Hydration study of homopolypeptides by (2)H NMR

Deuteron T(1) and T(2) was studied as a function of hydration in homopolyglycine (PG) and homopolyproline (PP). Water deuteron relaxation rates in PG conform to a hydration model involving two types of primary hydration sites where water is directly bonded to the polymer. Once these sites are filled, additional water only bonds to water molecules at the primary sites and in so doing affect their dynamics. PP exhibits an anomalous T(1) and T(2) hydration dependence which has been interpreted in terms of a cooperative water molecule-PP molecule helical conformational rearrangement which occurs once a certain hydration level is reached. The proposal of a water-PP structure is tested using molecular dynamics simulations.     

Analysis of membrane lipids by 500 MHz 1H NMR

A nondestructive method has been developed for rapid analysis of lipid content of membrane extracts based on high field proton NMR spectroscopy. Lipid extraction is done by stepwise sonication of purified membranes into chloroform:methanol:water mixtures, and 1H spectra are recorded at 35 degrees C on final preparations consisting of at least 1 mg dried lipid solubilized in 2:1 CD3OD:CDCl3. Spectral peaks of lipid mixtures are assigned to lipid classes using a data base of standard lipid characteristic resonances derived from purified single membrane lipids and known mixtures of them. Peak intensities of characteristic peaks yield ratios of various lipids such as cholesterol:phospholipid and phosphatidylcholine:phosphatidylethanolamine, degree of unsaturation, average acyl chain length, total glycerol lipid content, and presence or absence of particular lipids, such as glycolipids or lysolipids. This procedure of membrane lipid analysis has been verified using known mixtures of purified standard lipids.     

Analysis of the Composition of Mixed Lipid Phases by the Moments of 2H NMR Spectra

The use of ²H NMR spectral moments to determine the composition of biphasic lipid mixtures is outlined. The analysis has been applied to phosphatidylethanolamine-cholesterol (1:1), potassium palmitate, 30% (wt/wt) water and phosphatidylcholine-cholesterol (4:1) systems, as well as to membrances of Escherichia coli during phase transitions. The advantages and disadvantages of the use of spectral moments to determine fractions of coexistent phases are discussed.     

Sources of glucose production in cirrhosis by 2H2O ingestion and 2H NMR analysis of plasma glucose

Plasma glucose 2H enrichment was quantified by 2H NMR in patients with cirrhosis (n=6) and healthy subjects (n=5) fasted for 16 h and given 2H(2)O to approximately 0.5% body water. The percent contribution of glycogenolysis and gluconeogenesis to glucose production (GP) was estimated from the relative enrichments of hydrogen 5 and hydrogen 2 of plasma glucose. Fasting plasma glucose levels were normal in both groups (87+/-7 and 87+/-24 mg/dl for healthy and cirrhotic subjects, respectively). The percent contribution of glycogen to GP was smaller in cirrhotics than controls (22+/-7% versus 46+/-4%, P<0.001), while the contribution from gluconeogenesis was larger (78+/-7% versus 54+/-4%, P<0.001). In all subjects, glucose 6R and 6S hydrogens had similar enrichments, consistent with extensive exchange of 2H between body water and the hydrogens of gluconeogenic oxaloacetate (OAA). The difference in 2H-enrichment between hydrogen 5 and hydrogen 6S was significantly larger in cirrhotics, suggesting that the fractional contribution of glycerol to the glyceraldehyde-3-phosphate (G3P)-moiety of plasma glucose was higher compared to controls (19+/-6% versus 7+/-6%, P<0.01). In all subjects, hydrogens 4 and 5 of glucose had identical enrichments while hydrogen 3 enrichments were systematically lower. This reflects incomplete exchange between the hydrogen of water and that of 1-R-dihydroxyacetone phosphate (DHAP) or incomplete exchange of DHAP and G3P pools via triose phosphate isomerase.     

