The binding of cytochrome c to neuroglobin: a docking and surface plasmon resonance study.

It has recently been proposed that the role of neuroglobin in the protection of neurons from ischaemia induced cell death requires the formation of a transient complex with cytochrome c. No such complex has yet been isolated. Here, we present the results of soft docking calculations, which indicate one major binding site for cytochrome c to neuroglobin. The results yield a plausible structure for the most likely complex structure in which the hemes of each protein are in close contact. NMR analysis identifies the formation of a weak complex in which the heme group of cytochrome c is involved. surface plasmon resonance studies provide a value of 45 microM for the equilibrium constant for cytochrome c binding to neuroglobin, which increases significantly as the ionic strength of the solution increases. The temperature dependence of the binding constant indicates that the complex formation is associated with a small unfavourable enthalpy change (1.9 kcal mol(-1)) and a moderately large, favourable entropy change (14.8 cal mol(-1) deg(-1)). The sensitivity of the binding constant to the presence of salt suggests that the complex formation involves electrostatic interactions.

Direct identification of NH...N hydrogen bonds in non-canonical base pairs of RNA by NMR spectroscopy.

It is shown that the recently developed quantitative J(NN)HNN-COSY experiment can be used for the direct identification of hydrogen bonds in non-canonical base pairs in RNA. Scalar(2h)J(NN)couplings across NH.N hydrogen bonds are observed in imino hydrogen bonded GA base pairs of the hpGA RNA molecule, which contains a tandem GA mismatch, and in the reverse Hoogsteen AU base pairs of the E-loop of Escherichia coli 5S rRNA. These scalar couplings correlate the imino donor(15)N nucleus of guanine or uridine with the acceptor N1 or N7 nucleus of adenine. The values of the corresponding(2h)J(NN)coupling constants are similar in size to those observed in Watson-Crick base pairs. The reverse Hoogsteen base pairs could be directly detected for the E-loop of E.coli 5S rRNA both in the free form and in a complex with the ribosomal protein L25. This supports the notion that the E-loop is a pre-folded RNA recognition site that is not subject to significant induced conformational changes. Since Watson-Crick GC and AU base pairs are also readily detected the HNN-COSY experiment provides a useful and sensitive tool for the rapid identification of RNA secondary structure elements.

1H-NMR visible neutral lipids in activated T lymphocytes: relationship to phosphatidylcholine cycling.

Two-dimensional 1H-NMR spectroscopy was used to compare changes in the concentration of isotropically-tumbling neutral lipid during the activation of splenic and thymic T lymphocytes. The concentration of mobile neutral lipid (MNL) was similar in splenic and thymic T cells after 72 h of activation with phorbol myristate acetate and ionomycin. However, after 120 h of activation, MNL concentrations in splenic T cells were more than 3-fold higher than in thymic T cells. An increase in choline (Cho), phosphocholine (PCho) and glycerophosphocholine (GPC) was also observed in both thymic and splenic T cells after 24 h of activation. However, after 72 h of stimulation, Cho and PCho levels had decreased and continued to decline at 96-120 h, while GPC continued to be maintained at elevated levels. The simultaneous increase in MNL and GPC and the decline in Cho and PCho leads us to propose that the synthesis of NMR-visible MNL in activated lymphocytes is linked to the phosphatidylcholine cycle.

Identification of key residues involved in adrenomedullin binding to the AM1 receptor.

