Toward the characterization of peptidoglycan structure and protein-peptidoglycan interactions by solid-state NMR spectroscopy

Solid-state NMR spectroscopy is applied to intact peptidoglycan sacculi of the Gram-negative bacterium Escherichia coli. High-quality solid-state NMR spectra allow atom-resolved investigation of the peptidoglycan structure and dynamics as well as the study of protein-peptidoglycan interactions.     

NMR spectroscopy techniques for screening and identifying ligand binding to protein receptors

Binding events of ligands to receptors are the key for an understanding of biological processes. Gaining insight into protein-protein and protein-ligand interactions in solution has recently become possible on an atomic level by new NMR spectroscopic techniques. These experiments identify binding events either by looking at the resonance signals of the ligand or the protein. Ideally, both techniques together deliver a complete picture of ligand binding to a receptor. The approaches discussed in this review allow screening of compound libraries as well as a detailed identification of the groups involved in the binding events. Also, characterization of the binding strength and kinetics is possible, competitive binding as well as allosteric effects can be identified, and it has even been possible to identify ligand binding to intact viruses and membrane-bound proteins.     

Observation of ligand binding to cytochrome P450 BM-3 by means of solid-state NMR spectroscopy

A broad understanding of the binding modes of ligands and inhibitors to cytochrome P450 is vital for the development of new drugs. We investigated ligand binding in a site-specific fashion on cytochrome P450 BM-3 from Bacillus megaterium, a 119 kDa paramagnetic enzyme, using solid-state magic angle spinning nuclear magnetic resonance methods. Selective labeling and longitudinal relaxation effects were utilized to identify the peaks in a site-specific fashion and to provide evidence for binding. Well-resolved one-dimensional and two-dimensional NMR spectra of cytochrome P450 BM-3 reveal shifts upon binding of its substrate, N-palmitoylglycine. These data are consistent with the crystallographic result that a biochemically important amino acid residue, Phe87, moves upon ligation. This experimental scheme provides a tool for probing ligand binding for complex systems.     

Summing up ligand binding interactions

Artificial molecular recognition systems show negligible positive binding cooperativity compared to biological systems, possibly because rigid ligands cannot accommodate numerous partly bound states that comprise overall ligand binding affinity. This directly correlates with the phenomenon of enthalpy-entropy compensation.     

Molecular complexation and binding studied by electrophoretic NMR spectroscopy

Electrophoretic mobilities obtained on a molecularly selective manner by electrophoretic NMR can be used to provide a quantitative characterization of the composition and stoichiometry of molecular complexes. This is demonstrated in complexes formed by uncharged cyclodextrins which attain an electrophoretic mobility upon inclusion of charged surfactants.     

Characterization of protein-ligand interactions by high-resolution solid-state NMR spectroscopy

A novel approach for detection of ligand binding to a protein in solid samples is described. Hydrated precipitates of the anti-apoptotic protein Bcl-xL show well-resolved (13)C-(13)C 2D solid-state NMR spectra that allow site-specific assignment of resonances for many residues in uniformly (13)C-enriched samples. Binding of a small peptide or drug-like organic molecule leads to changes in the chemical shift of resonances from multiple residues in the protein that can be monitored to characterize binding. Differential chemical shifts can be used to distinguish between direct protein-ligand contacts and small conformational changes of the protein induced by ligand binding. The agreement with prior solution-state NMR results indicates that the binding pocket in solid and liquid samples is similar for this protein. Advantages of different labeling schemes involving selective (13)C enrichment of methyl groups of Ala, Val, Leu, and Ile (Cdelta1) for characterizing protein-ligand interactions are also discussed. It is demonstrated that high-resolution solid-state NMR spectroscopy on uniformly or extensively (13)C-enriched samples has the potential to screen proteins of moderate size ( approximately 20 kDa) for ligand binding as hydrated solids. The results presented here suggest the possibility of using solid-state NMR to study ligand binding in proteins not amenable to solution NMR.     

