1
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Varghese CN, Jaladeep A, Sekhar A. Measuring Hydroxyl Exchange Rates in Glycans Using a Synergistic Combination of Saturation Transfer and Relaxation Dispersion NMR. J Am Chem Soc 2024; 146:3825-3835. [PMID: 38293947 PMCID: PMC7615893 DOI: 10.1021/jacs.3c10982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Molecular recognition events mediated by glycans play pivotal roles in controlling the fate of diverse biological processes such as cellular communication and the immune response. The affinity of glycans for their target receptors is governed primarily by the hydrogen bonds formed by hydroxyl groups decorating the glycan surface. Hydroxyl exchange rate constants are therefore vital parameters that report on glycan structure and dynamics. Here we present a strategy for characterizing hydroxyl hydrogen/deuterium (H/D) exchange in glycans that employs a synergistic combination of 13C chemical exchange saturation transfer (CEST) and Carr-Purcell-Meiboom-Gill relaxation dispersion (CPMG) NMR methods. We show that the combination of CEST and CPMG experiments facilitates the sensitive detection of the small (∼0.1 ppm) two-bond deuterium isotope shift on a 13C nucleus when the attached hydroxyl group fluctuates between protonated and deuterated states. This shift is leveraged for measuring site-specific kinetic H/D exchange rate constants as well as thermodynamic free energies of isotope fractionation. The CEST and CPMG modules are integrated with a selective J-cross-polarization scheme that provides the flexibility for rapid characterization of H/D exchange at a specific hydroxyl site. Moreover, our approach enables the precise isothermal measurement of hydroxyl exchange rate constants without the need for cumbersome isotope labeling. The H/D exchange rate constants of three different glycans assessed using this method highlight its potential for detecting transient intra- and intermolecular hydrogen bonds. In addition, the trends in H/D exchange rate constants establish site-specific steric accessibility as a key determinant of solvent exchange dynamics in glycans.
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Affiliation(s)
- Claris Niya Varghese
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, Karnataka, India
| | - Ahallya Jaladeep
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, Karnataka, India
| | - Ashok Sekhar
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, Karnataka, India
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2
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Abstract
Glycans, carbohydrate molecules in the realm of biology, are present as biomedically important glycoconjugates and a characteristic aspect is that their structures in many instances are branched. In determining the primary structure of a glycan, the sugar components including the absolute configuration and ring form, anomeric configuration, linkage(s), sequence, and substituents should be elucidated. Solution state NMR spectroscopy offers a unique opportunity to resolve all these aspects at atomic resolution. During the last two decades, advancement of both NMR experiments and spectrometer hardware have made it possible to unravel carbohydrate structure more efficiently. These developments applicable to glycans include, inter alia, NMR experiments that reduce spectral overlap, use selective excitations, record tilted projections of multidimensional spectra, acquire spectra by multiple receivers, utilize polarization by fast-pulsing techniques, concatenate pulse-sequence modules to acquire several spectra in a single measurement, acquire pure shift correlated spectra devoid of scalar couplings, employ stable isotope labeling to efficiently obtain homo- and/or heteronuclear correlations, as well as those that rely on dipolar cross-correlated interactions for sequential information. Refined computer programs for NMR spin simulation and chemical shift prediction aid the structural elucidation of glycans, which are notorious for their limited spectral dispersion. Hardware developments include cryogenically cold probes and dynamic nuclear polarization techniques, both resulting in enhanced sensitivity as well as ultrahigh field NMR spectrometers with a 1H NMR resonance frequency higher than 1 GHz, thus improving resolution of resonances. Taken together, the developments have made and will in the future make it possible to elucidate carbohydrate structure in great detail, thereby forming the basis for understanding of how glycans interact with other molecules.
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Affiliation(s)
- Carolina Fontana
- Departamento
de Química del Litoral, CENUR Litoral Norte, Universidad de la República, Paysandú 60000, Uruguay
| | - Göran Widmalm
- Department
of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden,
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3
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Fronius M. Epithelial Na+ channel and the glycocalyx: a sweet and salty relationship for arterial shear stress sensing. Curr Opin Nephrol Hypertens 2022; 31:142-150. [PMID: 34966089 DOI: 10.1097/mnh.0000000000000779] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW The ability of endothelial cells to sense mechanical force, and shear stress in particular, is crucial for normal vascular function. This relies on an intact endothelial glycocalyx that facilitates the production of nitric oxide (NO). An emerging arterial shear stress sensor is the epithelial Na+ channel (ENaC). This review highlights existing and new evidence for the interdependent activity of the glycocalyx and ENaC and its implications for vascular function. RECENT FINDINGS New evidence suggests that the glycocalyx and ENaC are physically connected and that this is important for shear stress sensing. The connection relies on N-glycans attached to glycosylated asparagines of α-ENaC. Removal of specific N-glycans reduced ENaC's shear stress response. Similar effects were observed following degradation of the glycocalyx. Endothelial specific viral transduction of α-ENaC increased blood pressure (∼40 mmHg). This increase was attenuated in animals transduced with an α-ENaC version lacking N-glycans. SUMMARY These observations indicate that ENaC is connected to the glycocalyx and their activity is interdependent to facilitate arterial shear stress sensation. Future research focusing on how N-glycans mediate this interaction can provide new insights for the understanding of vascular function in health and disease.
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Affiliation(s)
- Martin Fronius
- Department of Physiology, School of Biomedical Sciences
- HeartOtago, University of Otago, Dunedin
- Healthy Hearts Aotearoa New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Centre of Research Excellence, Auckland, New Zealand
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4
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Methods for Measuring Exchangeable Protons in Glycosaminoglycans. Methods Mol Biol 2021. [PMID: 34626393 DOI: 10.1007/978-1-0716-1398-6_29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Recent NMR studies of the exchangeable protons of GAGs in aqueous solution, including those of the amide, sulfamate, and hydroxyl moieties, have demonstrated potential for the detection of intramolecular hydrogen bonds providing insights into secondary structure preferences. GAG amide protons are observable by NMR over wide pH and temperature ranges; however, specific solution conditions are required to reduce the exchange rate of the sulfamate and hydroxyl protons and allow their detection by NMR. Building on the vast body of knowledge on detection of hydrogen bonds in peptides and proteins, a variety of methods can be used to identify hydrogen bonds in GAGs including temperature coefficient measurements, evaluation of chemical shift differences between oligo- and monosaccharides, and relative exchange rates measured through line shape analysis and EXSY spectra. Emerging strategies to allow direct detection of hydrogen bonds through heteronuclear couplings offer promise for the future. Molecular dynamic simulations are important in this effort both to predict and confirm hydrogen bond donors and acceptors.
