1
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Kwon J, Ruda A, Azurmendi HF, Zarb J, Battistel MD, Liao L, Asnani A, Auzanneau FI, Widmalm G, Freedberg DI. Glycan Stability and Flexibility: Thermodynamic and Kinetic Characterization of Nonconventional Hydrogen Bonding in Lewis Antigens. J Am Chem Soc 2023; 145:10022-10034. [PMID: 37099481 PMCID: PMC10176581 DOI: 10.1021/jacs.2c13104] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/27/2023]
Abstract
We provide evidence for CH-based nonconventional hydrogen bonds (H-bonds) for 10 Lewis antigens and two of their rhamnose analogues. We also characterize the thermodynamics and kinetics of the H-bonds in these molecules and present a plausible explanation for the presence of nonconventional H-bonds in Lewis antigens. Using an alternative method to simultaneously fit a series of temperature-dependent fast exchange nuclear magnetic resonance (NMR) spectra, we determined that the H-bonded conformation is favored by ∼1 kcal/mol over the non-H-bonded conformation. Additionally, a comparison of temperature-dependent 13C linewidths in various Lewis antigens and the two rhamnose analogues reveals H-bonds between the carbonyl oxygen of the N-acetyl group of N-acetylglucosamine and the OH2 group of galactose/fucose. The data presented herein provide insight into the contribution of nonconventional H-bonding to molecular structure and could therefore be used for the rational design of therapeutics.
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Affiliation(s)
- Jeahoo Kwon
- Division of Bacterial Products and Allergenic Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, Maryland 20993, United States
| | - Alessandro Ruda
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
| | - Hugo F Azurmendi
- Division of Bacterial Products and Allergenic Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, Maryland 20993, United States
| | - Jasmin Zarb
- Division of Bacterial Products and Allergenic Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, Maryland 20993, United States
| | - Marcos D Battistel
- Division of Bacterial Products and Allergenic Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, Maryland 20993, United States
| | - Liang Liao
- Department of Chemistry, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Ari Asnani
- Department of Chemistry, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | | | - Göran Widmalm
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
| | - Darón I Freedberg
- Division of Bacterial Products and Allergenic Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, Maryland 20993, United States
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2
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Hargett AA, Marcella AM, Yu H, Li C, Orwenyo J, Battistel MD, Wang LX, Freedberg DI. Glycosylation States on Intact Proteins Determined by NMR Spectroscopy. Molecules 2021; 26:molecules26144308. [PMID: 34299586 PMCID: PMC8303171 DOI: 10.3390/molecules26144308] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 07/05/2021] [Accepted: 07/06/2021] [Indexed: 12/23/2022] Open
Abstract
Protein glycosylation is important in many organisms for proper protein folding, signaling, cell adhesion, protein-protein interactions, and immune responses. Thus, effectively determining the extent of glycosylation in glycoprotein therapeutics is crucial. Up to now, characterizing protein glycosylation has been carried out mostly by liquid chromatography mass spectrometry (LC-MS), which requires careful sample processing, e.g., glycan removal or protein digestion and glycopeptide enrichment. Herein, we introduce an NMR-based method to better characterize intact glycoproteins in natural abundance. This non-destructive method relies on exploiting differences in nuclear relaxation to suppress the NMR signals of the protein while maintaining glycan signals. Using RNase B Man5 and RNase B Man9, we establish reference spectra that can be used to determine the different glycoforms present in heterogeneously glycosylated commercial RNase B.
