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Tichotová MC, Tučková L, Kocek H, Růžička A, Straka M, Procházková E. Exploring the impact of alignment media on RDC analysis of phosphorus-containing compounds: a molecular docking approach. Phys Chem Chem Phys 2024; 26:2016-2024. [PMID: 38126374 DOI: 10.1039/d3cp04099b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
Residual dipolar couplings (RDCs) are employed in NMR analysis when conventional methods, such as J-couplings and nuclear Overhauser effects (NOEs) fail. Low-energy (optimized) conformers are often used as input structures in RDC analysis programs. However, these low-energy structures do not necessarily resemble conformations found in anisotropic environments due to interactions with the alignment medium, especially if the analyte molecules are flexible. Considering interactions with alignment media in RDC analysis, we developed and evaluated a molecular docking-based approach to generate more accurate conformer ensembles for compounds in the presence of the poly-γ-benzyl-L-glutamate alignment medium. We designed chiral phosphorus-containing compounds that enabled us to utilize 31P NMR parameters for the stereochemical analysis. Using P3D/PALES software to evaluate diastereomer discrimination, we found that our conformer ensembles outperform moderately the standard, low-energy conformers in RDC analysis. To further improve our results, we (i) averaged the experimental values of the molecular docking-based conformers by applying the Boltzmann distribution and (ii) optimized the structures through normal mode relaxation, thereby enhancing the Pearson correlation factor R and even diastereomer discrimination in some cases. Nevertheless, we presume that significant differences between J-couplings in isotropic and in anisotropic environments may preclude RDC measurements for flexible molecules. Therefore, generating conformer ensembles based on molecular docking enhances RDC analysis for mildly flexible systems while flexible molecules may require applying more advanced approaches, in particular approaches including dynamical effects.
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Affiliation(s)
- Markéta Christou Tichotová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 160 00 Prague, Czech Republic.
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, 116 28 Prague, Czech Republic
| | - Lucie Tučková
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 160 00 Prague, Czech Republic.
| | - Hugo Kocek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 160 00 Prague, Czech Republic.
| | - Aleš Růžička
- Department of General and Inorganic Chemistry, Faculty of Chemical Technology, University of Pardubice, Pardubice 532 10, Czech Republic
| | - Michal Straka
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 160 00 Prague, Czech Republic.
| | - Eliška Procházková
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 160 00 Prague, Czech Republic.
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2
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Venturi L, Bua E, Caputo G, Mileo V. Residual Dipolar Coupling Based Conformational Analysis Allows the Configurational Assessment of Steroids with up to Eight Stereocenters. Chempluschem 2023; 88:e202200391. [PMID: 36811319 DOI: 10.1002/cplu.202200391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 02/20/2023] [Accepted: 02/21/2023] [Indexed: 02/24/2023]
Abstract
Residual dipolar couplings (RDCs) induced by anisotropic media have been proved as a powerful tool for the structure elucidation of organic molecules in solution in nuclear magnetic resonance (NMR) based analysis. The value of dipolar couplings to solve complex conformational and configurational problems represents indeed an appealing analytical tool for the pharmaceutical industry particularly focusing on the stereochemistry characterization of NCEs since the early phase of the drug development process. In our work, RDCs were used for the conformational and configurational study of synthetic steroids with multiple stereocenters - prednisone and beclomethasone dipropionate (BDP) -. For both molecules the correct relative configuration was identified among all the possible diastereoisomers (32 and 128 respectively) arising from the compounds stereogenic carbons. Only for prednisone the use of additional experimental data (i. e. rOes) was necessary to resolve the right stereochemical structure.
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Affiliation(s)
- Luca Venturi
- Preclinical Analytics and Early Formulations Department, Chiesi Farmaceutici Spa, Largo Belloli 11/A, 43123, Parma, PR, Italy
| | - Emanuela Bua
- Food and Drug Department, University of Parma, Parco Area delle Scienze 27/A, 43124, Parma, PR, Italy
| | - Giulia Caputo
- Pharmacy Department, University "G. d'Annunzio" of Chieti-Pescara, Via dei Vestini, 66100, Chieti, CH, Italy
| | - Valentina Mileo
- Preclinical Analytics and Early Formulations Department, Chiesi Farmaceutici Spa, Largo Belloli 11/A, 43123, Parma, PR, Italy
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3
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Poveda A, Fittolani G, Seeberger PH, Delbianco M, Jiménez-Barbero J. The Flexibility of Oligosaccharides Unveiled Through Residual Dipolar Coupling Analysis. Front Mol Biosci 2021; 8:784318. [PMID: 34859057 PMCID: PMC8631391 DOI: 10.3389/fmolb.2021.784318] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 10/14/2021] [Indexed: 11/13/2022] Open
Abstract
The intrinsic flexibility of glycans complicates the study of their structures and dynamics, which are often important for their biological function. NMR has provided insights into the conformational, dynamic and recognition features of glycans, but suffers from severe chemical shift degeneracy. We employed labelled glycans to explore the conformational behaviour of a β(1-6)-Glc hexasaccharide model through residual dipolar couplings (RDCs). RDC delivered information on the relative orientation of specific residues along the glycan chain and provided experimental clues for the existence of certain geometries. The use of two different aligning media demonstrated the adaptability of flexible oligosaccharide structures to different environments.
