High-pressure NMR Spectroscopy Research Articles

Solution NMR investigation of the response of the lactose repressor core domain dimer to hydrostatic pressure

Previous investigations of the sensitivity of the lac repressor to high-hydrostatic pressure have led to varying conclusions. Here high-pressure solution NMR spectroscopy is used to provide an atomic level view of the pressure induced structural transition of the lactose repressor regulatory domain (LacI* RD) bound to the ligand IPTG. As the pressure is raised from ambient to 3kbar the native state of the protein is converted to a partially unfolded form. Estimates of rotational correlation times using transverse optimized relaxation indicates that a monomeric state is never reached and that the predominate form of the LacI* RD is dimeric throughout this pressure change. Spectral analysis suggests that the pressure-induced transition is localized and is associated with a volume change of approximately −115mlmol−1 and an average pressure dependent change in compressibility of approximately 30mlmol−1kbar−1. In addition, a subset of resonances emerge at high-pressures indicating the presence of a non-native but folded alternate state.

Unexpected CO Dependencies, Catalyst Speciation, and Single Turnover Hydrogenolysis Studies of Hydroformylation via High Pressure NMR Spectroscopy

Rhodium bis(diazaphospholane) (BDP) catalyzed hydroformylation of styrene is sensitive to CO concentration, and drastically different kinetic regimes are affected by modest changes in gas pressure. The Wisconsin High Pressure NMR Reactor (WiHP-NMRR) has enabled the observation of changes in catalyst speciation in these different regimes. The apparent discrepancy between catalyst speciation and product distribution led us to report the first direct, noncatalytic quantitative observation of hydrogenolysis of acyl dicarbonyls. Analysis and modeling of these experiments show that not all catalyst is shunted through the off-cycle intermediates and this contributes to the drastic mismatch in selectivities. The data herein highlight the complex kinetics of Rh(BDP) catalyzed hydroformylation. In this case, the complexity arises from competing kinetic and thermodynamic preferences involving formation and isomerization of the acyl mono- and dicarbonyl intermediates and their hydrogenolysis to give aldehydes.

Conformational Substates of Amyloidogenic hIAPP Revealed by High Pressure NMR Spectroscopy

The islet amyloid polypeptide (IAPP) is a peptide hormone that is secreted by pancreatic beta cells along with glucagon and insulin. The development of type-2 diabetes mellitus (T2DM) is accompanied by aggregation and amyloid deposits of IAPP. Here we report pressure-induced changes of NMR chemical shifts for the elucidation of conformational substates of IAPP in bulk solution. Comparison with a similar peptide, the Alzheimer peptide Ab, reveals that the area around amino acid residues 3-20 displays large differences in the first and second order pressure coefficients, pinpointing to a different structural ensemble in this sequence element, while the area around amino acid residues 28-37 displays similar transient structural conformations for both peptides. Knowledge of the structural nature of the highly amyloidogenic IAPP and the differences with respect to the conformational ensemble of Ab will help facilitate the rational design of drugs for therapeutic treatment of T2DM.

The Chemical Shift Baseline for High-Pressure NMR Spectra of Proteins.

High-pressure (HP) NMR spectroscopy is an important method for detecting rare functional states of proteins by analyzing the pressure response of chemical shifts. However, for the analysis of the shifts it is mandatory to understand the origin of the observed pressure dependence. Here we present experimental HP NMR data on the (15) N-enriched peptide bond model, N-methylacetamide (NMA), in water, combined with quantum-chemical computations of the magnetic parameters using a pressure-sensitive solvation model. Theoretical analysis of NMA and the experimentally used internal reference standard 4,4-dimethyl-4-silapentane-1-sulfonic (DSS) reveal that a substantial part of observed shifts can be attributed to purely solvent-induced electronic polarization of the backbone. DSS is only marginally responsive to pressure changes and is therefore a reliable sensor for variations in the local magnetic field caused by pressure-induced changes of the magnetic susceptibility of the solvent.

Structural transitions in full-length human prion protein detected by xenon as probe and spin labeling of the N-terminal domain.

