Solid-state deuterium nuclear magnetic resonance spectroscopy of proteins.
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Bacteriorhodopsins↗
Biomedical subjects
M A Keniry
Publications and source records attributed to M A Keniry.
Location and activity of ubiquinone 10 and ubiquinone analogues in model and biological membranes.
Deuteriated analogues of ubiquinone 10 (Q10) have been dispersed with plasma membranes of Escherichia coli and with the inner membranes of beetroot mitochondria. Orientational order at various deuteriated sites was measured by solid-state deuterium nuclear magnetic resonance (2H NMR). Similar measurements were made, using the compounds dispersed in dimyristoylphosphatidylcholine (DMPC) and egg yolk lecithin and dispersions prepared from the lipid extracts of beetroot mitochondria. In all cases only a single unresolved 2H NMR spectrum (typically 1000-Hz full width at half-height) was observed at concentrations down to 0.02 mol % Q10 per membrane lipid. This result shows that most Q10 is in a mobile environment which is physically separate from the orientational constraints of the bilayer lipid chains. In contrast, a short-chain analogue of Q10, in which the 10 isoprene groups have been replaced by a perdeuteriated tridecyl chain, showed 2H NMR spectra with quadrupolar splittings typical of an ordered lipid that is intercalated into the bilayer. The NADH oxidase activity and O2 uptake in Escherichia coli and in mitochondria were independent of which analogue was incorporated into the membrane. Thus, despite the major difference in their physical association with membranes, or their lipid extracts, the electron transport function of the long- and short-chain ubiquinones is similar, suggesting that the bulk of the long-chain ubiquinone does not have a direct function in electron transporting activity. The physiologically active Q10 may only be a small fraction of the total ubiquinone, a fraction that is below the level of detection of the present NMR equipment.(ABSTRACT TRUNCATED AT 250 WORDS)
Escherichia coli↗
NMR studies of the interaction of chromomycin A3 with small DNA duplexes I.
1H and 31P NMR spectral analysis of a chromomycin/d(ATGCAT)2 complex provides strong evidence for a nonintercalative mode of drug binding. Investigation of the imino proton region of the duplex suggests a protection of one of the two guanine imino protons from fast exchange with the bulk water up to at least 45 degrees C by the drug. Subsequent one-dimensional nuclear Overhauser enhancement experiments place the exchangeable chromomycin chromophoric hydroxyl proton less than 0.45 nm from this guanine imino proton and the chromophore 7-methyl less than 0.45 from the internal thymine 6-proton and/or the guanine 8-proton. 1H two-dimensional NMR reveals that the duplex retains a right-handed B conformation but there are distortions at the TGC region of one chain and large deviations in the chemical shift of protons relative to the uncomplexed duplex in the other chain in the same TGC region. The data suggest that the chromomycin chromophore is oriented such that the hydrophilic side of the ring system is proximal to the helix center in the major groove near the TG region while the aromatic side of the ring is oriented away from the helix but is partially protected from the solvent by the aliphatic chain, which bends back over the two aromatic protons. Changes in the 31P spectrum of the duplex on binding of the drug are different from the effect of either actinomycin or netropsin on nucleic acid fragments.
Base Composition↗
Comparison of lactate concentration determinations in ischemic and hypoxic rat brains by in vivo and in vitro 1H NMR spectroscopy.
An experimental protocol for the quantitation of lactate is demonstrated for in vivo 1H NMR surface coil spectroscopy. The in vivo lactate concentration can be calculated by comparing the in vivo and in vitro ratios of lactate and N-acetylaspartate (NAA) NMR signals. With this protocol, approximately 25% of lactate present in the hypoxic or ischemic rat brain is observed by NMR.
Animals↗
Measurement of lactate accumulation by in vivo proton NMR spectroscopy during global cerebral ischemia in rats.
In vivo 1H NMR spectral editing techniques were used to monitor cerebral lactate production during remotely controlled temporary forebrain ischemia in rats. The lactate/N-acetylaspartate (NAA) ratio correlated with survival after ischemia and subsequent reperfusion. The lactate/NAA ratio that predicted death after ischemia in rats was estimated to be approximately 1.3.
Animals↗
The conformation of the d(ACCCGGGT) duplex in aqueous solution.
