Dipolar Decoupled-magic Angle Spinning Research Articles

Network structures and dynamics of dry and swollen poly(acrylate)s. Characterization of high- and low-frequency motions as revealed by suppressed or recovered intensities (SRI) analysis of 13C NMR

We recorded temperature-dependent high-resolution 13C NMR spectra of dry and swollen poly(acrylate)s [poly(2-methoxyethyl acrylate) (PMEA), poly(2-hydroxyethyl methacrylate) (PHEMA), and poly(tetrahydrofurfuryl acrylate) (PTHFA)] by dipolar decoupled-magic angle spinning (DD-MAS) and cross-polarization-magic angle spinning (CP-MAS) methods, to gain insight into their network structures and dynamics. Suppressed or recovered intensities (SRI) analysis of 13C CP-MAS and DD-MAS NMR was successfully utilized, to reveal portions of dry and swollen polymers which undergo fast and slow motions with fluctuation frequencies in the order of 10 8 Hz and 10 4–10 5 Hz, respectively. Fast isotropic motions with frequency higher than 10 8 Hz at ambient temperature were located to the portions in which 13C CP-MAS NMR signals of swollen PMEA were selectively suppressed. In contrast, low-frequency motion was identified to the portions in which 13C DD-MAS (and CP-MAS) signals are most suppressed at the characteristic suppression temperature(s) T s. Network of PMEA gels (containing 7 wt% of water) turns out to be formed by partial association of backbones only, as manifested from their T s gradient at lowered temperature, whereas networks of PHEMA (containing 40 wt% of water) and PTHFA (9 wt% of water) gels are tightly formed through mutual inter-chain associations of both backbones and side-chains, as viewed from the raised T s values for both near at ambient temperature. It is also interesting to note that flexibility of gel network (PMEA > PTHFA > PHEMA) characterized by the suppression temperature T s (PMEA < PTHFA < PHEMA) is well related with a characteristic parameter for biocompatibility such as the production of TAT (thrombin–antithrombin III complex) as a marker of activation of the coagulation system.

NMR of Microencapsulated Fish Oil Samples During In Vitro Digestion

The use of nuclear magnetic resonance (NMR) spectroscopy for characterising microencapsulated tuna oil powders (25% and 50% w/w oil) and assessing the behaviour of the microcapsules on their exposure to water, simulated gastric fluid or to sequential exposure of simulated gastric and intestinal fluids was examined. The matrices used for encapsulation were physical mixtures of casein or whey protein in combination with carbohydrates (dextrose monohydrate with either dried glucose syrup or a physically modified resistant starch) or heated mixtures of these matrices. Solid-state 13C cross-polarised magic angle spinning NMR and dipolar de-coupled magic angle spinning NMR record the 13C NMR signals of the encapsulant material and that of the encapsulated oil, respectively. 1H and 13C solution NMR were used to investigate the relative increase in mobility of the various encapsulant matrices due to their dissolution on exposure to gastrointestinal fluids. The results suggested that the dissolution characteristics of matrices of microencapsulated oil powders were dependent on the type of milk protein and carbohydrate used and whether the protein–carbohydrate matrices were heat-treated prior to encapsulation of the oil.

Conformation and Dynamics of the [3- 13C]Ala, [1- 13C]Val-Labeled Truncated pharaonis Transducer, pHtrII(1–159), as Revealed by Site-Directed 13C Solid-State NMR: Changes Due to Association with Phoborhodopsin (Sensory Rhodopsin II)

