Nuclear magnetic resonance at high pressure

Practical aspects of high-pressure NMR spectroscopy and its applications in protein biophysics and structural biology

Pressure and temperature are the two fundamental variables of thermodynamics. Temperature and chemical perturbation are central experimental tools for the exploration of macromolecular structure and dynamics. Though it has long been recognized that hydrostatic pressure offers a complementary and often unique view of macromolecular structure, stability and dynamics, it has not been employed nearly as much. For solution NMR applications the limited use of high-pressure is undoubtedly traced to difficulties of employing pressure in the context of modern multinuclear and multidimensional NMR. Limitations in pressure tolerant NMR sample cells have been overcome and enable detailed studies of macromolecular energy landscapes, hydration, dynamics and function. Here we review the practical considerations for studies of biological macromolecules at elevated pressure, with a particular emphasis on applications in protein biophysics and structural biology.

The energetics of a three-state protein folding system probed by high-pressure relaxation dispersion NMR spectroscopy

The energetic and volumetric properties of a three-state protein folding system, comprising a metastable triple mutant of the Fyn SH3 domain, have been investigated using pressure-dependent (15) N-relaxation dispersion NMR from 1 to 2500 bar. Changes in partial molar volumes (ΔV) and isothermal compressibilities (ΔκT ) between all the states along the folding pathway have been determined to reasonable accuracy. The partial volume and isothermal compressibility of the folded state are 100 mL mol(-1) and 40 μL mol(-1)  bar(-1) , respectively, higher than those of the unfolded ensemble. Of particular interest are the findings related to the energetic and volumetric properties of the on-pathway folding intermediate. While the latter is energetically close to the unfolded state, its volumetric properties are similar to those of the folded protein. The compressibility of the intermediate is larger than that of the folded state reflecting the less rigid nature of the former relative to the latter.

Cavities and Excited States in Proteins

Protein cavities or voids are observed as defects in atomic packing. Cavities have long been suggested to play important roles in protein dynamics and function, but the underlying origin and mechanism remains elusive. Here, recent studies about the cavities characterized by high-pressure NMR spectroscopy have been reviewed. Analysis of the pressure-dependent chemical shifts showed both linear and nonlinear response of proteins to pressure. The linear response corresponded to compression within the native ensemble, while the nonlinear response indicated the involvement of low-lying excited states that were different from the native state. The finding of non-linear pressure shifts in various proteins suggested that the existence of the low-lying excited states was common for globular proteins. However, the absolute nonlinear coefficient values varied significantly from protein to protein, and showed a good correlation with the density of cavities. Extensive studies on hen lysozyme as a model system showed that the cavity hydration and water penetration into the interior of proteins was an origin of the conformational transition to the excited states. The importance of cavities for protein function and evolution has also been explained. In addition to these "equilibrium" cavities, there are also "transient" cavities formed in the interior of the protein structure, as manifested by the ring flip motions of aromatic rings. The significance of transient cavities, reflecting an intrinsic dynamic nature within the native state, has also been discussed.

Thermodynamic properties of bulk and confined water

The thermodynamic response functions of water display anomalous behaviors. We study these anomalous behaviors in bulk and confined water. We use nuclear magnetic resonance (NMR) to examine the configurational specific heat and the transport parameters in both the thermal stable and the metastable supercooled phases. The data we obtain suggest that there is a behavior common to both phases: that the dynamics of water exhibit two singular temperatures belonging to the supercooled and the stable phase, respectively. One is the dynamic fragile-to-strong crossover temperature (T(L) ≃ 225 K). The second, T* ∼ 315 ± 5 K, is a special locus of the isothermal compressibility K(T)(T, P) and the thermal expansion coefficient α(P)(T, P) in the P-T plane. In the case of water confined inside a protein, we observe that these two temperatures mark, respectively, the onset of protein flexibility from its low temperature glass state (T(L)) and the onset of the unfolding process (T*).

The thermodynamical response functions and the origin of the anomalous behavior of liquid water

The density maximum of water dominates the thermodynamics of the system under ambient conditions, is strongly P-dependent, and disappears at a crossover pressure P(cross) approximately 1.8 kbar. We study this variable across a wide area of the T-P phase diagram. We consider old and new data of both the isothermal compressibility K(T)(T, P), the pressure constant specific heat C(P)(T) and the coefficient of thermal expansion alpha(P) (T, P). We observe that K(T)(T) shows a minimum at T* approximately 315 +/- 5 K for all of the studied pressures, whereas, at the same temperature, C(P)(T) has the minimal variation as a function of P in the interval 1 bar-4 kbar. We find the behavior of alpha(P) also to be surprising: all the alpha(P)(T) curves measured at different P cross at T*. The experimental data show a "singular and universal expansivity point" at T* approximately 315 K and alpha(P)(T*) = 0.44 10(-3) K(-1). Unlike other water singularities, we find this temperature to be thermodynamically consistent in the relationship connecting the three response functions. By considering also the P-T behavior of the self-diffusion coefficient D(S) and of the NMR proton chemical shift delta we have the information that at T* the water local order points out, with decreasing T, the crossover from a normal fluid to the anomalous and complex liquid characterized by the many anomalies.

