Assigning the NMR spectra of aromatic amino acids in proteins: analysis of two Ets pointed domains

The measurement of interproton nuclear Overhauser enhancements (NOEs) and dihedral angle restraints of aromatic amino acids is a critical step towards determining the structure of a protein. The complete assignment of the resonances from aromatic rings and the subsequent resolution and identification of their associated NOEs, however, can be a difficult task. Shown here is a strategy for assigning the 1H, 13C, and 15N signals from the aromatic side chains of histidine, tryptophan, tyrosine, and phenylalanine using a suite of homo- and hetero-nuclear scalar and NOE correlation experiments, as well as selective deuterium isotope labelling. In addition, a comparison of NOE information obtained from homonuclear NOE spectroscopy (NOESY) and 13C-edited NOESY-heteronuclear single quantum correlation experiments indicates that high-resolution homonuclear two-dimensional NOESY spectra of selectively deuterated proteins are invaluable for obtaining distance restraints to the aromatic residues.     

Solid-state NMR studies of proteins: the view from static 2H NMR experiments

The application of solid-state 2H NMR spectroscopy to the study of protein and peptide structure and dynamics is reviewed. The advantages of solid-state NMR for the study of proteins are considered, and the particular advantages of solid-state 2H NMR are summarized. Examples of work on the integral membrane protein bacteriorhodopsin, and the membrane peptide gramicidin, are used to highlight the major achievements of the 2H NMR technique. These examples demonstrate that through the use of oriented samples, it is possible to obtain both structural and dynamic information simultaneously.     

Characterization of azo coupling adducts of benzenediazonium ions with aromatic amino acids in peptides and proteins

A synthetic peptide, VLSPADKTNWGHEYRMF(cmC)QIG, was reacted with 4-chlorobenzenediazonium hexafluorophosphate as a model for reactions of aromatic diazonium ions with proteins. At a ratio of diazonium ion to peptide of 0.8:1, three products could be seen by reversed-phase HPLC. Electrospray mass spectrometric analysis of the isolated products revealed that two of the products had the same mass of 2648 Da, being 138 Da higher than the parent peptide and corresponding to the addition of a 4-chlorobenzenediazo group. The third isolated product had a mass of 2787 Da which corresponded to the addition of two 4-chlorobenzenediazo groups (276 Da). Digestion of the monoadducted intact peptides with trypsin or endoproteinase Glu-C and HPLC separation of adduct oligopeptides followed by sequencing with electrospray ionization tandem mass spectrometry showed unambiguously that histidine and tyrosine residues were the major sites of modification. Incubation of human serum albumin with 4-chlorobenzenediazonium hexafluorophosphate at molar ratios of 1:1, 1:2, and 1:10 resulted in adduct formation as detected by shifts in the HPLC retention time of the protein and also by an increase in mass as determined by electrospray mass spectrometry.     

Global folds of highly deuterated, methyl-protonated proteins by multidimensional NMR

The development of 15N, 13C, 2H multidimensional NMR spectroscopy has facilitated the assignment of backbone and side chain resonances of proteins and protein complexes with molecular masses of over 30 kDa. The success of these methods has been achieved through the production of highly deuterated proteins; replacing carbon-bound protons with deuterons significantly improves the sensitivity of many of the experiments used in chemical shift assignment. Unfortunately, uniform deuteration also radically depletes the number of interproton distance restraints available for structure determination, degrading the quality of the resulting structures. Here we describe an approach for improving the precision and accuracy of global folds determined from highly deuterated proteins through the use of deuterated, selectively methyl-protonated samples. This labeling profile maintains the efficiency of triple-resonance NMR experiments while retaining a sufficient number of protons at locations where they can be used to establish NOE-based contacts between different elements of secondary structure. We evaluate how this deuteration scheme affects the sensitivity and resolution of experiments used to assign 15N, 13C, and 1H chemical shifts and interproton NOEs. This approach is tested experimentally on a 14 kDa SH2/phosphopeptide complex, and a global protein fold is obtained from a set of methyl-methyl, methyl-NH, and NH-NH distance restraints. We demonstrate that the inclusion of methyl-NH and methyl-methyl distance restraints greatly improves the precision and accuracy of structures relative to those generated with only NH-NH distance restraints. Finally, we examine the general applicability of this approach by determining the structures of several proteins with molecular masses of up to 40 kDa from simulated distance and dihedral angle restraint tables.     

