Peptide structural analysis by solid-state NMR spectroscopy.

Solid-state nmr spectroscopy provides a robust method for investigating polypeptides that have been prepared by chemical synthesis and that are immobilized by strong interactions with solid surfaces or large macroscopic complexes. Solid-state nmr spectroscopy has been widely used to investigate membrane polypeptides or peptide aggregates such as amyloid fibrils. Whereas magic angle spinning solid-state nmr spectroscopy allows one to measure distances and dihedral angles with high accuracy, static membrane samples that are aligned with respect to the magnetic field direction allow one to determine the secondary structure of bound polypeptides and their orientation with respect to the bilayer normal. Peptide dynamics and the effect of polypeptides on the macroscopic phase preference of phospholipid membranes have been investigated in nonoriented samples. Investigations of the structure and topology of membrane channels, peptide antibiotics, signal sequences as well as model systems that allow one to dissect the interaction contributions in phospholipid membranes will be presented in greater detail.     

Combination of NMR spectroscopy and X-ray crystallography offers unique advantages for elucidation of the structural basis of protein complex assembly

NMR spectroscopy and X-ray crystallography are two premium methods for determining the atomic structures of macro-biomolecular complexes. Each method has unique strengths and weaknesses. While the two techniques are highly complementary, they have generally been used separately to address the structure and functions of biomolecular complexes. In this review, we emphasize that the combination of NMR spectroscopy and X-ray crystallography offers unique power for elucidating the structures of complicated protein assemblies. We demonstrate, using several recent examples from our own laboratory, that the exquisite sensitivity of NMR spectroscopy in detecting the conformational properties of individual atoms in proteins and their complexes, without any prior knowledge of conformation, is highly valuable for obtaining the high quality crystals necessary for structure determination by X-ray crystallography. Thus NMR spectroscopy, in addition to answering many unique structural biology questions that can be addressed specifically by that technique, can be exceedingly powerful in modern structural biology when combined with other techniques including X-ray crystallography and cryo-electron microscopy.     

Structure elucidation of glycoprotein glycans and of polysaccharides by NMR spectroscopy

The applicability of 1H-NMR spectroscopy for the determination of the primary and tertiary structure of carbohydrate-containing molecules is demonstrated. For classes of known compounds the characterization can be based on chemical shifts observed in 1D NMR spectra with or without the aid of a computer database. For more complex structure determinations 2D NMR techniques are required. Here the application of 2D NMR is demonstrated for the primary structure determination of two bacterial exopolysaccharides, for the spatial structure determination of a disaccharide and a glycoprotein hormone.     

Isolation and structural elucidation of novel cholestane glycosides and spirostane saponins from Polygonatum odoratum

Much attention has been paid to cholestane-type steroidal glycosides because of their importance from the perspectives of both chemical diversity and significant biological activities. A phytochemical investigation of the rhizomes of Polygonatum odoratum (Liliaceae) resulted in the isolation of three novel cholestane-type steroidal glycosides (1–3) with unique Δ^14,16-unsaturated D-ring structures as well as two novel spirostane-type steroidal saponins (4 and 5) and three known steroidal glycosides (6–8). Their structures were determined by various spectroscopic methods and chemical reactions. Steroidal saponin 7 showed significant antifungal activity against Candida albicans JCM1542 (MIC 3.1 μg/mL) and Aspergillus fumigatus JCM1738 (MIC 6.3 μg/mL).     