Fatal neurodegenerative disorders termed transmissible spongiform encephalopathies (TSEs) are associated with the accumulation of fibrils of misfolded prion protein PrP. The noble gas xenon accommodates into four transiently enlarged hydrophobic cavities located in the well-folded core of human PrP(23–230) as detected by [1H, 15N]-HSQC spectroscopy. In thermal equilibrium a fifth xenon binding site is formed transiently by amino acids A120 to L125 of the presumably disordered N-terminal domain and by amino acids K185 to T193 of the well-folded domain. Xenon bound PrP was modelled by restraint molecular dynamics. The individual microscopic and macroscopic dissociation constants could be derived by fitting the data to a model including a dynamic opening and closing of the cavities. As observed earlier by high pressure NMR spectroscopy xenon binding influences also other amino acids all over the N-terminal domain including residues of the AGAAAAGA motif indicating a structural coupling between the N-terminal domain and the core domain. This is in agreement with spin labelling experiments at positions 93 or 107 that show a transient interaction between the N-terminus and the start of helix 2 and the end of helix 3 of the core domain similar to that observed earlier by Zn2+-binding to the octarepeat motif.

Evolution under Drug Pressure Remodels the Folding Free-Energy Landscape of Mature HIV-1 Protease

Using high-pressure NMR spectroscopy and differential scanning calorimetry, we investigate the folding landscape of the mature HIV-1 protease homodimer. The cooperativity of unfolding was measured in the absence or presence of a symmetric active site inhibitor for the optimized wild type protease (PR), its inactive variant PRD25N, and an extremely multidrug-resistant mutant, PR20. The individual fit of the pressure denaturation profiles gives rise to first order, ∆GNMR, and second order, ∆VNMR (the derivative of ∆GNMR with pressure); apparent thermodynamic parameters for each amide proton considered. Heterogeneity in the apparent ∆VNMR values reflects departure from an ideal cooperative unfolding transition. The narrow to broad distribution of ∆VNMR spanning the extremes from inhibitor-free PR20D25N to PR–DMP323 complex, and distinctively for PRD25N–DMP323 complex, indicated large variations in folding cooperativity. Consistent with this data, the shape of thermal unfolding transitions varies from asymmetric for PR to nearly symmetric for PR20, as dimer–inhibitor ternary complexes. Lack of structural cooperativity was observed between regions located close to the active site, including the hinge and tip of the glycine-rich flaps, and the rest of the protein. These results strongly suggest that inhibitor binding drastically decreases the cooperativity of unfolding by trapping the closed flap conformation in a deep energy minimum. To evade this conformational trap, PR20 evolves exhibiting a smoother folding landscape with nearly an ideal two-state (cooperative) unfolding transition. This study highlights the malleability of retroviral protease folding pathways by illustrating how the selection of mutations under drug pressure remodels the free-energy landscape as a primary mechanism.

Evolution under Drug Pressure Remodels the Folding Free-Energy Landscape of HIV-1 Protease

The HIV-1 Protease (PR) mediates its own release and promotes the proteolysis of the Gag-Pol polyprotein into mature structural and functional forms indispensable for viral maturation. Due to its central role in the virus life cycle, the HIV-1 PR has been a prominent target for clinical protease inhibitors for almost 25 years. However the short replication cycle of the virus together with the error-prone reverse transcriptase lead to the rapidly evolving selection of inhibitor-resistant mutations in HIV-1 PR. We use here high-pressure NMR spectroscopy to characterize the cooperativity of unfolding, in the absence and in the presence of a symmetric inhibitor, of the active mature PR, the inactive variant PRD25N and of the clinical multi-drug resistant PR20. We found that binding of the inhibitor drastically decreases the cooperativity of unfolding by trapping the closed flap conformation in a deep free-energy minimum. We show that in order to avoid this conformational trap, PR20 has evolved to exhibit a nearly ideal two-state unfolding transition. Our study highlights the malleability of the HIV-1 PR folding pathways and illustrates how selection for drug resistant mutations can lead to a major remodeling of the free-energy landscape.

Evolutionarily Conserved Pattern of Interactions in a Protein Revealed by Local Thermal Expansion Properties.

The way in which the network of intramolecular interactions determines the cooperative folding and conformational dynamics of a protein remains poorly understood. High-pressure NMR spectroscopy is uniquely suited to examine this problem because it combines the site-specific resolution of the NMR experiments with the local character of pressure perturbations. Here we report on the temperature dependence of the site-specific volumetric properties of various forms of staphylococcal nuclease (SNase), including three variants with engineered internal cavities, as measured with high-pressure NMR spectroscopy. The strong temperature dependence of pressure-induced unfolding arises from poorly understood differences in thermal expansion between the folded and unfolded states. A significant inverse correlation was observed between the global thermal expansion of the folded proteins and the number of strong intramolecular hydrogen bonds, as determined by the temperature coefficient of the backbone amide chemical shifts. Comparison of the identity of these strong H-bonds with the co-evolution of pairs of residues in the SNase protein family suggests that the architecture of the interactions detected in the NMR experiments could be linked to a functional aspect of the protein. Moreover, the temperature dependence of the residue-specific volume changes of unfolding yielded residue-specific differences in expansivity and revealed how mutations impact intramolecular interaction patterns. These results show that intramolecular interactions in the folded states of proteins impose constraints against thermal expansion and that, hence, knowledge of site-specific thermal expansivity offers insight into the patterns of strong intramolecular interactions and other local determinants of protein stability, cooperativity, and potentially also of function.

