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J L Markley

Publications and source records attributed to J L Markley.

At least 145 records · Page 8Linked to original sources

NMR assignments of the four histidines of staphylococcal nuclease in native and denatured states.

NMR signals from all four histidine ring C epsilon protons and three of the four histidine C delta protons in the protein staphylococcal nuclease have been assigned by comparing spectra of the wild-type (Foggi strain) protein to spectra of three variants that each lack a different histidine residue. All proteins studied were cloned and overproduced in Escherichia coli. The NMR spectra of the three mutant proteins (H8R, H46Y, and H124L) used to make these assignments were similar to one another and to those of the wild type, except for signals from the mutated residues. The pKa values of those histidines conserved between the wild type and the mutants remained essentially unchanged. Multiple histidine C epsilon proton resonances due to non-native forms of nuclease were observed in both thermally induced and acid-induced unfolding. Residue-specific assignments of H epsilon protons in the thermally denatured forms of the mutant H46Y were obtained from connectivities to the native state by saturation transfer.

Escherichia coli↗

Flavodoxin from Anabaena 7120: uniform nitrogen-15 enrichment and hydrogen-1, nitrogen-15, and phosphorus-31 NMR investigations of the flavin mononucleotide binding site in the reduced and oxidized states.

Interactions between flavin mononucleotide (FMN) and apoprotein have been investigated in the reduced and oxidized states of the flavodoxin isolated from Anabaena 7120 (Mr approximately 21,000). 1H, 15N, and 31P NMR have been used to characterize the FMN-protein interactions in both redox states. These are compared with those seen in other flavodoxins. Uniformly enriched [15N]flavodoxin (greater than 95% isotopic purity) was isolated from Anabaena 7120 grown on K15NO3 as the sole nitrogen source. 15N insensitive nucleus enhanced by polarization transfer (INEPT) and nuclear Overhauser effect (NOE) studies of this sample provided information regarding protein structure and dynamics. A 1H-detected 15N experiment allowed the correlation of nitrogen resonances to those of their attached protons. Over 90% of the expected N-H cross peaks could be resolved in this experiment.

Binding Sites↗

Water is allocated differently to chloroplasts in sun and shade leaves.

Hydrogen-1 nuclear magnetic resonance spectroscopy was used to study water allocation in cell compartments of sun and shade leaves. NMR spectra of Acer platanoides were resolved into two peaks that were assigned to chloroplast and nonchloroplast water. Sun leaves contained 1.7 times more water per unit area of surface than shade leaves, and the water was allocated differently. Chloroplasts in sun leaves contained 17% of the total leaf water versus 47% in shade leaves. Comparing equal leaf surface areas, the chloroplasts in shade leaves contained 60% more water than those in sun leaves.

Journal Article↗

The solution conformation of sucrose: concentration and temperature dependence.

13C-N.m.r. spin-lattice relaxation measurements were used to study molecular motion in aqueous sucrose. Results show that sucrose tumbles anisotropically in solution, and that its conformation is independent of temperature and concentration. Internal rotation occurs with distinctly different rates and activation energies in the three hydroxymethyl groups. Our data are consistent with results of calculations by Bock and Lemieux who predicted that the conformation of aqueous sucrose is similar to the crystal conformation but with the loss of one intramolecular hydrogen-bond.

Carbohydrate Conformation↗

Observation of the terminal methyl group in fatty acids of the linolenic series by a new 1H NMR pulse sequence providing spectral editing and solvent suppression. Application to excised frog muscle and rat brain.

A new 1H NMR pulse sequence is described that combines water suppression with the selective observation of signals from coupled spin systems. The pulse sequence is easy to set up and compensates for pulse width inhomogeneity in the biological sample. Suppression of the water signal is achieved by pulses that return the water spins to their equilibrium position; spectral editing is based on the J modulation present in spin-echo spectra and its inhibition by coherent decoupling at one of the resonances of the spin system of interest. The pulse sequence, which was designed for 1H NMR spectroscopy of tissue, was tested at 470 MHz on excised frog muscle and rat brain. The lactate methyl resonance of caffeine-treated frog sartorius muscle was observed selectively by irradiation at the position of its alcoholic proton. The terminal methyl signal of linolenic acid, along with other fatty acids of the linolenic series (first double bond in the omega-3 position), was observed selectively by irradiation at the position of its omega-1 methylene group. 1H NMR spectra of rat brain were edited to reveal the terminal methyl of either linolenic series or all other fatty acids. The results suggest that the terminal methyl groups of fatty acids of the linolenic series (mostly docosahexaenoic acid, 22:6) have higher mobility than those of all other fatty acids.

