High-pressure NMR Research Articles

Characteristics of water alternating CO2 injection in low-permeability beach-bar sand reservoirs

Water flooding can be ineffective in highly heterogeneous low-permeability beach-bar sand reservoirs. The introduction of CO2 flooding helps boost the oil production of the reservoirs but only in an early stage. During the late stage of flooding, gas channeling would occur. Water alternating gas (CO2) (WAG) process can be used to delay gas channeling and improve the effect of CO2 injection, though its adaptability to beach-bar sand reservoirs remains unclear. In order to clarify CO2 injection characteristics in these reservoirs, experiments were carried out in high-temperature high-pressure NMR on-line displacement experiment apparatus to simulate different flooding modes on synthetic cores that can reflect the vertical heterogeneity of beach-bar reservoirs. Different CO2 injection modes were implemented on these cores and the displacement characteristics and residual oil distribution features during both WAG injection and continuous CO2 injection were analyzed quantitatively and qualitatively. The results show that the scheme of WAG injection after continuous CO2 injection can obtain better oil displacement efficiency than that of the scheme of continuous CO2 injection after WAG injection, but there is no significant difference in respect of oil displacement efficiency of WAG flooding between the mode of bar-injection – beach-production (injection into bar sand – production from beach sand) and the mode of beach-injection – beach-production (injection into and production from beach sand), with the former mode having a higher oil recovery rate. The wider pore-size distribution range of microscopic residual oil after WAG injection shows great potential of enhancing oil recovery from subsequent continuous gas injection. When WAG injection is implemented prior to continuous CO2 injection, the displacement effect of the latter is more significant. This research may provide a theoretical basis for CO2 EOR in this type of reservoirs.

Combining High-Pressure NMR and Geometrical Sampling to Obtain a Full Topological Description of Protein Folding Landscapes: Application to the Folding of Two MAX Effectors from Magnaporthe oryzae.

Despite advances in experimental and computational methods, the mechanisms by which an unstructured polypeptide chain regains its unique three-dimensional structure remains one of the main puzzling questions in biology. Single-molecule techniques, ultra-fast perturbation and detection approaches and improvement in all-atom and coarse-grained simulation methods have greatly deepened our understanding of protein folding and the effects of environmental factors on folding landscape. However, a major challenge remains the detailed characterization of the protein folding landscape. Here, we used high hydrostatic pressure 2D NMR spectroscopy to obtain high-resolution experimental structural information in a site-specific manner across the polypeptide sequence and along the folding reaction coordinate. We used this residue-specific information to constrain Cyana3 calculations, in order to obtain a topological description of the entire folding landscape. This approach was used to describe the conformers populating the folding landscape of two small globular proteins, AVR-Pia and AVR-Pib, that belong to the structurally conserved but sequence-unrelated MAX effectors superfamily. Comparing the two folding landscapes, we found that, in spite of their divergent sequences, the folding pathway of these two proteins involves a similar, inescapable, folding intermediate, even if, statistically, the routes used are different.

NMR Analysis Method of Gas Flow Pattern in the Process of Shale Gas Depletion Development

Shale gas reservoirs have pores of various sizes, in which gas flows in different patterns. The coexistence of multiple gas flow patterns is common. In order to quantitatively characterize the flow pattern in the process of shale gas depletion development, a physical simulation experiment of shale gas depletion development was designed, and a high-pressure on-line NMR analysis method of gas flow pattern in this process was proposed. The signal amplitudes of methane in pores of various sizes at different pressure levels were calculated according to the conversion relationship between the NMR T 2 relaxation time and pore radius, and then, the flow patterns of methane in pores of various sizes under different pore pressure conditions were analyzed as per the flow pattern determination criteria. It is found that there are three flow patterns in the process of shale gas depletion development, i.e., continuous medium flow, slip flow, and transitional flow, which account for 73.5%, 25.8%, and 0.7% of total gas flow, respectively. When the pore pressure is high, the continuous medium flow is dominant. With the gas production in shale reservoir, the pore pressure decreases, the Knudsen number increases, and the pore size range of slip flow zone and transitional flow zone expands. When the reservoir pressure is higher than the critical desorption pressure, the adsorbed gas is not desorbed intensively, and the produced gas is mainly free gas. When the reservoir pressure is lower than the critical desorption pressure, the adsorbed gas is gradually desorbed, and the proportion of desorbed gas in the produced gas gradually increases.