We have recorded 13C NMR spectra of the [3- 13C]Ala, [1- 13C]Val-labeled pharaonis transducer pHtrII(1–159) in the presence and absence of phoborhodopsin ( ppR or sensory rhodopsin II) in egg phosphatidylcholine or dimyristoylphosphatidylcholine bilayers by means of site-directed (amino acid specific) solid-state NMR. Two kinds of 13C NMR signals of [3- 13C]Ala- pHtrII complexed with ppR were clearly seen with dipolar decoupled magic angle spinning (DD-MAS) NMR. One of these resonances was at the peak position of the low-field α-helical peaks ( α II-helix) and is identified with cytoplasmic α-helices protruding from the bilayers; the other was the high-field α-helical peak ( α I-helix) and is identified with the transmembrane α-helices. The first peaks, however, were almost completely suppressed by cross-polarization magic angle spinning (CP-MAS) regardless of the presence or absence of ppR or by DD-MAS NMR in the absence of ppR. This is caused by an increased fluctuation frequency of the cytoplasmic α-helix from 10 5 Hz in the uncomplexed states to >10 6 Hz in the complexed states, leading to the appearance of peaks that were suppressed because of the interference of the fluctuation frequency with the frequency of proton decoupling (10 5 Hz), as viewed from the 13C NMR spectra of [3- 13C]Ala-labeled pHtrII. Consistent with this view, the 13C DD-MAS NMR signals of the cytoplasmic α-helices of the complexed [3- 13C]Ala- pHtrII in the dimyristoylphosphatidylcholine (DMPC) bilayer were partially suppressed at 0°C due to a decreased fluctuation frequency at the low temperature. In contrast, examination of the 13C CP-MAS spectra of [1- 13C]Val-labeled complexed pHtrII showed that the 13C NMR signals of the transmembrane α-helix were substantially suppressed. These spectral changes are again interpreted in terms of the increased fluctuation frequency of the transmembrane α-helices from 10 3 Hz of the uncomplexed states to 10 4 Hz of the complexed states. These findings substantiate the view that the transducers alone are in an aggregated or clustered state but the ppR- pHtrII complex is not aggregated. We show that 13C NMR is a very useful tool for achieving a better understanding of membrane proteins which will serve to clarify the molecular mechanism of signal transduction in this system.

Secondary structure and backbone dynamics of Escherichia coli diacylglycerol kinase, as revealed by site-directed solid-state 13C NMR

To gain insight into secondary structure and backbone dynamics, we have recorded 13C NMR spectra of [3- 13C]Ala-, [1- 13C]Val-labeled Escherichia coli diacylglycerol kinase (DGK), using cross-polarization-magic angle spinning (CP-MAS) and single-pulse excitation with dipolar decoupled-magic angle spinning (DD-MAS) methods. DGK was either solubilized in n-decyl-β-maltoside (DM) micelle or integrated into 1-palmitoyl-2-oleoyl- sn-glycero-3-phosphocholine (POPC) or 1,2-dipalmitoyl- sn-glycero-3-phosphocholine (DPPC) bilayers. Surprisingly, the 13C NMR spectra were broadened to yield rather featureless peaks at physiological temperatures, both in DM solution or lipid bilayers at liquid crystalline phase, due to interference of motional frequencies of DGK with frequencies of magic angle spinning (MAS) or proton decoupling (10 4 or 10 5 Hz, respectively). In gel phase lipids, however, up to six distinct 13C NMR peaks were well-resolved due to lowered fluctuation frequencies (<10 5 Hz) for the transmembrane region, the amphipathic α-helices and loops. While DGK can be tightly packed in gel phase lipids, DGK is less tightly packed at physiological temperatures, where it becomes more mobile. The fact that the enzymatic activity is low under conditions where motion is restricted and high when conformational fluctuations can occur suggests that acquisition of low frequency backbone motions, on the microsecond to millisecond time scale, may facilitate the efficient enzymatic activity of DGK.

Local protein structure and dynamics at kinked transmembrane α-helices of [1- 13C]Pro-labeled bacteriorhodopsin as revealed by site-directed solid-state 13C NMR

