Heteronuclear saturation transfer difference (HSTD) experiment for detection of ligand binding to proteins

This report presents a modified saturation transfer difference experiment for protein–ligand binding studies. A heteronuclear saturation transfer difference (HSTD) is suggested, where in a hetero atom, such as carbon is utilized for monitoring the binding instead of proton. This method is free from some of the problems associated with proton STD experiment, such as lack of sufficient number of protons at the binding site or crowding of spectra due to smaller chemical shift dispersion. The present method has been demonstrated on three systems namely caffeine–HSA, salicylic acid–HSA and glucose–lysozyme, illustrating the utility of the method.     

Sensitivity enhancement in saturation transfer difference (STD) experiments through optimized excitation schemes

Investigation of ligand-protein interactions by the saturation transfer difference (STD) experiment has been well established in the drug discovery process through numerous examples. Thus, binding epitopes may be mapped by comparing signals of the ligand with and without saturation of the protein. Herein, it is shown that a less selective process allows more protons to assist in the saturation of the protein, thereby considerably enhancing the sensitivity of the STD experiment. Increasing the saturation power entails a greater risk of perturbing the ligand; however, an amplitude modulation of the waveform assists this procedure by distributing the applied energy in sidebands.     

Analysis of nucleotides binding to chromatography supports provided by nuclear magnetic resonance spectroscopy

The epitope mapping of nucleotides bound to three chromatography supports is accomplished using saturation transfer difference (STD)-NMR spectroscopy. This experiment involves subtracting a spectrum in which the support was selectively saturated from one recorded without support saturation. In the difference spectrum only the signals of the ligands that bind to the support and received saturation transfer remain. The nucleotide protons in closer contact with the support have more intense signals due to a more efficient transfer of saturation. We investigate the effects on the binding to the nucleotides by the introduction of a spacer arm between l-histidine and Sepharose. Our NMR experiments evidence a clear contribution of the spacer to the interaction with all the nucleotides, increasing the mobility of the amino acid and giving different STD responses. This enhanced mobility originates the reinforcement of the interactions with the sugar moiety and phosphate group of 5'-CMP and 5'-TMP or the base of 5'-GMP and 5'-UMP. Hence, with this study we show that by using STD NMR technique on chromatographic systems it is possible to provide a fast, robust and efficient way of screening the atoms involved in the binding to the supports.     

Clean SEA-TROSY Experiments to Map Solvent Exposed Amides in Large Proteins

It is well known that the SEA-TROSY experiment could alleviate some of the problems of resonance overlap in ^15N/^2H labeled proteins as it was designed to selectively map solvent exposed amide protons. However, SEATROSY spectra may be contaminated with exchange-relayed NOE contributions from fast exchanged hydroxyl or amine protons and contributions from longitudinal relaxation. Also, perdeuteration of the protein sample is a prerequisite for this experiment. In this communication, a modified version, clean SEA-TROSY, was proposed to eliminate these artifacts and to allow the experiment to be applied to protonated or partially deuterated proteins and protein complexes.     

Complete NMR analysis of oxytocin in phosphate buffer

Complete NMR analysis of oxytocin (OXT) in phosphate buffer was elucidated by one‐dimensional (1D)‐ and two‐dimensional (2D)‐NMR techniques, which involve the assignment of peptide amide NH protons and carbamoyl NH₂ protons. The ¹H? ¹⁵N correlation of seven amide NH protons and three carbamoyl NH₂ protons were also shown by HSQC NMR of OXT without ¹⁵N enrichment. Copyright © 2009 John Wiley & Sons, Ltd.     

Measurements of carbon to amide-proton distances by C-H dipolar recoupling with 15N NMR detection

A new magic-angle spinning NMR method for measuring internuclear distances between a 13C-labeled site and amide protons is described. The magnetization of the protons evolves under homonuclear decoupling and the recoupled 13C-1H dipolar interaction, which provides simple spin-pair REDOR curves if only one 13C-labeled site is present. The modulation of the amide proton HN is detected via short 1H-15N cross polarization followed by 15N detection. The method is demonstrated on two specifically 13C- and 15N-labeled peptides, with 13C-HN distances from 2.2 to ca. 6 A. This technique promises to be particularly useful for measuring distances between 13C=O and H-15N groups, to identify hydrogen bonds in peptides and proteins.     

