Metabolism of lactic acid bacteria studied by nuclear magnetic resonance

The complexity of metabolic and regulatory networks presents a great scientific challenge to an integrated view of how individual components contribute to the overall function. Nuclear magnetic resonance (NMR) spectroscopy is undoubtedly a suitable technique for global investigations of microbial metabolism, since it allows a view into living cells without disturbing the cellular organisation. Therefore, metabolic processes can be monitored in real time under physiological conditions. In the present paper, examples of the application of NMR to study the metabolism of lactic acid bacteria will be given. These include the analysis of labelling patterns in end-products using ¹³C as a tracer, thereby establishing metabolic pathways, the detection and quantification of intermediates in the pathway of exopolysaccharide biosynthesis, and on line monitoring of glycolytic kinetics to assess the effect of metabolic engineering strategies.     

Water binding and phase structures for different Acholeplasma laidlawii membrane lipids studied by deuteron nuclear magnetic resonance and x-ray diffraction

Water binding capability and phase structures for different lipid species extracted from Acholeplasma laidlawii A membranes have been studied using deuteron nuclear magnetic resonance and low-angle X-ray diffraction.The dominating membrane lipids are monoglucosyldiglyceride and diglucosyldiglyceride and each of them takes up limited amounts of water (bound plus trapped), i.e., up to 13% (w/w), whereas the phospholipids and phosphoglycolipids have larger hydration capacities.Addition of magnesium and calcium ions, but not sodium ions, to the diglucosyldiglyceride increases the hydration capability. This increase is accompanied by the formation of a metastable liquid crystalline phase and a hysteresis effect for the transition temperature.Large differences in water deuteron quadrupole splitting were observed between mono- and diglucosyldiglyceride. Both ²H nuclear magnetic resonance and low-angle X-ray diffraction studies on lipids containing biosynthetically incorporated ω-d₃-palmitic acid clearly indicate the existence of a reverse hexagonal phase structure for the monoglucosyldiglyceride and lamellar structures for the diglucosyldiglyceride and the other membrane lipids.The low hydration capability of the large diglucosyldiglyceride polar head is discussed in terms of polar head configuration.Both mono- and diglucosyldiglyceride have several physical properties similar to those of phosphatidylethanolamine.     

Lecithin translational diffusion studied by pulsed nuclear magnetic resonance.

The translational diffusion coefficient of egg yolk and dilauroyl lecithin in optically isotropic phases containing sodium cholate has been measured using the pulsed NMR magnetic field gradient method. After a correction for geometrical factors the measured diffusion coefficient is found to agree well with previous determinations in phospholipid systems. The experimental data imply that the cubic mesophase of the lecithin-sodium cholate-water system contains continuous lipid aggregates. A possible model of the arrangement of the different amphiphile molecules in the cubic phase is discussed.     

Binding modes of inhibitors to ribonuclease T1 as studied by nuclear magnetic resonance

The binding modes of inhibitors to ribonuclease T1 (RNase T1) were studied by the analyses of 270-MHz proton NMR spectra. The chemical shift changes upon binding of phosphate, guanosine, 2'-GMP, 3'-GMP, 5'-GMP, and guanosine 3',5'-bis(phosphate) were observed as high field shifted methyl proton resonances of RNase T1. One methyl resonance was shifted upon binding of phosphate and guanosine nucleotides but not upon binding of guanosine. Four other methyl resonances were shifted upon binding of guanosine and guanosine nucleotides but not upon binding of phosphate. From the analyses of nuclear Overhauser effects for the pair of H8 and H1' protons, together with the vicinal coupling constants for the pair of H1' and H2' protons, the conformation of the guanosine moiety as bound to RNase T1 is found to be C3'-endo-syn for 2'-GMP and 3'-GMP and C3'-endo-anti for 5'-GMP and guanosine 3',5'-bis(phosphate). These observations suggest that RNase T1 probably has specific binding sites for the guanine base and 3'-phosphate group (P1 site) but not for the 5'-phosphate group (PO site) or the ribose ring. The weak binding of guanosine 3',5'-bis(phosphate) and 5'-GMP to RNase T1 is achieved by taking the anti form about the glycosyl bond. The productive binding to RNase T1 probably requires the syn form of the guanosine moiety of RNA substrates.     