Probing paeonol-pluronic polymer interactions by 1H NMR spectroscopy

By using a combination of 1H NMR spectroscopy, two-dimensional heteronuclear single-quantum coherence-resolved (1)H{(13)C} and homonuclear rotating-frame Overhauser enhancement NMR correlation experiments with diffusion ordered spectroscopy (DOSY), the location and distribution of a hydrophobic drug, paeonol, have been established with respect to the methyl groups of the poly(ethylene oxide)-poly(propylene oxide) -poly(ethylene oxide) (PEO-PPO-PEO) triblock copolymer. The interaction between them is adjustable according to the different temperature-dependent hydrophilicities or hydrophobicities of the triblock copolymer components. On the other hand, such interactions influence the self-assembly properties of the block copolymer amphiphiles in solution. The amount of anhydrous methyl groups of PPO segments shows an increase with increasing paeonol concentration. It was also demonstrated that the shell-crosslinking of the Pluronic polymer has an effect in increasing the amount of anhydrous methyl groups and thus increasing the hydrophobicity of Pluronic micelles. This might be the deeper reason underlying the increase in drug-loading capacity and prolongation in release time of Pluronic micelles for drug delivery after the shell-crosslinking. Changes in self-diffusion coefficients of paeonol with varying copolymer concentrations and types were also determined by the diffusion-based NMR DOSY technique, and values of K(a), DeltaG, and n were calculated.     

Synthesis and characterization of sulphonated PEES copolymers by NMR spectroscopy

Two sulphonated PEES copolymers were synthesized by reacting 75 or 60 mol% silylated hydroquinone sulphonic acid and 25 or 40 mol% of hydroquinone with 4,4′-difluorodiphenyl sulphone. The number average molecular weights determined by GPC were 13.250 and 12.050 g/mol. In the FTIR spectra, in addition to the characteristic absorption bands due to aromatic skeleton, absorption bands associated with sulphonic acid groups were observed at ∼3500, 1172, 1080, 1026, and 706 cm⁻¹. In ¹H NMR, the aromatic proton resonance signals were observed between δ = 6.99 and 7.96 ppm. ¹³C{¹H} NMR spectra of these copolymers were complex and in order to resolve this, two-dimensional (2D) NMR techniques were utilized. Heteronuclear single quantum coherence (HSQC), total correlated spectroscopy (TOCSY), and heteronuclear multiple bond correlation (HMBC) were used for assigning the structure of the copolymers.     

Mass spectrometry and NMR analysis of ligand binding by human liver fatty acid binding protein

Human liver fatty acid binding protein (hL‐FABP) is the most abundant cytosolic protein in the liver. This protein plays important roles associated to partitioning of fatty acids (FAs) to specific metabolic pathways, nuclear signaling and protection against oxidative damage. The protein displays promiscuous binding properties and can bind two internal ligands, unlike FABPs from other tissues. Different topologies for the ligand located in the more accessible site have been reported, with either a ‘head‐in’ or ‘head‐out’ orientation of the carboxylate end. Electrospray‐ionization mass spectrometry and nuclear magnetic resonance titrations are employed here in order to investigate in further detail the binding properties of this system, the equilibria established in solution and the pH dependence of the complexes. The results are consistent with two binding sites with different affinity and a unique head‐out topology for the second molecule of either ligand. Competition experiments indicate a higher affinity for oleic acid relative to palmitic acid at each binding site. Copyright © 2013 John Wiley & Sons, Ltd.     