Animals↗

Hydrogen-1 nuclear magnetic resonance investigation of Clostridium pasteurianum rubredoxin: previously unobserved signals.

Previously unobserved signals were located in the 470-MHz 1H NMR spectra of oxidized and reduced rubredoxin (Rd) from Clostridium pasteurianum. When the protein was oxidized, some of the resonances broadened beyond detection. Longitudinal relaxation (T1) measurements identified a number of these peaks as arising from residues close to the paramagnetic iron; these resonances exhibited short T1 values attributable to the dominant electron-nuclear dipolar relaxation mechanism. The chemical shifts of these peaks were not strongly dependent on the oxidation state of the protein, although relative ratios of line widths of several peaks in the spectra of oxidized and reduced Rd suggested localized conformational changes of the protein as a result of oxidation. Furthermore, spectra of the oxidized protein collected in the range 8-60 degrees C revealed no appreciable changes in the chemical shifts of these peaks with temperature. These results seem to point out a negligible dipolar contribution, due to either magnetic anisotropy or zero field splitting, to the observed shifts in the spectrum of oxidized Rd. Resonances were assigned to tyrosine-11 or phenylalanine-49 (but not to either specifically) on the basis of their T1 values and the X-ray diffraction data of the protein molecule [Watenpaugh, K. D., Sieker, L. C., Herriott, J. R., & Jensen, L. H. (1973) Acta Crystallogr., Sect. B: Struct. Crystallogr. Cryst. Chem. B29, 943-956; and a further refinement deposited with the Protein Data Bank]. An upfield-shifted peak at about -1.1 ppm in the spectra of both oxidized and reduced Rd was assigned to a methyl group.(ABSTRACT TRUNCATED AT 250 WORDS)

Clostridium↗

Hydrogen-1 nuclear magnetic resonance investigation of high-potential iron-sulfur proteins from Ectothiorhodospira halophila and Ectothiorhodospira vacuolata: a comparative study of hyperfine-shifted resonances.

Proton NMR spectra of the oxidized and reduced forms of high-potential iron-sulfur proteins (HiPIPs) were recorded at 200 MHz. The proteins studied were the HiPIPs I and II from Ectothiorhodospira halophila and Ectothiorhodospira vacuolata. Hyperfine-shifted peaks in spectra of the oxidized proteins were assigned to some of the protons of the cysteinyl ligands and aromatic residues at the active site on the basis of their chemical shifts, longitudinal relaxation times, and temperature-dependent behavior. The cysteinyl C beta-H protons were found to resonate downfield (about 100 ppm) and the C alpha-H protons upfield (about-25 ppm). This hyperfine shift pattern is consistent with the observed isotropic shift being contact in origin; it probably results from a pi-spin-transfer mechanism. The large magnitudes of the chemical shifts of peaks assigned to aromatic residues suggest that these residues interact with the iron-sulfur cluster via pi-pi overlap. Some of the hyperfine-shifted peaks observed in water were found to disappear in 2H2O solution. Such resonances probably arise from exchange-labile hydrogens of amino acid residues directly hydrogen bonded to the iron-sulfur cluster. In the case of HiPIPs I and II from E. vacuolata, whose spectra are similar except for the number of such peaks, the relative number of hydrogen bonds inferred to be present in the oxidized and reduced proteins qualitatively explains the difference between their midpoint redox potentials. On the other hand, for E. halophila HiPIPs I and II, consideration of the inferred number of hydrogen bonds alone fails to predict the sign of the difference between their midpoint redox potentials.(ABSTRACT TRUNCATED AT 250 WORDS)

Iron-Sulfur Proteins↗

One- and two-dimensional NMR spectral analysis of the consequences of single amino acid replacements in proteins.

The traditional approach of using homologous sequences to elucidate the role of specific amino acid residues in protein structure and function becomes more meaningful as the number of differences is minimized, with the limit being alteration of a single residue. For small proteins in solution, NMR spectroscopy offers a means of obtaining detailed information about each residue and its response to a given change in the protein sequence. Extraction of this information has been aided by recent progress in spectrometer technology (higher magnetic fields, more sensitive signal detection, more sophisticated computers) and experimental strategies (new NMR pulse sequences including multiple-quantum and two-dimensional NMR methods). The set of avian ovomucoid third domains, which consists of the third domain proper plus a short leader (connecting peptide) and has a maximum of 56 amino acid residues, offers an attractive system for developing experimental methods for investigating sequence-structure and structure-function relationships in proteins. Our NMR results provide examples of sequence effects on pKa' values, average conformation, and internal motion of amino acid side chains.