BACKGROUND AND PURPOSE: Adrenomedullin (AM) is a peptide hormone whose receptors are members of the class B GPCR family. They comprise a heteromer between the GPCR, the calcitonin receptor-like receptor and one of the receptor activity-modifying proteins 1-3. AM plays a significant role in angiogenesis and its antagonist fragment AM22-52 can inhibit blood vessel and tumour growth. The mechanism by which AM interacts with its receptors is unknown. EXPERIMENTAL APPROACH: We determined the AM22-52 binding epitope for the AM1 receptor extracellular domain using biophysical techniques, heteronuclear magnetic resonance spectroscopy and alanine scanning. KEY RESULTS: Chemical shift perturbation experiments located the main binding epitope for AM22-52 at the AM1 receptor to the C-terminal 8 amino acids. Isothermal titration calorimetry of AM22-52 alanine-substituted peptides indicated that Y52, G51 and I47 are essential for AM1 receptor binding and that K46 and P49 and R44 have a smaller role to play. Characterization of these peptides at the full-length AM receptors was assessed in Cos7 cells by cAMP assay. This confirmed the essential role of Y52, G51 and I47 in binding to the AM1 receptor, with their substitution resulting in ≥100-fold reduction in antagonist potency compared with AM22-52 . R44A, K46A, S48A and P49A AM22-52 decreased antagonist potency by approximately 10-fold. CONCLUSIONS AND IMPLICATIONS: This study localizes the main binding epitope of AM22-52 to its C-terminal amino acids and distinguishes essential residues involved in this binding. This will inform the development of improved AM receptor antagonists.

A DFT study of the interresidue dependencies of scalar J-coupling and magnetic shielding in the hydrogen-bonding regions of a DNA triplex.

Scalar coupling constants and magnetic shieldings in the imino hydrogen-bonding region of Hoogsteen-Watson-Crick T.A-T and C(+).G-C triplets have been calculated as a function of the distance between proton donor and acceptor nitrogen atoms. The Fermi contact contributions to (h2)J((15)N-H...(15)N), (1)J((15)N-(1)H), and (h1)J((1)H...(15)N) were computed using density functional theory/finite perturbation theory (DFT/FPT) methods for the full base triplets at the unrestricted B3PW91/6-311G level. Chemical shifts delta((1)H) and delta((15)N) were obtained at the same level using the gauge including atomic orbital (GIAO) method for magnetic shielding. All three scalar couplings and all three chemical shifts are strongly interrelated and exhibit monotonic changes with base pair separation. These correlations are in conformity with experimental data for a 32-nucleotide DNA triplex. The results suggest that both chemical shifts and coupling constants can be used to gain information on H-bond donor-acceptor distances in nucleic acids. In addition to the DFT/FPT calculations, a simple three-orbital model of the N-H...H bond and a sum-over-states analysis is presented. This model reproduces the basic features of the H-bond coupling effect. In accordance with this model and the DFT calculations, a positive sign for the (h2)J(NN) coupling is determined from an E.COSY experiment.

An NMR investigation of the changes in plasma membrane triglyceride and phospholipid precursors during the activation of T-lymphocytes.

Two-dimensional 1H-NMR spectroscopy was used to quantify the level of isotropically tumbling plasma membrane triglyceride and the intracellular concentrations of water-soluble phospholipid precursors during the activation of thymic T-lymphocytes. The concentration of "mobile" triglyceride in the plasma membrane was seen to increase 25-fold during 72 h of activation of murine thymic T-lymphocytes with ionomycin and phorbol myristate acetate. This is the first unequivocal demonstration of such a dramatic increase in mobile plasma membrane triglyceride during T-lymphocyte activation and leads to the suggestion that immune cell activation is associated with increased plasma membrane fluidity. The intracellular concentrations of choline- and ethanolamine-based phospholipid precursors were shown to increase during the early stages of T-lymphocyte activation and then remain at levels above those in resting cells. This may facilitate de novo phospholipid biosynthesis, which is presumably necessary since cell volume, and hence the plasma membrane surface area, was demonstrated to increase significantly during thymocyte activation.

A doublet-separated sensitivity-enhanced HSQC for the determination of scalar and dipolar one-bond J-couplings.

A simple, sensitivity-enhanced HSQC experiment is described which separates the upfield and downfield components in the indirect dimension into different subspectra. The sequence is similar to the generalized TROSY scheme; however, decoupling of the X-nucleus is used during detection. A detailed analysis of relaxation effects, precision and sensitivity of the method is presented. The approach is demonstrated in a two-dimensional water flip-back 1H-15N HSQC which measures 1JHN splittings in isotropic and oriented samples of ubiquitin and the hepatitis C protease. The results are in excellent agreement with splittings obtained from a conventional 1H-coupled HSQC.

