Heteronuclear NOE Measurements Research Articles

Molecular Dynamics-Assisted Optimization of Protein NMR Relaxation Analysis.

NMR relaxation analysis of the mobile residues in globular proteins is sensitive to the form of the experimentally fitted internal autocorrelation function, which is used to represent that motion. Different order parameter representations can precisely fit the same set of 15N R1, R2, and heteronuclear NOE measurements while yielding significantly divergent predictions of the underlying autocorrelation functions, indicating the insufficiency of these experimental relaxation data for assessing which order parameter representation provides the most physically realistic predictions. Molecular dynamics simulations offer an unparalleled capability for discriminating among different order parameter representations to assess which representation can most accurately model a wide range of physically realistic autocorrelation functions. Six currently utilized AMBER and CHARMM force fields were applied to calculate autocorrelation functions for the backbone H–N bond vectors of ubiquitin as an operational test set. An optimized time constant-constrained triexponential (TCCT) representation was shown to markedly outperform the widely used (Sf2,τs,S2) extended Lipari–Szabo representation and the more closely related (Sf2,SH2, SN2) Larmor frequency-selective representation. Optimization of the TCCT representation at both 600 and 900 MHz 1H converged to the same parameterization. The higher magnetic field yielded systematically larger deviations in the back-prediction of the autocorrelation functions for the mobile amides, indicating little added benefit from multiple field measurements in analyzing amides that lack slower (∼ms) exchange line-broadening effects. Experimental 15N relaxation data efficiently distinguished among the different force fields with regard to their prediction of ubiquitin backbone conformational dynamics in the ps–ns time frame. While the earlier AMBER 99SB and CHARMM27 force fields underestimate the scale of backbone dynamics, which occur in this time frame, AMBER 14SB provided the most consistent predictions for the well-averaged highly mobile C-terminal residues of ubiquitin.

Using Structural and Dynamic NMR Analyses to Dissect the Pathologic Function of a Novel Chemokine

Chemokines are small, secreted proteins that bind G protein-coupled receptors (GPCRs) to orchestrate cellular chemotaxis in the immune system and beyond. While the ∼50 members of the chemokine family share a remarkably conserved tertiary structure, they still manage to coordinate diverse, non-redundant physiologic and pathologic functions in the human body. It is therefore assumed that more subtle nuances in the structure and dynamics of each chemokine-receptor pair are the key determinants of their biologic function. Here we present the molecular structure of CCL28, an especially intriguing chemokine recently identified to play a major role in asthma pathogenesis, solved by solution-state nuclear magnetic resonance spectroscopy (NMR). The structure reveals that while CCL28 adopts the conserved chemokine tertiary fold, it has a particularly curious structural feature not seen in other chemokines. An intrinsically disordered C-terminal domain of ∼30 residues extends from the globular core of the chemokine, part of which is tethered by a non-conserved disulfide bond. Dynamic NMR experiments including backbone 1H-15N heteronuclear NOE measurements, heteronuclear single quantum coherence (HSQC) titrations, and pulsed field gradient (PFG) diffusion measurements collectively indicate the disordered, dynamic nature of the C-terminal extension. Combined with mutational and in vitro functional studies, our findings suggest that the unique structural and dynamic features of CCL28 may be key determinants of its pathologic function.

Supramolecular complexes of podand ligands with xenon

Abstract Formation of stable complexes between xenon and podand polyoxyethylene ligands was ascertained. The complexation process was studied by 129Xe NMR titration, NMR diffusiometry and heteronuclear NOE measurements. The ligands studied form a 1:1 complexes with Xe(0). Their stability constants depend on the ligand structure, i.e., polyoxyethylene chain length, number of complexating polyether units and the topology of the anchoring centre.