Characterizing the use of perdeuteration in NMR studies of large proteins: 13C, 15N and 1H assignments of human carbonic anhydrase II

Perdeuteration of all non-exchangeable proton sites can significantly increase the size of proteins and protein complexes for which NMR resonance assignments and structural studies are possible. Backbone 1H, 15N, 13CO, 13C alpha and 13C beta chemical shifts and aliphatic side-chain 13C and 1H(N)/15N chemical shifts for human carbonic anhydrase II (HCA II), a 259 residue 29 kDa metalloenzyme, have been determined using a strategy based on 2D, 3D and 4D heteronuclear NMR experiments, and on perdeuterated 13C/15N-labeled protein. To date, HCA II is one of the largest monomeric proteins studied in detail by high-resolution NMR. Of the backbone resonances, 85% have been assigned using fully protonated 15N and 3C/15N-labeled protein in conjunction with established procedures based on now standard 2D and 3D NMR experiments. HCA II has been perdeuterated both to complete the backbone resonance assignment and to assign the aliphatic side-chain 13C and 1H(N)/15N resonances. The incorporation of 2H into HCA II dramatically decreases the rate of 13C and 1H(N)T2 relaxation. This, in turn, increases the sensitivity of several key 1H/13C/15N triple-resonance correlation experiments. Many otherwise marginal heteronuclear 3D and 4D correlation experiments, which are important to the assignment strategy detailed herein, can now be executed successfully on HCA II. Further analysis suggests that, from the perspective of sensitivity, perdeuteration should allow other proteins with rotational correlation times significantly longer than HCA II (tau c = 11.4 ns) to be studied successfully with these experiments. Two different protocols have been used to characterize the secondary structure of HCA II from backbone chemical-shift data. Secondary structural elements determined in this manner compare favorably with those elements determined from a consensus analysis of the HCA II crystal structure. Finally, having outlined a general strategy for assigning backbone and side-chain resonances in a perdeuterated large protein, we propose a strategy whereby this information can be used to glean more detailed structural information from the partially or fully protonated protein equivalent.     

Solid-state NMR studies of the prion protein H1 fragment

Conformational changes in the prion protein (PrP) seem to be responsible for prion diseases. We have used conformation-dependent chemical-shift measurements and rotational-resonance distance measurements to analyze the conformation of solid-state peptides lacking long-range order, corresponding to a region of PrP designated H1. This region is predicted to undergo a transformation of secondary structure in generating the infectious form of the protein. Solid-state NMR spectra of specifically 13C-enriched samples of H1, residues 109-122 (MKHMAGAAAAGAVV) of Syrian hamster PrP, have been acquired under cross-polarization and magic-angle spinning conditions. Samples lyophilized from 50% acetonitrile/50% water show chemical shifts characteristic of a beta-sheet conformation in the region corresponding to residues 112-121, whereas samples lyophilized from hexafluoroisopropanol display shifts indicative of alpha-helical secondary structure in the region corresponding to residues 113-117. Complete conversion to the helical conformation was not observed and conversion from alpha-helix back to beta-sheet, as inferred from the solid-state NMR spectra, occurred when samples were exposed to water. Rotational-resonance experiments were performed on seven doubly 13C-labeled H1 samples dried from water. Measured distances suggest that the peptide is in an extended, possibly beta-strand, conformation. These results are consistent with the experimental observation that PrP can exist in different conformational states and with structural predictions based on biological data and theoretical modeling that suggest that H1 may play a key role in the conformational transition involved in the development of prion diseases.     

Vitamin E dose-response studies in humans with use of deuterated RRR-alpha-tocopherol

A prospective double-blind randomized trial was initiated to examine two types of laparoscopic fundoplication (Nissen and anterior). Thirty-two patients with proven gastroesophageal reflux disease presenting for primary laparoscopic antireflux surgery were randomized to undergo either Nissen fundoplication (N = 13) or anterior hemifundoplication (N = 19). Postoperative fluoroscopic and manometric examination was carried out concomitantly. Nissen fundoplication resulted in significantly greater elevation of resting (33.5 vs 23 mm Hg) and residual lower esophageal sphincter pressures (17 vs 6.5 mm Hg) and lower esophageal ramp pressure (26 vs 20.5 mm Hg) than the anterior partial fundoplication. A smaller radiologically measured sphincter opening diameter was seen following Nissen fundoplication (9 mm) compared with anterior fundoplication (12 mm). Lower esophageal ramp pressure correlated weakly (r = 0.37, P = 0.04) with postoperative dysphagia. It is concluded that the type of fundoplication performed significantly influences postoperative manometric and video barium radiology outcomes. The clinical relevance of this requires further investigation.     

