H2BC: a new technique for NMR analysis of complex carbohydrates

Petersen, Bent O.; Vinogradov, Evguenii; Kay, William W.; Würtz, Peter; Nyberg, Nils T.; Duus, Jens Øllgaard; Sørensen, Ole W.

doi:10.1016/j.carres.2005.11.020

Cited by 73 publications

(46 citation statements)

References 11 publications

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“…This exchange process was repeated three times. All NMR spectra were recorded in D 2 O at 308 K using a Bruker Avance 500 spectrometer equipped with a TXI xyz-three gradient probe for 1 H detection or BBO z-gradient probe for 13 C detection. Chemical shifts are reported in ppm relative to acetone-d 6 as an internal standard (d H ϭ2.189 ppm, d C ϭ31.45 ppm).…”

Section: Methodsmentioning

confidence: 99%

“…The spectral width was 4006 Hz in each dimension and 512 increments of 4096 data points with 48 scans per t 1 increment were recorded. Two-dimensional 13 Cedited hetero nuclear single quantum coherence spectroscopy (HSQC) was conducted with 512 increments of 2048 data points with 32 scans per t 1 increment using the Bruker standard pulse sequence. The spectral width was 3501 Hz for t 2 and 12500 Hz for t 1 .…”

Section: Methodsmentioning

confidence: 99%

“…The spectral width was 3501 Hz for t 2 and 12500 Hz for t 1 . Two-dimensional 1 H, 13 C-hetero nuclear multiple bond coherence spectroscopy (HMBC) was performed with 256 increments of 2048 data points with 132 scans per t 1 increment using the Bruker standard pulse sequence. The delay time for evolution long range coupling was set to 62.5 ms (optimized for 8 Hz).…”

Section: Methodsmentioning

confidence: 99%

“…12) However, in some cases, the assignment can be empirically based due to signals that heavily overlap and small J coupling constants. For the reasons mentioned above, we attempted to apply recently developed pulse sequences, the heteronuclear 2-bond correlation (H2BC) experiments [13][14][15] in order to achieve an unambiguous assignment of the high mannose type polysaccharide, the O-antigen from O9 LPS.…”

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confidence: 99%

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An Unambiguous Assignment and Structural Analysis Using Solution NMR Experiments of O-Antigen from Escherichia coli ATCC23505 (Serotype O9)

et al. 2007

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Bacterial lipopolysaccharides (LPSs) are major surfaceexposed structural components of the outer membrane of Gram-negative bacteria. LPSs consist of lipid A, a core region, and an O-antigen region in many bacteria.1) LPSs play an important role in the pathogenicity of Gram-negative infections. In experimental animals, purified LPSs induce numerous pathophysiological activities that can lead to shock and death, a condition called "Sepsis".2) Most of these biological activities, including the induction of inflammatory cytokines, are expressed by the lipid A moiety, a ubiquitous component of LPSs that is structurally similar and serologically cross-reacting among Enterobacteriaceae, via toll-like receptor 4 (TLR4). [3][4][5] However, numerous recent studies have revealed that LPSs possessing the mannose homopolymer (MHP) as the O-antigen region, such as the LPS from Escherichia coli (E. coli) O9 (O9 LPS), exhibit several characteristic immunological activities differ from those of the well-known endotoxic shock. In addition, we previously described that the mannan moieties of Candida albicans water-soluble fraction, CAWS, from fungi shows similar immunological properties to Gramnegative bacterial O9 LPS.6) These characteristic activities should be exhibited by recognizing mannose residues via lectins, such as mannose-binding lectin (MBL). 7,8) Therefore, analyzing the structure of O-antigens, especially mannoserich regions, is important for understanding some of the biological activities of LPSs.The O-antigen structure of O9 LPS has been studied using methylation analysis, smith degradation, optical rotation and enzymatic methods, [9][10][11] however, a precise assignment by NMR spectroscopy has not been conducted.In general, focusing on the anomeric proton as the starting point for assignment, TOCSY and HSQC-TOCSY experiments are useful for the analysis of individual sugar components in polysaccharides.12) However, in some cases, the assignment can be empirically based due to signals that heavily overlap and small J coupling constants. For the reasons mentioned above, we attempted to apply recently developed pulse sequences, the heteronuclear 2-bond correlation (H2BC) experiments [13][14][15] in order to achieve an unambiguous assignment of the high mannose type polysaccharide, the O-antigen from O9 LPS.In the present study, we report on the structure of the Oantigen of O9 LPS, and completely assign all protons and carbons using 1D-, 2D-NMR spectroscopy including the DQF-COSY, TOCSY, NOESY, HSQC, H2BC, HSQC-TOCSY, and HMBC methods. ExperimentalBacterial Strain and Conditions for Growth E. coli ATCC23505 was obtained from American Type Culture Collection (ATCC). The strain was grown in Luria Bertani (LB) medium.Preparation of LPS O9 LPS was extracted from E. coli ATCC23505 (O9:K9B:H12) by the phenol water method.16) The acetone-dried cells (10 g) cultured in LB medium were suspended in 175 ml of distilled water (preheated at 65°C), and then 175 ml of 90% liquid phenol (preheated at 65°C) was added under vigorous st...

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 99%

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An Unambiguous Assignment and Structural Analysis Using Solution NMR Experiments of O-Antigen from Escherichia coli ATCC23505 (Serotype O9)

et al. 2007

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“…Two-dimensional NMR spectra of heteronuclear single quantum coherence (HSQC), 19) HSQC total correlation spectroscopy (HSQC-TOCSY), 19) heteronuclear multiple bond correlation (HMBC), 20) and heteronuclear 2 bond correlation 21) were recorded in the cases of acarbose, AC5, and AC6. 1 H NMR spectra were recorded in the cases of AC7-AC10.…”

Section: )mentioning

confidence: 99%

Enzymatic Synthesis of Acarviosyl-maltooligosaccharides Using Disproportionating Enzyme 1

Tagami

Tanaka

Mori

et al. 2013

Bioscience, Biotechnology, and Biochemistry

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Biomolecular Structures by Solution Nuclear Magnetic Resonance

Blumenschein

2009

Digital Encyclopedia of Applied Physics

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The article contains sections titled: Introduction Spectra Acquisition Nuclei Sample Preparation Pulse Sequences and Processing Strategies Chemical Shift Assignment Chemical Shift Assignment in Proteins Chemical Shift Assignment in Nucleic Acids Chemical Shift Assignment in Carbohydrates Structural Restraints Nuclear Overhauser Effect Torsion Angles Residual Dipolar Couplings ( RDCs ) Hydrogen Bonds Paramagnetic Centers Structural Information from Chemical Shifts Molecular Modeling and Structure Calculation

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H2BC: a new technique for NMR analysis of complex carbohydrates

Cited by 73 publications

References 11 publications

An Unambiguous Assignment and Structural Analysis Using Solution NMR Experiments of O-Antigen from Escherichia coli ATCC23505 (Serotype O9)

An Unambiguous Assignment and Structural Analysis Using Solution NMR Experiments of O-Antigen from Escherichia coli ATCC23505 (Serotype O9)

Enzymatic Synthesis of Acarviosyl-maltooligosaccharides Using Disproportionating Enzyme 1

Biomolecular Structures by Solution Nuclear Magnetic Resonance

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