Structural Characterization of Hsp12, the Heat Shock Protein from Saccharomyces cerevisiae, in Aqueous Solution Where It Is Intrinsically Disordered and in Detergent Micelles Where It Is Locally α-Helical

Hsp12 (heat shock protein 12) belongs to the small heat shock protein family, partially characterized as a stress response, stationary phase entry, late embryonic abundant-like protein located at the plasma membrane to protect membrane from desiccation. Here, we report the structural characterization of Hsp12 by NMR and biophysical techniques. The protein was labeled uniformly with nitrogen-15 and carbon-13 so that its conformation could be determined in detail both in aqueous solution and in two membrane-mimetic environments, SDS and dodecylphosphocholine (DPC) micelles. Secondary structural elements determined from assigned chemical shifts indicated that Hsp12 is dynamically disordered in aqueous solution, whereas it gains four helical stretches in the presence of SDS micelles and a single helix in presence of DPC. These conclusions were reinforced by circular dichroism spectra of the protein in all three environments. The lack of long range interactions in NOESY spectra indicated that the helices present in SDS micelles do not pack together. R(1) and R(2), relaxation and heteronuclear NOE measurements showed that the protein is disordered in aqueous solution but becomes more ordered in presence of detergent micelles. NMR spectra collected in presence of paramagnetic spin relaxation agents (5DSA, 16DSA, and Gd(DTPA-BMA)) indicated that the amphipathic α-helices of Hsp12 in SDS micelles lie on the membrane surface. These observations are in agreement with studies suggesting that Hsp12 functions to protect the membrane from desiccation.

Structural and thermodynamic investigations of an unusual enantiomeric separation: Lipodex E and compound B

Compound B (1,1,3,3,3-pentafluoro-2-fluoromethoxy-1-methoxypropane) can be separated by gas chromatography with an extraordinary chiral separation factor on a column coated with Lipodex E (octakis(3- O-butanoyl-2,6-di- O- n-pentyl)-γ-cyclodextrin). The enantioselectivity is greatly reduced when employing the β-cyclodextrin analogue. To further investigate the background of this unusual separation, the complexation between ‘compound B’ and Lipodex E (octakis(3- O-butanoyl-2,6-di- O- n-pentyl)-γ-cyclodextrin) and heptakis(3- O-butanoyl-2,6-di- O- n-pentyl)-β-cyclodextrin were studied by NMR. Association constants of the interaction of the two enantiomers of compound B with Lipodex E and its β-cyclodextrin analogue were determined by NMR chemical shift titration and showed a large difference corroborating earlier GC results. Heteronuclear NOE measurements proved that inclusion complex formation is taking place with compound B situated inside the cavity of the cyclodextrin moiety. Differences between the inclusion complex structures and their connection to association constants are discussed.

The pH-dependence of preferential solvation as studied by intermolecular homo- and heteronuclear NOE measurements of adenosine in water-trifluoroethanol mixtures.

A study of the state of solvation of the adenine ring in adenosine and adenosine 5'-monophosphate disodium salt in water and in a (7.5:2.5) water-TFE mixture has been carried out by measurement of homo- and heteronuclear intermolecular NOE enhancements between water or TFE and the aromatic protons of these compounds. The results give evidence of site specificity in solute-solvent interaction for both solvent systems and preferential solvation of the solute by TFE in the water-TFE mixture. Significant pH dependence of these interactions has been discovered.

Evidence of complete hydrophobic coating of bombesin by trifluoroethanol in aqueous solution: an NMR spectroscopic and molecular dynamics study.

Bombesin is a tetradecapeptide that possesses a random coil structure in pure water. In the presence of 30 % (v/v) 2,2,2-trifluoroethanol (TFE), it adopts a partial helical conformation involving the C-terminal amino acids 6-14. This conformational change, known as the TFE effect, is studied here in terms of the solvation state of the peptide at different TFE concentrations by means of intermolecular homo- and heteronuclear NOE measurements. When an aqueous solution of bombesin is titrated with TFE, a continual decrease in the water/peptide interactions and a concomitant increase in the TFE/peptide interactions is observed, and at 30 % (v/v) TFE no homonuclear NOEs between water and the peptide can be detected. The conformational transition of the bombesin molecule is thus accompanied by a complete surface covering with TFE. A parallel molecular dynamics (MD) study of the peptide in aqueous solution with the single-point charge (SPC) water model and in a 30 % (v/v) TFE/water mixture with a recently developed TFE model has also been performed. The 10 ns simulations were in agreement with the experimental data. The calculations indicate stabilisation of the alpha-helix in the H(2)O/TFE mixture, in contrast to the situation in pure water, and clustering of the TFE molecules around the peptide.