13C NMR Analysis of some simple tetrahydroisoquinolines

¹³C NMR resonances of 15 simple tetrahydroisoquinolines have been assigned on the basis of chemical shift theory, ¹³C-¹H coupling constants     

Mobility of Core Water in Bacillus subtilis Spores by 2H NMR

Bacterial spores in a metabolically dormant state can survive long periods without nutrients under extreme environmental conditions. The molecular basis of spore dormancy is not well understood, but the distribution and physical state of water within the spore is thought to play an important role. Two scenarios have been proposed for the spore’s core region, containing the DNA and most enzymes. In the gel scenario, the core is a structured macromolecular framework permeated by mobile water. In the glass scenario, the entire core, including the water, is an amorphous solid and the quenched molecular diffusion accounts for the spore’s dormancy and thermal stability. Here, we use ²H magnetic relaxation dispersion to selectively monitor water mobility in the core of Bacillus subtilis spores in the presence and absence of core Mn²⁺ ions. We also report and analyze the solid-state ²H NMR spectrum from these spores. Our NMR data clearly support the gel scenario with highly mobile core water (∼25 ps average rotational correlation time). Furthermore, we find that the large depot of manganese in the core is nearly anhydrous, with merely 1.7% on average of the maximum sixfold water coordination.     

Contribution of proteolytic and metabolic sources to hepatic glutamine by 2H NMR analysis of urinary phenylacetylglutamine 2H-enrichment from 2H2O

Proteolytic and cataplerotic sources of hepatic glutamine were determined by ²H NMR analysis of urinary phenylacetylglutamine (PAGN) ²H-enrichments in eight healthy subjects after ²H₂O and phenylbutyric acid ingestion. Body water enrichment was 0.49±0.03%. PAGN was enriched to lower levels with significant differences between the various glutamine positions. PAGN position 2 enrichment=0.33±0.02%; 3R=0.27±0.02%; 3S=0.27±0.02% and position 4=0.17±0.01%. Position 3R,S enrichments are conditional with the net conversion of citrate to glutamate and are therefore markers of cataplerosis. From the ratio of positions 3R,S to body water enrichment, 55±3% of hepatic glutamine was derived from cataplerosis and 45±3% from proteolysis. In conclusion, enrichment of PAGN 3R,S hydrogens relative to that of body water reflects the contribution of cataplerotic and proteolytic sources to hepatic glutamine.     

Active-site modification of superoxide dismutase by H2O2 studied through 1H NMR of the cobalt derivatives

It is known that H2O2 at pH 10, inactivates copper(II)-zinc(II)-SOD although not much information is available on what happens at the ligands coordinated to the two metal ions. We have reinvestigated the system through the electronic and 1H NMR spectra of the cobalt(II) and copper(II)-cobalt(II) derivatives. Such studies indicate that the coordinated residues are maintained although there is evidence of some flexibility of the donor groups. The coordination around copper is slightly more tetragonal. Azide binding to the copper ion does not cause the complete detachment of one of the histidines from the copper coordination sphere, as happens with the untreated enzyme.     

High-field 1H NMR studies of prostaglandin H2 and its decomposition pathways

Prostaglandin H2 displays at 500 MHz a detailed 1H-NMR in which all methylene groups are non-equivalent in C6D6 solution. The spectrum was assigned by analogy to isosteric structures. The dissymmetric perturbation and steric hindrance of the bicyclo [2.2.1] core caused by the side-chains provides a rationale for the selective fragmentations which PGH2 undergoes. Purified PGH2 is considerably more robust than previous literature accounts suggest. The following transformations were monitored by 1H-NMR: 1) O-O bond cleavage by Ph3P , 2) aqueous media fragmentation to PGE2 and PGD2, 3) base catalyzed fragmentation to ketoaldehydes , and 4) thermolysis attempts.     