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5
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Novakovic M, Battistel MD, Azurmendi HF, Concilio MG, Freedberg DI, Frydman L. The Incorporation of Labile Protons into Multidimensional NMR Analyses: Glycan Structures Revisited. J Am Chem Soc 2021; 143:8935-8948. [PMID: 34085814 PMCID: PMC8297728 DOI: 10.1021/jacs.1c04512] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Glycan structures
are often stabilized by a repertoire of hydrogen-bonded
donor/acceptor groups, revealing longer-lived structures that could
represent biologically relevant conformations. NMR provides unique
data on these hydrogen-bonded networks from multidimensional experiments
detecting cross-peaks resulting from through-bond (TOCSY) or through-space
(NOESY) interactions. However, fast OH/H2O exchange, and
the spectral proximity among these NMR resonances, hamper the use
of glycans’ labile protons in such analyses; consequently,
studies are often restricted to aprotic solvents or supercooled aqueous
solutions. These nonphysiological conditions may lead to unrepresentative
structures or to probing a small subset of accessible conformations
that may miss “active” glycan conformations. Looped,
projected spectroscopy (L-PROSY) has been recently shown to substantially
enhance protein NOESY and TOCSY cross-peaks, for 1Hs that
undergo fast exchange with water. This study shows that even larger
enhancements can be obtained for rapidly exchanging OHs in saccharides,
leading to the retrieval of previously undetectable 2D TOCSY/NOESY
cross-peaks with nonlabile protons. After demonstrating ≥300%
signal enhancements on model monosaccharides, these experiments were
applied at 1 GHz to elucidate the structural network adopted by a
sialic acid homotetramer, used as a model for α,2–8 linked
polysaccharides. High-field L-PROSY NMR enabled these studies at higher
temperatures and provided insight previously unavailable from lower-field
NMR investigations on supercooled samples, involving mostly nonlabile
nuclei. Using L-PROSY’s NOEs and other restraints, a revised
structural model for the homotetramer was obtained combining rigid
motifs and flexible segments, that is well represented by conformations
derived from 40 μs molecular dynamics simulations.
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Affiliation(s)
- Mihajlo Novakovic
- Department of Chemical and Biological Physics, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Marcos D Battistel
- Laboratory of Bacterial Polysaccharides, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, Maryland 20993, United States
| | - Hugo F Azurmendi
- Laboratory of Bacterial Polysaccharides, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, Maryland 20993, United States
| | - Maria-Grazia Concilio
- Department of Chemical and Biological Physics, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Darón I Freedberg
- Laboratory of Bacterial Polysaccharides, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, Maryland 20993, United States
| | - Lucio Frydman
- Department of Chemical and Biological Physics, Weizmann Institute of Science, 76100 Rehovot, Israel
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6
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Watson A, Simmermaker C, Aung E, Do S, Hackbusch S, Franz AH. NMR analysis and molecular dynamics conformation of α-1,6-linear and α-1,3-branched isomaltose oligomers as mimetics of α-1,6-linked dextran. Carbohydr Res 2021; 503:108296. [PMID: 33813322 DOI: 10.1016/j.carres.2021.108296] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 03/21/2021] [Accepted: 03/22/2021] [Indexed: 01/01/2023]
Abstract
The conformational preferences of several α-1,6-linear and α-1,3-branched isomalto-oligosaccharides were investigated by NMR and MD-simulations. Right-handed helical structure contributed to the solution geometry in isomaltotriose and isomaltotetraose with one nearly complete helix turn and stabilizing intramolecular hydrogen bonds in the latter by MD-simulation. Decreased helix contribution was observed in α-1,3-glucopyranosyl- and α-1,3-isomaltosyl-branched saccharide chains. Especially the latter modification was predicted to cause a more compact structure consistent with literature rheology measurements as well as with published dextranase-resistant α-1,3-branched oligosaccharides. The findings presented here are significant because they shed further light on the conformational preference of isomalto-oligosaccharides and provide possible help for the design of dextran-based drug delivery systems or for the targeted degradation of capsular polysaccharides by dextranases in multi-drug resistant bacteria.
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Affiliation(s)
- Amelia Watson
- Department of Chemistry, University of the Pacific, 3601 Pacific Avenue, Stockton, CA, 95211, USA
| | - Cate Simmermaker
- Department of Chemistry, University of the Pacific, 3601 Pacific Avenue, Stockton, CA, 95211, USA
| | - Ei Aung
- Department of Chemistry, University of the Pacific, 3601 Pacific Avenue, Stockton, CA, 95211, USA
| | - Stephen Do
- Department of Chemistry, University of the Pacific, 3601 Pacific Avenue, Stockton, CA, 95211, USA
| | - Sven Hackbusch
- Department of Chemistry, University of the Pacific, 3601 Pacific Avenue, Stockton, CA, 95211, USA
| | - Andreas H Franz
- Department of Chemistry, University of the Pacific, 3601 Pacific Avenue, Stockton, CA, 95211, USA.
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7
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Yao HYY, Wang JQ, Yin JY, Nie SP, Xie MY. A review of NMR analysis in polysaccharide structure and conformation: Progress, challenge and perspective. Food Res Int 2021; 143:110290. [PMID: 33992390 DOI: 10.1016/j.foodres.2021.110290] [Citation(s) in RCA: 133] [Impact Index Per Article: 44.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 02/28/2021] [Accepted: 02/28/2021] [Indexed: 12/31/2022]
Abstract
Nuclear magnetic resonance (NMR) has been widely used as an analytical chemistry technique to investigate the molecular structure and conformation of polysaccharides. Combined with 1D spectra, chemical shifts and coupling constants in both homo- and heteronuclear 2D NMR spectra are able to infer the linkage and sequence of sugar residues. Besides, NMR has also been applied in conformation, quantitative analysis, cell wall in situ, degradation, polysaccharide mixture interaction analysis, as well as carbohydrates impurities profiling. This review summarizes the principle and development of NMR in polysaccharides analysis, and provides NMR spectra data collections of some common polysaccharides. It will help to promote the application of NMR in complex polysaccharides of biochemical interest, and provide valuable information on commercial polysaccharide products.
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Affiliation(s)
- Hao-Ying-Ye Yao
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology (Nanchang), Nanchang University, 235 Nanjing East Road, Nanchang 330047, China.
| | - Jun-Qiao Wang
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology (Nanchang), Nanchang University, 235 Nanjing East Road, Nanchang 330047, China.
| | - Jun-Yi Yin
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology (Nanchang), Nanchang University, 235 Nanjing East Road, Nanchang 330047, China.
| | - Shao-Ping Nie
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology (Nanchang), Nanchang University, 235 Nanjing East Road, Nanchang 330047, China.
| | - Ming-Yong Xie
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology (Nanchang), Nanchang University, 235 Nanjing East Road, Nanchang 330047, China; National R&D Center for Freshwater Fish Processing, Jiangxi Normal University, Nanchang, Jiangxi 330022, China.
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8
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Abraham RJ, Cooper MA, Reid M. The use of MM/QM calculations of 13C chemical shifts in the conformational analysis of some monosaccharides and sucrose. NEW J CHEM 2021. [DOI: 10.1039/d0nj04227g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The 13C NMR chemical shifts of some common pyranose monosaccharides in D2O solution were predicted using a combined molecular mechanics (Pcmod 9.1/MMFF94) and ab initio (GIAO (B3LYP/DFT, 6-31G(d))) model.
