Heteronuclear Experiments Research Articles

Unexpected effects of third-order cross-terms in heteronuclear spin systems under simultaneous radio-frequency irradiation and magic-angle spinning NMR

We recently noted [R. K. Harris, P. Hodgkinson, V. Zorin, J.-N. Dumez, B. Elena, L. Emsley, E. Salager, and R. Stein, Magn. Reson. Chem. 48, S103 (2010)] anomalous shifts in apparent (1)H chemical shifts in experiments using (1)H homonuclear decoupling sequences to acquire high-resolution (1)H NMR spectra for organic solids under magic-angle spinning (MAS). Analogous effects were also observed in numerical simulations of model (13)C,(1)H spin systems under homonuclear decoupling and involving large (13)C,(1)H dipolar couplings. While the heteronuclear coupling is generally assumed to be efficiently suppressed by sample spinning at the magic angle, we show that under conditions typically used in solid-state NMR, there is a significant third-order cross-term from this coupling under the conditions of simultaneous MAS and homonuclear decoupling for spins directly bonded to (1)H. This term, which is of the order of 100 Hz under typical conditions, explains the anomalous behaviour observed on both (1)H and (13)C spins, including the fast dephasing observed in (13)C{(1)H} heteronuclear spin-echo experiments under (1)H homonuclear decoupling. Strategies for minimising the impact of this effect are also discussed.

The relative signs of NMR proton–carbon coupling constants in quinolines

The relative signs of spin–spin coupling constants are of practical significance in spectral analysis and in structural elucidation. The signs, however, cannot be obtained directly from usual NMR spectra. In the present study, we measured 1H and 13C NMR spectra of three quinolines and used the Selective Population Transfer (SPT) to determine the relative sign of their proton–carbon coupling constants. For the determination of the relative signs of JCH, hetero-nuclear SPT experiments accompanied with proton decoupling were applied to systems in which a carbon nucleus couples with four or more protons. SPT was applied to the lowest or highest field 13C satellite of the 1H spectrum. The value of 2JH3C2 of 6-chloro-2-methyl-quinolines (1) was determined to be +2.2 Hz by hetero-nuclear SPT with the decoupling of CH3 protons. Similarly, 2JH6C7 of 7-chloro-8-methylqionoline (2) and 2JH7C8 of 8-hydroxyquinoline (3) were determined to be −2 and −4.0 Hz with the decoupling of CH3 protons of Compound (2) and H4 of Compound (3), respectively.

Localized in vivo hyperpolarization transfer sequences

In vivo localized and fully adiabatic homonuclear and heteronuclear polarization transfer experiments were designed and performed in the rat brain at 9.4 T after infusion of hyperpolarized sodium [1,2-(13)C(2)] and sodium [1-(13)C] acetate. The method presented herein leads to highly enhanced in vivo detection of short-T(1) (13)C as well as attached protons. This indirect detection scheme allows for probing additional molecular sites in hyperpolarized substrates and their metabolites and can thus lead to improved spectral resolution such as in the case of (13)C-acetate metabolism.

Structures and Interaction Analyses of Integrin αMβ2 Cytoplasmic Tails

Integrins are heterodimeric (α and β subunits) signal transducer proteins involved in cell adhesions and migrations. The cytosolic tails of integrins are essential for transmitting bidirectional signaling and also implicated in maintaining the resting states of the receptors. In addition, cytosolic tails of integrins often undergo post-translation modifications like phosphorylation. However, the consequences of phosphorylation on the structures and interactions are not clear. The leukocyte-specific integrin αMβ2 is essential for myeloid cell adhesion, phagocytosis, and degranulation. In this work, we determined solution structures of the myristoylated cytosolic tail of αM and a Ser phosphorylated variant in dodecylphosphocholine micelles by NMR spectroscopy. Furthermore, the interactions between non-phosphorylated and phosphorylated αM tails with β2 tail were investigated by NMR and fluorescence resonance energy transfer (FRET). The three-dimensional structures of the 24-residue cytosolic tail of αM or phosphorylated αM are characterized by an N-terminal amphipathic helix and a loop at the C terminus. The residues at the loop are involved in packing interactions with the hydrophobic face of the helix. 15N-1H heteronuclear single quantum coherence experiments identified residues of αM and β2 tails that may be involved in the formation of a tail-tail heterocomplex. We further examined interactions between myristoylated β2 tail in dodecylphosphocholine micelles with dansylated αM tail peptides by FRET. These studies revealed enhanced interactions between αM or phosphorylated αM tails with β2 tail with Kd values ∼5.2±0.6 and ∼4.4±0.7 μm, respectively. Docked structures of tail-tail complexes delineated that the αM/β2 interface at the cytosolic region could be sustained by a network of polar interactions, ionic interactions, and/or hydrogen bonds.