Bilayers of arachidonic acid containing phospholipids studied by 2H and 31P NMR spectroscopy

The configurational properties and dynamics of the arachidonic acyl chains of phospholipid bilayers have been investigated for the first time by solid-state 2H NMR techniques, with the goal of achieving a better understanding of the biological roles of polyunsaturated phospholipids. Vinyl perdeuterated arachidonic acid (20:4 delta 5,8,11,14-d8) was prepared from eicosatetraynoic acid (ETYA) and was esterified with 1-palmitoyl-sn-glycero-3-phosphocholine to yield 1-palmitoyl-2-vinylperdeuterioarachidonoyl-sn-glycero-3-phosphocho line [(16:0)(20:4-d8)PC]. 31P NMR spectra of aqueous dispersions of (16:0)(20:4-d8)PC as well as 1-perdeuteriopalmitoyl-2-arachidonoyl-sn-glycero-3-phosphocholine [(per-2H-16:0)(20:4)PC] were characteristic of the lamellar liquid-crystalline state. The dispersions had similar 31P chemical shift anisotropies, with little apparent motional averaging of the lineshapes due to macroscopic reorientation of liposomes or lateral diffusion of phospholipids about their curved surfaces. Comparison to other phosphatidylcholines indicated that both samples comprised the fully hydrated L alpha phase plus excess water. However, the dispersion of (16:0)(20:4-d8)PC yielded relatively narrow powder-type 2H NMR spectra, compared to (per-2H-16:0)(20:4)PC in the liquid-crystalline state. The differences in the 2H NMR powder patterns thus reflect differences in the configurational properties of the polyunsaturated sn-2 arachidonic acyl chain compared to the saturated sn-1 palmitic chain. When the powder-type 2H NMR spectra of the (16:0)(20:4-d8)PC bilayer were dePaked (theta = 0 degrees), they showed three kinds of deuterons upon integration: one with a large splitting (approximately 25-35 kHz), two with intermediate splittings (approximately 10-15 kHz), and the remainder with smaller splittings (approximately 0.3-5 kHz).(ABSTRACT TRUNCATED AT 250 WORDS)     

Structure, dynamics and topology of membrane polypeptides by oriented 2H solid-state NMR spectroscopy

Knowledge of the structure, dynamics and interactions of polypeptides when associated with phospholipid bilayers is key to understanding the functional mechanisms of channels, antibiotics, signal- or translocation peptides. Solid-state NMR spectroscopy on samples uniaxially aligned relative to the magnetic field direction offers means to determine the alignment of polypeptide bonds and domains relative to the bilayer normal. Using this approach the ¹⁵N chemical shift of amide bonds provides a direct indicator of the approximate helical tilt, whereas the ²H solid-state NMR spectra acquired from peptides labelled with 3,3,3-²H₃-alanines contain valuable complimentary information for a more accurate analysis of tilt and rotation pitch angles. The deuterium NMR line shapes are highly sensitive to small variations in the alignment of the C_α–C_β bond relative to the magnetic field direction and, therefore, also the orientational distribution of helices relative to the membrane normal. When the oriented membrane samples are investigated with their normal perpendicular to the magnetic field direction, the rate of rotational diffusion can be determined in a semi-quantitative manner and thereby the aggregation state of the peptides can be analysed. Here the deuterium NMR approach is first introduced showing results from model amphipathic helices. Thereafter investigations of the viral channel peptides Vpu_1–27 and Influenza A M2_22–46 are shown. Whereas the ¹⁵N chemical shift data confirm the transmembrane helix alignments of these hydrophobic sequences, the deuterium spectra indicate considerable mosaic spread in the helix orientations. At least two peptide populations with differing rotational correlation times are apparent in the deuterium spectra of the viral channels suggesting an equilibrium between monomeric peptides and oligomeric channel configurations under conditions where solid-state NMR structural studies of these peptides have previously been performed. Dedicated to Prof. K. Arnold on the occasion of his 65th birthday.     