We have recorded 13C NMR spectra of [1- 13C]Pro-labeled bacteriorhodopsin (bR) and P50G, P91G, and P186A mutants under fully hydrated condition, by high-resolution solid-state NMR utilizing cross polarization-magic angle spinning (CP-MAS) and dipolar decoupled-magic angle spinning (DD-MAS) techniques. Seven well-resolved 13C NMR signals including a shoulder peak were distinguished by CP-MAS NMR, although only two signals were resolved by DD-MAS NMR. We assigned these 13C NMR signals among them to Pro50, 91 and 186 residues at the kinks in the inner part of the transmembrane α-helices, on the basis of compared peak-intensities between wild type bR and the above-mentioned site-directed mutants, together with aid of Mn 2+-induced suppression of peaks from residues located near at the surfaces due to accelerated spin–spin relaxation times. It turned out that these Pro 13C NMR signals of wild type were appreciably broadened at temperature below −40 °C as in [3- 13C]Ala-bR, as a result of superposition of a variety of frozen conformers of the transmembrane α-helices exhibiting dispersion of chemical shifts. This means that the dynamic behavior of bR as viewed from Pro residue is very similar to that of ordinary amino acid residues such as Ala, Val, Phe, etc. Further, it was found that no appreciable conformational change was noted for wild type bR within a temperature range between −20 and 35 °C at these kinked portions, although such change was noted at 35 °C for Y185F mutant which lacks interchain hydrogen bonding interaction as observed for wild type bR between the side-chains of Asp212 and Tyr185.

Surface dynamics of bacteriorhodopsin as revealed by (13)C NMR studies on [(13)C]Ala-labeled proteins: detection of millisecond or microsecond motions in interhelical loops and C-terminal alpha-helix.

We have recorded (13)C NMR spectra of [2-(13)C]-, [1-(13)C]-, [3-(13)C],- and [1,2,3-(13)C(3)]Ala-labeled bacteriorhodopsin (bR), and its mutants, A196G, A160G, and A103C, by means of cross polarization-magic angle spinning (CP-MAS) and dipolar decoupled-magic angle spinning (DD-MAS) techniques, to reveal the conformation and dynamics of bR, with emphasis on the loop and C-terminus structures. The (13)C NMR signals of the loop (C-D, E-F, and F-G) regions were almost completely suppressed from [2-(13)C]-, [1-(13)C]Ala-, and [1-(13)C]Gly-labeled bR, due to the presence of conformational fluctuation with correlation times of 10(-4) s that interfered with the peak-narrowing by magic angle spinning. The observation of such suppressed peaks for specific residues provides a unique means of detecting intermediate frequency motions on the time scale of ms or micros in the surface loops of membrane proteins. Instead, the three well-resolved (13)C CP-MAS NMR signals of [2-(13)C]Ala-bR, at 50.38, 49.90, and 47.96 ppm, were ascribed to the C-terminal alpha-helix previously proposed from the data for [3-(13)C]Ala-bR: the former two peaks were assigned to Ala 232 and 238, in view of the results of successive proteolysis experiments, while the highest-field peak was ascribed to Ala 235 prior to Pro 236. Even such (13)C NMR signals were substantially broadened when (13)C NMR spectra of fully labeled [1,2,3-(13)C]Ala-bR were recorded, because the broadening and splitting of peaks due to the accelerated transverse relaxation rate caused by the increased number of relaxation pathways through a number of (13)C-(13)C homo-nuclear dipolar interactions and scalar J couplings, respectively, are dominant among (13)C-labeled nuclei. In addition, approximate correlation times for local conformational fluctuations of different domains, including the C-terminal tail, C-terminal alpha-helix, loops, and transmembrane alpha-helices, were estimated by measurement of the spin-lattice relaxation times in the laboratory frame and spin-spin relaxation times under the conditions of cross-polarization-magic angle spinning, and comparative study of suppressed specific peaks between the CP-MAS and DD-MAS experiments.

Irreversible conformational change of bacterio-opsin induced by binding of retinal during its reconstitution to bacteriorhodopsin, as studied by (13)C NMR.