Amino Acid Sequence↗

Turnip yellow mosaic virus and its capsid have thermal stabilities with opposite pH dependence: studies by differential scanning calorimetry and 31P nuclear magnetic resonance spectroscopy.

In the differential scanning calorimetry (DSC) scans of turnip yellow mosaic virus (TYMV) or its capsid a single endotherm was observed. The endotherm was attributed to disruption of the virion or capsid structure with accompanying protein denaturation. At pH 4.5 the thermal stabilities of the TYMV virion and capsid were similar. With increasing pH, the capsid stability increased while the virion stability decreased. At neutral pH the capsid disrupted at 83.5 degrees, and the virion disrupted at 69 degrees. Our results suggest that packaging of viral RNA in the TYMV capsid imparts instability. The pHmid for disruption of the TYMV capsid is 5.7, which is in the pKa range expected for histidine side chains. Hence repulsive interactions involving one or more of the three histidines of the TYMV coat protein may explain the decreased stability of the TYMV capsid at low pH. This conclusion is supported further by the observation that belladonna mottle virus (BDMV) capsid (BDMV and TYMV belong to the tymo virus group), which contains no histidine in its coat protein, did not exhibit pH-dependent stability. The size of the cooperative unit in the disruption of TYMV capsid was estimated to be approximately that of a dimer of the coat protein, at pH 7.0, but a larger oligomer at low pH. Several reports implicate pH-dependent protein-RNA interactions with a pHmid near 7 as important in stabilizing tymovirus virions. Both DSC and 31P nuclear magnetic resonance linewidth analyses of the TYMV virion showed a transition midpoint at pH 7.0.

Calorimetry, Differential Scanning↗

Thermal stability of cowpea mosaic virus components: differential scanning calorimetry studies.

Differential scanning calorimetry studies show that the thermal stability of cowpea mosaic virus (CPMV) is pH dependent in the pH range 5 to 8. The four different components of CPMV, top (protein shell devoid of RNA), middle (virus particle containing the smaller RNA), bottom upper and bottom lower (virus particle containing the larger RNA), are stable up to 64-70 degrees at pH 5.0 and up to 43-46 degrees at pH 8.25. These components did not exhibit any difference in their thermal stability between pH 6.0 and 8.0.

Calorimetry, Differential Scanning↗

Active-site serine phosphate and histidine residues of phosphoglucomutase: pH titration studies monitored by 1H and 31P NMR spectroscopy.

1H and 31P NMR pH titrations were conducted to monitor changes in the environment and protonation state of the histidine residues and phosphoserine group of rabbit muscle phosphoglucomutase on binding of metal ions at the activating site and of substrate (glucose phosphate) at the catalytic site. Imidazole C epsilon-H signals from 8 of the 10 histidines present in the free enzyme were observed in 1H NMR spectra obtained by a spin-echo pulse sequence at 470 MHz; their pH (uncorrected pH meter reading of a 2H2O solution measured with a glass electrode standardized with H2O buffer) titration properties (in 99% 2H2O) were determined. Three of these histidine residues, which have pKa values ranging from 6.5 to 7.9, exhibited an atypical pH-dependent perturbation of their chemical shifts with a pHmid of 5.8 and a Hill coefficient of about 2. Since none of the observed histidines has a pKa near 5.8, it appears that these three histidines interact with a cluster consisting of two or more groups which become protonated cooperatively at this pH. Binding of Cd2+ at the activating site of the enzyme abolishes the pH-dependent transition of these histidines; hence, the putative anion cluster may constitute the metal ion binding site, or part of it. Two separate 31P NMR peaks from phosphoserine-116 of the phosphoenzyme were observed between pH 6 and 9. Apparently, the metal-free enzyme exists as a pH-dependent mixture of conformers that provide two different environments, I and II, for the enzymic phosphate group; the transition of the phosphate group between these two environments is slow on the NMR time scale.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗

Location and mobility of ubiquinones of different chain lengths in artificial membrane vesicles.