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Affiliation(s)
| | - M. Ashley Cooper
- The Chemistry Department
- University of Liverpool
- Liverpool L69 7ZD
- UK
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9
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Li W, Battistel MD, Reeves H, Oh L, Yu H, Chen X, Wang LP, Freedberg DI. A combined NMR, MD and DFT conformational analysis of 9-O-acetyl sialic acid-containing GM3 ganglioside glycan and its 9-N-acetyl mimic. Glycobiology 2020; 30:787-801. [PMID: 32350512 PMCID: PMC8179627 DOI: 10.1093/glycob/cwaa040] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 04/22/2020] [Accepted: 04/22/2020] [Indexed: 01/30/2023] Open
Abstract
O-Acetylation of carbohydrates such as sialic acids is common in nature, but its role is not clearly understood due to the lability of O-acetyl groups. We demonstrated previously that 9-acetamido-9-deoxy-N-acetylneuraminic acid (Neu5Ac9NAc) is a chemically and biologically stable mimic of the 9-O-acetyl-N-acetylneuraminic acid (Neu5,9Ac2) of the corresponding sialoglycans. Here, a systematic nuclear magnetic resonance (NMR) spectroscopic and molecular dynamics (MD) simulation study was undertaken for Neu5,9Ac2-containing GM3 ganglioside glycan (GM3-glycan) and its Neu5Ac9NAc analog. GM3-glycan with Neu5Ac as the non-O-acetyl form of Neu5,9Ac2 was used as a control. Complete 1H and 13C NMR chemical shift assignments, three-bond 1H-13C trans-glycosidic coupling constants (3JCH), accurate 1H-1H coupling constants (3JHH), nuclear Overhauser effects and hydrogen bonding detection were carried out. Results show that structural modification (O- or N-acetylation) on the C-9 of Neu5Ac in GM3 glycan does not cause significant conformational changes on either its glycosidic dihedral angles or its secondary structure. All structural differences are confined to the Neu5Ac glycerol chain, and minor temperature-dependent changes are seen in the aglycone portion. We also used Density Functional Theory (DFT) quantum mechanical calculations to improve currently used 3JHH Karplus relations. Furthermore, OH chemical shifts were assigned at -10°C and no evidence of an intramolecular hydrogen bond was observed. The results provide additional evidence regarding structural similarities between sialosides containing 9-N-acetylated and 9-O-acetylated Neu5Ac and support the opportunity of using 9-N-acetylated Neu5Ac as a stable mimic to study the biochemical role of 9-O-acetylated Neu5Ac.
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Affiliation(s)
- Wanqing Li
- Department of Chemistry, University of California-Davis, One Shields Avenue, Davis, California 95616, USA
| | - Marcos D Battistel
- Laboratory of Bacterial Polysaccharides, Food and Drug Administration (FDA), Silver Spring, MD 20993, USA
| | - Hannah Reeves
- Department of Chemistry, University of California-Davis, One Shields Avenue, Davis, California 95616, USA
| | - Lisa Oh
- Department of Chemistry, University of California-Davis, One Shields Avenue, Davis, California 95616, USA
| | - Hai Yu
- Department of Chemistry, University of California-Davis, One Shields Avenue, Davis, California 95616, USA
| | - Xi Chen
- Department of Chemistry, University of California-Davis, One Shields Avenue, Davis, California 95616, USA
| | - Lee-Ping Wang
- Department of Chemistry, University of California-Davis, One Shields Avenue, Davis, California 95616, USA
| | - Darón I Freedberg
- Laboratory of Bacterial Polysaccharides, Food and Drug Administration (FDA), Silver Spring, MD 20993, USA
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10
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Abstract
The conformation of a molecule strongly affects its function, as demonstrated for peptides and nucleic acids. This correlation is much less established for carbohydrates, the most abundant organic materials in nature. Recent advances in synthetic and analytical techniques have enabled the study of carbohydrates at the molecular level. Recurrent structural features were identified as responsible for particular biological activities or material properties. In this Minireview, recent achievements in the structural characterization of carbohydrates, enabled by systematic studies of chemically defined oligosaccharides, are discussed. These findings can guide the development of more potent glycomimetics. Synthetic carbohydrate materials by design can be envisioned.
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Affiliation(s)
- Yang Yu
- Department of Biomolecular SystemsMax-Planck-Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
- Department of Chemistry and BiochemistryFreie Universität BerlinArnimallee 2214195BerlinGermany
| | - Martina Delbianco
- Department of Biomolecular SystemsMax-Planck-Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
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11
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Leong SX, Koh LK, Koh CSL, Phan-Quang GC, Lee HK, Ling XY. In Situ Differentiation of Multiplex Noncovalent Interactions Using SERS and Chemometrics. ACS APPLIED MATERIALS & INTERFACES 2020; 12:33421-33427. [PMID: 32578974 DOI: 10.1021/acsami.0c08053] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Probing changes of noncovalent interactions is crucial to study the binding efficiencies and strengths of (bio)molecular complexes. While surface-enhanced Raman scattering (SERS) offers unique molecular fingerprints to examine such interactions in situ, current platforms are only able to recognize hydrogen bonds because of their reliance on manual spectral identification. Here, we differentiate multiple intermolecular interactions between two interacting species by synergizing plasmonic liquid marble-based SERS platforms, chemometrics, and density functional theory. We demonstrate that characteristic 3-mercaptobenzoic acid (probe) Raman signals have distinct peak shifts upon hydrogen bonding and ionic interactions with tert-butylamine, a model interacting species. Notably, we further quantify the contributions from each noncovalent interaction coexisting in different proportions. As a proof-of-concept, we detect and categorize biologically important nucleotide bases based on molecule-specific interactions. This will potentially be useful to study how subtle changes in biomolecular interactions affect their structural and binding properties.
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Affiliation(s)
- Shi Xuan Leong
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 637371, Singapore
| | - Li Keng Koh
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 637371, Singapore
| | - Charlynn Sher Lin Koh
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 637371, Singapore
| | - Gia Chuong Phan-Quang
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 637371, Singapore
| | - Hiang Kwee Lee
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 637371, Singapore
| | - Xing Yi Ling
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 637371, Singapore
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12
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Yamada K, Yamaguchi Y, Uekusa Y, Aoki K, Shimada I, Yamaguchi T, Kato K. Solid-state 17O NMR analysis of synthetically 17O-enriched d-glucosamine. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2020.137455] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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13
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Affiliation(s)
- Darón I. Freedberg
- Center for Biologics Evaluation and ResearchFood and Drug Administration 10903 New Hampshire Ave. Silver Spring MD. 20993
| | - Jeahoo Kwon
- Center for Biologics Evaluation and ResearchFood and Drug Administration 10903 New Hampshire Ave. Silver Spring MD. 20993
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14
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Bezerra FF, Vignovich WP, Aderibigbe AO, Liu H, Sharp JS, Doerksen RJ, Pomin VH. Conformational properties of l-fucose and the tetrasaccharide building block of the sulfated l-fucan from Lytechinus variegatus. J Struct Biol 2019; 209:107407. [PMID: 31698075 DOI: 10.1016/j.jsb.2019.107407] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 10/07/2019] [Accepted: 10/23/2019] [Indexed: 01/19/2023]
Abstract
Although the 3D structure of carbohydrates is known to contribute to their biological roles, conformational studies of sugars are challenging because their chains are flexible in solution and consequently the number of 3D structural restraints is limited. Here, we investigate the conformational properties of the tetrasaccharide building block of the Lytechinus variegatus sulfated fucan composed of the following structure [l-Fucp4(SO3-)-α(1-3)-l-Fucp2,4(SO3-)-α(1-3)-l-Fucp2(SO3-)-α(1-3)-l-Fucp2(SO3-)] and the composing monosaccharide unit Fucp, primarily by nuclear magnetic resonance (NMR) experiments performed at very low temperatures and using H2O as the solvent for the sugars rather than using the conventional deuterium oxide. By slowing down the fast chemical exchange rates and forcing the protonation of labile sites, we increased the number of through-space 1H-1H distances that could be measured by NMR spectroscopy. Following this strategy, additional conformational details of the tetrasaccharide and l-Fucp in solution were obtained. Computational molecular dynamics was performed to complement and validate the NMR-based measurements. A model of the NMR-restrained 3D structure is offered for the tetrasaccharide.