Unraveling complex small-molecule binding mechanisms by using simple NMR spectroscopy

Heteronuclear NMR spectroscopy provides a unique way to obtain site-specific information about protein-ligand interactions. Usually, such studies rely on the availability of isotopically labeled proteins, thereby allowing both editing of the spectra and ligand signals to be filtered out. Herein, we report that the use of the methyl SOFAST correlation experiment enables the determination of site-specific equilibrium binding constants by using unlabeled proteins. By using the binding of L- and D-tryptophan to serum albumin as a test case, we determined very accurate dissociation constants for both the high- and low-affinity sites present at the protein surface. The values of site-specific dissociation constants were closer to those obtained by isothermal titration calorimetry than those obtained from ligand-observed methods, such as saturation transfer difference. The possibility of measuring ligand binding to serum albumin at physiological concentrations with unlabeled proteins may open up new perspectives in the field of drug discovery.     

Bilayer in small bicelles revealed by lipid-protein interactions using NMR spectroscopy

Intermolecular nuclear Overhauser effects (NOEs) between the integral outer membrane protein OmpX from Escherichia coli and small bicelles of dihexanoyl phosphatidylcholine (DHPC) and dimyristoyl phosphatidylcholine (DMPC) give insights into protein-lipid interactions. Intermolecular NOEs between hydrophobic tails of lipid and protein in the bicelles cover the surface area of OmpX forming a continuous cylindric jacket of approximately 2.7 nm in height. These NOEs originate only from DMPC molecules, and no NOEs from DHPC are observed. Further, these NOEs are mainly from methylene groups of the hydrophobic tails of DMPC, and only a handful of NOEs arise from methyl groups of the hydrophobic tails. The observed contacts indicate that the hydrophobic tails of DMPC are oriented parallel to the surface of OmpX and thus DMPC molecules form a bilayer in the vicinity of the protein. Thus, a bilayer exists in the small bicelles not only in the absence of but also in the presence of a membrane protein. In addition, the number of NOEs between the polar head groups of lipid molecules and protein is increased in the bicelles compared with those in micelles. This observation may be due to the closely packed head groups of the bilayer. Moreover, irregularity of hydrophobic interactions in the middle of the bilayer environment was observed. This observation together with the interactions between polar head groups and proteins gives a possible rationale for structural and functional differences of membrane proteins solubilized in micelles and in bilayer systems and hints at structural differences between protein-free and protein-loaded bilayers.     

Supramolecular interactions probed by 13C-13C solid-state NMR spectroscopy

We present a robust solid-state NMR approach for the accurate determination of molecular interfaces in insoluble and noncrystalline protein-protein complexes. The method relies on the measurement of intermolecular (13)C-(13)C distances in mixtures of [1-(13)C]glucose- and [2-(13)C]glucose-labeled proteins. We have applied this method to Parkinson's disease-associated α-synuclein fibrils and found that they are stacked in a parallel in-register arrangement. Additionally, intermolecular distance restraints for the structure determination of the fibrils at atomic resolution were measured.     

Fast 2D NMR ligand screening using Hadamard spectroscopy

Fast 2D NMR-based screening can be achieved using Hadamard encoded spectroscopy to focus on the signals of interest (e.g., enzyme active or ligand recognition sites). By recording a set of Hadamard spectra (a "Hadamard constellation") with relative offsets comparable to the excitation bandwidth, quantitative ligand-induced shifts can be obtained from peak intensities.     

Dissecting functional interactions in coagulation protein complexes by use of NMR spectroscopy

The blood coagulation cascade can be considered as a system of well-orchestrated protein activation reactions involving and leading to the formation of large macromolecular assemblies. NMR investigations performed during the last six years have focused on the structural, motional and binding properties of some protein domains and interfaces critical for the formation of these protein complexes, outlining sophisticated intermolecular adaptations. The studied protein domains are either single molecules or covalently-linked heterodimers of the epidermal growth factor (EGF) homology domains, calcium-binding EGF domains and gamma-carboxyglutamic(Gla)-containing domains responsible for calcium-dependent binding to cell membranes. The characterized binding interfaces have included those between thrombin and fibrinogen, between thrombin and thrombomodulin, between factor VIIIa and the cell membrane, between tissue factor and factor VIIa, and most recently between factor Va and prothrombin. The obtained results indicate that the regulation of blood coagulation by protein and low molecular weight cofactors may involve a significant degree of protein folding transitions with changes in molecular and conformational motions coupled to enzymatic activities. This new level of complexity of the molecular processes controlling coagulation may lead to novel strategies for the development of more effective therapeutic anticoagulants.     