Allosteric modulation of the adenosine A2A receptor by cholesterol.

Cholesterol is a major component of the cell membrane and commonly regulates membrane protein function. Here, we investigate how cholesterol modulates the conformational equilibria and signaling of the adenosine A2A receptor (A2AR) in reconstituted phospholipid nanodiscs. This model system conveniently excludes possible effects arising from cholesterol-induced phase separation or receptor oligomerization and focuses on the question of allostery. GTP hydrolysis assays show that cholesterol weakly enhances the basal signaling of A2AR while decreasing the agonist EC50. Fluorine nuclear magnetic resonance (19F NMR) spectroscopy shows that this enhancement arises from an increase in the receptor's active state population and a G-protein-bound precoupled state. 19F NMR of fluorinated cholesterol analogs reveals transient interactions with A2AR, indicating a lack of high-affinity binding or direct allosteric modulation. The combined results suggest that the observed allosteric effects are largely indirect and originate from cholesterol-mediated changes in membrane properties, as shown by membrane fluidity measurements and high-pressure NMR.

Equilibria between conformational states of the Ras oncogene protein revealed by high pressure crystallography.

In this work, we experimentally investigate the allosteric transitions between conformational states on the Ras oncogene protein using high pressure crystallography. Ras protein is a small GTPase involved in central regulatory processes occurring in multiple conformational states. Ras acts as a molecular switch between active GTP-bound, and inactive GDP-bound states, controlling essential signal transduction pathways. An allosteric network of interactions between the effector binding regions and the membrane interacting regions is involved in Ras cycling. The conformational states which coexist simultaneously in solution possess higher Gibbs free energy than the ground state. Equilibria between these states can be shifted by applying pressure favouring conformations with lower partial molar volume, and has been previously analyzed by high-pressure NMR spectroscopy. High-pressure macromolecular crystallography (HPMX) is a powerful tool perfectly complementary to high-pressure NMR, allowing characterization at the molecular level with a high resolution the different allosteric states involved in the Ras cycling. We observe a transition above 300 MPa in the crystal leading to more stable conformers. Thus, we compare the crystallographic structures of Ras(wt)·Mg2+·GppNHp and Ras(D33K)·Mg2+·GppNHp at various high hydrostatic pressures. This gives insight into per-residue descriptions of the structural plasticity involved in allosteric equilibria between conformers. We have mapped out at atomic resolution the different segments of Ras protein which remain in the ground-state conformation or undergo structural changes, adopting excited-energy conformations corresponding to transient intermediate states. Such in crystallo phase transitions induced by pressure open the possibility to finely explore the structural determinants related to switching between Ras allosteric sub-states without any mutations nor exogenous partners.

Refined high-pressure tube design for improved resolution in high-pressure NMR spectroscopy.

High-pressure NMR spectroscopy has become a valuable analytical tool in many activities, including the energy sector, chemical research, and biophysics. Many pressure-based applications could benefit from low-field NMR. In this context, a novel, simple, and low-cost high-pressure tube design improving the signal-to-noise ratio by more than 80% is presented.

Asphaltene precipitation and reservoir damage characteristics of CO2 flooding in different microscopic structure types in tight light oil reservoirs

Asphaltene precipitation is often accompanied by CO2 injection in tight light oil reservoirs. In tight oil reservoirs, the traditional studies of reservoir damage by asphaltene precipitation after CO2 flooding have limitations that the influence of reservoir microscopic pore structure characteristic parameters is not considered. In order to accurately evaluate the asphaltene precipitation characteristics and reservoir damage degree of different microscopic structure types, SEM, high pressure mercury injection and NMR have been used. In this study, the asphaltene precipitation characteristics under different CO2 flooding conditions have been clarified. The damage degree of asphaltene precipitation on the pore throat blockage characteristics, porosity, permeability and wettability of different types of reservoirs and the effect on oil displacement efficiency have been evaluated. The results show that the Chang 8 reservoir can be divided into type I, type II, and type III. The percolation capacity and storage space of the three pore structure reservoirs decrease successively. The asphaltene precipitation of three types of reservoirs increases with the increase of threshold pressure and injection volume. The blockage rate of large and small pores is the highest in type III reservoirs, followed by type II reservoir, and type I reservoir is the lowest. The oil displacement efficiency is the highest for type II reservoir and the lowest for type I reservoir. Asphaltene precipitation has little effect on porosity of three types of reservoirs, but has high damage on permeability. Asphaltene precipitation easily causes wettability reversal to lipophilicity and the reversal index increases with the injection pressure. The wettability reversal index of type I reservoir is the highest and that of type III reservoir is the lowest. The surfactant can be injected in reservoir to reduce the wettability reversal index caused by asphaltene precipitation. This paper has evaluated the asphaltene precipitation characteristics of CO2 flooding in tight light oil reservoirs, which further supplements the mechanism of CO2 flooding and provides reference and guidance for the optimization of field parameters.