Ubiquinone (UQn with n = 2, 3, or 10 isoprenoid groups) was incorporated into small, sonicated vesicles made of dipalmitoylphosphatidylcholine (DPPC) or dimyristoylphosphatidylcholine (DMPC). (1) The accessibility of oxidized UQ in DPPC or DMPC vesicles to the reductant sodium borohydride (NaBH4), measured by UV spectroscopy, was UQ2 greater than UQ3 greater than UQ10 (DPPC) and UQ2 greater than UQ3 approximately UQ10 (DMPC). (2) Catalysis of the reduction of entrapped ferricyanide by exogenous NaBH4 was more effective with UQ2 than UQ10 but was slower with all quinones than reduction by added dithionite. (3) The methoxy protons of UQ2 and UQ3 in DPPC and DMPC vesicles exhibited a single NMR resonance centered at approximately 3.95 ppm, whereas the methoxy groups of UQ10 gave rise to two separate proton resonances, at 3.93 ppm and a more narrow resonance at 3.78 ppm. The UQ10 population characterized by the 3.78 ppm resonance was present at a higher concentration in DPPC than in DMPC vesicles and was relatively insensitive to reduction by NaBH4. (4) UQ10 perturbed the melting temperature (Tm) of DPPC vesicles to a smaller extent (delta Tm = -1 degrees C) than did UQ2 and UQ3 (delta Tm = -3 to -4 degrees C). The combined UV and NMR data imply the following: The UQ10 pool characterized by the 3.78 ppm peak corresponds to a more mobile UQ10 fraction that is not reduced by NaBH4 in 2-3 min and is thought to be localized close to the center of the DPPC bilayer since it has little effect on the DPPC Tm.(ABSTRACT TRUNCATED AT 250 WORDS)

Dimyristoylphosphatidylcholine↗

Multinuclear magnetic resonance studies of metal ion binding sites of phosphoglucomutase.

Metal binding at the activating site of rabbit muscle phosphoglucomutase has been studied by 31P, 7Li, and 113Cd NMR spectroscopy. A 7Li NMR signal of the binary Li+ complex of the phosphoenzyme was not observed probably because of rapid transverse relaxation of the bound ion due to chemical exchange with free Li+. The phosphoenzyme-Li+-glucose 6-phosphate ternary complex is more stable, kinetically, and yields a well-resolved peak from bound Li+ at -0.24 ppm from LiCl with a line width of 5 Hz and a T1 relaxation time of 0.51 +/- 0.07 s at 78 MHz. When glucose 1-phosphate was bound, instead, the chemical shift of bound 7Li+ was -0.13 ppm; and in the Li+ complex of the dephosphoenzyme and glucose bisphosphate a partially broadened 7Li+ peak appeared at -0.08 ppm. Thus, the bound metal ion has a somewhat different environment in each of these three ternary complexes. The 113Cd NMR signal of the binary Cd2+ complex of the phosphoenzyme appears at 22 ppm relative to Cd(ClO4)2 with a line width of 20 Hz at 44.4 MHz. Binding of substrate and formation of the Cd2+ complex of the dephosphoenzyme and glucose bisphosphate broaden the 113Cd NMR signal to 70 Hz and shift it to 75 ppm. The 53 ppm downfield shift upon the addition of substrate along with 1H NMR data suggests that one oxygen ligand to Cd2+ in the binary complex is replaced by a nitrogen ligand at some intermediate point in the enzymic reaction.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗

Water permeability of chloroplast envelope membranes. In vivo measurement by saturation-transfer NMR.

In tulip tree (Liriodendron tulipifera) leaves, the proton NMR signal from chloroplast water is resolved from that of water in other leaf compartments. We used the saturation-transfer NMR method to measure the mean water molecule residence time within a chloroplast, (88 +/- 17) ms at 20 degrees C. From the measured chloroplast dimensions, we calculate an effective permeability coefficient of (9 +/- 2) X 10(-4) cm/s for the chloroplast envelope membrane. This is the first in vivo measurement of chloroplast water permeability.

Cell Membrane↗

1H, 13C, and 31P nuclear magnetic resonance studies of cowpea mosaic virus: detection and exchange of polyamines and dynamics of the RNA.