Characterization of the myristoyl lipid modification of membrane-bound GCAP-2 by 2H solid-state NMR spectroscopy

Guanylate cyclase-activating protein-2 (GCAP-2) is a retinal Ca2+ sensor protein. It is responsible for the regulation of both isoforms of the transmembrane photoreceptor guanylate cyclase, a key enzyme of vertebrate phototransduction. GCAP-2 is N-terminally myristoylated and full activation of its target proteins requires the presence of this lipid modification. The structural role of the myristoyl moiety in the interaction of GCAP-2 with the guanylate cyclases and the lipid membrane is currently not well understood. In the present work, we studied the binding of Ca2+-free myristoylated and non-myristoylated GCAP-2 to phospholipid vesicles consisting of dimyristoylphosphatidylcholine or of a lipid mixture resembling the physiological membrane composition by a biochemical binding assay and 2H solid-state NMR. The NMR results clearly demonstrate the full-length insertion of the aliphatic chain of the myristoyl group into the membrane. Very similar geometrical parameters were determined from the 2H NMR spectra of the myristoyl group of GCAP-2 and the acyl chains of the host membranes, respectively. The myristoyl chain shows a moderate mobility within the lipid environment, comparable to the acyl chains of the host membrane lipids. This is in marked contrast to the behavior of other lipid-modified model proteins. Strikingly, the contribution of the myristoyl group to the free energy of membrane binding of GCAP-2 is only on the order of -0.5 kJ/mol, and the electrostatic contribution is slightly unfavorable, which implies that the main driving forces for membrane localization arises through other, mainly hydrophobic, protein side chain-lipid interactions. These results suggest a role of the myristoyl group in the direct interaction of GCAP-2 with its target proteins, the retinal guanylate cyclases.     

Flexibility of ras lipid modifications studied by 2H solid-state NMR and molecular dynamics simulations

Human posttranslationally modified N-ras oncogenes are known to be implicated in numerous human cancers. Here, we applied a combination of experimental and computational techniques to determine structural and dynamical details of the lipid chain modifications of an N-ras heptapeptide in 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) membranes. Experimentally, 2H NMR spectroscopy was used to study oriented membranes that incorporated ras heptapeptides with two covalently attached perdeuterated hexadecyl chains. Atomistic molecular dynamics simulations of the same system were carried out over 100 ns including 60 DMPC and 4 ras molecules. Several structural and dynamical experimental parameters could be directly compared to the simulation. Experimental and simulated 2H NMR order parameters for the methylene groups of the ras lipid chains exhibited a systematic difference attributable to the absence of collective motions in the simulation and to geometrical effects. In contrast, experimental 2H NMR spin-lattice relaxation rates for Zeeman order were well reproduced in the simulation. The lack of slower collective motions in the simulation did not appreciably influence the relaxation rates at a Larmor frequency of 115.1 MHz. The experimental angular dependence of the 2H NMR relaxation rates with respect to the external magnetic field was also relatively well simulated. These relaxation rates showed a weak angular dependence, suggesting that the lipid modifications of ras are very flexible and highly mobile in agreement with the low order parameters. To quantify these results, the angular dependence of the 2H relaxation rates was calculated by an analytical model considering both molecular and collective motions. Peptide dynamics in the membrane could be modeled by an anisotropic diffusion tensor with principal values of Dparallel=2.1x10(9) s(-1) and Dperpendicular=4.5x10(5) s(-1). A viscoelastic fitting parameter describing the membrane elasticity, viscosity, and temperature was found to be relatively similar for the ras peptide and the DMPC host matrix. Large motional amplitudes and relatively short correlation times facilitate mixing and dispersal with the lipid bilayer matrix, with implications for the role of the full-length ras protein in signal transduction and oncogenesis.     

