis (venous or arterial). On the contrary, in the patients with primary APS, the presence of the 3 aCL isotypes plus LAC was associated with a higher number of recurrent spontaneous abortions compared to other possible combinations of aCL isotypes.

Abortion, Spontaneous↗

PubMed1998

Probing residue-level unfolding during lysozyme precipitation.

We have employed nuclear magnetic resonance (NMR) measurements of hydrogen exchange to identify residue-level conformational changes in hen egg white lysozyme (HEWL) as induced by salt precipitation. Deuterated HEWL was dissolved into a phosphate (H2O) buffer and precipitated at pH 2.1 upon addition of solid KSCN or (ND4)2SO4, allowing isotope labeling of unfolded regions. After 1 h, each precipitate was then dissolved at pH 3.8 to initiate refolding and preserve labeling and subsequently purified for NMR analysis. HEWL precipitated by 1.0 M KSCN exhibited increased hydrogen exchange at 14 residues out of 42 normally well-protected in the native state. Of the affected residues, 9 were situated in the beta-sheet/loop domain. A similar, though less extensive, effect was observed at 0.2 M KSCN. Precipitation by 1.2 M (ND4)2SO4 resulted in none of the changes detected with KSCN. The popularity of ammonium sulfate as a precipitant is thus supported by this observed preservation of structural integrity. KSCN, in comparison, produced partial unfolding of specific regions in HEWL due most likely to known preferential interactions between -SCN and proteins. The severity of unfolding increased with KSCN concentration such that, at 1.0 M KSCN, almost the entire beta-sheet/loop domain of HEWL was disrupted. Even so, a portion of the HEWL core encompassed by three alpha-helices remained intact, possibly facilitating precipitate dissolution.

Animals↗

PubMed1998

Crystal structure of chemically synthesized [N33A] stromal cell-derived factor 1alpha, a potent ligand for the HIV-1 "fusin" coreceptor.

Stromal cell-derived factor-1alpha (SDF-1alpha ) is a member of the chemokine superfamily and functions as a growth factor and chemoattractant through activation of CXCR4/LESTR/Fusin, a G protein-coupled receptor. This receptor also functions as a coreceptor for T-tropic syncytium-inducing strains of HIV-1. SDF-1alpha antagonizes infectivity of these strains by competing with gp120 for binding to the receptor. The crystal structure of a variant SDF-1alpha ([N33A]SDF-1alpha ) prepared by total chemical synthesis has been refined to 2.2-A resolution. Although SDF-1alpha adopts a typical chemokine beta-beta-beta-alpha topology, the packing of the alpha-helix against the beta-sheet is strikingly different. Comparison of SDF-1alpha with other chemokine structures confirms the hypothesis that SDF-1alpha may be either an ancestral protein from which all other chemokines evolved or the chemokine that is the least divergent from a primordial chemokine. The structure of SDF-1alpha reveals a positively charged surface ideal for binding to the negatively charged extracellular loops of the CXCR4 HIV-1 coreceptor. This ionic complementarity is likely to promote the interaction of the mobile N-terminal segment of SDF-1alpha with interhelical sites of the receptor, resulting in a biological response.

Binding Sites↗

PubMed1998

Effect of extracellular glutamine concentration on primary and secondary metabolism of a murine hybridoma: an in vivo 13C nuclear magnetic resonance study.

The effect of changes in extracellular glutamine level on metabolism of a murine hybridoma was examined with in vivo nuclear magnetic resonance (NMR) spectroscopy. Cells were cultured in a hollow-fiber bioreactor at high cell density to allow intracellular metabolite levels to be determined on a metabolically relevant time scale. Steady infusions of [1-13C] glucose were used to label glycolytic and tricarboxylic acid cycle intermediates, which permitted continuous monitoring with NMR spectroscopy during changes in environmental glutamine level. Samples of the extracellular medium were also analyzed to determine the effect of glutamine on other metabolites associated with primary and secondary metabolism. The changes in glutamine concentration had several effects on primary and secondary metabolism, depending on the rate the changes were made. For a brief reduction in feed glutamine concentration from 4 to 0 mM (which produced a rapid change from 0.67 to approximately 0 mM in residual glutamine), large changes were observed in the rate of consumption of metabolites normally associated with energy production. Antibody synthesis was strongly stimulated and nitrogen metabolism was significantly altered. For a more prolonged reduction from 2.4 to 1.2 mM (which produced a slower reduction from 0.30 to 0. 08 mM in residual glutamine), much smaller changes were observed even though the concentration of glutamine at the reduced feed level was very low. Energy metabolism did not appear to be limited by glutamine at 0.08 mM, which suggests that significant futile cycling may occur in energy producing pathways when excess glucose and glutamine are available. However, this concentration of extracellular glutamine appeared to affect some anabolic pathways, which require amino groups from glutamine.