A singular thermodynamically consistent temperature at the origin of the anomalous behavior of liquid water

The density maximum of water dominates the thermodynamics of the system under ambient conditions, is strongly P-dependent, and disappears at a crossover pressure P(cross) ~ 1.8 kbar. We study this variable across a wide area of the T-P phase diagram. We consider old and new data of both the isothermal compressibility K(T)(T, P) and the coefficient of thermal expansion α(P)(T, P). We observe that K(T)(T) shows a minimum at T* ~ 315±5 K for all the studied pressures. We find the behavior of α(P) to also be surprising: all the α(P)(T) curves measured at different P cross at T*. The experimental data show a "singular and universal expansivity point" at T* ~ 315 K and α(P)(T*) ≃ 0.44 10(-3) K(-1). Unlike other water singularities, we find this temperature to be thermodynamically consistent in the relationship connecting the two response functions.

Coupled motion in proteins revealed by pressure perturbation

The cooperative nature of protein substructure and internal motion is a critical aspect of their functional competence about which little is known experimentally. NMR relaxation is used here to monitor the effects of high pressure on fast internal motion in the protein ubiquitin. In contrast to the main chain, the motions of the methyl-bearing side chains have a large and variable pressure dependence. Within the core, this pressure sensitivity correlates with the magnitude of motion at ambient pressure. Spatial clustering of the dynamic response to applied hydrostatic pressure is also seen, indicating localized cooperativity of motion on the sub-nanosecond time scale and suggesting regions of variable compressibility. These and other features indicate that the native ensemble contains a significant fraction of members with characteristics ascribed to the recently postulated "dry molten globule". The accompanying variable side-chain conformational entropy helps complete our view of the thermodynamic architecture underlying protein stability, folding, and function.

High pressure magnetic resonance imaging with metallic vessels

High pressure measurements in most scientific fields rely on metal vessels given the superior tensile strength of metals. We introduce high pressure magnetic resonance imaging (MRI) measurements with metallic vessels. The developed MRI compatible metallic pressure vessel concept is very general in application. Macroscopic physical systems are now amenable to spatially resolved nuclear magnetic resonance (NMR) study at variable pressure and temperature. Metallic pressure vessels not only provide inherently high tensile strengths and efficient temperature control, they also permit optimization of the MRI RF probe sensitivity. An MRI compatible pressure vessel is demonstrated with a rock core holder fabricated using non-magnetic stainless steel. Water flooding through a porous rock under pressure is shown as an example of its applications. High pressure NMR spectroscopy plays an indispensable role in several science fields. This work will open new vistas of study for high pressure material science MRI and MR.

Repulsive reference potential reproducing the dynamics of a liquid with attractions

A well-known result of liquid state theory is that the structure of dense fluids is mainly determined by their repulsive forces. The Weeks-Chandler-Andersen potential, which cuts intermolecular potentials at their minima, is therefore often used as a reference. However, this cannot reproduce the viscous dynamics of the Kob-Andersen binary Lennard-Jones liquid [Berthier and Tarjus, Phys. Rev. Lett. 103, 170601 (2009)]. This paper shows that repulsive inverse-power-law potentials provide a reference for this liquid that reproduces its structure, dynamics, and isochoric heat capacity.

Nonperturbative effect of attractive forces in viscous liquids

We study the role of the attractive intermolecular forces in the viscous regime of a simple glass-forming liquid by using computer simulations. To this end, we compare the structure and the dynamics of a standard Lennard-Jones glass-forming liquid model with and without the attractive tail of the interaction potentials. The viscous slowing down of the two systems is found to be quantitatively and qualitatively different over a broad density range, whereas the static pair correlations remain close. The common assumption that the behavior of dense nonassociated liquids is determined by the short-ranged repulsive part of the intermolecular potentials dramatically breaks down for the relaxation in the viscous liquid regime.

Thermodynamics of coarse-grained models of supercooled liquids

In recent papers, we have argued that kinetically constrained coarse-grained models can be applied to understand dynamic properties of glass-forming materials, and we have used this approach in various applications that appear to validate this view. In one such paper [J. P. Garrahan and D. Chandler, Proc. Natl. Acad. Sci. U.S.A. 100, 9710 (2003)], among other things we argued that this approach also explains why the heat-capacity discontinuity at the glass transition is generally larger for fragile materials than for strong materials. In the preceding article, Biroli, Bouchaud, and Tarjus have objected to our explanation on this point, arguing that the class of models we apply is inconsistent with both the absolute size and the temperature dependence of the experimental specific heat. Their argument, however, neglects parameters associated with the coarse graining. Accounting for these parameters, we show here that our treatment of dynamics is not inconsistent with heat-capacity discontinuities.