The asparagine-linked oligosaccharides on bovine fetuin. Structural analysis of N-glycanase-released oligosaccharides by 500-megahertz 1H NMR spectroscopy

The structures of the entire population of sialylated asparagine-linked oligosaccharides present on bovine fetuin were elucidated. Asparagine-linked oligosaccharides were released from fetuin with N-glycanase, radiolabeled by reduction with NaB[3H]4, and fractionated by anion-exchange high performance liquid chromatography (HPLC), ion-suppression amine adsorption HPLC, and concanavalin A affinity chromatography. The 3H-labeled oligosaccharide fractions obtained were analyzed by 500-MHz 1H nuclear magnetic resonance spectroscopy, revealing the presence of 23 distinct oligosaccharide structures. These oligosaccharides differed in extent of sialylation (3% mono-, 35% di-, 54% tri-, and 8% tetrasialylated), number of peripheral branches (17% di- and 83% tribranched), linkage (alpha 2,3 versus alpha 2,6) and location of sialic acid moieties, and linkage (beta 1,4 versus beta 1,3) of galactose residues. This represents the first time that the asparagine-linked oligosaccharides of fetuin have been successfully fractionated and characterized as sialylated species. The sialylated oligosaccharides derived from fetuin were also used to further define the specificities of the lectins leukoagglutinating phytohemagglutinin and Ricinus communis agglutinin I. The behavior of these oligosaccharides during lectin affinity HPLC further establishes the structural features which predominate in the interaction of oligosaccharides with leukoagglutinating phytohemagglutinin and R. communis agglutinin I.     

Structure elucidation by NMR spectroscopy of a new acetylated saponin from Centratherum anthelminticum

A new glycosylated triterpene has been isolated from the seeds of Centratherum anthelminticum, a medicinally important plant. The structural analysis of its acetylated derivative was performed by 1H, 13C NMR, 1H-1H COSY, HMQC, HMBC and DEPT spectroscopy. The saponin was shown to contain hederagenin and six sugar residues forming two glycosyl chains. The complete structure of the saponin was established as 3-O-[beta-D-glucopyranosyl-(1-->3)-alpha-L-rhamnopyranosyl-(1-->2)-alpha-L-arabinopyranosyl]-28-O-[beta-D-glucuronopyranosyl-(1-->4)-alpha-L-rhamnopyranosyl-(1-->3)-beta-D-glucopyranosyl]-hederagenin.     

Structural elucidation of two capsular polysaccharides from one strain of Bacteroides fragilis using high-resolution NMR spectroscopy.

The capsule of Bacteroides fragilis is unusual in that it consists of two distinct capsular polysaccharides. Using a combination of high-resolution NMR spectroscopy, theoretical calculations, and as few chemical procedures as required, the structure of both polysaccharide antigens (polysaccharides A and B) was elucidated. Using the above procedures, it was possible to obtain the complete structures using minimal quantities of polysaccharides A and B (8 and 5 mg, respectively). Only small amounts of each subjected to chemical analysis were not recoverable. Polysaccharide A is composed of the following repeating unit: [----3)alpha-D-AATp(1----4)[beta-D-Galf(1----3)]alpha-D- GalpNAc(1----3)beta-D-Galp(1----], where AAT is 2-acetamido-4-amino-2,4,6-trideoxygalactose. A pyruvate substituent having the R configuration spans O-4 and O-6 of the beta-D-galactopyranosyl residue. Polysaccharide B is composed of the following repeating unit: [----4)alpha-L-QuipNAc(1----3)beta-D-QuipNAc(1----4)[alpha-L - Fucp(1----2)beta-D-GalpA(1----3)beta-D-GlcpNAc(1----3)]alpha -D-Galp(1----]. A 2-aminoethylphosphonate substituent is situated on O-4 of the N-acetyl-beta-D-glucopyranosyl residue.     

Interaction of a goose-type lysozyme with chitin oligosaccharides as determined by NMR spectroscopy