6-O-(10-Undecylenoyl)-D-Glucose: Controlled Enzymatic Synthesis and Structure Elucidation by <sup>1</sup>H and <sup>13</sup>C NMR

A direct esterification synthesis of glucose undecylenic acid sugar monoester is described, using the immobilized lipase enzyme NOVO-435 in 2-methyl-2-butonal and in ethyl methyl ketone (EMK). conditions were optimized in order to produce the monoester more rapidly and in higher yield. After the reaction product was purified, mass spectroscopy revealed that it had a molecular weight of 346.2 AMU. Further characterization by 1H and 13C NMR spectroscopy was carried out, including two-dimensional (2D) 1H-1H COSY and heteronuclear 1H-13C HSQC experiments. These data enabled identification of the monoester product to be 6-O-(10-undercylenoyl)α-D-glucose (74%), and 6-O-(10-undercylenoyl)β-D-glucose (26%) in methanol solution.

Anti-GM1/GD1a complex antibodies in GBS sera specifically recognize the hybrid dimer GM1-GD1a

It is now emerging the new concept that the antibodies from some patients with Guillain-Barré syndrome (GBS) recognize an antigenic epitope formed by two different gangliosides, a ganglioside complex (GSC). We prepared the dimeric GM1-GD1a hybrid ganglioside derivative that contains two structurally different oligosaccharide chains to mimic the GSC. We use this compound to analyze sera from GBS patients by high-performance thin-layer chromatography immunostaining and enzyme-linked immunosorbent assay. We also synthesized the dimeric GM1-GM1 and GD1a-GD1a compounds that were used in control experiments together with natural gangliosides. The hybrid dimeric GM1-GD1a was specifically recognized by human sera from GBS patients that developed anti-oligosaccharide antibodies specific for grouped complex oligosaccharides, confirming the information that GBS patients developed antibodies against a GSC. High-resolution (1)H-(13)C heteronuclear single-quantum coherence-nuclear overhauser effect spectroscopy nuclear magnetic resonance experiments showed an interaction between the IV Gal-H1 of GM1 and the IV Gal-H2 of GD1a suggesting that the two oligosaccharide chains of the dimeric ganglioside form a single epitope recognized by a single-antibody domain. The availability of a method capable to prepare several hybrid gangliosides, and the availability of simple analytical approaches, opens new perspectives for the understanding and the therapy of several neuropathies.

Cutting Off Functional Loops from Homodimeric Enzyme Superoxide Dismutase 1 (SOD1) Leaves Monomeric β-Barrels

Demetallation of the homodimeric enzyme Cu/Zn-superoxide dismutase (SOD1) is known to unleash pronounced dynamic motions in the long active-site loops that comprise almost a third of the folded structure. The resulting apo species, which shows increased propensity to aggregate, stands out as the prime disease precursor in amyotrophic lateral sclerosis (ALS). Even so, the detailed structural properties of the apoSOD1 framework have remained elusive and controversial. In this study, we examine the structural interplay between the central apoSOD1 barrel and the active-site loops by simply cutting them off; loops IV and VII were substituted with short Gly-Ala-Gly linkers. The results show that loop removal breaks the dimer interface and leads to soluble, monomeric β-barrels with high structural integrity. NMR-detected nuclear Overhauser effects are found between all of the constituent β-strands, confirming ordered interactions across the whole barrel. Moreover, the breathing motions of the SOD1 barrel are overall insensitive to loop removal and yield hydrogen/deuterium protection factors typical for cooperatively folded proteins (i.e. the active-site loops act as a "bolt-on" domain with little dynamic influence on its structural foundation). The sole exceptions are the relatively low protection factors in β-strand 5 and the turn around Gly-93, a hot spot for ALS-provoking mutations, which decrease even further upon loop removal. Taken together, these data suggest that the cytotoxic function of apoSOD1 does not emerge from its folded ground state but from a high energy intermediate or even from the denatured ensemble.