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Affiliation(s)
- Francisco F Bezerra
- Institute of Medical Biochemistry Leopoldo de Meis, University Hospital Clementino Fraga Filho, Federal University of Rio de Janeiro, Rio de Janeiro 21941, RJ, Brazil
| | - William P Vignovich
- BioMolecular Sciences Department, School of Pharmacy, University of Mississippi, University, 38677 MS, USA
| | - AyoOluwa O Aderibigbe
- BioMolecular Sciences Department, School of Pharmacy, University of Mississippi, University, 38677 MS, USA
| | - Hao Liu
- BioMolecular Sciences Department, School of Pharmacy, University of Mississippi, University, 38677 MS, USA
| | - Joshua S Sharp
- BioMolecular Sciences Department, School of Pharmacy, University of Mississippi, University, 38677 MS, USA; Research Institute of Pharmaceutical Sciences, School of Pharmacy, University of Mississippi, University, 38677 MS, USA
| | - Robert J Doerksen
- BioMolecular Sciences Department, School of Pharmacy, University of Mississippi, University, 38677 MS, USA; Research Institute of Pharmaceutical Sciences, School of Pharmacy, University of Mississippi, University, 38677 MS, USA
| | - Vitor H Pomin
- Institute of Medical Biochemistry Leopoldo de Meis, University Hospital Clementino Fraga Filho, Federal University of Rio de Janeiro, Rio de Janeiro 21941, RJ, Brazil; BioMolecular Sciences Department, School of Pharmacy, University of Mississippi, University, 38677 MS, USA; Research Institute of Pharmaceutical Sciences, School of Pharmacy, University of Mississippi, University, 38677 MS, USA.
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15
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Rönnols J, Engström O, Schnupf U, Säwén E, Brady JW, Widmalm G. Inter-residual Hydrogen Bonding in Carbohydrates Unraveled by NMR Spectroscopy and Molecular Dynamics Simulations. Chembiochem 2019; 20:2519-2528. [PMID: 31066963 DOI: 10.1002/cbic.201900301] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Indexed: 12/15/2022]
Abstract
Carbohydrates, also known as glycans in biological systems, are omnipresent in nature where they as glycoconjugates occur as oligo- and polysaccharides linked to lipids and proteins. Their three-dimensional structure is defined by two or three torsion angles at each glycosidic linkage. In addition, transglycosidic hydrogen bonding between sugar residues may be important. Herein we investigate the presence of these inter-residue interactions by NMR spectroscopy in D2 O/[D6 ]DMSO (70:30) or D2 O and by molecular dynamics (MD) simulations with explicit water as solvent for disaccharides with structural elements α-d-Manp-(1→2)-d-Manp, β-d-GlcpNAc-(1→2)-d-Manp, and α-d-Glcp-(1→4)-β-d-Glcp, all of which have been suggested to exhibit inter-residue hydrogen bonding. For the disaccharide β-d-GlcpNAc-(1→2)-β-d-Manp-OMe, the large extent of O5'⋅⋅⋅HO3 hydrogen bonding as seen from the MD simulation is implicitly supported by the 1 H NMR chemical shift and 3 JHO3,H3 value of the hydroxy proton. In the case of α-d-Glcp-(1→4)-β-d-Glcp-OMe, the existence of a transglycosidic hydrogen bond O2'⋅⋅⋅HO3 was proven by the presence of a cross-peak in 1 H,13 C HSQC-TOCSY experiments as a result of direct TOCSY transfer between HO3 of the reducing end residue and H2' (detected at C2') of the terminal residue. The occurrence of inter-residue hydrogen bonding, albeit transient, is judged important for the stabilization of three-dimensional structures, which may be essential in maintaining a conformational state for carbohydrate-protein interactions of glycans to take place in biologically important environments.
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Affiliation(s)
- Jerk Rönnols
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, 106 91, Stockholm, Sweden
| | - Olof Engström
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, 106 91, Stockholm, Sweden
| | - Udo Schnupf
- Department of Chemistry and Biochemistry, Bradley University, Peoria, IL, 61625, USA
| | - Elin Säwén
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, 106 91, Stockholm, Sweden
| | - John W Brady
- Department of Food Science, Cornell University, Ithaca, NY, 14853, USA
| | - Göran Widmalm
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, 106 91, Stockholm, Sweden
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16
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Valverde P, Quintana JI, Santos JI, Ardá A, Jiménez-Barbero J. Novel NMR Avenues to Explore the Conformation and Interactions of Glycans. ACS OMEGA 2019; 4:13618-13630. [PMID: 31497679 PMCID: PMC6714940 DOI: 10.1021/acsomega.9b01901] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 08/02/2019] [Indexed: 05/12/2023]
Abstract
This perspective article is focused on the presentation of the latest advances in NMR methods and applications that are behind the exciting achievements in the understanding of glycan receptors in molecular recognition events. Different NMR-based methodologies are discussed along with their applications to scrutinize the conformation and dynamics of glycans as well as their interactions with protein receptors.
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Affiliation(s)
- Pablo Valverde
- CIC
bioGUNE, Bizkaia Technology
Park, Building 800, 48160 Derio, Bizkaia, Spain
| | - Jon I. Quintana
- CIC
bioGUNE, Bizkaia Technology
Park, Building 800, 48160 Derio, Bizkaia, Spain
| | - Jose I. Santos
- SGIker
UPV/EHU, Centro Joxe Mari Korta, Tolosa Hiribidea 72, 20018 Donostia, Spain
| | - Ana Ardá
- CIC
bioGUNE, Bizkaia Technology
Park, Building 800, 48160 Derio, Bizkaia, Spain
- E-mail: (A.A.)
| | - Jesús Jiménez-Barbero
- CIC
bioGUNE, Bizkaia Technology
Park, Building 800, 48160 Derio, Bizkaia, Spain
- Ikerbasque, Basque Foundation for Science, Maria Diaz de Haro 3, 48013 Bilbao, Spain
- Department
Organic Chemistry II, Faculty Science &
Technology, EHU-UPV, 48940 Leioa, Bizkaia, Spain
- E-mail: (J.J.-B.)
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17
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Affiliation(s)
- Giulio Fittolani
- Department of Biomolecular SystemsMax Planck Institute of Colloids and Interfaces Potsdam Germany
| | - Peter H. Seeberger
- Department of Biomolecular SystemsMax Planck Institute of Colloids and Interfaces Potsdam Germany
- Institute of Chemistry and BiochemistryFreie Universität Berlin Berlin Germany
| | - Martina Delbianco
- Department of Biomolecular SystemsMax Planck Institute of Colloids and Interfaces Potsdam Germany
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18
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Green AR, Li K, Lockard B, Young RP, Mueller LJ, Larive CK. Investigation of the Amide Proton Solvent Exchange Properties of Glycosaminoglycan Oligosaccharides. J Phys Chem B 2019; 123:4653-4662. [PMID: 31067054 DOI: 10.1021/acs.jpcb.9b01794] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
One-dimensional 1H NMR experiments were conducted for aqueous solutions of glycosaminoglycan oligosaccharides to measure the amide proton temperature coefficients and activation energy barriers for solvent exchange and evaluate the effect of pH on the solvent exchange properties. A library of mono- and oligosaccharides was prepared by enzymatic depolymerization of amide-containing polysaccharides and by chemical modification of heparin and heparan sulfate saccharides including members that contain a 3- O-sulfated glucosamine residue. The systematic evaluation of this saccharide library facilitated assessment of the effects of structural characteristics, such as size, sulfation number and site, and glycosidic linkage, on amide proton solvent exchange rates. Charge repulsion by neighboring negatively charged sulfate and carboxylate groups was found to have a significant impact on the catalysis of amide proton solvent exchange by hydroxide. This observation leads to the conclusion that solvent exchange rates must be interpreted within the context of a given chemical environment. On their own, slow exchange rates do not conclusively establish the involvement of a labile proton in a hydrogen bond, and additional supporting experimental evidence such as reduced temperature coefficients is required.