Amide-Exchange-Rate-Edited NMR （AERE-NMR） Experiment： A Novel Method for Resolving Overlapping Resonances

This paper describes an amide-exchange-rate-edited （AERE） NMR method that can effectively alleviate the problem of resonance overlap for proteins and peptides. This method exploits the diversity of amide proton exchange rates and consists of two complementary experiments： （1） SEA （solvent exposed amide）-type NMR experiments to map exchangeable surface residues whose amides are not involved in hydrogen bonding, and （2） presat-type NMR experiments to map solvent inaccessibly buried residues or nonexchangeable residues located in hydrogen-bonded secondary structures with properly controlled saturation transfer via amide proton exchanges with the solvent. This method separates overlapping resonances in a spectrum into two complementary spectra. The AERE-NMR method was demonstrated with a sample of ^15N/^13C/^2H（70%） labeled ribosome-inactivating protein trichosanthin of 247 residues.     

An Approach to NMR Assignment of Intrinsically Disordered Proteins

An efficient approach to NMR assignments in intrinsically disordered proteins is presented, making use of the good dispersion of cross peaks observed in [¹⁵N,¹³C′]‐ and [¹³C′,¹H^N]‐correlation spectra. The method involves the simultaneous collection of {3D (H)NCO(CAN)H and 3D (HACA)CON(CA)HA} spectra for backbone assignments via sequential H^N and H^α correlations and {3D (H)NCO(CACS)HS and 3D (HS)CS(CA)CO(N)H} spectra for side‐chain ¹H and ¹³C assignments, employing sequential ¹H data acquisitions with direct detection of both the amide and aliphatic protons. The efficacy of the approach for obtaining resonance assignments with complete backbone and side‐chain chemical shifts is demonstrated experimentally for the 61‐residue [¹³C,¹⁵N]‐labelled peptide of a voltage‐gated potassium channel protein of the Kv1.4 channel subunit. The general applicability of the approach for the characterisation of moderately sized globular proteins is also demonstrated.     

Multiple-quantum relaxation dispersion NMR spectroscopy probing millisecond time-scale dynamics in proteins: theory and application

New relaxation dispersion experiments are presented that probe millisecond time-scale dynamical processes in proteins. The experiments measure the relaxation of (1)H-(15)N multiple-quantum coherence as a function of the rate of application of either (1)H or (15)N refocusing pulses during a constant time relaxation interval. In contrast to the dispersion profiles generated from more conventional (15)N((1)H) single-quantum relaxation experiments that depend on changes in (15)N((1)H) chemical shifts between exchanging states, (1)H-(15)N multiple-quantum dispersions are sensitive to changes in the chemical environments of both (1)H and (15)N spins. The resulting multiple-quantum relaxation dispersion profiles can, therefore, be quite different from those generated by single-quantum experiments, so that an analysis of both single- and multiple-quantum profiles together provides a powerful approach for obtaining robust measures of exchange parameters. This is particularly the case in applications to protonated proteins where other methods for studying exchange involving amide proton spins are negatively influenced by contributions from neighboring protons. The methodology is demonstrated on protonated and perdeuterated samples of a G48M mutant of the Fyn SH3 domain that exchanges between folded and unfolded states in solution.     

Über die Struktur der Thioamide und ihrer Derivate—XXIII: 14N-Entkoppelte H-NMR-Spektren und Messung der Rotationsbarrieren bei primären Amiden und Thioamiden

By saturation of the ¹⁴N resonance, hindered internal rotation around the CN bond of the (thio)amide system is detected in the H-NMR spectra of the primary amides ( 1a to 1d ) and the thioamides ( 2a to 2g ). With the aid of coupling constants and benzene dilution shifts, it is possible to assign the signals of the amino group to the cis and the trans NH protons. From coalescence results free enthalpies of activation of hindered internal rotation are obtained, and their dependence on steric and electronic effects as well as the influence of the solvent are discussed.     

Group epitope mapping by saturation transfer difference NMR to identify segments of a ligand in direct contact with a protein receptor.