Animals↗

PubMed1997

In situ analysis of protein chromatography and column efficiency using magnetic resonance imaging.

Magnetic resonance imaging has been used to visualize size-based protein separations inside operating chromatography columns. The effects of flow nonuniformity have been observed and analyzed quantitatively through concentration profiles of tracers measured inside the column. Analysis of these profiles provides local and averaged intracolumn plate height values for characterization of dispersion and flow nonuniformity. The magnetic resonance measurements compare favorably with conventional chromatographic measurements of column efficiency and provide more detailed insights into nonideal column performance.

Animals↗

PubMed1997

Histological and 1H magnetic resonance spectroscopic imaging analysis of quinolinic acid-induced damage to the rat striatum.

NAA has been described as a neuron-specific compound. NAA levels as determined by magnetic resonance spectroscopic imaging (MRSI) have been used to determine degree of neuronal loss in several neurological diseases, but there has been limited work to document the accuracy and reliability of this technique. This study addresses this question quantitatively with histological analysis of cell viability and tissue shrinkage in quinolinic acid (QA)-induced damage of the rat striatum compared with 1H MRSI measurement of N-acetyl aspartate (NAA) as a noninvasive measure of neuronal loss. Both 1H MRSI and histology detect damage to the lesioned striatum; however, there are differences in the degree of damage as assessed by the two methods. Although partial-volume effects and tissue shrinkage may decrease the sensitivity of MR to such damage, the sparing of axons by QA may be another important factor in the differences in assessment. These results indicate that further studies of NAA metabolism and its distribution within neurons are warranted.

Animals↗

PubMed1997

Effects of severe global ischemia on N-acetylaspartate and other metabolites in the rat brain.

N-acetylaspartate (NAA) is found exclusively in neurons and their processes in the adult brain. Since the regional distribution of NAA may be imaged using magnetic resonance spectroscopic imaging (1H-MRSI), a regional measure of neuronal density may be noninvasively obtained. The technique may be particularly useful in the diagnosis of diseases where neurons are selectively injured, since these diseases do not result in definitive changes on conventional imaging studies. The goal of this study was to determine whether 1H-MRSI measurement of NAA defects neuronal loss following global ischemia. 1H-MRSI was performed in rats 24 h after global ischemia was induced by bilateral carotid occlusion plus hypotension. 1-H-MRSI showed that NAA was decreased by 28-74% in vulnerable regions, including the cortex, striatum, hippocampus, and, to a lesser extent, the thalamus. No change was observed in the brain stem or cerebellum. Regions where 1H-MRSI observed NAA was decreased also had histological evidence of selective neuronal necrosis and showed marked increase of lactate and alanine. These results show that 1H-MRSI detected loss of NAA in brain regions with selective neuronal loss, suggesting that 1H-MRSI measurements of NAA could detect neuronal loss in a variety of disease states where there is selective neuronal necrosis.

Alanine↗

PubMed1997

Modeling NMR lineshapes using logspline density functions.

Distortions in the FID and spin echo due to magnetic field inhomogeneity are proved to have a representation as the characteristic function of some probability distribution. In the special case that the distribution is Cauchy, the model reduces to the conventional Lorentzian model. A more general and flexible representation is presented using the Fourier transform of a logspline density. An algorithm for fitting the model is described, the performance of the model and algorithm is investigated in applications to real and simulated data sets, and the logspline approach is compared to a previous Hermitian spline approach and to the Lorentzian model. The logspline model is more parsimonious than the Hermitian spline model, provides a better fit to real data, and is much less biased than the Lorentzian model.

Algorithms↗

PubMed1997

Three dimensional outer volume suppression for short echo time in vivo 1H spectroscopic imaging in rat brain.