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Affiliation(s)
- Audra A. Hargett
- Center for Biologics Evaluation and Review, Laboratory of Bacterial Polysaccharides, Food and Drug Administration (FDA), Silver Spring, MD 20993, USA; (A.A.H.); (A.M.M.); (H.Y.); (M.D.B.)
| | - Aaron M. Marcella
- Center for Biologics Evaluation and Review, Laboratory of Bacterial Polysaccharides, Food and Drug Administration (FDA), Silver Spring, MD 20993, USA; (A.A.H.); (A.M.M.); (H.Y.); (M.D.B.)
| | - Huifeng Yu
- Center for Biologics Evaluation and Review, Laboratory of Bacterial Polysaccharides, Food and Drug Administration (FDA), Silver Spring, MD 20993, USA; (A.A.H.); (A.M.M.); (H.Y.); (M.D.B.)
| | - Chao Li
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA; (C.L.); (J.O.); (L.-X.W.)
| | - Jared Orwenyo
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA; (C.L.); (J.O.); (L.-X.W.)
| | - Marcos D. Battistel
- Center for Biologics Evaluation and Review, Laboratory of Bacterial Polysaccharides, Food and Drug Administration (FDA), Silver Spring, MD 20993, USA; (A.A.H.); (A.M.M.); (H.Y.); (M.D.B.)
| | - Lai-Xi Wang
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA; (C.L.); (J.O.); (L.-X.W.)
| | - Darón I. Freedberg
- Center for Biologics Evaluation and Review, Laboratory of Bacterial Polysaccharides, Food and Drug Administration (FDA), Silver Spring, MD 20993, USA; (A.A.H.); (A.M.M.); (H.Y.); (M.D.B.)
- Correspondence:
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3
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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5
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Battistel MD, Freedberg DI. Dispersing the crowd: Adopting 13C direct detection for glycans. J Magn Reson 2020; 318:106792. [PMID: 32759046 DOI: 10.1016/j.jmr.2020.106792] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 07/08/2020] [Accepted: 07/12/2020] [Indexed: 06/11/2023]
Abstract
As a direct consequence of technological advancements, the interest in direct detection of low-gamma/low-sensitivity heteronuclei for NMR experiments has been revived. Until recently, experimental development of 13C/15N detected experiments has been focused on protein NMR. In the present report, we extend the use of 13C-detected experiments to structural studies of glycans in natural abundance. The narrow 1H and wider 13C signal dispersion make glycans ideal candidates for heteronuclear detection. We show that 13C-detected HSQC offers a ten-fold increase in 13C dimension resolution compared to the analogous 1H-detected HSQC, when the experiments are acquired for the same amount of time. The enhanced resolution comes at the expense of 2 to 3-fold loss in SNR; however, the observed signal loss is a fraction of the theoretical 8-fold difference expected between experiments. Further, we show that by combining a 1H constant time element (CT), SMILE data reconstruction and 13C-direct detection, complete resonance assignments of highly degenerate glycan signals are possible. Finally, we demonstrate the potential of our strategy to aid in the assignment of complex glycans, by using a novel 13C-detected version of the CT-HSQC-TOCSY experiment performed on sialyl Lewis X pentasaccharide model system.
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Affiliation(s)
- Marcos D Battistel
- Laboratory of Bacterial Polysaccharides, Food and Drug Administration (FDA), Silver Spring, MD 20993, United States
| | - Darón I Freedberg
- Laboratory of Bacterial Polysaccharides, Food and Drug Administration (FDA), Silver Spring, MD 20993, United States.
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6
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Fricke SN, Seymour JD, Battistel MD, Freedberg DI, Eads CD, Augustine MP. Data processing in NMR relaxometry using the matrix pencil. J Magn Reson 2020; 313:106704. [PMID: 32179433 DOI: 10.1016/j.jmr.2020.106704] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 02/12/2020] [Accepted: 02/28/2020] [Indexed: 06/10/2023]
Abstract
The matrix pencil method (MPM) is explored for stable, reproducible data processing in nuclear magnetic resonance (NMR) relaxometry. Data from one-dimensional and two-dimensional relaxometry experiments designed to measure transverse relaxation T2, longitudinal relaxation T1, diffusion coefficient D values, and their correlations in a standard olive oil/water mixture serve as a platform available to any NMR spectroscopist to compare the performance of the MPM to the benchmark inverse Laplace transform (ILT). The data from two practical examples, including the drying of a solvent polymer system and the enzymatic digestion of polysialic acid, were also explored with the MPM and ILT. In the cases considered here, the MPM appears to outperform the ILT in terms of resolution and stability in the determination of fundamental constants for complex materials and mixtures.