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Affiliation(s)
- Andrew R Green
- Department of Chemistry , University of California-Riverside , Riverside , California 92501 , United States
| | - Kecheng Li
- Department of Chemistry , University of California-Riverside , Riverside , California 92501 , United States.,Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology , Chinese Academy of Sciences , Qingdao 266071 , China.,Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology , Qingdao 266237 , China
| | - Blake Lockard
- Department of Chemistry , University of California-Riverside , Riverside , California 92501 , United States
| | - Robert P Young
- Department of Chemistry , University of California-Riverside , Riverside , California 92501 , United States.,Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , Washington 99352 , United States
| | - Leonard J Mueller
- Department of Chemistry , University of California-Riverside , Riverside , California 92501 , United States
| | - Cynthia K Larive
- Department of Chemistry , University of California-Riverside , Riverside , California 92501 , United States
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19
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Zhang W, Meredith R, Yoon MK, Wang X, Woods RJ, Carmichael I, Serianni AS. Synthesis and O-Glycosidic Linkage Conformational Analysis of 13C-Labeled Oligosaccharide Fragments of an Antifreeze Glycolipid. J Org Chem 2019; 84:1706-1724. [PMID: 30624062 DOI: 10.1021/acs.joc.8b01411] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
NMR studies of two 13C-labeled disaccharides and a tetrasaccharide were undertaken that comprise the backbone of a novel thermal hysteresis glycolipid containing a linear glycan sequence of alternating [βXyl p-(1→4)-βMan p-(1→4)] n dimers. Experimental trans-glycoside NMR J-couplings, parameterized equations obtained from density functional theory (DFT) calculations, and an in-house circular statistics package ( MA'AT) were used to derive conformational models of linkage torsion angles ϕ and ψ in solution, which were compared to those obtained from molecular dynamics simulations. Modeling using different probability distribution functions showed that MA'AT models of ϕ in βMan(1→4)βXyl and βXyl(1→4)βMan linkages are very similar in the disaccharide building blocks, whereas MA'AT models of ψ differ. This pattern is conserved in the tetrasaccharide, showing that linkage context does not influence linkage geometry in this linear system. Good agreement was observed between the MA'AT and MD models of ψ with respect to mean values and circular standard deviations. Significant differences were observed for ϕ, indicating that revision of the force-field employed by GLYCAM is probably needed. Incorporation of the experimental models of ϕ and ψ into the backbone of an octasaccharide fragment leads to a helical amphipathic topography that may affect the thermal hysteresis properties of the glycolipid.
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Affiliation(s)
| | | | | | - Xiaocong Wang
- Complex Carbohydrate Research Center , University of Georgia , Athens , Georgia 30602 , United States
| | - Robert J Woods
- Complex Carbohydrate Research Center , University of Georgia , Athens , Georgia 30602 , United States
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20
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Turney T, Pan Q, Zhang W, Oliver AG, Serianni AS. O-Benzoyl side-chain conformations in 2,3,4,6-tetra-O-benzoyl-β-D-galactopyranosyl-(1→4)-1,2,6-tri-O-benzoyl-β-D-glucopyranose (ethyl acetate solvate) and 1,2,4,6-tetra-O-benzoyl-β-D-glucopyranose (acetone solvate). ACTA CRYSTALLOGRAPHICA SECTION C-STRUCTURAL CHEMISTRY 2019; 75:161-167. [DOI: 10.1107/s2053229619000822] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 01/17/2019] [Indexed: 05/30/2023]
Abstract
The crystal structures of 2,3,4,6-tetra-O-benzoyl-β-D-galactopyranosyl-(1→4)-1,2,6-tri-O-benzoyl-β-D-glucopyranose ethyl acetate hemisolvate, C61H50O18·0.5C4H8O2, and 1,2,4,6-tetra-O-benzoyl-β-D-glucopyranose acetone monosolvate, C34H28O10·C3H6O, were determined and compared to those of methyl β-D-galactopyranosyl-(1→4)-β-D-glucopyranoside (methyl β-lactoside) and methyl β-D-glucopyranoside hemihydrate, C7H14O6·0.5H2O, to evaluate the effects of O-benzoylation on bond lengths, bond angles and torsion angles. In general, O-benzoylation exerts little effect on exo- and endocyclic C—C and endocyclic C—O bond lengths, but exocyclic C—O bonds involved in O-benzoylation are lengthened by 0.02–0.04 Å depending on the site of substitution. The conformation of the O-benzoyl side-chains is highly conserved, with the carbonyl O atom either eclipsing the H atom attached to a 2°-alcoholic C atom or bisecting the H—C—H bond angle of an 1°-alcoholic C atom. Of the three bonds that determine the side-chain geometry, the C—O bond involving the alcoholic C atom exhibits greater rotational variability than the remaining C—O and C—C bonds involving the carbonyl C atom. These findings are in good agreement with recent solution NMR studies of the O-acetyl side-chain conformation in saccharides.
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21
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Brown GD, Bauer J, Osborn HMI, Kuemmerle R. A Solution NMR Approach To Determine the Chemical Structures of Carbohydrates Using the Hydroxyl Groups as Starting Points. ACS OMEGA 2018; 3:17957-17975. [PMID: 31458388 PMCID: PMC6644132 DOI: 10.1021/acsomega.8b02136] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 12/07/2018] [Indexed: 06/10/2023]
Abstract
An efficient NMR approach is described for determining the chemical structures of the monosaccharide glucose and four disaccharides, namely, nigerose, gentiobiose, leucrose and isomaltulose. This approach uses the 1H resonances of the -OH groups, which are observable in the NMR spectrum of a supercooled aqueous solution, as the starting point for further analysis. The 2D-NMR technique, HSQC-TOCSY, is then applied to fully define the covalent structure (i.e., the topological relationship between C-C, C-H, and O-H bonds) that must be established for a novel carbohydrate before proceeding to further conformational studies. This process also leads to complete assignment of all 1H and 13C resonances. The approach is exemplified by analyzing the monosaccharide glucose, which is treated as if it were an "unknown", and also by fully assigning all the NMR resonances for the four disaccharides that contain glucose. It is proposed that this technique should be equally applicable to the determination of chemical structures for larger carbohydrates of unknown composition, including those that are only available in limited quantities from biological studies. The advantages of commencing the structure elucidation of a carbohydrate at the -OH groups are discussed with reference to the now well-established 2D-/3D-NMR strategy for investigation of peptides/proteins, which employs the -NH resonances as the starting point.
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Affiliation(s)
- Geoffrey D. Brown
- Department of Chemistry and Reading School of Pharmacy, The University of Reading, Whiteknights, Reading RG6 6AP, United Kingdom
| | - Julia Bauer
- Department of Chemistry and Reading School of Pharmacy, The University of Reading, Whiteknights, Reading RG6 6AP, United Kingdom
| | - Helen M. I. Osborn
- Department of Chemistry and Reading School of Pharmacy, The University of Reading, Whiteknights, Reading RG6 6AP, United Kingdom
| | - Rainer Kuemmerle
- Bruker
Biospin AG, NMR Division, Industriestrasse 26, CH-8117 Fallanden, Switzerland
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22
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Nestor G, Anderson T, Oscarson S, Gronenborn AM. Direct Observation of Carbohydrate Hydroxyl Protons in Hydrogen Bonds with a Protein. J Am Chem Soc 2017; 140:339-345. [PMID: 29227646 DOI: 10.1021/jacs.7b10595] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydroxyl proton resonances of uniformly 13C-labeled Manα(1-2)Manα(1-2)ManαOMe (Man3) bound to cyanovirin-N (CV-N) were detected at ambient temperature in aqueous solution by NMR spectroscopy. The directions of the hydroxyl groups were determined on the basis of NOEs, and a previously unknown hydrogen-bonding network between Man3 and CV-N was discovered. This is the first report on detecting hydroxyl protons of a protein-bound carbohydrate in aqueous solution by NMR. Approaches such as those presented here may open the door for accurately determining intermolecular hydrogen bonds in carbohydrate-protein complexes.