Combined High-Pressure and Multiquantum NMR and Molecular Simulation Propose a Role for N-Terminal Salt Bridges in Amyloid-Beta.

Several lines of evidence point to the important role of the N-terminal region of amyloid-beta (Aβ) peptide in its toxic aggregation in Alzheimer’s disease (AD). It is known that charge-altering modifications such as Ser8 phosphorylation promote Aβ fibrillar aggregation. In this Letter, we combine high-pressure NMR, multiquantum chemical exchange saturation transfer (MQ-CEST) NMR, and microseconds-long molecular dynamics simulation and provide evidence of the presence of several salt bridges between Arg5 and its nearby negatively charged residues, in particular, Asp7 and Glu3. The presence of these salt bridges is correlated with less extended structures in the N-terminal region of Aβ. Through density functional theory calculations, we demonstrate how the introduction of negatively charged phosphoserine 8 influences the network of adjacent salt bridges in Aβ and favors more extended N-terminal structures. Our data propose a structural mechanism for the Ser8-phosphorylation-promoted Aβ aggregation and define the N-terminal salt bridges as potential targets for anti-AD drug design.

Comparative Assessment of NMR Probes for the Experimental Description of Protein Folding Pathways with High-Pressure NMR.

Simple SummaryDuring the last decade, high-pressure multidimensional NMR has emerged as a very powerful tool to describe the folding landscapes of proteins. This is (i) because pressure is a gentle perturbation, the effects of which originate from local properties of the folded state, contrary to chemical or thermal denaturation, and (ii) because multidimensional NMR intrinsically provides multiple probes strategically scattered on the three-dimensional structure of the protein, allowing a quasi-atomic resolution to describe the folding pathway. Residue-specific information obtained from these probes can be used to describe protein folding pathways through the calculation of NMR-derived fractional probabilities of contact at increasing pressure. Here, we used this strategy to evaluate and compare the results obtained from NH amide, CαHα, and CH3 groups when used as NMR probes to explore the folding pathway of the model protein ∆+PHS Staphylococcal Nuclease. Multidimensional NMR intrinsically provides multiple probes that can be used for deciphering the folding pathways of proteins: NH amide and CαHα groups are strategically located on the backbone of the protein, while CH3 groups, on the side-chain of methylated residues, are involved in important stabilizing interactions in the hydrophobic core. Combined with high hydrostatic pressure, these observables provide a powerful tool to explore the conformational landscapes of proteins. In the present study, we made a comparative assessment of the NH, CαHα, and CH3 groups for analyzing the unfolding pathway of ∆+PHS Staphylococcal Nuclease. These probes yield a similar description of the folding pathway, with virtually identical thermodynamic parameters for the unfolding reaction, despite some notable differences. Thus, if partial unfolding begins at identical pressure for these observables (especially in the case of backbone probes) and concerns similar regions of the molecule, the residues involved in contact losses are not necessarily the same. In addition, an unexpected slight shift toward higher pressure was observed in the sequence of the scenario of unfolding with CαHα when compared to amide groups.

High-Pressure NMR Experiments for Detecting Protein Low-Lying Conformational States

High-Pressure NMR Experiments for Detecting Protein Low-Lying Conformational States

High-Pressure NMR Experiments for Detecting Protein Low-Lying Conformational States.