Investigation of dipolar-mediated water-protein interactions in microcrystalline Crh by solid-state NMR spectroscopy

Water-protein interactions play a major role in protein folding, structure, and function, and solid-state NMR has recently been shown to be a powerful tool for the site-resolved observation of these interactions in solid proteins. In this article we report investigations on possible water-protein dipolar transfer mechanisms in the microcrystalline deuterated protein Crh by a set of solid-state NMR techniques. Double-quantum (DQ) filtered and edited heteronuclear correlation experiments are used to follow direct dipolar water-protein magnetization transfers. Experimental data reveal no evidence for "solid-like" water molecules, indicating that residence times of solvent molecules are shorter than required for DQ creation, typically a few hundred microseconds. An alternative magnetization pathway, intermolecular cross-relaxation via heteronuclear nuclear Overhauser effects (NOEs), is probed by saturation transfer experiments. The significant additional enhancements observed when irradiating at the water frequency can possibly be attributed to direct heteronuclear water-protein NOEs; however, a contribution from relayed magnetization transfer via chemical exchange or proton-proton dipolar mechanisms cannot be excluded.     

Probing hydrogen bonding and ion-carbonyl interactions by solid-state 17O NMR spectroscopy: G-ribbon and G-quartet

We report solid-state 17O NMR determination of the 17O NMR tensors for the keto carbonyl oxygen (O6) of guanine in two 17O-enriched guanosine derivatives: [6-17O]guanosine (G1) and 2',3',5'-O-triacetyl-[6-17O]guanosine (G2). In G1.2H2O, guanosine molecules form hydrogen-bonded G-ribbons where the guanine bases are linked by O6...H-N2 and N7...H-N7 hydrogen bonds in a zigzag fashion. In addition, the keto carbonyl oxygen O6 is also weakly hydrogen-bonded to two water molecules of hydration. The experimental 17O NMR tensors determined for the two independent molecules in the asymmetric unit of G1.2H2O are: Molecule A, CQ=7.8+/-0.1 MHz, etaQ=0.45+/-0.05, deltaiso=263+/-2, delta11=460+/-5, delta22=360+/-5, delta33=-30+/-5 ppm; Molecule B, CQ=7.7+/-0.1 MHz, etaQ=0.55+/-0.05, deltaiso=250+/-2, delta11=440+/-5, delta22=340+/-5, delta33=-30+/-5 ppm. In G1/K+ gel, guanosine molecules form extensively stacking G-quartets. In each G-quartet, four guanine bases are linked together by four pairs of O6...H-N1 and N7...H-N2 hydrogen bonds in a cyclic fashion. In addition, each O6 atom is simultaneously coordinated to two K+ ions. For G1/K+ gel, the experimental 17O NMR tensors are: CQ=7.2+/-0.1 MHz, etaQ=0.68+/-0.05, deltaiso=232+/-2, delta11=400+/-5, delta22=300+/-5, delta33=-20+/-5 ppm. In the presence of divalent cations such as Sr2+, Ba2+, and Pb2+, G2 molecules form discrete octamers containing two stacking G-quartets and a central metal ion, that is, (G2)4-M2+-(G2)4. In this case, each O6 atom of the G-quartet is coordinated to only one metal ion. For G2/M2+ octamers, the experimental 17O NMR parameters are: Sr2+, CQ=6.8+/-0.1 MHz, etaQ=1.00+/-0.05, deltaiso=232+/-2 ppm; Ba2+, CQ=7.0+/-0.1 MHz, etaQ=0.68+/-0.05, deltaiso=232+/-2 ppm; Pb2+, CQ=7.2+/-0.1 MHz, etaQ=1.00+/-0.05, deltaiso=232+/-2 ppm. We also perform extensive quantum chemical calculations for the 17O NMR tensors in both G-ribbons and G-quartets. Our results demonstrate that the 17O chemical shift tensor and quadrupole coupling tensor are very sensitive to the presence of hydrogen bonding and ion-carbonyl interactions. Furthermore, the effect from ion-carbonyl interactions is several times stronger than that from hydrogen-bonding interactions. Our results establish a basis for using solid-state 17O NMR as a probe in the study of ion binding in G-quadruplex DNA and ion channel proteins.     