The nonexchangeable base and sugar protons of the octanucleotide d(ACCCGGGT)2 have been assigned using two dimensional homonuclear Hartmann-Hahn relayed spectroscopy (HOHAHA), double quantum filtered homonuclear correlation spectroscopy (DQFCOSY) and nuclear Overhauser spectroscopy (NOESY) in D2O at 12 degrees C. The observed NOE's between the base protons and their own H2' protons and between the base protons and the H2' protons of the 5' adjacent nucleotide and the observed coupling constants between the deoxyribose 1' and 2',2'' protons indicate that this duplex assumes a right-handed B-type helix conformation in solution.
Magnetic Resonance Spectroscopy↗
New DNA polymorphism: evidence for a low salt, left-handed form of poly(dG-m5dC).
Spectroscopic studies on solutions of poly(dG-m5dC) over a wide range of salt concentration are presented. Low salt solutions [( Na+]) less than 2 mM) of poly(dG-m5dC) produce circular dichroism (CD) spectra typical of the left-handed, Z form at high salt [( Na+] = 1.75 M). Solutions of poly(dG-m5dC) at intermediate salt concentrations, e.g., 142 mM, yield CD spectra characteristic of the right-handed, B conformation. 31p NMR spectra of the low salt form of poly(dG-m5dC) reveal two well separated peaks, split by 1.4 ppm, consistent with a dinucleotide repeat. Kinetic studies show that the transition from the low salt form to teh right-handed B form is slow, as expected for a major conformational change. These results suggest that the Z conformation in poly(dG-m5dC) can be stabilized at very low salt as well as at high salt.
Circular Dichroism↗
Nuclear magnetic resonance studies of amino acids and proteins. Deuterium nuclear magnetic resonance relaxation of deuteriomethyl-labeled amino acids in crystals and in Halobacterium halobium and Escherichia coli cell membranes.
We have obtained deuterium (2H) Fourier transform nuclear magnetic resonance (NMR) spectra of zwitterionic L-[beta-2H3]alanine, DL-[gamma-2H6]valine, DL-[beta, gamma-2H4]threonine, L-[delta-2H3]leucine, and L-[alpha, beta, gamma, gamma', delta-2H10]isoleucine in the crystalline solid state and have determined the deuteriomethyl group spin-lattice relaxation rates as a function of temperature. The results yield the Arrhenius activation energies (delta E) for methyl rotation, and through use of a suitable mathematical model, rotational correlation times, tau c. For alanine, valine, threonine, leucine, and isoleucine at 37 degrees C, tau c and delta E values are 780, 100, 40, 38, and 18 ps and 22, 14.0, 17.6, 15.5, and 8.6 kJ, respectively. For L-[beta-2H3]alanine in the zwitterionic lattice, a spin-lattice relaxation time (T1) minimum of 2.1 +/- 0.3 ms is observed (at 0 degree C), in excellent agreement with the 1.92-ms prediction of the mathematical model. Similar tau c and delta E measurements are reported for bacteriorhodopsin in the purple membrane of Halobacterium halobium R1 and for Escherichia coli cell membranes. Overall, our results demonstrate a great similarity between the dynamics in amino acid crystals and in membrane proteins. However, threonine exhibits a nonlinear Arrhenius behavior in bacteriorhodopsin, and in the valine-, leucine-, and isoleucine-labeled membrane samples at higher temperatures (approximately greater than 37 degrees C), there is evidence of an additional slow side-chain motion. The lipid phase state in E. coli does not appear to influence, on the average, the dynamics of the valine side chains. These results indicate that the sensitivity of the deuterium NMR technique is now adequate to study in moderate detail the dynamics of most types of amino acids in a membrane protein and that adequate sensitivity, in some instances, should be available for the study of individual amino acids in suitably labeled membrane proteins.
Amino Acids↗
31P nuclear magnetic resonance studies of the association of basic proteins with multilayers of diacyl phosphatidylserine.