High-pressure is a well-known perturbation method that can be used to destabilize globular proteins and dissociate protein complexes in a reversible manner. Hydrostatic pressure drives thermodynamical equilibria toward the state(s) with the lower molar volume. Increasing pressure offers, therefore, the opportunities to finely tune the stability of globular proteins and the oligomerization equilibria of protein complexes. High-pressure NMR experiments allow a detailed characterization of the factors governing the stability of globular proteins, their folding mechanisms, and oligomerization mechanisms by combining the fine stability tuning ability of pressure perturbation and the site resolution offered by solution NMR spectroscopy. Here we present a protocol to probe the local folding stability of a protein via a set of 2D 1H-15N experiments recorded from 1 bar to 2.5 kbar. The steps required for the acquisition and analysis of such experiments are illustrated with data acquired on the RRM2 domain of hnRNPA1.

Protein-Ligand Binding Volume Determined from a Single 2D NMR Spectrum with Increasing Pressure.

Proteins undergo changes in their partial volumes in numerous biological processes such as enzymatic catalysis, unfolding–refolding, and ligand binding. The change in the protein volume upon ligand binding—a parameter termed the protein–ligand binding volume—can be extensively studied by high-pressure NMR spectroscopy. In this study, we developed a method to determine the protein–ligand binding volume from a single two-dimensional (2D) 1H–15N heteronuclear single quantum coherence (HSQC) spectrum at different pressures, if the exchange between ligand-free and ligand-bound states of a protein is slow in the NMR time-scale. This approach required a significantly lower amount of protein and NMR time to determine the protein–ligand binding volume of two carbonic anhydrase isozymes upon binding their ligands. The proposed method can be used in other protein–ligand systems and expand the knowledge about protein volume changes upon small-molecule binding.

Thermodynamic Stability of hnRNP A1 Low Complexity Domain Revealed by High-Pressure NMR

Low-complexity (LC) domains found in RNA-binding proteins associated with liquid-liquid phase separation form a specific class of intrinsically disordered domains. LC domains have distinct amino acid compositions; they are enriched in polar amino acids (especially Ser and Gly), and feature conserved patterns of aromatic residues. in many cases, these disordered LC domains are necessary and sufficient for driving phase separation. Liquid condensates are believed to be the result of multivalent weak interactions between multiple interacting motifs in LC domains, including electrostatic, cation-pi and pi-pi interactions.

Volume and compressibility differences between protein conformations revealed by high-pressure NMR

Proteins often interconvert between different conformations in ways critical to their function. Although manipulating such equilibria for biophysical study is often challenging, the application of pressure is a potential route to achieve such control by favoring the population of lower volume states. Here, we use this feature to study the interconversion of ARNT PAS-B Y456T, which undergoes a dramatic +3 slip in the β-strand register as it switches between two stably folded conformations. Using high-pressure biomolecular NMR approaches, we obtained the first, to our knowledge, quantitative data testing two key hypotheses of this process: the slipped conformation is both smaller and less compressible than the wild-type equivalent, and the interconversion proceeds through a chiefly unfolded intermediate state. Data collected in steady-state pressure and time-resolved pressure-jump modes, including observed pressure-dependent changes in the populations of the two conformers and increased rate of interconversion between conformers, support both hypotheses. Our work exemplifies how these approaches, which can be generally applied to protein conformational switches, can provide unique information that is not easily accessible through other techniques.

High-pressure NMR measurements provide insights into the different structural states that proteins can adopt

In structural biology, we are often familiar with the well-defined ground-state structure that a biomolecule adopts. As of today, combined efforts from x-ray crystallography, NMR spectroscopy, and cryo-electron microscopy have revealed over 170,000 static snapshots of proteins, RNAs, DNAs, and complexes thereof. These structures provide indispensable insights into the mechanisms that drive molecular function. At the same time, it is clear that biomolecules are highly dynamic entities that can populate distinct structural states that differ from the ground-state structure (1).

水中におけるナフタレン骨格超分子チューブと1,4-ジオキサンの複合体形成と圧力効果

Host-guest interactions between a pair of naphthalene-based molecular tubes (i.e., anti-isomer and syn-isomer) and 1,4-dioxiane have been studied to understand selective recognition. Volume changes for complexation of the amide naphthotubes with 1,4-dioxane were investigated using high-pressure fluorescence and high-pressure NMR spectroscopy. We found that the partial molar volume change (ΔV°) for the association of 1,4-dioxane with the naphthotubes was －6.3±0.1 mL mol－1 for the anti-isomer and 3.2±0.4 mL mol－1 for the syn-isomer. To elucidate the molecular basis of ΔV°, molecular dynamics simulations of the complexation process were also performed. The difference in ΔV° was attributed to variations in the shape and hydration of naphthotube hydrophobic cavities.