Determination of three-dimensional structures of proteins and nucleic acids in solution by nuclear magnetic resonance spectroscopy

Nuclear magnetic resonance (NMR) spectroscopy has evolved over the last decade into a powerful method for determining three-dimensional structures of biological macromolecules in solution. Key advances have been the introduction of two-dimensional experiments, high-field superconducting magnets, and computational procedures for converting the NMR-derived interproton distances and torsion angles into three-dimensional structures. This article outlines the methodology employed, describes the major NMR experiments necessary for the spectral analysis of macromolecules, and discusses the computational approaches employed to date. The present state of the art is illustrated using a variety of examples, and future developments are indicated.     

Validation of nuclear magnetic resonance structures of proteins and nucleic acids: hydrogen geometry and nomenclature

A statistical analysis is reported of 1,200 of the 1,404 nuclear magnetic resonance (NMR)-derived protein and nucleic acid structures deposited in the Protein Data Bank (PDB) before 1999. Excluded from this analysis were the entries not yet fully validated by the PDB and the more than 100 entries that contained < 95% of the expected hydrogens. The aim was to assess the geometry of the hydrogens in the remaining structures and to provide a check on their nomenclature. Deviations in bond lengths, bond angles, improper dihedral angles, and planarity with respect to estimated values were checked. More than 100 entries showed anomalous protonation states for some of their amino acids. Approximately 250,000 (1.7%) atom names differed from the consensus PDB nomenclature. Most of the inconsistencies are due to swapped prochiral labeling. Large deviations from the expected geometry exist for a considerable number of entries, many of which are average structures. The most common causes for these deviations seem to be poor minimization of average structures and an improper balance between force-field constraints for experimental and holonomic data. Some specific geometric outliers are related to the refinement programs used. A number of recommendations for biomolecular databases, modeling programs, and authors submitting biomolecular structures are given.     

Molecular conformation and function of erabutoxins as studied by nuclear magnetic resonance

The 270-MHz proton NMR spectra of erabutoxins a, b and c from Laticauda semifasciata in 2H2O solution were observed together with [15-N6-acetyllysine]erabutoxin b, [27-N6-acetyllysine]-erabutoxin b and [47-N6-acetyllysine]erabutoxin b. The lysine epsilon-methylene proton resonances of erabutoxin b are assigned to individual residues. The epsilon-methylene proton resonance of Lys-27 is significantly broad, indicating that the mobility of this residue is restricted. Upon acetylation of Lys-27 of erabutoxin b, the pKa values of three other lysine residues are lowered by about 0.2, indicating long-range interactions among lysine residues. All the methyl proton resonances are assigned to amino acid types, primarily by the spin-echo double-resonance method. The pH dependences of proton chemical shifts were analyzed by the nonlinear least-square method, for obtaining pKa values and protonation shifts. The interproton nuclear Overhauser effect enhancements were measured for elucidating the spatial proximity of methyl-bearing residues and aromatic residues. On the basis of these NMR data and with the crystal structures by Low et al. and by Petsko et al., the methyl proton resonances of all the valine, leucine, and isoleucine residues and Thr-45 have been identified. The microenvironments of Tyr-25, His-26, Trp-29, four lysines and eight methyl-bearing residues have been elucidated. The addition of the paramagnetic hexacyanochromate ion causes broadening of the proton resonances of Thr-45, Lys-47, Ile-50, Trp-29 and Ile-36 residues located on one end of the molecule of erabutoxin b. The positively charged invariant residues of Lys-47 and Arg-33 at this part of the molecule are probably involved in the binding to the receptor protein.     

Mechanisms of transmembrane cation transport studied by nuclear magnetic resonance spectroscopy

Several molecules like ionophores, vitamins, ion-binding cyclic peptides, acidic phospholipids, surfactants are known to expose the inner side of vesicles, to the externally added cations. Whereas ionophores and certain other systems bring about these changes by a selective transport (influx) of the cation by specialized mechanisms known as the carrier and channel mechanism, other systems cause lysis and vesicle fusion. These systems have been successfully studied using¹H,³¹ P and¹³C nuclear magnetic resonance spectroscopy after the demonstration, fifteen years ago, of the ability of paramagnetic lanthanide ions to distinguish the inside of the vesicle from the outside. The results of these ’nuclear magnetic resonance kinetics’ experiments are reviewed.     