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Affiliation(s)
- Ana Poveda
- CICbioGUNE, Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Giulio Fittolani
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces, Potsdam, Germany.,Department of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Peter H Seeberger
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces, Potsdam, Germany.,Department of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Martina Delbianco
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces, Potsdam, Germany
| | - Jesús Jiménez-Barbero
- CICbioGUNE, Basque Research and Technology Alliance (BRTA), Derio, Spain.,Ikerbasque, Basque Foundation for Science, Bilbao, Spain.,Department of Organic Chemistry II, Faculty of Science and Technology, University of the Basque Country, EHU-UPV, Leioa, Spain.,Centro de Investigacion Biomedica En Red de Enfermedades Respiratorias, Madrid, Spain
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4
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Ibáñez de Opakua A, Zweckstetter M. Extending the applicability of P3D for structure determination of small molecules. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2021; 2:105-116. [PMID: 37904779 PMCID: PMC10539764 DOI: 10.5194/mr-2-105-2021] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 03/15/2021] [Indexed: 11/01/2023]
Abstract
The application of anisotropic nuclear magnetic resonance (NMR) parameters for the correct structural assignment of small molecules requires the use of partially ordered media. Previously we demonstrated that the use of P3D simulations using poly(γ -benzyl-L-glutamate) (PBLG) as an alignment medium allows for the determination of the correct diastereomer from extremely sparse NMR data. Through the analysis of the structural characteristics of small molecules in different alignment media, here we show that when steric or electrostatic factors dominate the alignment, P3D-PBLG retains its diastereomer discrimination power. We also demonstrate that P3D simulations can define the different conformations of a flexible small molecule from sparse NMR data.
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Affiliation(s)
- Alain Ibáñez de Opakua
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold-Str. 3a, 37075 Göttingen, Germany
| | - Markus Zweckstetter
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold-Str. 3a, 37075 Göttingen, Germany
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, 37077 Göttingen, Germany
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5
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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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6
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Pitoux D, Hu Z, Plainchont B, Merlet D, Farjon J, Bonnaffé D, Giraud N. Combining pure shift and J-edited spectroscopies: A strategy for extracting chemical shifts and scalar couplings from highly crowded proton spectra of oligomeric saccharides. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2018; 56:954-962. [PMID: 29396911 DOI: 10.1002/mrc.4715] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 01/12/2018] [Accepted: 01/16/2018] [Indexed: 06/07/2023]
Abstract
We report the application of pure shift and J-edited nuclear magnetic resonance spectroscopies to the structural analysis of a protected maltotrioside synthetic intermediate whose crowded 1 H spectrum displays highly crowded regions. The analytical strategy is based on the implementation of J-edited and TOCSY experiments whose resolution is optimized by the use of broadband homonuclear decoupling and selective refocusing techniques, to assign and measure chemical shifts and homonuclear scalar couplings with high accuracy. The resulting data show a high level of complementarity, providing a detailed insight into each subunit of this oligomeric saccharide, even for proton sites whose nuclear magnetic resonance signals strongly overlap. This approach allowed for fully assigning proton chemical shifts and extracting 80% of the 3 JHH couplings that are in excellent agreement with those expected for D-gluco-pyranosyl units in 4 C1 conformations.