Proton dynamics in high-pressure ice-VII from density functional theory

Using a density-functional-theory-based approach, we explore the symmetrization and proton dynamics in ice-VII, for which recent high-pressure NMR experiments indicate significant proton dynamics in the pressure-range of $20-95$ GPa. We directly sample the potential seen by the proton and find a continuous transition from double- to single-well character over the pressure range of 2 to 130 GPa accompanied by proton dynamics in agreement with the NMR experiments.

Insight into decomposition of formic acid to syngas required for Rh-catalyzed hydroformylation of olefins

Formic acid (FA) is one kind of important bulk chemicals, which is recognized as a sustainable and eco-friendly energy carrier to transport H2 via dehydrogenation or CO via decarbonylation. Expectantly, FA upon decomposition into H2 and CO could be used as the syngas alternative for hydroformylation. In this paper, the behaviors of FA to release H2 as well as CO following the distinct pathways were carefully investigated for the first time, and then established a new hydroformylation protocol free of syngas. It was found that the atmospheric hydroformylation of olefins with formic acid (FA) as syngas alternative was smoothly fulfilled over Xantphos (L1) modified Rh-catalyst under mild conditions (80 °C, Rh concentration 1 mol %, 14 h), resulting in >90% conversion of the olefins along with the high selectivity to the target aldehydes (>93%). By using FA as syngas source, the side-reaction of olefin-hydrogenation was greatly depressed. The in situ FT-IR and the high-pressure 1H NMR spectroscopic analyses were applied to reveal how FA behaves dually as CO surrogate and hydrogen source over L1-Rh(acac)(CO)2 catalytic system, based on which the deeply insight into the catalytic mechanism of hydroformylation of olefins with FA as syngas alternative was offered.

Proton mobility in metallic copper hydride from high-pressure nuclear magnetic resonance

Atomic and electronic structures of Cu2H and CuH have been investigated by high pressure NMR spectroscopy, X-ray diffraction and ab-initio calculations. Metallic Cu2H was synthesized at a pressure of 40 GPa, and semi-metallic CuH at 90 GPa, found stable up to 160 GPa. Experiments and computations suggest the formation of a metallic 1H-sublattice as well as a high 1H mobility of ~10-7 cm2/s in Cu2H. Comparison of Cu2H and FeH data suggests that deviations from Fermi gas behavior, formation of conductive hydrogen networks, and high 1H mobility could be common features of metal hydrides.

Aliphatic polycarbonates derived from epoxides and CO2: A comparative study of poly(cyclohexene carbonate) and poly(limonene carbonate)

The ring-opening copolymerization (ROCOP) of epoxides and CO2 provides an alternative approach towards polycarbonates and due to their aliphatic nature, they represent an interesting alternative to bisphenol-A based polycarbonates. A Lewis acidic β-diiminate (BDI)CF3-Zn-(SiMe3)2 complex 1 is used in the ROCOP of CO2 with cyclohexene oxide (CHO) and limonene oxide (LO), respectively. The knowledge gained from polymerizations monitored via in situ IR spectroscopy was used to upscale the reactions to a 1 L reactor. The two products poly(cyclohexene carbonate) (PCHC) and poly(limonene carbonate) (PLC) were then characterized via thermal analysis, a multiaxial pressure test, and dynamic mechanical analysis and compared with commercial polymers. While PCHC and PLC were both thermally stable at 150 °C for 20 min and only minor decomposition occurred at 180 °C, PLC is prone to cross-linking at elevated temperatures. This could be prevented by hydrogenation of the double bond or by the addition of an antioxidant. In the mechanical performance, the aliphatic polymers ranged between the highly impact resistant Durabio® and the brittle PMMA but broke without a splintering of the material. Overall, this study enabled a classification of CO2-based polycarbonates, especially of the novel PLC. Additionally, complex 1 was active in the terpolymerization of CHO, LO, and CO2. The formation of an actual terpolymer was confirmed via aliquot gel-permeation chromatography and diffusion-ordered NMR spectroscopy. High-pressure NMR techniques reveal an interesting kinetic feature. CHO gets copolymerized with CO2 exclusively, and LO incorporation only starts when CHO is fully consumed.