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Affiliation(s)
- S N Fricke
- Department of Chemistry, 69 Chemistry Building, University of California, Davis, CA 95616, USA
| | - J D Seymour
- Department of Chemical and Biological Engineering, 306 Cobleigh Hall, Montana State University, Bozeman, MT 59717, USA
| | - M D Battistel
- Laboratory of Bacterial Polysaccharides, Center for Biologics Evaluation and Research, United States Food and Drug Administration, 10903 New Hampshire Ave., Silver Spring, MD 20993, USA
| | - D I Freedberg
- Laboratory of Bacterial Polysaccharides, Center for Biologics Evaluation and Research, United States Food and Drug Administration, 10903 New Hampshire Ave., Silver Spring, MD 20993, USA
| | - C D Eads
- The Procter & Gamble Company, 8700 S. Mason-Montgomery Road, Mason, OH 45040, USA
| | - M P Augustine
- Department of Chemistry, 69 Chemistry Building, University of California, Davis, CA 95616, USA.
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7
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Yu H, An Y, Battistel MD, Cipollo JF, Freedberg DI. Improving Analytical Characterization of Glycoconjugate Vaccines through Combined High-Resolution MS and NMR: Application to Neisseria meningitidis Serogroup B Oligosaccharide-Peptide Glycoconjugates. Anal Chem 2018; 90:5040-5047. [DOI: 10.1021/acs.analchem.7b04748] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Huifeng Yu
- Laboratory of Bacterial Polysaccharides, Center for Biologics Evaluation and Research, Food and Drug Administration (FDA), Silver Spring, Maryland 20993, United States
| | - Yanming An
- Laboratory of Bacterial Polysaccharides, Center for Biologics Evaluation and Research, Food and Drug Administration (FDA), Silver Spring, Maryland 20993, United States
| | - Marcos D. Battistel
- Laboratory of Bacterial Polysaccharides, Center for Biologics Evaluation and Research, Food and Drug Administration (FDA), Silver Spring, Maryland 20993, United States
| | - John F. Cipollo
- Laboratory of Bacterial Polysaccharides, Center for Biologics Evaluation and Research, Food and Drug Administration (FDA), Silver Spring, Maryland 20993, United States
| | - Darón I. Freedberg
- Laboratory of Bacterial Polysaccharides, Center for Biologics Evaluation and Research, Food and Drug Administration (FDA), Silver Spring, Maryland 20993, United States
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8
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Azurmendi HF, Battistel MD, Zarb J, Lichaa F, Negrete Virgen A, Shiloach J, Freedberg DI. The β-reducing end in α(2-8)-polysialic acid constitutes a unique structural motif. Glycobiology 2017; 27:900-911. [PMID: 28369425 PMCID: PMC6283323 DOI: 10.1093/glycob/cwx025] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 03/10/2017] [Accepted: 03/14/2017] [Indexed: 12/13/2022] Open
Abstract
Over the years, structural characterizations of α(2-8)-polysialic acid (polySia) in solution have produced inconclusive results. Efforts for obtaining detailed information in this important antigen have focused primarily on the α-linked residues and not on the distinctive characteristics of the terminal ones. The thermodynamically preferred anomeric configuration for the reducing end of sialic acids is β, which has the [I]CO2- group equatorial and the OH ([I]OH2) axial, while for all other residues the CO2- group is axial. We show that this purportedly minor difference has distinct consequences for the structure of α(2-8)-polySia near the reducing end, as the β configuration places the [I]OH2 in a favorable position for the formation of a hydrogen bond with the carboxylate group of the following residue ([II]CO2-). Molecular dynamics (MD) simulations predicted the hydrogen bond, which we subsequently directly detected by NMR. The combination of MD and residual dipolar couplings shows that the net result for the structure of Sia2-βOH is a stable conformation with well-defined hydration and charge patterns, and consistent with experimental NOE-based hydroxyl and aliphatic inter-proton distances. Moreover, we provide evidence that this distinct conformation is preserved on Sia oligosaccharides, thus constituting a motif that determines the structure and dynamics of α(2-8)-polySia for at least the first two residues of the polymer. We suggest the hypothesis that this structural motif sheds light on a longtime puzzling observation for the requirement of 10 residues of α(2-8)-polySia in order to bind effectively to specific antibodies, about four units more than for analogous cases.