Lysozyme, cytochrome c, poly(L-lysine), myelin basic protein and ribonuclease were used to form multilayer dispersions containing about 50% protein (by weight) with bovine brain diacyl phosphatidylserine (PS). 31P nuclear magnetic resonance shift anisotropies, spin-spin (T2) and spin-lattice (T1) relaxation times for the lipid headgroup phosphorus were measured at 36.44 MHz. At pH 7.5, lysozyme, cytochrome c, poly(L-lysine) and ribonuclease were shown to increase the chemical shift anisotropy of PS by between 12-20%. Myelin basic protein altered the shape of the phosphate resonance, suggesting the presence of two lipid components, one of which had a modified headgroup conformation. The presence of cytochrome c led to the formation of a narrow spike at the isotropic shift position of the spectrum. Of the various proteins or peptides we have studied, only poly(L-lysine) and cytochrome c had any effect on the T1 of PS (1050 ms). Both caused a 20-30% decrease in T1 of the lamellar-phase phosphate peak. The narrow peak in the presence of cytochrome c had a very short T1 of 156 ms. The possibility is considered that the cytochrome Fe3+ contributes to the phosphate relaxation in this case. The effect of all proteins on the T2 of the phosphorus resonance was to cause an increase from the value for pure PS (1.6 ms) to between 2 and 5 ms. The results obtained with proteins are compared with the effects of small ions and intrinsic membrane proteins on the order and motion of the headgroups of lipids in bilayers.
Animals↗
Nuclear magnetic resonance studies of amino acids and proteins. Side-chain mobility of methionine in the crystalline amino acid and in crystalline sperm whale (Physeter catodon) myoglobin.
We have obtained deuterium (2H) nuclear magnetic resonance (NMR) spectra and spin-lattice relaxation times (T1) of L-[epsilon-2H3]methionine, L-[epsilon-2H3]methionine in a D,L lattice, and [S-methyl-2H3]methionine in the crystalline solid state, as a function of temperature, in addition to obtaining 2H T1 and line-width results as a function of temperature on [epsilon-2H3]methionine-labeled sperm whale (Physeter catodon) myoglobins by using the method of magnetic ordering [Rothgeb, T. M., & Oldfield, E. (1981) J. Biol. Chem. 256, 1432-1446]. The results indicate that in the L-amino acid, methyl rotation having an activation energy (delta E) of 8.3 +/- 1 kJ dominates T1 at low temperatures (less than or equal to 10 degrees C), while at higher temperatures an additional large-amplitude side-chain motion occurs which causes changes in the 2H NMR line shape and T1. This motion is inhibited in the D,L lattice, indicating that lattice effects may have a strong effect on the mobility of anhydrous amino acids in the solid state. Further substitution at S delta to form the sulfonium salt [S-methyl-2H3]-methionine causes a large increase in delta E, to 15.9 +/- 2 kJ, a value comparable to the 14-16 kJ found in valine and leucine, which contain the structurally similar isopropyl moiety. These results suggest that the very low barriers to methyl rotation in the methionine side chain are due to long C-S bond lengths and the presence of only two substituents on sulfur, while the anomalous high-temperature behavior is due to a lattice-packing effect. 2H T1 results with methionine-labeled myoglobin are complex, reflecting the presence of fast large-amplitude side-chain motions, in addition to rapid methyl rotation. Our data indicate that Met-55 and Met-131 are motionally inequivalent in crystalline cyanoferrimyoglobin, in contrast to solution NMR results. We have also recorded 13C cross-polarization "magic-angle" sample-spinning NMR spectra of [epsilon-13C]methionine-labeled crystalline cyanoferrimyoglobin (at 37.7 MHz, corresponding to a magnetic field strength of 3.52 T) and of the same protein in aqueous solution. Cross-polarization transfer rates and proton rotating-frame relaxation time results again indicate that Met-55 and Met-131 are motionally inequivalent in the solid state, and the TCH data indicate that Met-55 is more solidlike. However, we find that 13C chemical shifts in solution and those in the crystalline solid state are in very close agreement, suggesting that the average solution and crystal conformations are the same, in the area of Met-55 and Met-131.
Animals↗
Dependence on lipid structure of the coil-to-helix transition of bovine myelin basic protein.
In aqueous solution bovine myelin basic protein has a close-to-random coil structure that is partially transformed to helix on interaction with lipids. Circular dichroism spectra have been used to follow this conformational transition which, with phospholipids, decreases in the order phosphatidylglycerol, phosphatidic acid approximately equal to phospholipids, decreases in the order phosphatidylethanolamine. There appears to be a strong correlation between the extent of alpha-helix formation and the degree of penetration of the hydrophobic region of the bilayer, as assessed by other methods. Cholesterol mixed in bilayers with phosphatidylserine has little effect on the protein secondary structure. Although basic protein binds strongly to cerebroside and to cerebroside sulphate, two of the other major myelin lipids, the intrinsic chirality of these lipids precludes assessment of their effect on the protein conformation. No significant changes in the circular dichroism spectra accompany the protein association with either of the zwitterionic bilayer-forming lipids, phosphatidylethanolamine and phosphatidylcholine. This seems to exclude extensive penetration into bilayers of these lipids and hence to exclude appreciable hydrophobic interactions; on the other hand, it is argued that little evidence exists for ionic attractions to these lipids. The optical activity of peptides derived from the basic protein by cleavage at the 42-43 and 88-89 peptides bonds (with cathepsin D) and at the 115-116 bond (with a skatole derivative) has also been measured in an attempt to locate the helix-forming regions within the primary structure.