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Affiliation(s)
- Gustav Nestor
- Department of Structural Biology, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15261, United States
| | - Taigh Anderson
- Centre for Synthesis and Chemical Biology, University College Dublin , Belfield, Dublin 4, Ireland
| | - Stefan Oscarson
- Centre for Synthesis and Chemical Biology, University College Dublin , Belfield, Dublin 4, Ireland
| | - Angela M Gronenborn
- Department of Structural Biology, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15261, United States
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23
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Blasco P, Patel DS, Engström O, Im W, Widmalm G. Conformational Dynamics of the Lipopolysaccharide from Escherichia coli O91 Revealed by Nuclear Magnetic Resonance Spectroscopy and Molecular Simulations. Biochemistry 2017; 56:3826-3839. [DOI: 10.1021/acs.biochem.7b00106] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Pilar Blasco
- Department
of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106
91 Stockholm, Sweden
| | - Dhilon S. Patel
- Department
of Biological Sciences and Bioengineering Program, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Olof Engström
- Department
of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106
91 Stockholm, Sweden
| | - Wonpil Im
- Department
of Biological Sciences and Bioengineering Program, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Göran Widmalm
- Department
of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106
91 Stockholm, Sweden
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24
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Battistel MD, Azurmendi HF, Freedberg DI. Glycan OH Exchange Rate Determination in Aqueous Solution: Seeking Evidence for Transient Hydrogen Bonds. J Phys Chem B 2017; 121:683-695. [PMID: 27995788 DOI: 10.1021/acs.jpcb.6b10594] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hydrogen bonds (Hbonds) are important stabilizing forces in biomolecules. However, for glycans in aqueous solution, direct NMR detection of Hbonds is elusive because of their transient nature. Here, we present Isotope-based Natural-abundance TOtal correlation eXchange SpectroscopY (INTOXSY), a new 1H-13C heteronuclear single quantum coherence-total correlation spectroscopy based method, to extract OH groups' exchange rate constants (kex) for molecules in natural 13C abundance and show that OH Hbonds can be inferred from "slower" H/D kex. We evaluate kex measured with INTOXSY in light of those extracted with line-shape analysis. Subsequently, we use a set of common glycans to establish a kex reference basis set and to infer the existence of transient Hbonds involving OH donor groups. Then, we report kex values for a series of mono- and disaccharides, as well as for oligosaccharides sialyl Lewis X and β-cyclodextrin, and compare the results with those from the reference set to extract Hbond information. Finally, we utilize NMR experimental data in conjunction with molecular dynamics simulations to establish donor and acceptor Hbond pairs. Our exchange rate measurements indicate that OH/OD exchange rates, kHD, values <10 s-1 are consistent with transient Hbond OH groups and potential acceptor groups can be uncovered through MD simulations.
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Affiliation(s)
- Marcos D Battistel
- Laboratory of Bacterial Polysaccharides, Center for Biologics Evaluation and Research, Food and Drug Administration , 10903 New Hampshire Avenue, Silver Spring, Maryland 20903, United States
| | - Hugo F Azurmendi
- Laboratory of Bacterial Polysaccharides, Center for Biologics Evaluation and Research, Food and Drug Administration , 10903 New Hampshire Avenue, Silver Spring, Maryland 20903, United States
| | - Darón I Freedberg
- Laboratory of Bacterial Polysaccharides, Center for Biologics Evaluation and Research, Food and Drug Administration , 10903 New Hampshire Avenue, Silver Spring, Maryland 20903, United States
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25
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Lonardi A, Oborský P, Hünenberger PH. Solvent-Modulated Influence of Intramolecular Hydrogen-Bonding on the Conformational Properties of the Hydroxymethyl Group in Glucose and Galactose: A Molecular Dynamics Simulation Study. Helv Chim Acta 2016. [DOI: 10.1002/hlca.201600158] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Alice Lonardi
- Laboratory of Physical Chemistry; ETH Hönggerberg; HCI; CH-8093 Zürich Switzerland
| | - Pavel Oborský
- Laboratory of Physical Chemistry; ETH Hönggerberg; HCI; CH-8093 Zürich Switzerland
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26
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Pendrill R, Engström O, Volpato A, Zerbetto M, Polimeno A, Widmalm G. Flexibility at a glycosidic linkage revealed by molecular dynamics, stochastic modeling, and (13)C NMR spin relaxation: conformational preferences of α-L-Rhap-α-(1 → 2)-α-L-Rhap-OMe in water and dimethyl sulfoxide solutions. Phys Chem Chem Phys 2016; 18:3086-96. [PMID: 26741055 DOI: 10.1039/c5cp06288h] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The monosaccharide L-rhamnose is common in bacterial polysaccharides and the disaccharide α-L-Rhap-α-(1 → 2)-α-L-Rhap-OMe represents a structural model for a part of Shigella flexneri O-antigen polysaccharides. Utilization of [1'-(13)C]-site-specific labeling in the anomeric position at the glycosidic linkage between the two sugar residues facilitated the determination of transglycosidic NMR (3)JCH and (3)JCC coupling constants. Based on these spin-spin couplings the major state and the conformational distribution could be determined with respect to the ψ torsion angle, which changed between water and dimethyl sulfoxide (DMSO) as solvents, a finding mirrored by molecular dynamics (MD) simulations with explicit solvent molecules. The (13)C NMR spin relaxation parameters T1, T2, and heteronuclear NOE of the probe were measured for the disaccharide in DMSO-d6 at two magnetic field strengths, with standard deviations ≤1%. The combination of MD simulation and a stochastic description based on the diffusive chain model resulted in excellent agreement between calculated and experimentally observed (13)C relaxation parameters, with an average error of <2%. The coupling between the global reorientation of the molecule and the local motion of the spin probe is deemed essential if reproduction of NMR relaxation parameters should succeed, since decoupling of the two modes of motion results in significantly worse agreement. Calculation of (13)C relaxation parameters based on the correlation functions obtained directly from the MD simulation of the solute molecule in DMSO as solvent showed satisfactory agreement with errors on the order of 10% or less.
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Affiliation(s)
- Robert Pendrill
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden.
| | - Olof Engström
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden.
| | - Andrea Volpato
- Dipartimento di Scienze Chimiche, Università degli Studi di Padova, Padova 35131, Italy.
| | - Mirco Zerbetto
- Dipartimento di Scienze Chimiche, Università degli Studi di Padova, Padova 35131, Italy.
| | - Antonino Polimeno
- Dipartimento di Scienze Chimiche, Università degli Studi di Padova, Padova 35131, Italy.
| | - Göran Widmalm
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden.
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27
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Chalmers G, Glushka JN, Foley BL, Woods RJ, Prestegard JH. Direct NOE simulation from long MD trajectories. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2016; 265:1-9. [PMID: 26826977 PMCID: PMC4818662 DOI: 10.1016/j.jmr.2016.01.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 01/10/2016] [Accepted: 01/12/2016] [Indexed: 05/08/2023]
Abstract
A software package, MD2NOE, is presented which calculates Nuclear Overhauser Effect (NOE) build-up curves directly from molecular dynamics (MD) trajectories. It differs from traditional approaches in that it calculates correlation functions directly from the trajectory instead of extracting inverse sixth power distance terms as an intermediate step in calculating NOEs. This is particularly important for molecules that sample conformational states on a timescale similar to molecular reorientation. The package is tested on sucrose and results are shown to differ in small but significant ways from those calculated using an inverse sixth power assumption. Results are also compared to experiment and found to be in reasonable agreement despite an expected underestimation of water viscosity by the water model selected.