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Affiliation(s)
- D Pitoux
- Equipe de RMN en milieu orienté, ICMMO, UMR 8182 (CNRS-UPS), Université Paris-Sud, Université Paris-Saclay, 91405, Orsay Cedex, France
| | - Z Hu
- Equipe Méthodologies, Synthèses et Molécules Thérapeutiques, ICMMO, UMR 8182 (CNRS-UPS), Université Paris-Sud, Université Paris-Saclay, 91405, Orsay Cedex, France
| | - B Plainchont
- Equipe de RMN en milieu orienté, ICMMO, UMR 8182 (CNRS-UPS), Université Paris-Sud, Université Paris-Saclay, 91405, Orsay Cedex, France
| | - D Merlet
- Equipe de RMN en milieu orienté, ICMMO, UMR 8182 (CNRS-UPS), Université Paris-Sud, Université Paris-Saclay, 91405, Orsay Cedex, France
| | - J Farjon
- Equipe de RMN en milieu orienté, ICMMO, UMR 8182 (CNRS-UPS), Université Paris-Sud, Université Paris-Saclay, 91405, Orsay Cedex, France
| | - D Bonnaffé
- Equipe Méthodologies, Synthèses et Molécules Thérapeutiques, ICMMO, UMR 8182 (CNRS-UPS), Université Paris-Sud, Université Paris-Saclay, 91405, Orsay Cedex, France
| | - N Giraud
- Equipe de RMN en milieu orienté, ICMMO, UMR 8182 (CNRS-UPS), Université Paris-Sud, Université Paris-Saclay, 91405, Orsay Cedex, France
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7
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Li GW, Liu H, Qiu F, Wang XJ, Lei XX. Residual Dipolar Couplings in Structure Determination of Natural Products. NATURAL PRODUCTS AND BIOPROSPECTING 2018; 8:279-295. [PMID: 29943349 PMCID: PMC6102172 DOI: 10.1007/s13659-018-0174-x] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 06/14/2018] [Indexed: 05/16/2023]
Abstract
The determination of natural products stereochemistry remains a formidable task. Residual dipolar couplings (RDCs) induced by anisotropic media are a powerful tool for determination of the stereochemistry of organic molecule in solution. This review will provide a short introduction on RDCs-based methodology for the structural elucidation of natural products. Special attention is given to the current availability of alignment media in organic solvents. The applications of RDCs for structural analysis of some examples of natural products were discussed and summarized. This review provides a short introduction on RDCs-based methodology for the structural elucidation of natural products. Special attention is given to the current availability of alignment media in organic solvents. The applications of RDCs for structural analysis of some examples of natural products were discussed and summarized.
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Affiliation(s)
- Gao-Wei Li
- College of Chemistry and Chemical Engineering, Shangqiu Normal University, Shangqiu, 476000, People's Republic of China
| | - Han Liu
- School of Pharmaceutical Sciences, South Central University for Nationalities, Wuhan, 430074, People's Republic of China
| | - Feng Qiu
- School of Pharmaceutical Sciences, South Central University for Nationalities, Wuhan, 430074, People's Republic of China
| | - Xiao-Juan Wang
- College of Chemistry and Chemical Engineering, Shangqiu Normal University, Shangqiu, 476000, People's Republic of China
| | - Xin-Xiang Lei
- School of Pharmaceutical Sciences, South Central University for Nationalities, Wuhan, 430074, People's Republic of China.
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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] [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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Reller M, Wesp S, Koos MRM, Reggelin M, Luy B. Biphasic Liquid Crystal and the Simultaneous Measurement of Isotropic and Anisotropic Parameters by Spatially Resolved NMR Spectroscopy. Chemistry 2017. [DOI: 10.1002/chem.201702126] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Malin Reller
- Institut für Organische Chemie and Institut für Biologische Grenzflächen 4 - Magnetische Resonanz; Karlsruher Institut für Technologie (KIT); Fritz-Haber-Weg 6 76131 Karlsruhe Germany
| | - Svenja Wesp
- Organische Chemie; Technische Universität Darmstadt; Alarich-Weiss Str. 4 64287 Darmstadt Germany
| | - Martin R. M. Koos
- Institut für Organische Chemie and Institut für Biologische Grenzflächen 4 - Magnetische Resonanz; Karlsruher Institut für Technologie (KIT); Fritz-Haber-Weg 6 76131 Karlsruhe Germany
| | - Michael Reggelin
- Organische Chemie; Technische Universität Darmstadt; Alarich-Weiss Str. 4 64287 Darmstadt Germany
| | - Burkhard Luy
- Institut für Organische Chemie and Institut für Biologische Grenzflächen 4 - Magnetische Resonanz; Karlsruher Institut für Technologie (KIT); Fritz-Haber-Weg 6 76131 Karlsruhe Germany
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10
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Bose-Basu B, Zhang W, Kennedy JLW, Hadad MJ, Carmichael I, Serianni AS. 13C-Labeled Idohexopyranosyl Rings: Effects of Methyl Glycosidation and C6 Oxidation on Ring Conformational Equilibria. J Org Chem 2017; 82:1356-1370. [DOI: 10.1021/acs.joc.6b02399] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Bidisha Bose-Basu
- Department
of Chemistry and Physics, Fayetteville State University, Fayetteville, North Carolina 28301, United States
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11
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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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12
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Kato K, Yamaguchi T. Paramagnetic NMR probes for characterization of the dynamic conformations and interactions of oligosaccharides. Glycoconj J 2015; 32:505-13. [PMID: 26050258 DOI: 10.1007/s10719-015-9599-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 05/19/2015] [Accepted: 05/25/2015] [Indexed: 12/21/2022]
Abstract
Paramagnetism-assisted nuclear magnetic resonance (NMR) techniques have recently been applied to a wide variety of biomolecular systems, using sophisticated immobilization methods to attach paramagnetic probes, such as spin labels and lanthanide-chelating groups, at specific sites of the target biomolecules. This is also true in the field of carbohydrate NMR spectroscopy. NMR analysis of oligosaccharides is often precluded by peak overlap resulting from the lack of variability of local chemical structures, by the insufficiency of conformational restraints from nuclear Overhauser effect (NOE) data due to low proton density, and moreover, by the inherently flexible nature of carbohydrate chains. Paramagnetic probes attached to the reducing ends of oligosaccharides cause paramagnetic relaxation enhancements (PREs) and/or pseudocontact shifts (PCSs) resolve the peak overlap problem. These spectral perturbations can be sources of long-range atomic distance information, which complements the local conformational information derived from J couplings and NOEs. Furthermore, paramagnetic NMR approaches, in conjunction with computational methods, have opened up possibilities for the description of dynamic conformational ensembles of oligosaccharides in solution. Several applications of paramagnetic NMR techniques are presented to demonstrate their utility for characterizing the conformational dynamics of oligosaccharides and for probing the carbohydrate-recognition modes of proteins. These techniques can be applied to the characterization of transient, non-stoichiometric interactions and will contribute to the visualization of dynamic biomolecular processes involving sugar chains.