We compared (13)C NMR spectra of [3-(13)C]Ala- and [1-(13)C]Val-labeled bacterio-opsin (bO), produced either by bleaching bR with hydroxylamine or from a retinal-deficient strain, with those of bacteriorhodopsin (bR), in order to gain insight into the conformational changes of the protein backbone that lead to correct folding after retinal is added to bO. The observed (13)C NMR spectrum of bO produced by bleaching is not greatly different from that of bR, except for the presence of suppressed or decreased peak-intensities. From careful evaluation of the intensity differences between cross polarization magic angle spinning (CP-MAS) and dipolar decoupled-magic angle spinning (DD-MAS) spectra, it appears that the reduced peak-intensities arise from reduced efficiency of cross polarization or interference of internal motions with proton decoupling frequencies. In particular, the E-F and F-G loops and some transmembrane helices of the bleached bO have acquired internal motions whose frequencies interfere with proton decoupling frequencies. In contrast, the protein backbone of the bO from the retinal-negative cells is incompletely folded. Although it contains mainly a-helices, its very broad (13)C NMR signals indicate that its tertiary structure is different from bR. Importantly, this changed structure is identical in form to that of bleached bO from wild-type bR after it was regenerated with retinal in vitro, and bleached with hydroxylamine. We conclude that the binding of retinal is essential for the correct folding of bR after it is inserted in vitro into the lipid bilayer, and the final folded state does not revert to the partially folded form upon removal of the retinal.

Long-Distance Effects of Site-Directed Mutations on Backbone Conformation in Bacteriorhodopsin from Solid State NMR of [1-13C]Val-Labeled Proteins

We have recorded 13C cross-polarization-magic angle spinning and dipolar decoupled-magic angle spinning NMR spectra of [1-13C]Val-labeled wild-type bacteriorhodopsin (bR), and the V49A, V199A, T46V, T46V/V49A, D96N, and D85N mutants, in order to study conformational changes of the backbone caused by site-directed mutations along the extracellular surface and the cytoplasmic half channel. On the basis of spectral changes in the V49A and V199A mutants, and upon specific cleavage by chymotrypsin, we assigned the three well-resolved 13C signals observed at 172.93, 172.00, and 171.11ppm to [1-13C]Val 69, Val 49, and Val 199, respectively. The local conformations of the backbone at these residues are revealed by the conformation-dependent 13C chemical shifts. We find that at the ambient temperature of these measurements Val 69 is not in a β-sheet, in spite of previous observations by electron microscopy and x-ray diffraction at cryogenic temperatures, but in a flexible turn structure that undergoes conformational fluctuation. Results with the T46V mutant suggest that there is a long-distance effect on backbone conformation between Thr 46 and Val 49. From the spectra of the D85N and E204Q mutants there also appears to be coupling between Val 49 and Asp 85 and between Asp 85 and Glu 204, respectively. In addition, the T2 measurement indicates conformational interaction between Asp 96 and extracellular surface. The protonation of Asp 85 in the photocycle therefore might induce changes in conformation or dynamics, or both, throughout the protein, from the extracellular surface to the side chain of Asp 96.

Conformation and dynamics of membrane proteins and biologically active peptides as studied by high-resolution solid-state 13C NMR

We have explored an empirical approach to clarify the three-dimensional structure and dynamics of membrane proteins such as bacteriorhodopsin (bR) based on 13C NMR measurements, utilizing the concept of the conformation-dependent displacements of 13C chemical shifts as determined by cross polarization-magic angle spinning (CP-MAS) and dipolar decoupled-magic angle spinning (DD-MAS) methods. This is possible because 13C chemical shifts of the amino acid residues under consideration are appreciably displaced, up to 8 ppm, depending upon particular conformations from several portions of membrane proteins such as the transmembrane α-helices, loops, N- or C-terminus, etc. as referred to the data accumulated to date of an appropriate model system. It is also possible to distinguish a region characterized by a variety of backbone motions with at least three different time scales from NMR data: rapid motions with correlation times shorter than 10 −8 s, intermediate motions with correlation times of 10 −4 to 10 −5 s, and slow motions with a time scale of 10 −2 s. In addition, we also explored a non-empirical approach to reveal the three-dimensional structure of a smaller molecular system such as biologically active peptides as a messenger molecule in signal transduction, based on accurately determined appropriate sets of interatomic distances as determined by rotational echo double resonance (REDOR). Examination of 13C or 15N chemical shifts before and after REDOR experiments proved to be an indispensable means to examine whether or not conformations of several kinds of 13C, 15N-doubly labeled samples at different positions are not changed all the time. Here, we summarize some illustrative examples to this end, selected from our recent studies on [3- 13C]Ala-labeled bR and biologically active peptides such as enkephalins.