Solid-state NMR studies of 1H spin diffusion in adsorbed organic molecules

1H spin diffusion times of toluene (MB) and tetrahydrofuran (THF) adsorbed on a series of porous solids (charcoal, SiO2 and Al2O3) were measured by a selective inversion technique. The experimental results show that they cover a wide range (from less than one millisecond to several hundreds of milliseconds). For all samples, a tri-exponential behavior was observed in the magnetization recovery processes of the negative peaks. This is attributed to the existence of the two different kinds of spin diffusion processes in addition to the T1 relaxation. One is assigned to the intermolecular spin diffusion between the surface acidic protons of the adsorbent and the organic molecules adsorbed on the solid surface, the other to the intramolecular spin diffusion of adsorbed molecules. Due to hydrogen bonding between the surface hydroxyl groups and the adsorbate, the intermolecular spin diffusion of THF adsorbed on various solids is more effective compared to that of adsorbed MB. In addition, the intermolecular 1H spin diffusion between charcoal and adsorbed THF molecules was confirmed by indirect measurement suggested by Tekely et al.     

Two-dimensional 1H and 15N NMR titration studies of hisactophilin

We have used two-dimensional 1H-15N heteronuclear single quantum correlation spectroscopy to measure the pH dependence of backbone amide group chemical shifts in the actin binding protein hisactophilin over the pH range 5.7-11.1. Most of the resonances can be analyzed using a simple equation involving a single apparent ionization constant, pK(app). The majority of resonances in the protein titrate with pK(app) values of 5.6-7.4. The results can be rationalized in terms of titration of many histidine residues in hisactophilin. The titration data provide direct experimental support for the proposed models of the atomic basis of actin and membrane binding by hisactophilin.     

1H and 13C NMR studies of conformational behaviour of Leu-enkephalin

The presence of secondary sensory cells in the Octopus gravity receptor system has been demonstrated. In serial thin sections of the receptor cells (hair cells) no axons were found leaving the cells. Instead, synapses were observed with synaptic vesicles lying inside the receptor cells. Both data clearly indicate that the receptor hair cells represent secondary sensory cells. In addition, efferent contacts to the receptor cells could be confirmed.     

Recommendations for the presentation of NMR structures of proteins and nucleic acids

The recommendations presented here are designed to support easier communication of NMR data and NMR structures of proteins and nucleic acids through unified nomenclature and reporting standards. Much of this document pertains to the reporting of data in journal articles; however, in the interest of the future development of structural biology, it is desirable that the bulk of the reported information be stored in computer-accessible form and be freely accessible to the scientific community in standardized formats for data exchange. These recommendations stem from an IUPAC-IUBMB-IUPAB inter-union venture with the direct involvement of ICSU and CODATA. The Task Group has reviewed previous formal recommendations and has extended them in the light of more recent developments in the field of biomolecular NMR spectroscopy. Drafts of the recommendations presented here have been examined critically by more than 50 specialists in the field and have gone through two rounds of extensive modification to incorporate suggestions and criticisms.     

On choosing a detergent for solution NMR studies of membrane proteins

Acne is a common condition seen routinely by both primary care physicians and dermatologists. Most patients have no underlying pathology and respond to traditional treatment; others, however, require more individualized evaluation and aggressive therapy. New information regarding the pathogenesis and treatment of acne is now available. This update discusses the proper evaluation of early childhood acne, the emergence of Propionibacterium acnes resistance, and the rare but serious side effects occasionally seen with minocycline. Advances in the topical treatment of acne, the use of oral contraceptives in acne, and the use and efficacy of isotretinoin are also addressed.     

Characterizing semilocal motions in proteins by NMR relaxation studies

The understanding of protein function is incomplete without the study of protein dynamics. NMR spectroscopy is valuable for probing nanosecond and picosecond dynamics via relaxation studies. The use of 15N relaxation to study backbone dynamics has become virtually standard. Here, we propose to measure the relaxation of additional nuclei on each peptide plane allowing for the observation of anisotropic local motions. This allows the nature of local motions to be characterized in proteins. As an example, semilocal rotational motion was detected for part of a helix of the protein Escherichia coli flavodoxin.     