Two-dimensional 1H NMR studies of membrane changes during the activation of primary T lymphocytes.

Two-dimensional 1H NMR spectroscopy was used to quantify the level of "mobile" plasma membrane triglyceride and the intracellular concentrations of water-soluble phospholipid precursors during the activation of both mature and immature primary T lymphocytes. The concentration of mobile triglyceride in the plasma membrane was seen to increase approximately 35-fold during 72 h of activation of murine thymic and splenic T lymphocytes with ionomycin and phorbol 12-myristate 13-acetate. This dramatic increase in mobile plasma membrane triglyceride during the activation of both mature and immature T-lymphocyte populations supports the hypothesis that immune cell activation is associated with increased plasma membrane fluidity. The intracellular concentrations of various phospholipid precursors were shown to increase during the early stages of T-lymphocyte activation and then remain at levels above those in resting cells. This may facilitate de novo phospholipid biosynthesis, which is presumably necessary since cell volume, and hence the plasma membrane surface area, was demonstrated to increase significantly during T-lymphocyte activation. Various models that might explain the origin of the NMR-visible plasma membrane triglyceride that is observed during immune cell activation and malignant transformation are examined.

Determination of backbone nitrogen-nitrogen J correlations in proteins.

Recently, a quantitative J correlation technique has been presented which makes use of homonuclear Hartmann-Hahn cross-polarization (TOCSY) to measure (3)J(C)'(C)' in proteins isotopically enriched with (13)C [Grzesiek, S. and Bax, A. (1997) J. Biomol. NMR, 9, 207-211]. Since homonuclear Hartmann-Hahn is twice as fast as conventional COSY transfer, this method is much less sensitive to transverse relaxation, which is the principal limiting factor in achieving long-range J-coupling correlations in macromolecules. Here we describe a similar experiment which is used to measure(3) J(NN) coupling constants between sequential amide(15) N nuclei in the backbone of ubiquitin. As expected from the low magnetic moment of (15)N, the (3)J(NN) coupling constants are exceedingly small, with values between 0.14 and 0.36 Hz for residues in ß-conformations and values below 0.15 Hz for residues in α-conformations. In contrast to what is expected from a Karplus-type dependence on the backbone angle ψ, large differences in the values of(3) J(NN) are observed for a number of residues with very similar backbone ψ angles. A quantitative description of statistical and systematic errors, in particular of relaxation effects during the TOCSY transfer, shows that these differences are highly significant.

Characterization of the hydrogen bond network in guanosine quartets by internucleotide 3hJ(NC)' and 2hJ(NN) scalar couplings.

Scalar coupling correlations across hydrogen bonds with carbonyl groups as acceptors have been observed in a variety of proteins, but not in nucleic acids. Here we present a pulse scheme that allows such an observation and quantification of trans-hydrogen bond 3hJ(NC)' correlations in nucleic acid base pairs, between the imino nitrogen 15N1 and the carbonyl 13C6 nuclei within the guanine quartets of the Oxy-1.5 DNA-quadruplex. Intra- and internucleotide N-H...O=C connectivities can be traced around each guanine quartet, allowing the hydrogen bonding partners to be unambiguously assigned. Absolute values of the 3hJ(NC)' couplings are approximately 0.2 Hz as quantified by a selective long-range H(N)CO experiment and are thus on average smaller than the analogous 3hJ(NC)' couplings observed in proteins. In addition, an improved version of the pseudo-heteronuclear H(N)N-COSY [Majumdar et al. (1999) J. Biomol. NMR, 14, 67-70] is presented which allows simultaneous detection of the 15N-donor and 15N-acceptor resonances connected by 2hJ(NN) couplings in hydrogen bonds involving amino groups. Using this experiment, values ranging between 6 and 8 Hz are determined for the 2hJNN couplings between 15N2 and 15N7 nuclei in the guanine quartet. These values are not strongly influenced by the presence of a significant amount of chemical exchange broadening due to amino group rotations.