Animals↗
A 13C NMR spin-lattice relaxation study of the interaction of myelin proteins with lipid vesicles.
Natural abundance 13C nuclear magnetic spin-lattice relaxation times have been measured for bovine brain phosphatidylserine vesicles with and without bound proteins. The relaxation times were lower than published values for the corresponding nuclei in egg phosphatidylcholine, but showed the same trend, with relaxation times increasing along the acyl chains away from the polar headgroup. These times were inversely related to the degree of saturation of the lipid. Cytochrome c caused insignificant changes in the lipid acyl chain relaxation rates but reduced the resonance intensities, in agreement with Brown and Wüthrich (Biochem. Biophys. Acta 468 (1977) 389). In contrast, the basic protein from bovine myelin did not affect the intensities but reduced the relaxation times for 13C nuclei near the bilayer centre, and for nuclei near carbon-carbon double bonds. These proteins also dramatically broadened the serine headgroup carboxyl resonance. It appears, in accord with other recent evidence, that the basic protein does penetrate the hydrophobic region of the bilayer (possibly to the centre), producing quantitatively similar changes in the relaxation rates to proteolipid protein, an integral membrane protein.
Journal Article↗
A 13C NMR spin-lattice relaxation study of the interaction of myelin proteins with ipid vesicles.
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Animals↗
Circular dichroic analysis of the secondary structure of myelin basic protein and derived peptides bound to detergents and to lipid vesicles.
In aqueous solution bovine myelin basic protein exhibits no significant alpha-helical or beta-pleated sheet structure. However, in vivo this protein is associated largely with the myelin membrane: experiments have therefore been performed to determine the structure of the protein when bound to lipid bilayers. Circular dichroism spectra show that this protein undergoes a major conformational change on binding to lipid bilayer vesicles formed from diacylphosphatidylserine or diacylphosphatidic acid, and on binding to micelles of several detergents. Association with diacylphosphatidylcholine failed to induce a structural change: this observation is interpreted in terms of an earlier report that lysophosphatidylcholine does increase the alpha-helical content of basic protein. These circular dichroism measurements and studies of the binding to the bilayer-forming lipids appear to provide support for significant hydrophobic lipid-protein interactions. Similar studies using two peptides produced by cleavf basic protein indicate that a major structure-forming region in the middle of the protein has been disrupted by this scission.
Animals↗
Quadruplex structures in nucleic acids.
DNA oligonucleotides that have repetitive tracts of guanine bases can form G-quadruplex structures that display an amazing polymorphism. Structures of several new G-quadruplexes have been solved recently that greatly expand the known structural motifs observed in nucleic acid quadruplexes. Base triads, base hexads, and quartets that contain cytosine have recently been identified stacked over the familiar G-quartets. The current status of the diverse array of structural features in quadruplexes is described and used to provide insight into the polymorphism and folding pathways. This review also summarizes recent progress in the techniques used to probe the structures of G-quadruplexes and discusses the role of ion binding in quadruplex formation. Several of the quadruplex structures featured in this review can be accessed in the online version of this review as CHIME representations.
DNA↗
Surface dynamics of the integral membrane protein bacteriorhodopsin.
Recently, there has been great interest in determining the three-dimensional structures of membrane proteins, particularly bacteriorhodopsin, for which a variety of possible folding arrangements have been suggested. In this paper we present nuclear magnetic resonance (NMR) spectra of deuterated bacteriorhodopsin, and use the data to help interpret the various suggested bacteriorhodopsin folding patterns. The results strongly indicate that (1) a membrane surface (+/- 1 residue) may be defined by NMR in bacteriorhodopsin; (2) all amino acids inside the surface are essentially crystalline; (3) all amino acids outside the surface (surface residues) in bacteriorhodopsin are highly mobile on the time scale of the 2H NMR experiments; (4) NMR data may be used to help evaluate the various structural models that have been proposed; (5) aggregation of purple membrane sheets may lead to an immobilization of the surface residues.
Amino Acid Sequence↗