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Affiliation(s)
- G Chalmers
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, United States
| | - J N Glushka
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, United States
| | - B L Foley
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, United States
| | - R J Woods
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, United States
| | - J H Prestegard
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, United States.
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28
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Battistel MD, Azurmendi HF, Frank M, Freedberg DI. Uncovering Nonconventional and Conventional Hydrogen Bonds in Oligosaccharides through NMR Experiments and Molecular Modeling: Application to Sialyl Lewis-X. J Am Chem Soc 2015; 137:13444-7. [PMID: 26426963 DOI: 10.1021/jacs.5b03824] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We describe the direct NMR detection of a C-H···O nonconventional hydrogen bond (Hbond) and provide experimental and theoretical evidence for conventional Hbonds in the pentasaccharide sialyl Lewis-X (sLe(X)-5) between 5 and 37 °C in water. Extensive NMR structural studies together with molecular dynamics simulations offer strong evidence for significant local dynamics in the Le(X) core and for previously undetected conventional Hbonds in rapid equilibrium that modulate structure. These NMR studies also showed temperature-dependent (1)H and (13)C line broadening. The resulting model emerging from this study is more complex than a simple rigid core description of Le(X)-like molecules and improves our understanding of stabilizing interactions in glycans.
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Affiliation(s)
- Marcos D Battistel
- Laboratory of Bacterial Polysaccharides, Food and Drug Administration ,10903 New Hampshire Avenue, Silver Spring, Maryland 20903, United States
| | - Hugo F Azurmendi
- Laboratory of Bacterial Polysaccharides, Food and Drug Administration ,10903 New Hampshire Avenue, Silver Spring, Maryland 20903, United States
| | - Martin Frank
- Biognos AB , Generatorsgatan 1, 41705 Gothenburg, Sweden
| | - Darón I Freedberg
- Laboratory of Bacterial Polysaccharides, Food and Drug Administration ,10903 New Hampshire Avenue, Silver Spring, Maryland 20903, United States
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29
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Kapla J, Engström O, Stevensson B, Wohlert J, Widmalm G, Maliniak A. Molecular dynamics simulations and NMR spectroscopy studies of trehalose-lipid bilayer systems. Phys Chem Chem Phys 2015; 17:22438-47. [PMID: 26252429 DOI: 10.1039/c5cp02472b] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The disaccharide trehalose (TRH) strongly affects the physical properties of lipid bilayers. We investigate interactions between lipid membranes formed by 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and TRH using NMR spectroscopy and molecular dynamics (MD) computer simulations. We compare dipolar couplings derived from DMPC/TRH trajectories with those determined (i) experimentally in TRH using conventional high-resolution NMR in a weakly ordered solvent (bicelles), and (ii) by solid-state NMR in multilamellar vesicles (MLV) formed by DMPC. Analysis of the experimental and MD-derived couplings in DMPC indicated that the force field used in the simulations reasonably well describes the experimental results with the exception for the glycerol fragment that exhibits significant deviations. The signs of dipolar couplings, not available from the experiments on highly ordered systems, were determined from the trajectory analysis. The crucial step in the analysis of residual dipolar couplings (RDCs) in TRH determined in a bicelle-environment was access to the conformational distributions derived from the MD trajectory. Furthermore, the conformational behavior of TRH, investigated by J-couplings, in the ordered and isotropic phases is essentially identical, indicating that the general assumptions in the analyses of RDCs are well founded.
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Affiliation(s)
- Jon Kapla
- Department of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden.
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30
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Van der Heiden E, Delmarcelle M, Simon P, Counson M, Galleni M, Freedberg DI, Thompson J, Joris B, Battistel MD. Synthesis and Physicochemical Characterization of D-Tagatose-1-Phosphate: The Substrate of the Tagatose-1-Phosphate Kinase in the Phosphotransferase System-Mediated D-Tagatose Catabolic Pathway of Bacillus licheniformis. J Mol Microbiol Biotechnol 2015; 25:106-19. [PMID: 26159072 DOI: 10.1159/000370115] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We report the first enzymatic synthesis of D-tagatose-1-phosphate (Tag-1P) by the multicomponent phosphoenolpyruvate:sugar phosphotransferase system (PEP-PTS) present in tagatose-grown cells of Klebsiella pneumoniae. Physicochemical characterization by (31)P and (1)H nuclear magnetic resonance spectroscopy reveals that, in solution, this derivative is primarily in the pyranose form. Tag-1P was used to characterize the putative tagatose-1-phosphate kinase (TagK) of the Bacillus licheniformis PTS-mediated D-tagatose catabolic pathway (Bli-TagP). For this purpose, a soluble protein fusion was obtained with the 6 His-tagged trigger factor (TF(His6)) of Escherichia coli. The active fusion enzyme was named TagK-TF(His6). Tag-1P and D-fructose-1-phosphate are substrates for the TagK-TF(His6) enzyme, whereas the isomeric derivatives D-tagatose-6-phosphate and D-fructose-6-phosphate are inhibitors. Studies of catalytic efficiency (kcat/Km) reveal that the enzyme specificity is markedly in favor of Tag-1P as the substrate. Importantly, we show in vivo that the transfer of the phosphate moiety from PEP to the B. licheniformis tagatose-specific Enzyme II in E. coli is inefficient. The capability of the PTS general cytoplasmic components of B. subtilis, HPr and Enzyme I to restore the phosphate transfer is demonstrated.
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Affiliation(s)
- Edwige Van der Heiden
- Center for Protein Engineering, University of Liège, Institut de Chimie, Sart-Tilman, Belgium
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31
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Abstract
Recent NMR studies of the exchangeable protons of GAGs in aqueous solution, including those of the amide, sulfamate, and hydroxyl moieties, have demonstrated potential for the detection of intramolecular hydrogen bonds, providing insights into secondary structure preferences. GAG amide protons are observable by NMR over wide pH and temperature ranges; however, specific solution conditions are required to reduce the exchange rate of the sulfamate and hydroxyl protons and allow their detection by NMR. Building on the vast body of knowledge on detection of hydrogen bonds in peptides and proteins, a variety of methods can be used to identify hydrogen bonds in GAGs including temperature coefficient measurements, evaluation of chemical shift differences between oligo- and monosaccharides, and relative exchange rates measured through line shape analysis and EXSY spectra. Emerging strategies to allow direct detection of hydrogen bonds through heteronuclear couplings offer promise for the future. Molecular dynamic simulations are important in this effort both to predict and confirm hydrogen bond donors and acceptors.