A protocol based on saturation transfer difference (STD) NMR spectra was developed to characterize the binding interactions at an atom level, termed group epitope mapping (GEM). As an example we chose the well-studied system of galactose binding to the 120-kDa lectin Ricinus communis agglutinin I (RCA(120)). As ligands we used methyl beta-D-galactoside and a biantennary decasaccharide. Analysis of the saturation transfer effects of methyl beta-D-galactoside showed that the H2, H3, and H4 protons are saturated to the highest degree, giving evidence of their close proximity to protons of the RCA(120) lectin. The direct interaction of the lectin with this region of the galactose is in excellent agreement with results obtained from the analysis of the binding specificities of many chemically modified galactose derivatives (Bhattacharyya, L.; Brewer, C. F. Eur. J. Biochem. 1988, 176, 207-212). This new NMR technique can identify the binding epitope of even complex ligands very quickly, which is a great improvement over time-consuming chemical modifications. Efficient GEM benefits from a relatively high off rate of the ligand and a large excess of the ligand over the receptor. Even for a ligand like the biantennary decasaccharide with micromolar binding affinity, the binding epitopes could easily be mapped to the terminal beta-D-Gal-(1-4)-beta-D-GlcNAc (beta-D-GlcNAc = N-acetyl-D-glucosamine) residues located at the nonreducing end of the two carbohydrate chains. The binding contribution of the terminal galactose residue is stronger than those of the penultimate GlcNAc residues. We could show that the GlcNAc residues bind "edge-on" with the region from H2 to H4, making contact with the protein. Analysis of STD NMR experiments performed under competitive conditions proved that the two saccharides studied bind at the same receptor site, thereby ruling out unspecific binding.     

A 15N nuclear magnetic resonance study of the base-catalyzed NH2 exchange reactions of acetamide and thioacetamide

The base-catalyzed ? NH₂ exchange reactions of acetamide and thioacetamide were studied by ¹⁵N nuclear magnetic resonance spectroscopy by the use of line-shape analysis. The ¹⁵N NMR spectra of these primary amides at intermediate exchange rates were broad doublets, which indicated that the two amide protons were exchanging at different rates. The line-shape analysis indicated that the ratio of exchange rates was 6±1 for acetamide and 3±1 for thioacetamide.     

Analysis and optimization of saturation transfer difference NMR experiments designed to map early self-association events in amyloidogenic peptides

Saturation transfer difference (STD) methods recently have been proposed to be a promising tool for self-recognition mapping at residue and atomic resolution in amyloidogenic peptides. Despite the significant potential of the STD approach for systems undergoing oligomer/monomer (O/M) equilibria, a systematic analysis of the possible artifacts arising in this novel application of STD experiments is still lacking. Here, we have analyzed the STD method as applied to O/M peptides, and we have identified three major sources of possible biases: offset effects, intramonomer cross-relaxation, and partial spin-diffusion within the oligomers. For the purpose of quantitatively assessing these artifacts, we employed a comparative approach that relies on 1-D and 2-D STD data acquired at different saturation frequencies on samples with different peptide concentrations and filtration states. This artifact evaluation protocol was applied to the Abeta(12-28) model system, and all three types of artifacts appear to affect the measured STD spectra. In addition, we propose a method to minimize the biases introduced by these artifacts in the Halpha STD distributions used to obtain peptide self-recognition maps at residue resolution. This method relies on the averaging of STD data sets acquired at different saturation frequencies and provides results comparable to those independently obtained through other NMR pulse sequences that probe oligomerization, such as nonselective off-resonance relaxation experiments. The artifact evaluation protocol and the multiple frequencies averaging strategy proposed here are of general utility for the growing family of amyloidogenic peptides, as they provide a reliable analysis of STD spectra in terms of polypeptide self-recognition epitopes.     

Measurement of Very Fast Exchange Rates of Individual Amide Protons in Proteins by NMR Spectroscopy

NMR spectroscopy is a pivotal technique to measure hydrogen exchange rates in proteins. However, currently available NMR methods to measure backbone exchange are limited to rates of up to a few per second. To raise this limit, we have developed an approach that is capable of measuring proton exchange rates up to approximately 10⁴ s⁻¹. Our method relies on the detection of signal loss due to the decorrelation of antiphase operators 2N_xH_z by exchange events that occur during a series of pi pulses on the ¹⁵N channel. In practice, signal attenuation was monitored in a series of 2D H(CACO)N spectra, recorded with varying pi-pulse spacing, and the exchange rate was obtained by numerical fitting to the evolution of the density matrix. The method was applied to the small calcium-binding protein Calbindin D_9k, where exchange rates up to 600 s⁻¹ were measured for amides, where no signal was detectable in ¹⁵N−¹H HSQC spectra. A temperature variation study allowed us to determine apparent activation energies in the range 47–69 kJ mol⁻¹ for these fast exchanging amide protons, consistent with hydroxide-catalyzed exchange.     

Sensitivity enhancement in 1D heteronuclear NMR spectroscopy via single-scan inverse experiments.