Interaction of Actin with Carcinoembryonic Antigen-related Cell Adhesion Molecule 1 (CEACAM1) Receptor in Liposomes Is Ca2+- and Phospholipid-dependent

The regulation of binding of G-actin to cytoplasmic domains of cell surface receptors is a common mechanism to control diverse biological processes. To model the regulation of G-actin binding to a cell surface receptor we used the cell-cell adhesion molecule carcinoembryonic antigen-related cell adhesion molecule 1 (CEACAM1-S) in which G-actin binds to its short cytoplasmic domain (12 amino acids; Chen, C. J., Kirshner, J., Sherman, M. A., Hu, W., Nguyen, T., and Shively, J. E. (2007) J. Biol. Chem. 282, 5749-5760). A liposome model system demonstrates that G-actin binds to the cytosolic domain peptide of CEACAM1-S in the presence of negatively charged palmitoyl-oleoyl phosphatidylserine (POPS) liposomes and Ca(2+). In contrast, no binding of G-actin was observed in palmitoyl-oleoyl phosphatidylcholine (POPC) liposomes or when a key residue in the peptide, Phe-454, is replaced with Ala. Molecular Dynamics simulations on CEACAM1-S in an asymmetric phospholipid bilayer show migration of Ca(2+) ions to the lipid leaflet containing POPS and reveal two conformations for Phe-454 explaining the reversible availability of this residue for G-actin binding. NMR transverse relaxation optimized spectroscopic analysis of (13)C-labeled Phe-454 CEACAM1-S peptide in liposomes plus actin further confirmed the existence of two peptide conformers and the Ca(2+) dependence of actin binding. These findings explain how a receptor with a short cytoplasmic domain can recruit a cytosolic protein in a phospholipid and Ca(2+)-specific manner. In addition, this model system provides a powerful approach that can be applied to study other membrane protein interactions with their cytosolic targets.

Assembly of a Filamin Four-domain Fragment and the Influence of Splicing Variant-1 on the Structure

Filamins are scaffold proteins that bind to various proteins, including the actin cytoskeleton, integrin adhesion receptors, and adaptor proteins such as migfilin. Alternative splicing of filamin, largely constructed from 24 Ig-like domains, is thought to have a role in regulating its interactions with other proteins. The filamin A splice variant-1 (FLNa var-1) lacks 41 amino acids, including the last β-strand of domain 19, FLNa(19), and the first β-strand of FLNa(20) that was previously shown to mask a key binding site on FLNa(21). Here, we present a structural characterization of domains 18-21, FLNa(18-21), in the FLNa var-1 as well as its nonspliced counterpart. A model of nonspliced FLNa(18-21), obtained from small angle x-ray scattering data, shows that these four domains form an L-shaped structure, with one arm composed of a pair of domains. NMR spectroscopy reveals that in the splice variant, FLNa(19) is unstructured whereas the other domains retain the same fold as in their canonical counterparts. The maximum dimensions predicted by small angle x-ray scattering data are increased upon migfilin binding in the FLNa(18-21) but not in the splice variant, suggesting that migfilin binding is able to displace the masking β-strand and cause a rearrangement of the structure. Possible function roles for the spliced variants are discussed.

Liquid Chromatography-Solid Phase Extraction-NMR (LC-SPE-NMR) Analysis of Liquid Crystalline Mixtures

We have performed Liquid Chromatography-Solid Phase Extraction-NMR (LC-SPE-NMR) analysis for liquid crystalline mixture and elucidated the structures of selected components by NMR spectra. Combining the results of one-dimensional 1H experiments as well as homonuclear and heteronuclear two-dimensional experiments, we could analyze the molecular structure of the liquid crystal singles whose structure had not been interpretable by mass spectrometry alone.