Structure,dynamics and interactions in polymer systems as studied by NMR spectroscopy

The possibilities of NMR spectroscopy in studies of interactions in polymer systems are demonstrated on the example of two types of macromolecular complexes: (i) By measuring ¹H NMR high resolution line intensities, the formation of ordered associated structures of syndiotactic (s) poly(methyl methacrylate)(PMMA) in mixed solvents was quantitatively characterized. The obtained results permit us to assume that the mechanism by which the solvent affects self-association of s-PMMA involves specific interactions of the solvent molecules with PMMA units. Solid state high resolution ¹³C NMR spectra of associated s-PMMA gels were also measured and compared with the spectra of a solid s-PMMA sample. (ii) By using ¹³C solid state NMR spectroscopy, the differences in the structure of the amorphous and crystalline phases in pure poly(ethylene oxide) and its complexes with p-dichlorobenzene or p-nitrophenol were characterized. Prounounced differences also in the dynamic structure of the crystalline phase in these systems are indicated by the relaxation times T₁(C), T_1ρ(C) and T_1ρ(H).     

Diffusion NMR spectroscopy for the characterization of the size and interactions of colloidal matter: the case of vesicles and nanoparticles

We report the application of the pulse gradient spin-echo (PGSE) NMR technique (PGSE NMR) to the analysis of large colloidal materials, specifically vesicles formed from macromolecular amphiphiles and nanoparticles. Measurements of size and size distribution were demonstrated to be comparable to those obtained through dynamic light scattering or hydrodynamic chromatography. In comparison to these more common analytical methods, the use of PGSE NMR is particularly advantageous in that, as a spectroscopic technique, it adds chemical selectivity to the study of physical dimensions. In this way, chemically different species contemporarily present in a sample may be individually studied. In addition, we demonstrate the use of PGSE NMR to probe the existence of equilibria between macroamphiphiles present in solution and those present in vesicles or on the surface of nanoparticles. This feature in particular opens exciting possibilities for the characterization of the phase behavior and of the surface adsorption phenomena of colloids.     

Selective interface detection: mapping binding site contacts in membrane proteins by NMR spectroscopy

Intermolecular contact surfaces are important regions where specific interactions mediate biological function. We introduce a new magic angle spinning solid state NMR technique, dubbed "selective interface detection spectroscopy" (SIDY). In this technique, 13C-attached protons (1Hlig) are dephased by 1H-13C REDOR. A spin diffusion period is then used to enhance long distance 1H-1H correlations, and the results are detected by a short period of cross polarization to the 13C isotope labels. This SIDY approach allows selective observation of the interface between 13C-labeled and unlabeled moieties. We have used SIDY to probe the ligand-protein binding surface between a uniformly isotopically labeled ligand cofactor, U-13C20-11-cis-retinal, and its binding site in rhodopsin (Rho), an unlabeled, membrane-embedded G-protein coupled receptor (GPCR). The observed 1HGPCR-13Clig correlations indicate multiple close contacts between the protein and the ionone ring of the ligand, in agreement with binding studies. The polyene tail of the ligand displays fewer strong correlations in the SIDY spectrum. Some correlations can be assigned to the protein side chains lining the ligand binding site, in agreement with the crystal structure.