High-pressure fluorescence correlation spectroscopy

We demonstrate that a novel high-pressure cell is suitable for fluorescence correlation spectroscopy (FCS). The pressure cell consists of a single fused silica microcapillary. The cylindrical shape of the capillary leads to refraction of the excitation light, which affects the point spread function of the system. We characterize the influence of these beam distortions by FCS and photon-counting histogram (PCH) analysis and identify the optimal position for fluorescence fluctuation experiments in the capillary. At this position within the capillary, FCS and photon-counting histogram experiments are described by the same equations as used in standard FCS experiments. We report the first experimental realization of fluorescence fluctuation spectroscopy under high pressure. A fluorescent dye was used as a model system for evaluating the properties of the capillary under pressure. The autocorrelation function and the photon count distribution were measured in the pressure range from 0 to 300 MPa. The fluctuation amplitude and the diffusion coefficient show a small pressure dependence. The changes of these parameters, which are on the order of 10%, are due to the pressure changes of the viscosity and the density of the aqueous medium.

Acetone hydration in supercritical water: 13C-NMR spectroscopy and Monte Carlo simulation

The (13)C-NMR chemical shift of acetone delta((13)C[Double Bond]O) was measured in aqueous solution at high temperatures up to 400 degrees C and water densities of 0.10-0.60 g/cm(3) for the study of hydration structure in the supercritical conditions. The average number N(HB) of hydrogen bonds (HBs) between an acetone and solvent waters and the energy change DeltaE upon the HB formation were evaluated from the delta and its temperature dependence, respectively. At 400 degrees C, N(HB) is an increasing function of the water density, the increase being slower at higher water densities. The acetone-water HB formation is exothermic in supercritical water with larger negative DeltaE at lower water densities (-3.3 kcal/mol at 0.10 g/cm(3) and -0.3 kcal/mol at 0.60 g/cm(3)), in contrast to the positive DeltaE in ambient water (+0.078 kcal/mol at 4 degrees C). The corresponding Monte Carlo simulations were performed to calculate the radial and orientational distribution functions of waters around the acetone molecule. The density dependence of N(HB) calculated at 400 degrees C is in a qualitative agreement with the experimental results. In the supercritical conditions, the HB angle in a neighboring acetone-water pair is weakly influenced by the water density, because of the absence of collective HB structure. This is in sharp contrast to the hydration structure in ambient water, where the acetone-water HB formation is orientationally disturbed by the tetrahedral HB network formation among the surrounding waters.

High-resolution nuclear magnetic resonance studies of proteins

The combination of advanced high-resolution nuclear magnetic resonance (NMR) techniques with high-pressure capability represents a powerful experimental tool in studies of protein folding. This review is organized as follows: after a general introduction of high-pressure, high-resolution NMR spectroscopy of proteins, the experimental part deals with instrumentation. The main section of the review is devoted to NMR studies of reversible pressure unfolding of proteins with special emphasis on pressure-assisted cold denaturation and the detection of folding intermediates. Recent studies investigating local perturbations in proteins and the experiments following the effects of point mutations on pressure stability of proteins are also discussed. Ribonuclease A, lysozyme, ubiquitin, apomyoglobin, alpha-lactalbumin and troponin C were the model proteins investigated.

Effects of high hydrostatic pressures on living cells: a consequence of the properties of macromolecules and macromolecule-associated water

Sixty percent of the Earth's biomass is found in the sea, at depths greater than 1000 m, i.e., at hydrostatic pressures higher than 100 atm. Still more surprising is the fact that living cells can reversibly withstand pressure shifts of 1000 atm. One explanation lies in the properties of cellular water. Water forms a very thin film around macromolecules, with a heterogeneous structure that is an image of the heterogeneity of the macromolecular surface. The density of water in contact with macromolecules reflects the physical properties of their different domains. Therefore, any macromolecular shape variations involving the reorganization of water and concomitant density changes are sensitive to pressure (Le Chatelier's principle). Most of the pressure-induced changes to macromolecules are reversible up to 2000 atm. Both the effects of pressure shifts on living cells and the characteristics of pressure-adapted species are opening new perspectives on fundamental problems such as regulation and adaptation.