Domain 3 of NS5A Protein from the Hepatitis C Virus Has Intrinsic α-Helical Propensity and Is a Substrate of Cyclophilin A

Nonstructural protein 5A (NS5A) is essential for hepatitis C virus (HCV) replication and constitutes an attractive target for antiviral drug development. Although structural data for its in-plane membrane anchor and domain D1 are available, the structure of domains 2 (D2) and 3 (D3) remain poorly defined. We report here a comparative molecular characterization of the NS5A-D3 domains of the HCV JFH-1 (genotype 2a) and Con1 (genotype 1b) strains. Combining gel filtration, CD, and NMR spectroscopy analyses, we show that NS5A-D3 is natively unfolded. However, NS5A-D3 domains from both JFH-1 and Con1 strains exhibit a propensity to partially fold into an α-helix. NMR analysis identifies two putative α-helices, for which a molecular model could be obtained. The amphipathic nature of the first helix and its conservation in all genotypes suggest that it might correspond to a molecular recognition element and, as such, promote the interaction with relevant biological partner(s). Because mutations conferring resistance to cyclophilin inhibitors have been mapped into NS5A-D3, we also investigated the functional interaction between NS5A-D3 and cyclophilin A (CypA). CypA indeed interacts with NS5A-D3, and this interaction is completely abolished by cyclosporin A. NMR heteronuclear exchange experiments demonstrate that CypA has in vitro peptidyl-prolyl cis/trans-isomerase activity toward some, but not all, of the peptidyl-prolyl bonds in NS5A-D3. These studies lead to novel insights into the structural features of NS5A-D3 and its relationships with CypA.

Structural Dynamics of Phosphorylated Pentameric Phospholamban in Lipid Membranes using a Combination of Solution and Solid-State NMR Spectroscopy

Phospholamban (PLN) is a 52-residue membrane protein that regulates the cardiac sarcoplasmic reticulum Ca2+ATPase (SERCA). PLN is in equilibrium between monomeric and pentameric species. The monomer binds to and decreases the rate of Ca2+ transport of SERCA. This inhibitory action is relieved upon PLN phosphorylation at Serine-16 and Threonine-17. Here, we present the structural dynamics of fully phosphorylated pentameric PLN by a combination of solution and solid-state NMR spectroscopy. SDS-PAGE analysis revealed a higher thermal stability of the phosphorylated pentameric PLN (at Ser-16, Thr-17 and both) with respect to the unphosphorylated protein when reconstituted in different lipids and detergents.Conventional T1, T2, and heteronuclear steady state NOEs experiments were used to probe fast (ps-ns) dynamics of the amide backbone upon phosphorylation at Ser-16, revealing a significant increase of the dynamics in this time scale. Slower (µs-ms) dynamics were probed by measuring rotating frame R(1rho) and R(2rho) dispersion curves using a new adiabatic irradiation scheme.The structural and topological effects of phosphorylation in pentameric PLN were investigated using solid-state NMR experiments on mechanically and magnetically oriented lipid systems. For the mechanically oriented samples, phosphorylated PLN was reconstituted in DOPC/DOPE lipid bilayers and uniaxially aligned between glass plates. For magnetically oriented samples, the protein was reconstituted in DMPC/Triton X-100 bicelles. Two-dimensional PISEMA and SAMPI4 experiments were used to determine the topology of PLN in lipid membranes. Chemical shifts anisotropy and dipolar coupling values were also used in combination with solution NMR restraints to determine a preliminary high-resolution structure of fully phosphorylated pentameric PLN.These studies reveal residue-by-residue details of the pentameric PLN structure and topology upon phosphorylation.

The effect of ring size variation on the structure and stability of lanthanide(iii) complexes with crown ethers containing picolinate pendants