Measuring the nuclear magnetic resonance spectra of low-gamma heteronuclei such as 15N constitutes an important analytical tool for the characterization of molecular structure and dynamics. The reduced resonance frequencies and magnetic moments of these heteronuclei, however, make the sensitivity of this kind of spectroscopy inherently lower than that of comparable H NMR observations. A well-known solution to this sensitivity problem is indirect detection: a 2D NMR technique capable of enhancing the sensitivity of heteronuclear NMR by porting the actual data acquisition from the low-gamma nucleus to neighboring protons. This has become the standard method of observation in biomolecular NMR, where the resolution introduced by 2D spectroscopy is always a sought-after commodity. Indirect detection, however, has not gained a wide appeal in organic chemistry or in in vivo investigations, where one-dimensional heteronuclear NMR information usually suffices. The present study explores the possibility of retaining certain advantages derived from indirect detection while not giving up on the simple one-dimensional nature of heteronuclear NMR, by relying on the spatial-encoding scheme we have recently demonstrated for implementing single-scan multi-dimensional NMR spectroscopy. Preliminary results based on a 1D modification of this experiment confirm theoretical calculations suggesting that the sensitivity of 1D 15N NMR can be enhanced significantly in this manner; the relevance of this experiment given the advent of dedicated H-observing cryogenic probeheads with very high sensitivities is briefly discussed.     

Characterization of heparin–protein interaction by saturation transfer difference (STD) NMR

The binding affinity and specificity of heparin to proteins is widely recognized to be sulfation-pattern dependent. However, for the majority of heparin-binding proteins (HBPs), it still remains unclear what moieties are involved in the specific binding interaction. Here, we report our study using saturation transfer difference (STD) nuclear magnetic resonance (NMR) to map out the interactions of synthetic heparin oligosaccharides with HBPs, such as basic fibroblast growth factor (FGF2) and fibroblast growth factor 10 (FGF10), to provide insight into the critical epitopes of heparin ligands involved. The irradiation frequency of STD NMR was carefully chosen to excite the methylene protons so that enhanced sensitivity was obtained for the heparin–protein complex. We believe this approach opens up additional application avenues to further investigate heparin–protein interactions.     

(15N) acetamide in polar solvents: Hindered internal rotation and intermolecular interactions

The ¹H spectrum of (¹⁵N)acetamide has been measured in dimethyl sulphoxide (DMSO), methyl propyl ketone (MPK), 1,3-dioxane, 1,4-dioxane, D₂O, acetonitrile and pyridine-d₅ at various temperature intervals within the range of 278–343 K. From the temperature dependence of the NMR spectra of the amide protons, the free energy of activation, ΔG^≠, for hindered rotation about the central C? N bond was determined by means of total line shape analysis in the four solvents DMSO, MPK and the two dioxanes. Observed values of ΔG^≠ (298 K) (72.7 in DMSO, 70.1 in MPK, 70.0 in 1,3-dioxane and 70.1 kJ mol¹ in 1,4-dioxane) were not very sensitive to the choice of solvent or concentration. The concentration dependence of the internal chemical shift between the amide protons was studied in MPK, D₂O, acetonitrile and pyridine-d₅. The free energy of activation and the internal chemical shift are discussed on the basis of solvent-amide and amide–amide specific hydrogen bonding interactions, and in comparison to the results of molecular orbital calculations.     

Determinations of 15N chemical shift anisotropy magnitudes in a uniformly 15N,13C-labeled microcrystalline protein by three-dimensional magic-angle spinning nuclear magnetic resonance spectroscopy

Amide 15N chemical shift anisotropy (CSA) tensors provide quantitative insight into protein structure and dynamics. Experimental determinations of 15N CSA tensors in biologically relevant molecules have typically been performed by NMR relaxation studies in solution, goniometric analysis of single-crystal spectra, or slow magic-angle spinning (MAS) NMR experiments of microcrystalline samples. Here we present measurements of 15N CSA tensor magnitudes in a protein of known structure by three-dimensional MAS solid-state NMR. Isotropic 15N, 13C alpha, and 13C' chemical shifts in two dimensions resolve site-specific backbone amide recoupled CSA line shapes in the third dimension. Application of the experiments to the 56-residue beta1 immunoglobulin binding domain of protein G (GB1) enabled 91 independent determinations of 15N tensors at 51 of the 55 backbone amide sites, for which 15N-13C alpha and/or 15N-13C' cross-peaks were resolved in the two-dimensional experiment. For 37 15N signals, both intra- and interresidue correlations were resolved, enabling direct comparison of two experimental data sets to enhance measurement precision. Systematic variations between beta-sheet and alpha-helix residues are observed; the average value for the anisotropy parameter, delta (delta = delta(zz) - delta(iso)), for alpha-helical residues is 6 ppm greater than that for the beta-sheet residues. The results show a variation in delta of 15N amide backbone sites between -77 and -115 ppm, with an average value of -103.5 ppm. Some sites (e.g., G41) display smaller anisotropy due to backbone dynamics. In contrast, we observe an unusually large 15N tensor for K50, a residue that has an atypical, positive value for the backbone phi torsion angle. To our knowledge, this is the most complete experimental analysis of 15N CSA magnitude to date in a solid protein. The availability of previous high-resolution crystal and solution NMR structures, as well as detailed solid-state NMR studies, will enhance the value of these measurements as a benchmark for the development of ab initio calculations of amide 15N shielding tensor magnitudes.     