The aromatic residues of bovine pancreatic ribonuclease studied by 1H nuclear magnetic resonance.

1. The aromatic proton resonances in the 360-MHz 1H nuclear magnetic resonance (NMR) spectrum of bovine pancreatic ribonuclease were divided into histidine, tyrosine and phenylalanine resonances by means of pH titrations and double resonance experiments. 2. Photochemically induced dynamic nuclear polarization spectra showed that one histidine (His-119) and two tyrosines are accessibly to photo-excited flavin. This permitted the identification of the C-4 proton resonance of His-119. 3. The resonances of the ring protons of Tyr-25, Tyr-76 and Tyr-115 and the C-4 proton of His-12 were identified by comparison with subtilisin-modified and nitrated ribonucleases. Other resonances were assigned tentatively to Tyr-73, Tyr-92 and Phe-46. 4. On addition of active-site inhibitors, all phenylalanine resonances broadened or disappeared. The resonance that was most affected was assigned tentatively to Phe-120. 5. Four of the six tyrosines of bovine RNase, identified as Tyr-76, Tyr-115 and, tentatively, Tyr-73 and Tyr-92, are titratable above pH 9. The rings of Tyr-73 and Tyr-115 are rapidly rotating or flipping by 180 degrees about their C beta--C gamma bond and are accessible to flavin in photochemically induced dynamic nuclear polarization experiments. Tyr-25 is involved in a pH-dependent conformational transition, together with Asp-14 and His-48. A scheme for this transition is proposed. 6. Binding of active-site inhibitors to bovine RNase only influences the active site and its immediate surroundings. These conformational changes are probably not connected with the pH-dependent transition in the region of Asp-14, Tyr-25 and His-48. 7. In NMR spectra of RNase A at elevated temperatures, no local unfolding below the temperature of the thermal denaturation was observed. NMR spectra of thermally unfolded RNase A indicated that the deviations from a random coil are small and might be caused by interactions between neighbouring residues.     

Dipalmitoylphosphatidylcholine-palmitic acid phase diagram studied by 13C nuclear magnetic resonance

The phase diagram of dipalmitoylphosphatidylcholine (DPPC) and palmitic acid mixtures in excess D2O was studied by 13C-NMR. Phase boundaries were determined from plots of apparent spin-spin relaxation time T2 (for both choline methyl and fatty acid chain carbons) versus temperature. A peritectic transition in the 1-10 mol% region, whose existence has been theoretically inferred from the Gibbs phase rule but which was undetectable by differential thermal analysis (DTA) (S.E. Schullery et al. Biochemistry, 20 (1981) 6818-6824), was located by NMR at 41.6 degrees C. A second, nearby peritectic line at 44 degrees C, which had been shown by DTA to extend from about 3-25 mol% palmitic acid, was seen by NMR only above 10 mol%. The palmitic acid/DPPC complex (2:1), with a sharp melting point at 64 degrees C, reported in earlier studies, was also seen by NMR. A phase diagram including both NMR and DTA results is presented. Important general conclusions from this study are: (i) NMR and scanning thermal analysis are complementary techniques for phase studies; each can see transitions that are invisible to the other. (ii) The case for the applicability of the Gibbs phase rule to lipid bilayer systems has been strengthened by the observance of two predicted, close-spaced boundaries. (iii) Low concentrations of fatty acids and related molecules can not be assumed to disperse as simple ideal solutes in the bilayer matrix.     

A minimal transmembrane beta-barrel platform protein studied by nuclear magnetic resonance

In this study, we were concerned with the structural role of the surface-exposed extracellular loops of the N-terminal transmembrane (TM) domain of OmpA. A variant of the TM domain of outer membrane protein A (OmpA) with all four such loops shortened, which we call the beta-barrel platform (BBP), was successfully refolded. This indicates that the removed parts of the surface-exposed loops indeed do not contain amino acid sequences critical for this membrane protein's refolding in vitro. BBP has the potential to be used as a template beta-barrel membrane protein structure for the development of novel functions, although our results also highlight the potential difficulties that can arise when functionality is being engineered into the loop regions of membrane proteins. We have used solution nuclear magnetic resonance spectroscopy to determine the global fold of BBP+EF, BBP with a metal ion-binding EF-hand inserted in one of the shortened loops. BBP and BBP+EF in dihexanoylphosphatidylcholine micelles are eight-stranded antiparallel beta-barrels, and BBP represents the smallest beta-structured integral membrane protein known to date.     