2D 1H NMR studies of monomeric insulin

In order to establish the conditions required for the observation of monomeric insulin in solution, a series of proton nuclear magnetic resonance studies of insulin in a variety of solvents was undertaken. Optimal spectra were recorded in trifluoroethanol- water mixtures in a 1:2 ratio. Using the sequential assignment approach the proton nuclear magnetic resonance spectrum of insulin was then assigned. Aspects of the structure of monomeric insulin in solution have been determined using the observed NOE cross peaks and slow exchange protons.     

Measurement of 2H distribution in natural products by quantitative 2H NMR: An approach to understanding metabolism and enzyme mechanism?

During the biosynthesis of natural products, the intra-molecular distribution of isotopes is introduced as a result of different isotope effects associated with the reactions involved. Due to the sensitivity of certain enzymes to the presence of a heavy isotope, the isotope selection effects related to some transformations can be high, especially for hydrogen. The effect of a series of isotope effects specific to each enzyme-catalysed step are additive during a biosynthetic pathway, leading to fractionation of the isotopes between the starting substrate and the final product. As the individual reactions are acting on different positions in the substrate, the net effect is a non-statistical distribution of isotope within the final product. Quantitative ²H NMR spectroscopy can be used to measure the distribution of ²H at natural abundance in natural products. In the first example, the fermentation of glucose is examined. Glucose can act as a primary carbon source for a wide range of fermentation products, produced by a variety of pathways. In many cases, competing pathways are active simultaneously. The relative fluxes are influenced by both environmental and genetic parameters. Quantitative ²H NMR spectroscopy is being used to obtain mechanistic and regulatory information about isotopic fractionation from glucose during such fermentations. Quantitative ²H NMR spectroscopy can also be used to examine the fractionation in ²H that occurs in long-chain fatty acids during chain elongation and oxygenation. It has been found that the (²H/¹H) ratio shows an alternating pattern along the length of the chain and that the residual hydrogen atoms at the sites of desaturation are asymmetrically impoverished. The extent to which the non-statistical distribution of isotopes can be related to the mechanism of enzymes involved in the biosynthetic pathway via kinetic isotopic effects will be discussed.     

Conformational and NMR study of some furan derivatives by DFT methods

4′-substituted neutral/protonated furfurylidenanilines and trans-styrylfurans are able to exist in two different conformations related to the rotation around the furan ring-bridge double bond. In this work, the equilibrium geometry and the corresponding rotational barrier of the benzene ring for each furan derivative conformation were calculated by DFT methods. The trend and shape of the rotational barrier are rationalized within natural bond orbitals as well as atoms-in-molecules approach. For the corresponding equilibrium geometries, ¹H and ¹³C substituent induced shifts (SIS) were calculated and compared with experimental values. Calculated shielding constants are shown to be sensitive to the substituent effect through a linear fit with substituent’s Hammett constants. An alternative approach was followed for assessing the effect of substituents over SIS through comparing the differences in isotropic shielding constants with NBO charges as well as with ¹H and ¹³C experimental chemical shifts.     

Order and dynamics in mixtures of membrane glucolipids from Acholeplasma laidlawii studied by 2H NMR