A polymer NMR cell for the study of high-pressure and supercritical fluid solutions

Nuclear magnetic resonance (NMR) offers researchers unique, highly localized molecular information. The importance of this technique is well established in studies using chemical shift, spin coupling, and relaxation times providing detailed structural information, determining chemical equilibria and kinetics, and understanding molecular dynamic processes. However, the widespread application of NMR spectroscopy to high-pressure liquids and supercritical fluids has been limited due to the complexity of the necessary instrumentation. One approach to these studies is to build a dedicated high-pressure probe. Another involves the utilization of a high-pressure cell designed to fit in commercially available probes. Here we present the design and implementation of a simple, three-piece, high-pressure NMR cell constructed of high-performance polymers. The present cell has pressure capabilities of up to 400 bar; however, the ultimate temperature and pressure limits will be determined by the specific polymer chosen. High-resolution NMR spectra of methanol modified and tributyl phosphate (IBP) modified supercritical CO2 are presented. An example of supercritical fluid phase behavior monitored with NMR is demonstrated for the TBP system in which the chemical shift changes in the 31P nucleus as a function of density are indicative of solution phase separation. The multinuclear NMR data demonstrate the utility of this cell for studying supercritical fluid solution systems relevant to analytical separations and extractions.

Temperature effect on the 13C NMR chemical shift of pressurized CO2 containing selected modifiers

Temperature dependence of 13C NMR chemical shift of pressurized CO2 containing modifiers has been studied. Benzene, C6F6, C6F5OH, (CF3)2CHOH and [(CH3)2N]3PO were used as the modifiers. The 13C chemical shift of CO2 was found to show a different temperature dependence in the presence of selected modifiers.

High-resolution, high-pressure NMR studies of proteins

Advanced high-resolution NMR spectroscopy, including two-dimensional NMR techniques, combined with high pressure capability, represents a powerful new tool in the study of proteins. This contribution is organized in the following way. First, the specialized instrumentation needed for high-pressure NMR experiments is discussed, with specific emphasis on the design features and performance characteristics of a high-sensitivity, high-resolution, variable-temperature NMR probe operating at 500 MHz and at pressures of up to 500 MPa. An overview of several recent studies using 1D and 2D high-resolution, high-pressure NMR spectroscopy to investigate the pressure-induced reversible unfolding and pressure-assisted cold denaturation of lysozyme, ribonuclease A, and ubiquitin is presented. Specifically, the relationship between the residual secondary structure of pressure-assisted, cold-denatured states and the structure of early folding intermediates is discussed.

Molecular mechanisms of pressure induced conformational changes in BPTI

We have performed a 800 ps molecular dynamics simulation of bovine pancreatic trypsin inhibitor (BPTI) in water coupled to a pressure bath at 1, 10,000, 15,000, and 20,000 bar. The simulation reproduces quite well the experimental behavior of the protein under high pressure. The protein keeps its globular form, but adopts a different conformation with a very small reduction in volume. Some residues in the hydrophobic core become exposed to water and a large part of the secondary structure of the protein, (60% of the sheet structure and 40% of the helical structure) is denatured between 10 and 15 kbar. This is in good agreement with experimental data (Goossens, K., et al. Eur. J. Biochem, 236:254-262, 1996) that show denaturation of BPTI between 8 and 14 kbar. A further increase of the pressure results in a freezing of the protein as deduced from the large decrease of the mobility of the residues. During the simulation, the normal structure of water changes from an ice Ih-like to an ice VI-like structure, while keeping the liquid state. The driving force of the high pressure induced conformational transition seems be the higher compressibility of the water compared with the protein. This produces a change in the solvent properties and leads to penetration of the solvent into the hydrophobic core.

High-resolution 13C NMR study of pressure effects on the main phase transition in L-alpha-dipalmitoyl phosphatidylcholine vesicles

The effects of pressure on the liquid-crystalline to gel transition in vesicles of L-alpha-dipalmitoyl phosphatidylcholine were investigated by high-resolution proton-decoupled natural-abundance 13C NMR spectroscopy. The linewidths of several 13C resonances, including the choline methyl groups, carbonyl carbons, and choline methylene groups and the palmitoyl methyl groups are reported as a function of pressure at 52.7 degrees C. These preliminary NMR experiments clearly demonstrate that high-pressure, high-resolution proton-decoupled natural-abundance 13C NMR spectra are a promising tool to study the phase-transition behavior and the dynamics of model membrane systems.

The effect of high pressure upon proteins and other biomolecules

We shall not attempt here to enumerate the results or review in a systematic way the significant literature dealing with the use of high pressure in studies of proteins and other molecules of biological interest. Two recent reviews on this subject, one by MOrild (1981) and another by Heremans (1982), and a further article by Jaenicke (1981) on enzymes under extreme environmental conditions contain expositions and references that would render redundatn such a task. Rather we concentrate here on the examination of othe conceptual framework employed in the interpretation of high pressure experiments and in the critical discussion of our knowledge of selected areas of present interest and likely future significance.