High-resolution nuclear magnetic resonance studies of proteins

The combination of advanced high-resolution nuclear magnetic resonance (NMR) techniques with high-pressure capability represents a powerful experimental tool in studies of protein folding. This review is organized as follows: after a general introduction of high-pressure, high-resolution NMR spectroscopy of proteins, the experimental part deals with instrumentation. The main section of the review is devoted to NMR studies of reversible pressure unfolding of proteins with special emphasis on pressure-assisted cold denaturation and the detection of folding intermediates. Recent studies investigating local perturbations in proteins and the experiments following the effects of point mutations on pressure stability of proteins are also discussed. Ribonuclease A, lysozyme, ubiquitin, apomyoglobin, alpha-lactalbumin and troponin C were the model proteins investigated.     

Highly fluctuating protein structures revealed by variable-pressure nuclear magnetic resonance

Although our knowledge of basic folded structures of proteins has dramatically improved, the extent of our corresponding knowledge of higher-energy conformers remains extremely slim. The latter information is crucial for advancing our understanding of mechanisms of protein function, folding, and conformational diseases. Direct spectroscopic detection and analysis of structures of higher-energy conformers are limited, particularly under physiological conditions, either because their equilibrium populations are small or because they exist only transiently in the folding process. A new experimental strategy using pressure perturbation in conjunction with multidimensional NMR spectroscopy is being used to overcome this difficulty. A number of rare conformers are detected under pressure for a variety of proteins such as the Ras-binding domain of RalGDS, beta-lactoglobulin, dihydrofolate reductase, ubiquitin, apomyoglobin, p13(MTCP1), and prion, which disclose a rich world of protein structure between basically folded and globally unfolded states. Specific structures suggest that these conformers are designed for function and are closely identical to kinetic intermediates. Detailed structural determination of higher-energy conformers with variable-pressure NMR will extend our knowledge of protein structure and conformational fluctuation over most of the biologically relevant conformational space.     

Molecular conformation of alpha-bungarotoxin as studied by nuclear magnetic resonance and circular dichroism

We have examined the circular dichroism and nuclear magnetic resonance spectra of a long neurotoxin, alpha-bungarotoxin, over a wide range of pH values and temperatures, and under high salt conditions. The observations are interpreted partly in terms of the known crystal structure of this polypeptide. We support earlier findings of a greater degree of beta-sheet structure in solution than has been reported by X-ray crystallography and, importantly, the invariant residue associated with neurotoxicity, Trp29, is shown to be in a similar environment to that found in alpha-cobratoxin and LS III from Laticauda semifasciata. The implications of this observation for structure/function relationships are outlined.     

Conformation of 1- and 3-deazaadenosines in solution as studied by 1H nuclear magnetic resonance spectroscopy.

¹H nuclear magnetic resonance spectra of 1 - (II) and 3-deazaadenosines (III) together with adenosine (I) in dimethylsulfoxide have been examined. Features of coupling constants indicate that the furanose rings of I, II, and III have similar conformational preferences and that conformations about the 4′-C–5′-C bond are preferentially $\text{gauche-gauche}$. Nuclear Overhauser effect and spin-lattice relaxation-time measurements demonstrate that II predominantly adopts the $\text{syn}$-conformation similar to that of I, whereas that of III has a greater $\text{anti}$ (freely rotating) component. The results suggest that the $\text{syn}$-conformation in II as well as I is stabilized presumably through a hydrogen bond between the 3-N and 5′-hydroxyl group.     

New nuclear magnetic resonance structures and structural methodology.

Progress in the field of protein nuclear magnetic resonance spectroscopy during the past year has included the elucidation of a number of new structures. In addition, several critical developments in the experimental methodology have opened up the potential for applying the nuclear magnetic resonance-based approach to structure determination in solution of recombinant proteins in excess of 15 kD.