A Rational Approach to CO2 Capture by Imidazolium Ionic Liquids: Tuning CO2 Solubility by Cation Alkyl Branching.

Branching at the alkyl side chain of the imidazolium cation in ionic liquids (ILs) was evaluated towards its effect on carbon dioxide (CO2 ) solubilization at 10 and 80 bar (1 bar=1×10(5) Pa). By combining high-pressure NMR spectroscopy measurements with molecular dynamics simulations, a full description of the molecular interactions that take place in the IL-CO2 mixtures can be obtained. The introduction of a methyl group has a significant effect on CO2 solubility in comparison with linear or fluorinated analogues. The differences in CO2 solubility arise from differences in liquid organization caused by structural changes in the cation. ILs with branched cations have similar short-range cation-anion orientations as those in ILs with linear side chains, but present differences in the long-range order. The introduction of CO2 does not cause perturbations in the former and benefits from the differences in the latter. Branching at the cation results in sponge-like ILs with enhanced capabilities for CO2 capture.

Characteristics of flexibility in metal-organic framework solid solutions of composition [Zn2(BME-bdc)x(DB-bdc)2−xdabco]n: In situ powder X-ray diffraction, in situ NMR spectroscopy, and molecular dynamics simulations

Porosity switching in the crystalline solid state is a unique phenomenon observed only in a limited number of materials. The switching behavior of two metal-organic frameworks as well as their respective solid solutions of composition [Zn2(BME-bdc)x(DB-bdc)2−xdabco]n (x = 2; 1.5; 1.0; 0.5; 0) is studied in situ during the adsorption of CO2 and Xe using X-ray diffraction and NMR techniques. The diffraction data, measured during the adsorption suggest a direct one-step phase transition (switching) from the narrow pore phase to the large pore phase beyond the transition pressure. An intermediate phase was found only in one compound within a narrow pressure range around the phase transition pressure region. In situ high-pressure 13C NMR spectroscopy of adsorbed CO2 also allowed following the gating behavior of the studied materials by monitoring the signal of adsorbed CO2. The 13C NMR spectra exhibit a pronounced broadening indicating a certain degree of order for the adsorbed molecules inside the pores. This ordering effect and the resulting line broadening depend on the linker functionalization as could be confirmed by corresponding molecular dynamics (MD) simulations.

High-pressure NMR spectroscopy: An in situ tool to study tin-catalyzed synthesis of organic carbonates from carbon dioxide and alcohols. Part 2 [1

Dialkoxide diorganotin(IV) complexes are known to readily react with carbon dioxide under pressure and they are considered as suitable catalyst precursor models for the direct synthesis of organic carbonates. To gain a better understanding of CO2 insertion processes with Sn-OR bonds, the reactivity of n-Bu2Sn(OCH(CH3)2)2 (2) was investigated using high-pressure NMR (HP-NMR) spectroscopy. In deuterated solvents (isopropanol-d8 and toluene-d8) under 50 bar of CO2 pressure at 80 °C, 119Sn{1H} NMR experiments revealed the exclusive formation of an unprecedented tetraorganodistannoxane species, characterized as the bis[diisopropycarbonatotetrabutyldistannoxane] complex, {[n-Bu2Sn(OC(O)OCH(CH3)2)2]2O}2 {7}2. The formation of hemicarbonato ligands resulting from CO2 insertion was also confirmed by FT-IR and 13C NMR spectroscopies. To the best of our knowledge, spectroscopic detection of the distannoxane species 7 is unprecedented.

High Pressure NMR Spectroscopy.