NMR characterization of the metallo-beta-lactamase from Bacteroides fragilis and its interaction with a tight-binding inhibitor: role of an active-site loop.

Understanding the structure and dynamics of the enzymes that mediate antibiotic resistance of pathogenic bacteria will allow us to take steps to combat this increasingly serious public health hazard. Complete backbone NMR resonance assignments have been made for the broad-specificity metallo-beta-lactamase CcrA from Bacteroides fragilis in the presence and absence of a tight-binding inhibitor. Chemical shift indices show that the secondary structure of the CcrA molecule in solution is very similar to that in published crystal structures. A loop adjacent to the two-zinc catalytic site exhibits significant structural variation in the published structures, but appears from the NMR experiments to be a regular beta-hairpin. Backbone heteronuclear NOE measurements indicate that this region has slightly greater flexibility on a picosecond to nanosecond time scale than the molecule as a whole. The loop appears to have an important role in the binding of substrates and inhibitors. Binding of the inhibitor 3-[2'-(S)-benzyl-3'-mercaptopropanoyl]-4-(S)-carboxy-5, 5-dimethylthiazolidine causes a marked increase in the stability of the protein toward unfolding and aggregation, and causes changes in the NMR resonance frequencies of residues close to the active (zinc-binding) site, including the beta-hairpin loop. There is a small but significant increase in the heteronuclear NOE for this loop upon inhibitor binding, indicative of a decrease in flexibility. In particular, the NOE of the indole ring of tryptophan 49, at the tip of the beta-hairpin loop, changes from a low value characteristic of a random coil chain to a significantly higher value, close to that observed for the backbone amides in this region of the protein. These results strongly suggest that the hairpin loop participates in the binding of substrate and in the shielding of the zinc sites from solvent. The broad specificity of the CcrA metallo-beta-lactamase may in fact reside in the plasticity of this part of the protein, which allows it to accommodate and bind tightly to substrates of a variety of shapes and sizes.

Inherent flexibility in a potent inhibitor of blood coagulation, recombinant nematode anticoagulant protein c2.

Nematode anticoagulant proteins (NAPs) from the hematophagous nematode Ancylostoma caninum inhibit blood coagulation with picomolar inhibition constants, and have been targeted as novel pharmaceutical agents. NAP5 and NAP6 inhibit factor Xa by binding to its active site, whereas NAPc2 binds to factor Xa at a different, as yet unidentified, site and the resultant binary complex inhibits the tissue factor-factor VIIa complex. We have undertaken NMR studies of NAPc2, including the calculation of a solution structure, and found that the protein is folded, with five disulfide bonds, but is extremely flexible, especially in the acidic loop. The Halpha secondary shifts and 3JHNHalpha coupling constants indicate the presence of some beta structure and a short helix, but the intervening loops are highly conformationally heterogeneous. Heteronuclear NOE measurements showed the presence of large amplitude motions on a subnanosecond timescale at the N-terminus and C-terminus and in the substrate-binding loop, indicating that the conformational heterogeneity observed in the NMR structures is due to flexibility of the polypeptide chain in these regions. Flexibility may well be an important factor in the physiological function of NAPc2, because it must interact with other proteins in the inhibition of blood coagulation. We suggest that this inhibitor is likely to become structured on binding to factor Xa, because the inhibition of the tissue factor-factor VIIa complex requires both NAPc2 and factor Xa.