The two dominant glucolipids in Acholeplasma laidlawii, viz., 1,2-diacyl-3-O-(alpha-D-glucopyranosyl)-sn-glycerol (MGlcDG) and 1,2-diacyl-3-O-[alpha-D-glucopyranosyl-(1----2)-O-alpha-D-glucopyranosyl ]- sn-glycerol (DGlcDG), have markedly different phase behavior. MGlcDG has an ability to form nonlamellar phases, whereas DGlcDG only forms lamellar phases. For maintenance of a stable lipid bilayer, the polar headgroup composition in A. laidlawii is metabolically regulated in vivo, in response to changes in the growth conditions [Wieslander et al. (1980) Biochemistry 19, 3650; Lindblom et al. (1986) Biochemistry 25, 7502]. To investigate the mechanism behind the lipid regulation, we have here studied bilayers of mixtures of unsaturated MGlcDG and DGlcDG, containing a small fraction of biosynthetically incorporated perdeuterated palmitic acid, with 2H NMR. The order-parameter profile of the acyl chains and an apparent transverse spin relaxation rate (R2) were determined from dePaked quadrupole-echo spectra. The order of the acyl chains in DGlcDG-d31 increases upon addition of protonated MGlcDG, whereas the order of MGlcDG-d31 decreases when DGlcDG is added. The variation of order with lipid composition is rationalized from simple packing constraints. R2 increases linearly with the square of the order parameter (S2) up to S approximately 0.14; then, R2 goes through a maximum and decreases. The increase in R2 with S2, as well as the magnitude of R2, is largest for pure MGlcDG-d31, smallest for DGlcDG-d31, and similar for mixtures with the same molar ratio of MGlcDG/DGlcDG but with the deuterium label on different lipids.(ABSTRACT TRUNCATED AT 250 WORDS)     

Geometry and intrinsic tilt of a tryptophan-anchored transmembrane alpha-helix determined by (2)H NMR

We used solid-state deuterium NMR spectroscopy and an approach involving geometric analysis of labeled alanines (GALA method) to examine the structure and orientation of a designed synthetic hydrophobic, membrane-spanning alpha-helical peptide in phosphatidylcholine (PC) bilayers. The 19-amino-acid peptide consists of an alternating leucine and alanine core, flanked by tryptophans that serve as interfacial anchors: acetyl-GWW(LA)(6)LWWA-ethanolamine (WALP19). A single deuterium-labeled alanine was introduced at different positions within the peptide. Peptides were incorporated in oriented bilayers of dilauroyl- (di-C12:0-), dimyristoyl- (di-C14:0-), or dioleoyl- (di-C18:1(c)-) phosphatidylcholine. The NMR data fit well to a WALP19 orientation characterized by a distinctly nonzero tilt, approximately 4 degrees from the membrane normal, and rapid reorientation about the membrane normal in all three lipids. Although the orientation of WALP19 varies slightly in the different lipids, hydrophobic mismatch does not seem to be the dominant factor causing the tilt. We suggest rather that the peptide itself has an inherently preferred tilted orientation, possibly related to peptide surface characteristics or the disposition of tryptophan indole anchors relative to the lipids, the peptide backbone, and the membrane/water interface. Additionally, the data allow us to define more precisely the local alanine geometry in this membrane-spanning alpha-helix.     

Labelling strategy and membrane characterization of marine bacteria Vibrio splendidus by in vivo 2H NMR

Vibrio splendidus is a marine bacterium often considered as a threat in aquaculture hatcheries where it is responsible for mass mortality events, notably of bivalves' larvae. This bacterium is highly adapted to dynamic salty ecosystems where it has become an opportunistic and resistant species. To characterize their membranes as a first and necessary step toward studying bacterial interactions with diverse molecules, we established a labelling protocol for in vivo ²H solid-state nuclear magnetic resonance (SS-NMR) analysis of V. splendidus. ²H SS-NMR is a useful tool to study the organization and dynamics of phospholipids at the molecular level, and its application to intact bacteria is further advantageous as it allows probing acyl chains in their natural environment and study membrane interactions. In this study, we showed that V. splendidus can be labelled using deuterated palmitic acid, and demonstrated the importance of surfactant choice in the labelling protocol. Moreover, we assessed the impact of lipid deuteration on the general fitness of the bacteria, as well as the saturated-to-unsaturated fatty acid chains ratio and its impact on the membrane properties. We further characterize the evolution of V. splendidus membrane fluidity during different growth stages and relate it to fatty acid chain composition. Our results show larger membrane fluidity during the stationary growth phase compared to the exponential growth phase under labelling conditions - an information to take into account for future in vivo SS-NMR studies. Our lipid deuteration protocol optimized for V. splendidus is likely applicable other microorganisms for in vivo NMR studies.