The interaction between a goose-type lysozyme from ostrich egg white (OEL) and chitin oligosaccharides [(GlcNAc)(n) (n = 2, 4 and 6)] was studied by nuclear magnetic resonance (NMR) spectroscopy. A stable isotope-labelled OEL was produced in Pichia pastoris, and backbone resonance assignments for the wild-type and an inactive mutant (E73A OEL) were achieved using modern multi-dimensional NMR techniques. NMR titration was performed with (GlcNAc)(n) for mapping the interaction sites of the individual oligosaccharides based on the shifts in the two-dimensional heteronuclear single quantum correlation (HSQC) resonances. In wild-type OEL, the interaction sites for (GlcNAc)(n) were basically similar to those determined by X-ray crystallography. In E73A OEL, however, the interaction sites were spread more widely over the substrate-binding cleft than expected, due to the multiple modes of binding. The association constant for E73A OEL and (GlcNAc)(6) calculated from the shifts in the Asp97 resonance (7.2 × 10(3) M(-1)) was comparable with that obtained by isothermal titration calorimetry (5.3 × 10(3) M(-1)). The interaction was enthalpy-driven as judged from the thermodynamic parameters (ΔH = -6.1 kcal/mol and TΔS = -1.0 kcal/mol). This study provided novel insights into the oligosaccharide binding mechanism and the catalytic residues of the enzymes belonging to family GH-23.     

Steroidal alkaloids from Solanum khasian um: Application of 13C NMR spectroscopy to their structural elucidation

The solasodine glycosides, solasonine, solamargine and khasianine have been isolated from berries of Solanum khasianum and characterized by ¹³C NMR spectroscopy. By application of this method, the structure of khasianine has been elucidated as O-α-l-rhamnosyl (1→4_glu)-O (3)-β-d-glucopyranosyl-solasodine (β₂-solamargine).     

Rapid screening for structural integrity of expressed proteins by heteronuclear NMR spectroscopy.

A simple and rapid method based on 15N labeling and 1H-15N heteronuclear single quantum coherence spectroscopy is presented to directly assess the structural integrity of overexpressed proteins in crude Escherichia coli extracts without the need for any purification. The method is demonstrated using two different expression systems and two different proteins, the B1 immunoglobulin-binding domain of streptococcal protein G (56 residues) and human interleukin-1 beta (153 residues). It is shown that high quality 1H-15N correlation spectra, recorded in as little as 15 min and displaying only cross-peaks arising from the overexpressed protein of interest, can be obtained from crude E. coli extracts.     

In-cell NMR spectroscopy.

The recent development of "in-cell NMR" techniques by two independent groups has demonstrated that NMR spectroscopy can be used to characterize the conformation and dynamics of biological macromolecules inside living cells. In this article, we describe different methods and discuss current and future applications as well as critical parameters of this new technique. We show experimental results, compare them with traditional in vitro experiments, and demonstrate that differences between the in vitro and the in vivo state of a macromolecule exist and can be detected and characterized.     

Carbohydrate epitope structural elucidation by 1H-NMR spectroscopy of a new Mycobacterium kansasii phenolic glycolipid antigen.

The complete primary structure of the carbohydrate moiety of a new phenolic glycolipid antigen namely PheGl K-IV from Mycobacterium kansasii was successfully established from only one- and two-dimensional 1H-NMR data. Among the scalar two-dimensional techniques, correlated spectroscopy with a 45 degree mixing pulse and phase-sensitive double-quantum-filtered correlated spectroscopy were selected, combined with two-dimensional dipolar techniques (nuclear Overhauser effect). These techniques using milligram of quantities native PheGl K-IV allowed the following monoacetylated tetrasaccharide to be proposed for its carbohydrate part: 4-O-Me-alpha-Manp-(1----3)-4-O-Ac-2-O-Me-alpha-Fucp-(1----3) -2-O-Me-alpha-Rhap- (1----3)-2,4-di-O-Me-alpha-Rhap. The PheGl K-IV shares, with the other phenolic glycolipids isolated from M. kansasii (K-I, K-II), a common core assigned to the lipid aglycone glycosylated by the monoacetylated trisaccharide part. It differs in the structure of the distal monosaccharide residue.     

New structural insights into carbohydrate-protein interactions from NMR spectroscopy

Recently developed NMR methods have been applied to discover carbohydrate ligands for proteins and to identify their binding epitopes. The structural details of carbohydrate-protein complexes have also been examined by NMR, providing site-specific information on the architecture, binding selectivity and plasticity of the carbohydrate-binding sites of the proteins. New insights into the conformational behaviour of free and protein-bound glycomimetics pave the way for the design of carbohydrate-based therapeutics. Finally, recent progress towards elucidating the influence of glycosylation on peptide conformation will be of key importance to fully understanding the role of carbohydrates in the function of glycopeptides.     