Electron-mediating Cu(A) centers in proteins: a comparative high field (1)H ENDOR study

High field (W-band, 95 GHz) pulsed electron-nuclear double resonance (ENDOR) measurements were carried out on a number of proteins that contain the mixed-valence, binuclear electron-mediating Cu(A) center. These include nitrous oxide reductase (N(2)OR), the recombinant water-soluble fragment of subunit II of Thermus thermophilus cytochrome c oxidase (COX) ba(3) (M160T9), its M160QT0 mutant, where the weak axial methionine ligand has been replaced by a glutamine, and the engineered "purple" azurin (purpAz). The three-dimensional (3-D) structures of these proteins, apart from the mutant, are known. The EPR spectra of all samples showed the presence of a mononuclear Cu(II) impurity with EPR characteristics of a type II copper. At W-band, the g( perpendicular) features of this center and of Cu(A) are well resolved, thus allowing us to obtain a clean Cu(A) ENDOR spectrum. The latter consists of two types of ENDOR signals. The first includes the signals of the four strongly coupled cysteine beta-protons, with isotropic hyperfine couplings, A(iso), in the 7-15 MHz range. The second group consists of weakly coupled protons with a primarily anisotropic character with A(zz) < 3 MHz. Orientation selective ENDOR spectra were collected for N(2)OR, M160QT0, and purpAz, and simulations of the cysteine beta-protons signals provided their isotropic and anisotropic hyperfine interactions. A linear correlation with a negative slope was found between the maximum A(iso) value of the beta-protons and the copper hyperfine interaction. Comparison of the best-fit anisotropic hyperfine parameters with those calculated from dipolar interactions extracted from the available 3-D structures sets limit to the sulfur spin densities. Similarly, the small coupling spectral region was simulated on the basis of the 3-D structures and compared with the experimental spectra. It was found that the width of the powder patterns of the weakly coupled protons recorded at g(perpendicular) is mainly determined by the histidine H(epsilon)(1) protons. Furthermore, the splitting in the outer wings of these powder patterns indicates differences in the positions of the imidazole rings relative to the Cu(2)S(2) core. Comparison of the spectral features of the weakly coupled protons of M160QT0 with those of the other investigated proteins shows that they are very similar to those of purpAz, where the Cu(A) center is the most symmetric, but the copper spin density and the H(epsilon)(1)-Cu distances are somewhat smaller. All proteins show the presence of a proton with a significantly negative A(iso) value which is assigned to an amide proton of one of the cysteines. The simulations of both strongly and weakly coupled protons, along with the known copper hyperfine couplings, were used to estimate and compare the spin density distribution in the various Cu(A) centers. The largest sulfur spin density was found in M160T9, and the lowest was found in purpAz. In addition, using the relation between the A(iso) values of the four cysteine beta-protons and the H-C-S-S dihedral angles, the relative contribution of the hyperconjugation mechanism to A(iso) was determined. The largest contribution was found for M160T9, and the lowest was found for purpAz. Possible correlations between the spin density distribution, structural features, and electron-transfer functionality are finally suggested.     

A paramagnetic MRI-CEST agent responsive to lactate concentration

A paramagnetic Yb(III) complex bearing six exchangeable amide protons, [Yb(MBDO3AM)](3+), has been investigated with the aim of developing a MRI-CEST (chemical exchange saturation transfer) contrast agent responsive to the concentration of L-lactate. The complex binds the substrate quantitatively to yield [Yb(MBDO3AM)L-lactate](2+). The exchange between the free and the L-lactate-bound complex is slow on the NMR time scale, and the resonances of their corresponding amide protons are sufficiently separated (more than 10 ppm) to allow their selective irradiation. Therefore, the CEST properties of the two forms can be independently assessed. In turn, the resulting saturation transfer to the bulk water signal is dependent on the L-lactate concentration.