1H and 13C NMR studies on cowpea mosaic virus (CpMV) revealed that polyamines are present in the middle (M) and upper bottom (BU) components obtained by CsCl density gradient centrifugation but not in the top (T) component; the lower bottom (BL) component contains trace amounts of polyamine. Dialysis of the BL component against spermidine led to incorporation of spermidine which gave rise to NMR peaks very similar to those observed with the natural M and BU components. NMR results conclusively demonstrate that polyamines in the M and BU components of CpMV are exchangeable with cesium ions and the exchange process is pH dependent. They also provide experimental support for the hypothesis that the BU to BL conversion results from the displacement of polyamines and possibly other natural counter ions of the RNA by cesium ions [G. Bruening, (1977), In "Comprehensive Virology" (H. Fraenkel-Conrat and R. R. Wagner, eds.), Vol. 11, pp. 55-141. Plenum, New York]. No sharp peaks, attributable to mobile amino acid side chains, were seen in spectra of an intact CpMV particle or its empty protein shell (T component). 31P NMR spin-lattice relaxation time and nuclear Overhauser effect parameters, which are sensitive to high-frequency motions, suggest that the RNA and, when present, the bound polyamine undergo internal motions with correlation times in the nanosecond range.

Carbon Isotopes↗

A theory and a model for interpreting the proton nuclear magnetic resonance spectra of water in plant leaves.

Some plant leaves display complex, orientation-dependent, proton nuclear magnetic resonance (1H NMR) spectra. The spectral patterns vary as the angle between the leaf surface and the applied magnetic field is varied. They also vary with temperature and with the quantity of absorbed manganous ions, but they are independent of magnetic field strength. In this paper, we propose a theory to explain the origin of the spectra and a model from which the patterns can be calculated. The theory shows how heterogeneous magnetic susceptibilities and local dipolar magnetic fields in chloroplasts can shift the water-proton resonance field. The model describes a simplified leaf structure in which the chloroplasts are nonrandomly aligned with respect to the leaf surface. Model calculations are tested by comparison with experimental spectra from hawthorn leaves (Crataegus sp.).

Magnetic Resonance Spectroscopy↗

Enzyme-bound intermediates in the conversion of glucose 1-phosphate to glucose 6-phosphate by phosphoglucomutase. Phosphorus NMR studies.

The interactions between metal ions and the phospho form of rabbit muscle phosphoglucomutase (EC 2.7.5.1) have been studied by 31P NMR. In the metal-free enzyme, the width at half-height of the 31P signal is 10 +/- 1 Hz at 81 MHz. In enzyme-Cd2+ complexes, the presence of spin-spin coupling with 113Cd2+ (J113Cd-O-31P = 16 Hz) and the absence of such splitting with 114Cd2+ indicate that Cd2+ binds directly to the enzymic phosphate. The absence of detectable splitting on transfer of the phosphate group to the acceptor hydroxyl group of bound glucose 1-phosphate, or glucose 6-phosphate (to give the 113Cd2+ complex of the dephospho-enzyme and glucose 1,6-bisphosphate), indicates that this transfer eliminates the direct metal ion-phosphate interaction. The enzyme-catalyzed reaction is slowed sufficiently by the addition of Li+ to allow studies of three discrete intermediate complexes by NMR techniques: glucose 1-phosphate bound to the phosphoenzyme, glucose 1,6-bisphosphate bound to the dephosphoenzyme (only one complex of this type was observed), and glucose 6-phosphate bound to the phosphoenzyme. Complete assignments of the phosphorus resonances of these intermediates have been made by labeling the phosphate ester group of either the enzyme or the sugar with 17O and by NMR polarization transfer studies. The effect of bound metal ions on these resonances also was determined. A 31P NMR titration study of the Li+ complex of the dephosphoenzyme with glucose 1,6-bisphosphate and a 31P NMR polarization transfer experiment indicate that beta-glucose 1,6-bisphosphate binds to the enzyme less tightly than alpha-glucose 1,6-bisphosphate.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗

1H NMR of intact muscle at 11 T.

1H NMR spectra of intact frog, and chicken skeletal muscles, were recorded at 470 MHz with the Plateau and Guéron pulse sequence for the suppression of water [(1982) J. Am. Chem. Soc. 104, 7310]. Only a few transients were required to resolve the resonances from the protons of muscle metabolites. The previously unobserved exchangeable protons of muscles were also recorded and thereby phosphocreatine and creatine could be measured simultaneously. During aging of dissected frog muscle, changes in levels of phosphocreatine, creatine and lactic acid, and the decrease in the intracellular pH were followed by 1H NMR.

Animals↗