The combination of high-resolution NMR spectroscopy with pressure perturbation, known as variable-pressure NMR spectroscopy or simply high pressure NMR spectroscopy, is a relatively recent accomplishment, but is a technique expanding rapidly with high promise in future. The importance of the method is that it allows, for the first time in history, a systematic means of detecting and analyzing the structures and thermodynamic stability of high-energy sub-states in proteins. High-energy sub-states have been only vaguely known so far, as normally their populations are too low to be detected by conventional spectroscopic techniques including NMR spectroscopy. By now, however, high pressure NMR spectroscopy has established unequivocally that high-energy conformers are universally present in proteins in equilibrium with their stable folded counterparts. This chapter describes briefly the techniques of high pressure NMR spectroscopy and its unique and novel aspects as a method to explore protein structure in its high-energy paradigm with illustrative examples. It is now well established that high pressure NMR spectroscopy is a method to study intrinsic fluctuations of proteins, rather than those forced by pressure, by detecting structural changes amplified by pressure. Extension of the method to other bio-macromolecular systems is considered fairly straightforward.

High Pressure NMR Methods for Characterizing Functional Substates of Proteins.

Proteins usually exist in multiple conformational states in solution. High pressure NMR spectroscopy is a well-suited method to identify these states. In addition, these states can be characterized by their thermodynamic parameters, the free enthalpies at ambient pressure, the partial molar volumes, and the partial molar compressibility that can be obtained from the analysis of the high pressure NMR data. Two main types of states of proteins exist, functional states and folding states. There is a strong link between these two types, the functional states represent essential folding states (intermediates), other folding states may have no functional meaning (optional folding states). In this chapter, this concept is tested on the Ras protein, an important proto-oncogen in humans where all substates required by theory can be identified experimentally by high pressure NMR spectroscopy. Finally, we show how these data can be used to develop allosteric inhibitors of proteins.

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.

Cavity as a Source of Conformational Fluctuation and High-Energy State: High-Pressure NMR Study of a Cavity-Enlarged Mutant of T4Lysozyme

Although the structure, function, conformational dynamics, and controlled thermodynamics of proteins are manifested by their corresponding amino acid sequences, the natural rules for molecular design and their corresponding interplay remain obscure. In this study, we focused on the role of internal cavities of proteins in conformational dynamics. We investigated the pressure-induced responses from the cavity-enlarged L99A mutant of T4 lysozyme, using high-pressure NMR spectroscopy. The signal intensities of the methyl groups in the 1H/13C heteronuclear single quantum correlation spectra, particularly those around the enlarged cavity, decreased with the increasing pressure, and disappeared at 200 MPa, without the appearance of new resonances, thus indicating the presence of heterogeneous conformations around the cavity within the ground state ensemble. Above 200 MPa, the signal intensities of >20 methyl groups gradually decreased with the increasing pressure, without the appearance of new resonances. Interestingly, these residues closely matched those sensing a large conformational change between the ground- and high-energy states, at atmospheric pressure. 13C and 1H NMR line-shape simulations showed that the pressure-induced loss in the peak intensity could be explained by the increase in the high-energy state population. In this high-energy state, the aromatic side chain of F114 gets flipped into the enlarged cavity. The accommodation of the phenylalanine ring into the efficiently packed cavity may decrease the partial molar volume of the high-energy state, relative to the ground state. We suggest that the enlarged cavity is involved in the conformational transition to high-energy states and in the volume fluctuation of the ground state.

High-Pressure Fluorescence Spectroscopy.

The combination of fluorescence and pressure perturbation is a widely used technique to study the effect of pressure on a protein system to obtain thermodynamic, structural and kinetic information on proteins. However, we often encounter the situation where the available pressure range up to 400MPa of most commercial high-pressure fluorescence spectrometers is insufficient for studying highly pressure-stable proteins like inhibitors and allergenic proteins. To overcome the difficulty, we have recently developed a new high-pressure fluorescence system that allows fluorescence measurements up to 700MPa. Here we describe the basic design of the apparatus and its application to study structural and thermodynamic properties of a couple of highly stable allergenic proteins, hen lysozyme and ovomucoid, using Tryptophan and Tyrosine/Tyrosinate fluorescence, respectively. Finally, we discuss the utility and the limitation of Trp and Tyr fluorescence. We discuss pitfalls of fluorescence technique and importance of simultaneous use of other high-pressure spectroscopy, particularly high-pressure NMR spectroscopy.