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Affiliation(s)
- Hugo F Azurmendi
- Laboratory of Bacterial Polysaccharides, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20903, USA
| | - Marcos D Battistel
- Laboratory of Bacterial Polysaccharides, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20903, USA
| | - Jasmin Zarb
- Laboratory of Bacterial Polysaccharides, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20903, USA
| | - Flora Lichaa
- Laboratory of Bacterial Polysaccharides, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20903, USA
| | - Alejandro Negrete Virgen
- Laboratory of Bacterial Polysaccharides, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20903, USA
| | - Joseph Shiloach
- Biotechnology Unit, MSC 5522, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Darón I Freedberg
- Laboratory of Bacterial Polysaccharides, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20903, USA
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9
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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10
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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11
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Battistel MD, Azurmendi HF, Yu B, Freedberg DI. NMR of glycans: shedding new light on old problems. Prog Nucl Magn Reson Spectrosc 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] [What about the content of this article? (0)] [Affiliation(s)] [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] [What about the content of this article? (0)] [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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Battistel MD, Pendrill R, Widmalm G, Freedberg DI. Direct Evidence for Hydrogen Bonding in Glycans: A Combined NMR and Molecular Dynamics Study. J Phys Chem B 2013; 117:4860-9. [DOI: 10.1021/jp400402b] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Marcos D. Battistel
- Laboratory of Bacterial Polysaccharides, Center for Biologics Evaluation and Research, Food and Drug Administration, 1401 Rockville Pike, Rockville, Maryland 20852-1448, United States
| | - Robert Pendrill
- Department of Organic Chemistry,
Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
| | - Göran Widmalm
- Department of Organic Chemistry,
Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
| | - Darón I. Freedberg
- Laboratory of Bacterial Polysaccharides, Center for Biologics Evaluation and Research, Food and Drug Administration, 1401 Rockville Pike, Rockville, Maryland 20852-1448, United States
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Battistel MD, Shangold M, Trinh L, Shiloach J, Freedberg DI. Evidence for helical structure in a tetramer of α2-8 sialic acid: unveiling a structural antigen. J Am Chem Soc 2012; 134:10717-20. [PMID: 22703338 DOI: 10.1021/ja300624j] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Characteristic H-bonding patterns define secondary structure in proteins and nucleic acids. We show that similar patterns apply for α2-8 sialic acid (SiA) in H(2)O and that H-bonds define its structure. A (15)N,(13)C α2-8 SiA tetramer, (SiA)(4), was used as a model system for the polymer. At 263 K, we detected intra-residue through-H-bond J couplings between (15)N and C8 for residues R-I-R-III of the tetramer, indicating H-bonds between the (15)N's and the O8's of these residues. Additional J couplings between the (15)N's and C2's of the adjacent residues confirm the putative H-bonds. NH groups showing this long-range correlation also experience slower (1)H/(2)H exchange. Additionally, detection of couplings between H7 and C2 for R-II and R-III implies that the conformations of the linkers between these residues are different than in the monomers. These structural elements are consistent with two left-handed helical models: 2 residues/turn (2(4) helix) and 4 residues/turn (1(4) helix). To discriminate between models, we resorted to (1)H,(1)H NOEs. The 2(4) helical model is in better agreement with the experimental data. We provide direct evidence of H-bonding for (SiA)(4) and show how H-bonds can be a determining factor for shaping its 3D structure.