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Affiliation(s)
- Consuelo N Beecher
- Department of Chemistry, University of California, Riverside, Riverside, CA, 92521, USA,
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Fontana C, Kovacs H, Widmalm G. NMR structure analysis of uniformly 13C-labeled carbohydrates. JOURNAL OF BIOMOLECULAR NMR 2014; 59:95-110. [PMID: 24771296 DOI: 10.1007/s10858-014-9830-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 04/16/2014] [Indexed: 05/26/2023]
Abstract
In this study, a set of nuclear magnetic resonance experiments, some of them commonly used in the study of (13)C-labeled proteins and/or nucleic acids, is applied for the structure determination of uniformly (13)C-enriched carbohydrates. Two model substances were employed: one compound of low molecular weight [(UL-(13)C)-sucrose, 342 Da] and one compound of medium molecular weight ((13)C-enriched O-antigenic polysaccharide isolated from Escherichia coli O142, ~10 kDa). The first step in this approach involves the assignment of the carbon resonances in each monosaccharide spin system using the anomeric carbon signal as the starting point. The (13)C resonances are traced using (13)C-(13)C correlations from homonuclear experiments, such as (H)CC-CT-COSY, (H)CC-NOESY, CC-CT-TOCSY and/or virtually decoupled (H)CC-TOCSY. Based on the assignment of the (13)C resonances, the (1)H chemical shifts are derived in a straightforward manner using one-bond (1)H-(13)C correlations from heteronuclear experiments (HC-CT-HSQC). In order to avoid the (1) J CC splitting of the (13)C resonances and to improve the resolution, either constant-time (CT) in the indirect dimension or virtual decoupling in the direct dimension were used. The monosaccharide sequence and linkage positions in oligosaccharides were determined using either (13)C or (1)H detected experiments, namely CC-CT-COSY, band-selective (H)CC-TOCSY, HC-CT-HSQC-NOESY or long-range HC-CT-HSQC. However, due to the short T2 relaxation time associated with larger polysaccharides, the sequential information in the O-antigen polysaccharide from E. coli O142 could only be elucidated using the (1)H-detected experiments. Exchanging protons of hydroxyl groups and N-acetyl amides in the (13)C-enriched polysaccharide were assigned by using HC-H2BC spectra. The assignment of the N-acetyl groups with (15)N at natural abundance was completed by using HN-SOFAST-HMQC, HNCA, HNCO and (13)C-detected (H)CACO spectra.
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Affiliation(s)
- Carolina Fontana
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, 106 91, Stockholm, Sweden
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Battistel MD, Azurmendi HF, Yu B, Freedberg DI. NMR of glycans: shedding new light on old problems. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2014; 79:48-68. [PMID: 24815364 DOI: 10.1016/j.pnmrs.2014.01.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Accepted: 01/10/2014] [Indexed: 06/03/2023]
Abstract
The diversity in molecular arrangements and dynamics displayed by glycans renders traditional NMR strategies, employed for proteins and nucleic acids, insufficient. Because of the unique properties of glycans, structural studies often require the adoption of a different repertoire of tailor-made experiments and protocols. We present an account of recent developments in NMR techniques that will deepen our understanding of structure-function relations in glycans. We open with a survey and comparison of methods utilized to determine the structure of proteins, nucleic acids and carbohydrates. Next, we discuss the structural information obtained from traditional NMR techniques like chemical shifts, NOEs/ROEs, and coupling-constants, along with the limitations imposed by the unique intrinsic characteristics of glycan structure on these approaches: flexibility, range of conformers, signal overlap, and non-first-order scalar (strong) coupling. Novel experiments taking advantage of isotopic labeling are presented as an option for overcoming spectral overlap and raising sensitivity. Computational tools used to explore conformational averaging in conjunction with NMR parameters are described. In addition, recent developments in hydroxyl detection and hydrogen bond detection in protonated solvents, in contrast to traditional sample preparations in D2O for carbohydrates, further increase the tools available for both structure information and chemical shift assignments. We also include previously unpublished data in this context. Accurate determination of couplings in carbohydrates has been historically challenging due to the common presence of strong-couplings. We present new strategies proposed for dealing with their influence on NMR signals. We close with a discussion of residual dipolar couplings (RDCs) and the advantages of using (13)C isotope labeling that allows gathering one-bond (13)C-(13)C couplings with a recently improved constant-time COSY technique, in addition to the commonly measured (1)H-(13)C RDCs.
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Affiliation(s)
- Marcos D Battistel
- Laboratory of Bacterial Polysaccharides, Center for Biologics Evaluation and Research, Food and Drug Administration, 1401 Rockville Pike, Rockville, MD 20852-1448, United States
| | - Hugo F Azurmendi
- Laboratory of Bacterial Polysaccharides, Center for Biologics Evaluation and Research, Food and Drug Administration, 1401 Rockville Pike, Rockville, MD 20852-1448, United States
| | - Bingwu Yu
- Laboratory of Bacterial Polysaccharides, Center for Biologics Evaluation and Research, Food and Drug Administration, 1401 Rockville Pike, Rockville, MD 20852-1448, United States
| | - Darón I Freedberg
- Laboratory of Bacterial Polysaccharides, Center for Biologics Evaluation and Research, Food and Drug Administration, 1401 Rockville Pike, Rockville, MD 20852-1448, United States.
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Shinar H, Battistel MD, Mandler M, Lichaa F, Freedberg DI, Navon G. Sialo-CEST: chemical exchange saturation transfer NMR of oligo- and poly-sialic acids and the assignment of their hydroxyl groups using selective- and HSQC-TOCSY. Carbohydr Res 2014; 389:165-73. [DOI: 10.1016/j.carres.2014.02.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Revised: 02/03/2014] [Accepted: 02/06/2014] [Indexed: 11/28/2022]
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Beecher CN, Young RP, Langeslay DJ, Mueller LJ, Larive CK. Hydroxyl-proton hydrogen bonding in the heparin oligosaccharide Arixtra in aqueous solution. J Phys Chem B 2014; 118:482-91. [PMID: 24354321 DOI: 10.1021/jp410540d] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Heparin is best known for its anticoagulant activity, which is mediated by the binding of a specific pentasaccharide sequence to the protease inhibitor antithrombin-III (AT-III). Although heparin oligosaccharides are thought to be flexible in aqueous solution, the recent discovery of a hydrogen bond between the sulfamate (NHSO3(-)) proton and the adjacent 3-O-sulfo group of the 3,6-O-sulfated N-sulfoglucosamine residue of the Arixtra (fondaparinux sodium) pentasaccharide demonstrates that definable elements of local structure are accessed. Molecular dynamics simulations of Arixtra suggest the presence of additional hydrogen bonds involving the C3-OH groups of the glucuronic acid and 2-O-sulfo-iduronic acid residues. NMR measurements of temperature coefficients, chemical shift differences, and solvent exchange rate constants provide experimental confirmation of these hydrogen bonds. We note that the extraction of rate constants from cross-peak buildup curves in 2D exchange spectroscopy is complicated by the presence of radiation damping in aqueous solution. A straightforward model is presented that explicitly takes into account the effects of radiation damping on the water proton relaxation and is sufficiently robust to provide an accurate measure of the proton exchange rate between the analyte hydroxyl protons and water.
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Affiliation(s)
- Consuelo N Beecher
- Department of Chemistry, University of California-Riverside , Riverside, California 92521, United States
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Zhang Y, Yamaguchi T, Kato K. New NMR Tools for Characterizing the Dynamic Conformations and Interactions of Oligosaccharides. CHEM LETT 2013. [DOI: 10.1246/cl.130789] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Ying Zhang
- Institute for Molecular Science and Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences
- Department of Functional Molecular Science, The Graduate University for Advanced Studies
- Graduate School of Pharmaceutical Sciences, Nagoya City University
| | - Takumi Yamaguchi
- Institute for Molecular Science and Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences
- Department of Functional Molecular Science, The Graduate University for Advanced Studies
- Graduate School of Pharmaceutical Sciences, Nagoya City University
| | - Koichi Kato
- Institute for Molecular Science and Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences
- Department of Functional Molecular Science, The Graduate University for Advanced Studies
- Graduate School of Pharmaceutical Sciences, Nagoya City University
- The Glycoscience Institute, Ochanomizu University
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