Interconversion between Planar-Triangle, Trigonal-Pyramid and Tetrahedral Configurations of Boron (B(OH)<sub>3</sub> -B(OH)<sub>4</sub><sup>-</sup> ), Carbon (CH<sub>3</sub><sup>+</sup> -CH<sub>3</sub>X) and for the Group 15 Elements as Nitrogen (NH<sub>3</sub>-NH<sub>4</sub><sup>+</sup> ). A Modelling Description with <i>Ab</i> <i>Initio </i> Results and Pressure-Induced Experimental Evidence

Recently a mechanistic understanding of the pressure-and/or temperature-induced coordination change of boron in a borosilicate glass has been demonstrated by Edwards et al. In situ high-pressure 11B solid-state NMR spectroscopy has been used in combination with ab initio calculations in order to obtain insight in the molecular geometry for the pressure-induced conversion. The results indicate a deformation of the B(OH)3 planar triangle, under isotropic stress, into a trigonal pyramid that serves as a precursor for the formation of a tetrahedral boron configuration. From our point of view, the deformation controlling the out-of-plane transition of boron accompanied with a D3h into C3v geometric change is an interesting transformation because it matches with our molecular description based on Van’t Hoff modelling for the tetrahedral change of carbon in CH3X by substitution of X with nucleophiles via a trigonal bipyramid state in which the transferred carbon is present as a methyl planar triangle “cation”. Van’t Hoff modelling and ab initio calculations have been also applied on the dynamics of the out-of-plane geometry of a transient positively charged carbon in a trigonal pyramidal configuration into a planar trivalent carbon cation. Finally the same model is also used for the C3v trigonal pyramidal configurations as NH3 of the group 15 elements in their nucleophilic abilities.

Homogenous catalytic hydrogenation of bicarbonate with water soluble aryl phosphine ligands

The chemical transformation of CO2 and bicarbonates into useful products becomes increasingly important as the atmospheric CO2 level has reached 400ppm. Here a small library of sulfonated aryl monophosphines and aryl diphosphines was tested as stabilizing ligands for a ruthenium catalytic precursor in aqueous-phase bicarbonate hydrogenation to formate. The reactions were monitored by high pressure NMR (HPNMR) spectroscopy which also revealed the presence of stable hydride species possibly linked to the superior activity of certain ligands. The different behaviors observed could be related to variations in air stabilities of the ligands. In some cases a pre-activation step of the catalytic precursor was necessary. The effect of such parameters on the stability and recyclability of the catalytic systems is discussed.

Effect of the Partial Replacement of CaH2 with CaF2 in the Mixed System CaH2 + MgB2

In this work the effect of a partial replacement of CaH2 with CaF2 on the sorption properties of the system CaH2 + MgB2 has been studied. The first five hydrogen absorption and four desorption reactions of the CaH2 + MgB2 and 3CaH2 + CaF2 + 4MgB2 systems were investigated by means of volumetric measurements, high-pressure differential scanning calorimetric technique (HP-DSC), 11B and 19F MAS NMR spectroscopy, and in situ synchrotron radiation powder X-ray diffraction (SR-PXD). It was observed that already during the mixing of the reactants formation of a nonstoichiometric CaF2–xHx solid solution takes place. Formation of the CaF2–xHx solid solution sensibly affects the overall hydrogen sorption reactions of the system CaH2 + MgB2.

Unique Properties of Human β-Defensin 6 (hBD6) and Glycosaminoglycan Complex: Sandwich-Like Dimerization and Competition with The Chemokine Receptor 2 (CCR2) Binding Site

Defensins are components of the innate immune system that promote the directional migration and activation of dendritic cells, thereby modulating the adaptive immune response. Because matrix glycosaminoglycan (GAG) is known to be important for these functions, we characterized the structural features of human β-defensin 6 (hBD6) and GAG interaction using a combination of structural and in silico analyses. Our results showed that GAG model compounds, a pentasaccharide (fondaparinux, FX) and an octasaccharide heparin derivative (dp8) bind to the α-helix and in the loops between the β2 and β3 strands, inducing the formation of a ternary complex with a 2:1 hBD6:FX stoichiometry. Competition experiments indicated an overlap of GAG and chemokine receptor CCR2 binding sites. An NMR-derived model of the ternary complex revealed that FX interacts with hBD6 along the dimerization interface, primarily contacting the α-helices and β2-β3 loops from each monomer. We further demonstrated that high-pressure NMR spectroscopy could capture an intermediate stage of hBD6-FX interaction, exhibiting features of a cooperative binding mechanism. Collectively, these data suggest a "sandwich-like" model in which two hBD6 molecules bind a single FX chain and provide novel structural insights into how defensin orchestrates leukocyte recruitment through GAG binding and G protein-coupled receptor activation. Despite the similarity to chemokines and hBD2, our data indicate different properties for the hBD6-GAG complex. This work adds significant information to the currently limited data available for the molecular structures and dynamics of defensin carbohydrate binding.