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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, Maryland 20852-1448, USA
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Barb AW, Freedberg DI, Battistel MD, Prestegard JH. NMR detection and characterization of sialylated glycoproteins and cell surface polysaccharides. J Biomol NMR 2011; 51:163-71. [PMID: 21947924 PMCID: PMC3199143 DOI: 10.1007/s10858-011-9550-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Accepted: 06/25/2011] [Indexed: 05/03/2023]
Abstract
Few solution NMR pulse sequences exist that are explicitly designed to characterize carbohydrates (glycans). This is despite the essential role carbohydrate motifs play in cell-cell communication, microbial pathogenesis, autoimmune disease progression and cancer metastasis, and despite that fact that glycans, often shed to extra-cellular fluids, can be diagnostic of disease. Here we present a suite of two dimensional coherence experiments to measure three different correlations (H3-C2, H3-C1, and C1-C2) on sialic acids, a group of nine-carbon carbohydrates found on eukaryotic cell surfaces that often play a key role in disease processes. The chemical shifts of the H3, C2, and C1 nuclei of sialic acids are sensitive to carbohydrate linkage, linkage conformation, and ionization state of the C1 carboxylate. The experiments reported include rigorous filter elements to enable detection and characterization of isotopically labeled sialic acids with high sensitivity in living cells and crude isolates with minimal interference from unwanted signals arising from the ~1% (13)C-natural abundance of cellular metabolites. Application is illustrated with detection of sialic acids on living cells, in unpurified mixtures, and at the terminus of the N-glycan on the 55 kDa immunoglobulin G Fc.
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Affiliation(s)
- Adam W. Barb
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA, 30602
| | - Darón I. Freedberg
- Laboratory of Bacterial Polysaccharides, Building 29, Room 115 Center for Biologics Evaluation and Research, Food and Drug Administration, 1401 Rockville Pike, HFM-419, Rockville, MD 20852
| | - Marcos D. Battistel
- Laboratory of Bacterial Polysaccharides, Building 29, Room 115 Center for Biologics Evaluation and Research, Food and Drug Administration, 1401 Rockville Pike, HFM-419, Rockville, MD 20852
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Battistel MD, Grishaev A, An SSA, Castellino FJ, Llinás M. Solution structure and functional characterization of human plasminogen kringle 5. Biochemistry 2009; 48:10208-19. [PMID: 19821587 DOI: 10.1021/bi901433n] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The ligand binding properties of the kringle 5 (K5) domain of human plasminogen have been investigated via intrinsic tryptophan fluorescence. The oleic acid (OA) affinity for K5 was quantified, yielding an association constant K(a) approximately 2.08 x 10(4) mM(-1). Simultaneously, it was determined that OA and trans-4-(aminomethyl)cyclohexanecarboxylic acid (AMCHA) (K(a) approximately 50 mM(-1)) compete for binding to K5. The solution structure of K5 in the presence of 11 mM AMCHA was solved via NMR spectroscopy (protein heavy atom RMSD approximately 0.93 +/- 0.12 A). The AMCHA binding site was localized via (1)H/(15)N chemical shift perturbation mapping assisted by in silico docking. We have found that AMCHA binds at the canonical kringle lysine binding site (LBS), structured by the Pro54-Gly60 segment plus the neighboring Phe36, Thr37, Trp62, Leu71, and Tyr72 residues. The segment 30-42, encompassing LBS residues, appears to be endowed with a higher degree of structural flexibility as suggested by the relatively lower value of S(2), the generalized order parameter, consistent with a higher backbone heavy atom RMSD of approximately 1.22 A (vs 0.84 A overall) between the two monomeric units in the crystal unit cell, of potential significance for ligand binding. OA was found to perturb the same area of the protein, namely, the LBS, as well as Tyr74. Combined with previous studies, the observation of OA binding expands the range of ligands that interact with kringle 5 while it widens the scope of potential biological functions for kringle domains.
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Affiliation(s)
- Marcos D Battistel
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, USA
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