Altered flexibility in the substrate-binding site of related native and engineered high-alkaline Bacillus subtilisins

High-alkaline serine proteases have been successfully applied as protein degrading components of detergent formulations and are subject to extensive protein engineering efforts to improve their stability and performance. Dynamics has been suggested to play an important role in determining enzyme activity and specificity and it is therefore of interest to establish how local changes in internal mobility affect protein stability, specificity and performance. Here we present the dynamic properties of the 269 residue serine proteases subtilisin PB92 (Maxacal™) and subtilisin BLS (Savinase™), secreted by Bacillus lentus, and an engineered quadruple variant, DSAI, that has improved washing performance. T1, T2and heteronuclear NOE measurements of the 15N nuclei indicate that for all three proteins the majority of the backbone is very rigid, with only a limited number of residues being involved in local mobility. Many of the residues that constitute the S1 and S4 pockets, determining substrate specificity, are flexible in solution. In contrast, the backbone amides of the residues that constitute the catalytic triad do not exhibit any motion. Subtilisins PB92, BLS and DSAI demonstrate similar but not identical NMR relaxation rates. A detailed analysis of local flexibility indicates that the motion of residues Thr143 and Ala194 becomes more restricted in subtilisin BLS and DSAI. Noteworthy, the loop regions involved in substrate binding become more structured in the engineered variant as compared with the two native proteases, suggesting a relation between altered dynamics and performance. Similar conclusions have been established by X-ray crystallograpic methods, as shown in the accompanying paper.

Solution structure of the DNA-binding domain of a human papillomavirus E2 protein: evidence for flexible DNA-binding regions.

The three-dimensional structure of the DNA-binding domain of the E2 protein from human papillomavirus-31 was determined by using multidimensional heteronuclear nuclear magnetic resonance (NMR) spectroscopy. A total of 1429 NMR-derived distance and dihedral angle restraints were obtained for each of the 83-residue subunits of this symmetric dimer. The average root mean square deviations of 20 structures calculated using a distance geometry-simulated annealing protocol are 0.59 and 0.90 angstroms for the backbone and all heavy atoms, respectively, for residues 2-83. The structure of the human virus protein free in solution consists of an eight-stranded beta-barrel and two pairs of alpha-helices. Although the overall fold of the protein is similar to the crystal structure of the bovine papillomavirus-1 E2 protein when complexed to DNA, several small but interesting differences were observed between these two structures at the subunit interface. In addition, a beta-hairpin that contacts DNA in the crystal structure of the protein-DNA complex is disordered in the NMR structures, and steady-state 1H-15N heteronuclear NOE measurements indicate that this region is highly mobile in the absence of DNA. The recognition helix also appears to be flexible, as evidenced by fast amide exchange rates. This phenomenon has also been observed for a number of other DNA-binding proteins and may constitute a common theme in protein/DNA recognition.

Rotational dynamics of calcium-free calmodulin studied by 15N-NMR relaxation measurements.

The backbone motions of calcium-free Xenopus calmodulin have been characterized by measurements of the 15N longitudinal relaxation times (T1) at 51 and 61 MHz, and by conducting transverse relaxation (T2), spin-locked transverse relaxation (T1 rho), and 15N-[1H] heteronuclear NOE measurements at 61 MHz 15N frequency. Although backbone amide hydrogen exchange experiments indicate that the N-terminal domain is more stable than calmodulin's C-terminal half, slowly exchanging backbone amide protons are found in all eight alpha-helices and in three of the four short beta-strands. This confirms that the calcium-free form consists of stable secondary structure and does not adopt a 'molten globule' type of structure. However, the C-terminal domain of calmodulin is subject to conformational exchange on a time scale of about 350 microseconds, which affects many of the C-terminal domain residues. This results in significant shortening of the 15N T2 values relative to T1 rho, whereas the T1 rho and T2 values are of similar magnitude in the N-terminal half of the protein. A model in which the motion of the protein is assumed to be isotropic suggests a rotational correlation time for the protein of about 8 ns but quantitatively does not agree with the magnetic field dependence of the T1 values and does not explain the different T2 values found for different alpha-helices in the N-terminal domain. These latter parameters are compatible with a flexible dumb-bell model in which each of calmodulin's two domains freely diffuse in a cone with a semi-angle of about 30 degrees and a time constant of about 3 ns, whereas the overall rotation of the protein occurs on a much slower time scale of about 12 ns. The difference in the transverse relaxation rates observed between the amides in helices C and D suggests that the change in interhelical angle upon calcium binding is less than predicted by Herzberg et al. Strynadka and James [Strynadka, N. C. J. & James, M. N. G. (1988) Proteins Struct. Funct. Genet. 3, 1-17].