Measuring macromolecular diffusion using heteronuclear multiple-quantum pulsed-field-gradient NMR.

We have previously shown that (1)H pulsed-field-gradient(PFG) NMR spectroscopy provides a facile method for monitoring proteinself-association and can be used, albeit with some caveats, to measure theapparent molecular mass of the diffusant [Dingley et al. (1995) J. Biomol.NMR, 6, 321-328]. In this paper we show that, for(15)N-labelled proteins, selection of(1)H-(15)N multiple-quantum (MQ) coherences in PFGdiffusion experiments provides several advantages over monitoring(1)H single-quantum (SQ) magnetization. First, the use of agradient-selected MQ filter provides a convenient means of suppressingresonances from both the solvent and unlabelled solutes. Second,(1)H-(15)N zero-quantum coherence dephases morerapidly than (1)H SQ coherence under the influence of a PFG.This allows the diffusion coefficients of larger proteins to be measuredmore readily. Alternatively, the gradient length and/or the diffusion delaymay be decreased, thereby reducing signal losses from relaxation. In orderto extend the size of macromolecules to which these experiments can beapplied, we have developed a new MQ PFG diffusion experiment in which themagnetization is stored as longitudinal two-spin order for most of thediffusion period, thus minimizing sensitivity losses due to transverserelaxation and J-coupling evolution.

High-resolution solution structure of gurmarin, a sweet-taste-suppressing plant polypeptide.

Gurmarin is a 35-residue polypeptide from the Asclepiad vine Gymnema sylvestre. It has been utilised as a pharmacological tool in the study of sweet-taste transduction because of its ability to selectively inhibit the neural response to sweet tastants in rats. We have chemically synthesised and folded gurmarin and determined its three-dimensional solution structure to high resolution using two-dimensional NMR spectroscopy. Structure calculations utilised 612 interproton-distance, 19 dihedral-angle, and 18 hydrogen-bond restraints. The structure is well defined for residues 3-34, with backbone and heavy atom rms differences of 0.27 +/- 0.09 A and 0.73 +/- 0.09 A, respectively. Gurmarin adopts a compact structure containing an antiparallel beta-hairpin (residues 22-34), several well-defined beta-turns, and a cystine-knot motif commonly observed in toxic and inhibitory polypeptides. Despite striking structural homology with delta-atracotoxin, a spider neurotoxin known to slow the inactivation of voltage-gated Na+ channels, we show that gurmarin has no effect on a variety of voltage-sensitive channels.

Measuring protein self-association using pulsed-field-gradient NMR spectroscopy: application to myosin light chain 2.

At the millimolar concentrations required for structural studies, NMR spectra of the calcium-binding protein myosin light chain 2 (MLC2) showed resonance line widths indicative of extensive self-association. Pulsed-field-gradient (PFG) NMR spectroscopy was used to examine whether MLC2 aggregation could be prevented by the zwitterionic bile salt derivative 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate (CHAPS). PFG NMR measurements indicated that CHAPS was capable of preventing MLC2 self-association, but only at concentrations well above the critical micelle concentration of approximately 7.5 mM. CHAPS was most effective at a concentration of 22.5 mM, where the apparent molecular mass of MLC2 corresponded to a protein monomer plus seven molecules of bound detergent. The resolution and sensitivity of 2D 15N-1H HSQC spectra of MLC2 were markedly improved by the addition of 25 mM CHAPS, consistent with a reduction in aggregation following addition of the detergent. The average amide nitrogen T2 value for MLC2 increased from approximately 30 ms in the absence of CHAPS to approximately 56 ms in the presence of 25 mM CHAPS. The results of this study lead us to propose that PFG NMR spectroscopy can be used as a facile alternative to conventional techniques such as analytical ultracentrifugation for examining the self-association of biological macromolecules.