The coordination properties of the macrocyclic receptor N,N'-bis[(6-carboxy-2-pyridyl)methylene]-1,10-diaza-15-crown-5 (H(2)bp15c5) towards the lanthanide ions are reported. Thermodynamic stability constants were determined by pH-potentiometric titration at 25 °C in 0.1 M KCl. A smooth decrease in complex stability is observed upon decreasing the ionic radius of the Ln(III) ion from La [log K(LaL) = 12.52(2)] to Lu [log K(LuL) = 10.03(6)]. Luminescence lifetime measurements recorded on solutions of the Eu(III) and Tb(III) complexes confirm the absence of inner-sphere water molecules in these complexes. (1)H and (13)C NMR spectra of the complexes formed with the diamagnetic La(III) metal ion were obtained in D(2)O solution and assigned with the aid of HSQC and HMBC 2D heteronuclear experiments, as well as standard 2D homonuclear COSY and NOESY spectra. The (1)H NMR spectra of the paramagnetic Ce(III), Eu(III) and Yb(III) complex suggest nonadentate binding of the ligand to the metal ion. The syn conformation of the ligand in [Ln(bp15c5)](+) complexes implies the occurrence of two helicities, one associated with the layout of the picolinate pendant arms (absolute configuration Δ or Λ), and the other to the five five-membered chelate rings formed by the binding of the crown moiety (absolute configuration δ or λ). A detailed conformational analysis performed with the aid of DFT calculations (B3LYP model) indicates that the complexes adopt a Λ(λδ)(δδλ) [or Δ(δλ)(λλδ)] conformation in aqueous solution. Our calculations show that the interaction between the Ln(III) ion and several donor atoms of the crown moiety is weakened as the ionic radius of the metal ion decreases, in line with the decrease of complex stability observed on proceeding to the right across the lanthanide series.

Isolation, Structure and Cholesterol Esterase Inhibitory Activity of a Polysaccharide, PS-A, from Cordyceps sinensis

A heteropolysaccharide possessing strong inhibitory activity against cholesterol esterase, namely PS-A, was isolated from water extracts of Cordyceps sinensis by activity-guided fractionation. The molecular weight of PS-A was estimated as 4.6×105 Da. Compositional analysis revealed the presence of D-glucose, D-galactose, and D-mannose at a molar ratio of 2:1:1. The 1H and 13C nuclear magnetic resonance spectra, correlation spectroscopy, nuclear Overhauser effect spectroscopy, and heteronuclear multiple bond correlations experiment established the structure of PS-A as follows: {fx784-1} Results of the in vitro enzyme assay showed strong inhibition of cholesterol esterase by PS-A, with an IC50 value of 12.7 μg/mL, suggesting the possibility of its usefulness as a potential agent for control of hypercholesterolemia.

Detection and characterization of intermolecular multiple-quantum coherence NMR signals of IS ( I = 1/2; S = 3/2) spin systems

Intermolecular multiple-quantum coherences (iMQCs) have some intrinsic properties different from conventional single-quantum coherences in solution NMR. In this paper, we extended our study to heteronuclear iMQCs in IS ( I = 1/2, S = 3/2) spin systems. A sample of sodium chloride (NaCl) water solution was taken as an example. Heteronuclear COSY revamped by asymmetric Z-gradient echo detection (CRAZED) experiments were performed. One- and two-dimensional heteronuclear iMQC spectra were obtained. The quantum-mechanical treatment was used to deduce the signal expressions. Magic angle experiments validate that the signals are indeed from intermolecular dipolar interaction and insensitive to the imperfection of radio-frequency (RF) flip angles. Both experimental results and theoretical analysis indicate that heteronuclear CRAZED experiment allows coherence transfer from spin-3/2 nuclei to spin-1/2, and vice verse. Furthermore, the dependences of iMQC signal intensities on RF pulse flip angles follow the same rules as those for heteronuclear IS ( I = 1/2, S = 1/2 or 1) spin systems.

Effect of protein structural integrity on cross-linking by tyrosinase evidenced by multidimensional heteronuclear magnetic resonance spectroscopy

Enzymatic cross-linking of proteins can be catalyzed either by transferase-type enzymes, e.g., transglutaminases, or by oxidoreductases, e.g., tyrosinases or laccases. Three-dimensional structure of protein substrate plays a key role in these reactions, that is, the reactivity and end product are strongly modulated by the accessibility of target amino acid residues to the cross-linking enzyme. Typically structural integrity of protein can be distorted by heat, pH, or mechanical action, as well as by varying ionic concentration of the solution. In this study we used partially unfolded protein (wild-type DrkN SH3) and its structurally stabilized mutant (T22G) to investigate the impact of folded/unfolded conformations on cross-linking by Trichoderma reesei tyrosinase. Our results clearly showed formation of intermolecular cross-links solely between unfolded conformations, making them superior substrates to folded proteins when using tyrosinase as a cross-linking enzyme. Multidimensional heteronuclear magnetic resonance experiments in solution state were employed to investigate cross-linked end-products. The results presented in this study form basis for application development in food, medical, cosmetic, textile, packing and other sectors. In addition, the outcome of this study has a high value for the basic understanding of reaction mechanism of tyrosinases on proteins.