Stability of the C-terminal alpha-helical domain of bacteriorhodopsin that protrudes from the membrane surface, as studied by high-resolution solid-state 13C NMR.

We have recorded 13C NMR spectra of [1-(13)C]Ala- and [3-(13)C]Ala-bacteriorhodopsin (bR), [1-(13)C]Ala- and [3-(13)C]Ala-papain-cleaved bR, and [3-(13)C]Ala-labeled R227Q bR mutant by cross polarization-magic angle spinning (CP-MAS) and dipolar decoupled-magic angle spinning (DD-MAS) methods. The pH and temperature were varied, and Arg 227 was replaced with Gln (R227Q), in order to clarify their effects on the stability of the alpha-helical domain of the C-terminus that protrudes from the membrane surface. The comparative 13C CP- and DD-MAS NMR study of [3-(13)C]Ala-bR, rather than [1-(13)C]Ala-bR, turned out to be the best means to distinguish the 13C NMR signals of the C-terminus from those of the rest of the transmembrane helices or loops. The inner segment of the C-terminus, from Ala 228 to Ala 235, forms an alpha-helical domain (resonated at 15.9 ppm) either at neutral pH and/or at 10 to -10 degrees C. The alpha-helical peak was not seen, however, after either cleavage of the C-terminus with papain or lowering the pH to 4.25. This alpha-helical structure, and a part of the random coil which was produced from the helix at pH 4.25, were further converted to a low-temperature-type alpha-helix, as indicated by an upfield displacement of the 13C NMR signal, when the temperature was lowered to 10- -10 degrees C. Surprisingly, the corresponding helical structure in R227Q is more stable than in the wild type at the acidic pH. This alpha-helical peak was classified as an alphaII-helix from the 13C chemical shifts of Cbeta carbon, although it was ascribed to an alphaI-helix on the basis of the carbonyl shifts. This is in contrast to Ala 53 which adopts the alphaII-helix as judged from the 13C chemical shifts of Cbeta and the carbonyl carbons. Therefore, this discrepancy might be caused by differential sensitivity of the two types of carbon signals to conformation and to modes of hydrogen bonding when motional fluctuation is involved. It is likely that the alphaII-helix form present at the C-terminus is not always the type originally proposed but should be considered as a form undergoing large-amplitude conformational fluctuation around alpha-helix.

Synergistic effect of zeolite in an intumescence process: study of the carbonaceous structures using solid-state NMR

This work deals with the chemical effect of zeolite 4A added to the intumescent ammonium polyphosphate (APP)–pentaerythritol (PER) system [fire retardant (FR) polyethylene-based formulation]. The study of the thermal behaviour of the system using thermogravimetric (TG) analysis shows that the presence of the zeolite leads to an increase in the stability of the material at high temperature (T > 500 °C). Chemical analysis and cross-polarisation dipolar-decoupled magic-angle spinning (CP–DD–MAS)13C NMR reveals that the materials resulting from the thermal treatment of the APP–PER and APP–PER/4A systems are formed by carbonaceous and phosphocarbonaceous species and that the zeolite enhances the stability of the phosphocarbonaceous species. DD–MAS 31P NMR indicates that this stability may be due to an absence of pyrophosphate species in the heat-treated APP–PER/4A system. Micro-Raman spectroscopy and 1H NMR of the solid state provides information on the structure of the carbonaceous material. Thermal treatment led to the formation of a ‘turbostatic carbon’ with a local structure of this ‘carbon species’, with the zeolite permitting retention of the comparatively unorganised carbon species in the high-temperature range. Moreover, a low-resolution solid-state 1H NMR study of the spin–lattice and spin–spin relaxations of the samples allows an evaluation of the size of the slow relaxation domains using the Goldman–Shen procedure. It is shown that the zeolite hinders the formation of small molecules in the polyaromatic network. Finally, the relationship between the formation of a coherent macromolecular network and the improved FR performance of the APP–PER/4A system is proposed.