Computer-assisted structural analysis of oligosaccharides using CASPER.

The computer program CASPER for structural analysis has been tested on some oligosaccharides. The program is shown to predict the correct structure of five linear or branched tri- to hexasaccharides using information on components and linkage positions and NMR chemical shifts. Theoligosaccharides are either reducting or methyl glycosides.     

Synthesis and NMR elucidation of novel tetrapeptides

The synthesis and NMR elucidation of Ala‐Val‐Pro‐Ile and five novel peptide‐based derivatives are reported. These peptides mimic the natural second mitochondria‐derived activator of caspase (Smac) protein. Purification was achieved using preparative HPLC and the NMR elucidation of all compounds is reported for the first time. A series of overlapping signals were observed in the 1D NMR spectra thus making assignment a difficult task to undertake. The use of 2D NMR techniques with the inclusion of efficient adiabatic symmetrized ROESY proved to be an effective tool in overcoming these difficulties. Copyright © 2011 European Peptide Society and John Wiley & Sons, Ltd.     

Low-temperature-induced structural changes in human lysozyme elucidated by three-dimensional NMR spectroscopy

The three-dimensional solution structures of human lysozyme were determined at 35 and 4 degrees C using the heteronuclear multidimensional NMR spectroscopy, which were compared with each other to clarify the structural response of this enzyme to lowering of the temperature. Together with the data of the temperature dependence experiments of the lytic activity against Micrococcus luteus, we consider the implication of the observed structural change for the low-temperature-induced reduction of the activity of human lysozyme. The structures of human lysozyme determined at the two temperatures are found to be similar, both of which comprise four alpha-helices (A- to D-helices) and three antiparallel beta-strands (beta(1)-beta(3)), leading to the constructions of the alpha- and beta-domains as previously identified in the X-ray crystal structure. A significant structural change was observed for the "active site lobe" comprising the loop region connecting C- and D-helices and the following D-helix, which moves toward the active site cleft located between the alpha- and beta-domains so as to obstruct the cleft according to the temperature lowering. It further appeared that the total volume as well as the accessible surface area of human lysozyme decreases with lowering of the temperature, suggesting that the internal cavity of this enzyme shrinks under low temperature environment. Because in human lysozyme the region comprising the active site lobe is responsible for turnover of the enzymatic reaction against the substrate, the low-temperature-induced structural change of the active site lobe presumably controls the efficiency of the lytic activity under low temperatures.     

Isolation and structure elucidation of tetrameric procyanidins from unripe apples (Malus pumila cv. Fuji) by NMR spectroscopy

Procyanidins are plant secondary metabolites widely consumed and known to have various physiological functions, but their bioavailability and mechanism of action are still unclear especially for larger oligomers. One of the reasons is scarce information about the detailed structure of oligomeric procyanidins. As for apple, structures of procyanidin components larger than trimers are scarcely known. In this study, 11 tetrameric procyanidins including two known compounds were isolated from unripe apples (Malus pumila cv. Fuji) and identified by NMR spectroscopic analysis and phloroglucinol degradation. As a result, the detailed structural diversity of tetrameric procyanidins in apple was established.     

Combined use of COSY and double quantum two-dimensional NMR spectroscopy for elucidation of spin systems in polymyxin B

Two-dimensional single quantum correlation NMR spectroscopy (COSY) and two-dimensional double quantum NMR spectroscopy (2QT) are used to study spin systems in the 1H NMR spectrum of polymyxin B. Because of different frequency relationships, the two types of two-dimensional NMR experiments are found to be highly complementary. This is demonstrated by combined use of COSY and 2QT spectroscopy to obtain a complete analysis of the complicated spectral overlap which occurs in the 1H NMR spectrum of polymyxin B.