Integrin β3 Phosphorylation Dictates Its Complex with the Shc Phosphotyrosine-binding (PTB) Domain

Adaptor protein Shc plays a key role in mitogen-activated protein kinase (MAPK) signaling pathway, which can be mediated through a number of different receptors including integrins. By specifically recognizing the tyrosine-phosphorylated integrin β(3), Shc has been shown to trigger integrin outside-in signaling, although the structural basis of this interaction remains nebulous. Here we present the detailed structural analysis of Shc phosphotyrosine-binding (PTB) domain in complex with the bi-phosphorylated β(3)integrin cytoplasmic tail (CT). We show that this complex is primarily defined by the phosphorylation state of the integrin C-terminal Tyr(759), which fits neatly into the classical PTB pocket of Shc. In addition, we have identified a novel binding interface which concurrently accommodates phosphorylated Tyr(747) of the highly conserved NPXY motif of β(3). The structure represents the first snapshot of an integrin cytoplasmic tail bound to a target for mediating the outside-in signaling. Detailed comparison with the known Shc PTB structure bound to a target TrkA peptide revealed some significant differences, which shed new light upon the PTB domain specificity.

ChemInform Abstract: NMR of Peptides

AbstractReview: 62 refs.

Backbone 1H, 13C, and 15N assignments for the tandem ubiquitin binding domains of signal transducing adapter molecule 1

Signal transducing adapter molecule (STAM) forms the endosomal sorting complex required for transport-0 (ESCRT-0) complex with hepatocyte growth factor-regulated substrate (Hrs) to sort the ubiquitinated cargo proteins from the early endosomes to the ESCRT-1 complex. ESCRT-0 complex, STAM and Hrs, contains multiple ubiquitin binding domains, in which STAM has two ubiquitin binding domains, Vps27/Hrs/Stam (VHS) and ubiquitin interacting motif (UIM) at its N-terminus. By the cooperation of the multiple ubiquitin binding domains, the ESCRT-0 complex recognizes poly-ubiquitin, especially Lys63-linked ubiquitin. Here, we report the backbone resonance assignments and the secondary structure of the N-terminal 191 amino acids of the human STAM1 which includes the VHS domain and UIM. The {(1)H}-(15)N heteronuclear NOE experiments revealed that an unstructured and flexible loop region connects the VHS domain and UIM. Our work provides the basic information for the further NMR investigation of the interaction between STAM1 and poly-ubiquitin.

Lipid-protein correlations in nanoscale phospholipid bilayers determined by solid-state nuclear magnetic resonance.

Nanodiscs are examples of discoidal nanoscale lipid-protein particles that have been extremely useful for the biochemical and biophysical characterization of membrane proteins. They are discoidal lipid bilayer fragments encircled and stabilized by two amphipathic helical proteins named membrane scaffolding protein (MSP), ~10 nm in size. Nanodiscs are homogeneous, easily prepared with reproducible success, amenable to preparations with a variety of lipids, and stable over a range of temperatures. Here we present solid-state nuclear magnetic resonance (SSNMR) studies on lyophilized, rehydrated POPC Nanodiscs prepared with uniformly (13)C-, (15)N-labeled MSP1D1 (Δ1-11 truncated MSP). Under these conditions, by SSNMR we directly determine the gel-to-liquid crystal lipid phase transition to be at 3 ± 2 °C. Above this phase transition, the lipid (1)H signals have slow transverse relaxation, enabling filtering experiments as previously demonstrated for lipid vesicles. We incorporate this approach into two- and three-dimensional heteronuclear SSNMR experiments to examine the MSP1D1 residues interfacing with the lipid bilayer. These (1)H-(13)C and (1)H-(13)C-(13)C correlation spectra are used to identify and quantify the number of lipid-correlated and solvent-exposed residues by amino acid type, which furthermore is compared with molecular dynamics studies of MSP1D1 in Nanodiscs. This study demonstrates the utility of SSNMR experiments with Nanodiscs for examining lipid-protein interfaces and has important applications for future structural studies of membrane proteins in physiologically relevant formulations.