Combined use of 13C chemical shift and 1H??13C? heteronuclear NOE data in monitoring a protein NMR structure refinement

A large portion of the 13C resonance assignments for murine epidermal growth factor (mEGF) at pH 3.1 and 28 degrees C has been determined at natural isotope abundance. Sequence-specific 13C assignments are reported for 100% of the assignable C alpha, 96% of the C beta, 86% of the aromatic and 70% of the remaining peripheral aliphatic resonances of mEGF. A good correlation was observed between experimental and back-calculated C alpha chemical shifts for regions of regular beta-sheet structure. These assignments also provide the basis for interpreting 1H alpha-13C alpha heteronuclear NOE (HNOE) values in mEGF at natural isotope abundance. Some of the backbone polypeptide segments with high internal mobility, indicated by these 1H alpha-13C alpha HNOE measurements, correlate with locations of residues involved in the putative mEGF-receptor binding site. Using four families of mEGF structures obtained over the last few years, we demonstrate that standard deviations between experimental and back-calculated delta delta C alpha values can be used to monitor the refinement of this protein's structure, particularly for beta-sheet regions. Improved agreement between calculated and observed values of delta delta C alpha is correlated with other measures of structure quality, including lowered values of residual constraint violations and more negative values of conformational energy. These results support the view that experimental conformation-dependent chemical shifts, delta delta C alpha, can provide a reliable source of information for monitoring the process of protein structure refinement and are potentially useful restraints for driving the refinement.

Overcoming Solvent Saturation-Transfer Artifacts in Protein NMR at Neutral pH. Application of Pulsed Field Gradients in Measurements of 1H- 15N Overhauser Effects

Artifacts due to solvent saturation-transfer effects result in incorrect measurements of 1H- 15N heteronuclear NOE (HNOE). These artifacts are commonly observed in aqueous protein solutions at neutral pH. We describe the application of pulsed field gradients (PFGs) together with long recycle delays in overcoming errors in HNOE measurements which arise from H 2O solvent preirradiation and solvent saturation transfer. Even in the absence of explicit solvent irradiation, the HNOE pulse sequence itself results in a nonequilibrium spin-state distribution of solvent nuclei which can then be transferred by chemical exchange into amide-proton sites. This effect can be avoided by using PFGs for suppression of solvent H 2O together with a recycle delay sufficiently long for the magnetization of water to relax back to equilibrium values during the preparation period. These effects were studied in 15N-enriched human type α transforming growth factor at pH 7.1. Comparisons of PFG-HNOE experiments with and without selective H 2O irradiation and with different recycle times provide estimates of the effects of solvent irradiation on HNOE measurements, which are different for different amide nitrogen-15 nuclei. The amplitudes of these artificial HNOE enhancements are roughly correlated with solvent accessibilities of amide sites in the three-dimensional structure of hTGFα.

Quantitative 13C-{ 1H} NOE spectroscopy at natural abundance. The role of indirect effects

Indirect, three-spin effects in the 13C isotopomers arising from abundant or dilute spins are analyzed theoretically and by experiments including mono- and biselective heteronuclear NOE measurements, homonuclear NOE factors, and selective relaxation rates. An extension of the Kuhlmann-Grant-Harris heteronuclear NOE theory to dilute spins allows the determination of direct relaxation rates in AMX spin systems. This method was used successfully for carbon-proton distance measurement in the range of 0.1–0.4 nm in small, rigid, isotropically reorienting organic molecules even in the presence of negative, indirect NOE. The first example of such effects at quaternary carbons in their natural abundance is presented.