Three-dimensional in vivo spectroscopic imaging in rat brain requires additional localization to reduce the effects of lipid contamination. Outer volume suppression has been shown to be effective in two dimensions. We have extended this approach to three dimensions with additional outer volume suppression conforming to the shape of the rat brain. The technique suppresses the pericranial lipid effectively, allowing sampling of volumes close to the skull and effective localized shimming. These benefits permit three-dimensional 1H magnetic resonance spectroscopic imaging to be performed over most of the brain at shorter echo times, providing spectra more amenable to quantitative analysis.

Animals↗

PubMed1996

Mapping of lactate and N-acetyl-L-aspartate predicts infarction during acute focal ischemia: in vivo 1H magnetic resonance spectroscopy in rats.

The time course, anatomic distribution, and extent of changes in cerebral lactate, N-acetyl-L-aspartate (NAA), and other metabolite levels determined by three-dimensional in vivo 1H magnetic resonance spectroscopy and single-voxel spectral analysis after middle cerebral artery occlusion in rats. Increased lactate was detected in the central ischemic region within 1.3 hours after the onset of permanent occlusion (n = 22) or 0.5 hour after the onset of 1 hour of temporary occlusion and then reperfusion (n = 8). Permanent occlusion resulted in persistent lactate elevation and a 25.4 +/- 4.1% reduction in the NAA peak after 1.3 hours; NAA was almost completely depleted after 24 hours. Results also demonstrated delayed depletion of all other magnetic resonance spectroscopy-visible 1H metabolites, including creatine, choline, and glutamate, after permanent occlusion. After 1 hour of temporary focal ischemia, lactate returned to nearly normal levels within 0.4 hour after the onset of reperfusion; at 72 hours, a recurrent increase in lactate and a new decrease in NAA were observed, suggesting delayed tissue injury. Histological analysis, performed in 10 rats, demonstrated infarcts that corresponded in distribution to regions of NAA depletion at 72 hours. These findings indicate that lactate elevation is a sensitive early marker of ischemia; however, temporary recovery of lactate accumulation after reperfusion did not predict sustained metabolic recovery. In contrast, NAA depletion within 1.3 hours after the onset of ischemia identified central ischemic regions that were destined for infarction. Potential clinical applications include selection and monitoring of therapeutic intervention, as well as prediction of outcome, in patients with acute stroke.

Animals↗

PubMed1994

31P NMR investigation of energy metabolism in perifused MMQ cells.

The MMQ cell line is a unique prolactin-secreting rat pituitary cell line. MMQ cells entrapped in agarose gel threads are metabolically active, as determined by the uptake and phosphorylation of creatine and the maintenance of high energy phosphates for over 15 h. Forskolin activates the catalytic subunit of adenylyl cyclase and, in MMQ cells, elevates the level of cAMP and stimulates prolactin secretion. 31P NMR spectroscopy was used to investigate the energy metabolism of the MMQ cells during stimulation by forskolin. The ability to measure small changes in the energy status of these cells was enhanced by increasing the PCr levels in the cells. Administration of forskolin to the perifused MMQ cells resulted in acute, reversible, and dose-dependent changes in the 31P NMR spectra of the cells within 12 to 24 min of the beginning of forskolin exposure. Several lines of evidence indicate that the changes observed in the MMQ cells are the composite result of the interaction of forskolin with adenylyl cyclase and the plasma membrane glucose transporter. Also, preincubation of the MMQ cells with the dopamine agonist, bromocriptine, attenuates the forskolin-stimulated decrease in the PCr resonance by approximately 50%. This attenuation indicates that the forskolin-stimulated changes in energy metabolism are probably related to the prolactin secretion process.

Adenylyl Cyclases↗

PubMed1994

Detection of Streptococcus mutans by PCR amplification of spaP gene.

Synthetic oligonucleotide primers were used in the polymerase chain reaction (PCR) to amplify a sequence of the spaP gene, which encodes the surface protein antigen I/II of Streptococcus mutans. A DNA fragment of c. 192 bp was amplified from lysed S. mutans cells or isolated DNA. With S. mutans cells, the lower limit of detection was 4-40 cfu. With these primers, 13 reference and 50 clinical strains of S. mutans were identified. Amplification of the 192-bp product was not demonstrated when 41 strains of other streptococcal and non-streptococcal species were tested. The spaP gene PCR has potential for the rapid diagnosis of S. mutans infections.

Adult↗