Molecular motion and orientation distributions in melt-processed, fully aromatic liquid crystalline polyesters from 1H NMR

Fully-aromatic thermotropic liquid crystalline polymers (LCP) containing 4-hydroxybenzoic acid (HBA) and 6-hydroxy-2-naphthoic acid (HNA) were studied with 1H NMR. A two- or three-parameter nematic director distribution in molten or nearly molten samples was obtained via rigorous simulation of wideline spectral lineshapes. This methodology was further employed to yield the chain director distribution in macroscopic sections derived from a frozen contraction flow. In addition, the dynamic conformation of polymer chains through the melting transition was monitored via lineshape analysis of samples having (bulk) isotropic director distributions. Extension of rigorous 1H NMR spectral deconvolution to recently developed solid-state NMR imaging sequences is discussed.     

1H/27Al TRAPDOR NMR studies on aluminum species in dealuminated zeolites

Aluminum species in several dealuminated zeolites (ultrastable HY, HZSM-5 and mordenite) were investigated in detail by means of the newly introduced 1H/27Al TRAPDOR method in combination with 27Al MAS NMR, and the quadrupole coupling constants (Q[CC]s) for aluminum atoms associated with these species were obtained. A signal at ca. 6.8 ppm, due to water molecules adsorbed on Lewis acid sites, was observed in the 1H MAS spectra for all the three zeolites. The TRAPDOR NMR provides direct evidence that there is a strong interaction between the adsorbed water molecules and the aluminum atoms of the Lewis-acid sites. The Q(CC) values for this aluminum species of 8.3, 6.7 and 11.3 MHz were determined from the TRAPDOR profiles for the ultrastable HY, HZSM-5 and mordenite zeolites, respectively. The Q(CC)s calculated from the TRAPDOR curves are usually larger than 10 MHz for both Bronsted-acid sites (SiOHAI) and non-framework aluminum species in the three zeolites. Three narrow peaks at 54, 30 and 0 ppm are separately superimposed on a broad hump in the 27Al MAS spectra of the three dehydrated zeolites, while the latter is associated with the 'NMR invisible' Al. The NMR experimental results suggest that the three kinds of aluminum species (non-framework aluminum species, Bronsted- and Lewis-acid sites) are all responsible for the resonance of the broad hump in dehydrated zeolites, which makes it difficult to explain the 27Al MAS spectra. Fortunately, the TRAPDOR NMR provides a direct method for individually studying different aluminum species with large Q(CC)s via their dipolar coupling to nearby proton nuclei.     

Membrane transport of aromatic amino acids by Hymenolepis diminuta (Cestoda)

Aromatic amino acids (phenylalanine, tryptophan and tyrosine) are absorbed by Hymenolepis diminuta through a combination of mediated (non-Na+-sensitive) transport and diffusion. All 3 amino acids are accumulated against an apparent concentration difference during a 30-min incubation of tapeworms in 0.1 mM 3H-labelled amino acid. Inhibitor studies demonstrate that phenylalanine, tryptophan and tyrosine are mutually competitive inhibitors of the uptake of each other, and the uptake of these amino acids is inhibited by aliphatic amino acids but not by basic or dicarboxylic amino acids. The D- and L-isomers of aromatic amino acids are equally effective in inhibiting aromatic amino acid uptake. The data indicate that at least 3 amino acid transport loci are involved in aromatic amino acid transport by H. diminuta.     

Dynamic structure of proteins in solid state. 1H and 13C NMR relaxation study

Temperature dependencies of 1H non-selective NMR T1 and T2 relaxation times measured at two resonance frequencies and natural abundance 13C NMR relaxation times T1 and T1r measured at room temperature have been studied in a set of dry and wet solid proteins - Bacterial RNase, lysozyme and Bovine serum albumin (BSA). The proton and carbon data were interpreted in terms of a model supposing three kinds of internal motions in a protein. These are rotation of the methyl protons around the axis of symmetry of the methyl group, and fast and slow oscillations of all atoms. The correlation times of these motions in solid state are found around 10(-11), 10(-9) and 10(-6)s, respectively. All kinds of motion are characterized by the inhomogeneous distribution of the correlation times. The protein dehydration affects only the slow internal motion. The amplitude of the slow motion obtained from the carbon data is substantially less than that obtained from the proton data. This difference can be explained by taking into account different relative inter- and intra- chemical group contributions to the proton and carbon second moments. The comparison of the solid state and solution proton relaxation data showed that the internal protein dynamics in these states is different: the slow motion seems to be few orders of magnitude faster in solution.