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Affiliation(s)
- Koichi Kato
- Institute for Molecular Science and Okazaki Institute for Integrative Bioscience, 5-1 Higashiyama, Myodaiji, Okazaki, 444-8787, Japan.
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tababe-dori, Mizuho-ku, Nagoya, 467-8603, Japan.
- The Glycoscience Institute, Ochanomizu University, 2-1-1 Ohtsuka, Bunkyo-ku, Tokyo, 112-8610, Japan.
| | - Takumi Yamaguchi
- Institute for Molecular Science and Okazaki Institute for Integrative Bioscience, 5-1 Higashiyama, Myodaiji, Okazaki, 444-8787, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tababe-dori, Mizuho-ku, Nagoya, 467-8603, Japan
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13
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Yan S, Yao L. DFT application in conformational determination of cellobiose. Carbohydr Res 2015; 404:117-23. [DOI: 10.1016/j.carres.2014.12.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 12/08/2014] [Accepted: 12/16/2014] [Indexed: 11/26/2022]
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14
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Camilloni C, Vendruscolo M. A tensor-free method for the structural and dynamical refinement of proteins using residual dipolar couplings. J Phys Chem B 2014; 119:653-61. [PMID: 24824082 DOI: 10.1021/jp5021824] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Residual dipolar couplings (RDCs) are parameters measured in nuclear magnetic resonance spectroscopy that can provide exquisitely detailed information about the structure and dynamics of biological macromolecules. We describe here a method of using RDCs for the structural and dynamical refinement of proteins that is based on the observation that the RDC between two atomic nuclei depends directly on the angle ϑ between the internuclear vector and the external magnetic field. For every pair of nuclei for which an RDC is available experimentally, we introduce a structural restraint to minimize the deviation from the value of the angle ϑ derived from the measured RDC and that calculated in the refinement protocol. As each restraint involves only the calculation of the angle ϑ of the corresponding internuclear vector, the method does not require the definition of an overall alignment tensor to describe the preferred orientation of the protein with respect to the alignment medium. Application to the case of ubiquitin demonstrates that this method enables an accurate refinement of the structure and dynamics of this protein to be obtained.
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Affiliation(s)
- Carlo Camilloni
- Department of Chemistry, University of Cambridge , Cambridge CB2 1EW, U.K
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15
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Bell NGA, Rigg G, Masters S, Bella J, Uhrín D. Detecting low-level flexibility using residual dipolar couplings: a study of the conformation of cellobiose. Phys Chem Chem Phys 2014; 15:18223-34. [PMID: 24064673 DOI: 10.1039/c3cp52987h] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have developed novel NMR methods for the measurement of heteronuclear residual dipolar couplings (RDCs) in molecules with severely overlapping NMR resonances. These and other methods enabled us to obtain 31 RDCs for α-D-cellobiose and 24 RDCs for β-D-cellobiose. The interpretation of the data in the approximation of a rigid disaccharide structure, using RDCs and interglycosidic (3)J coupling constants, yielded conformation that is very close to that determined using X-ray crystallography. However, depending on which ring was used to calculate the order parameters, the dihedral angle ψH varied up to 30° or 40°, while the φH angle was always the same. This indicates residual flexibility of the glycosidic linkage between the two monosaccharide rings and was observed for both α- and β-D-cellobiose. The RDC analysis using rigid fragments rather than a complete molecule has thus shown that the glycosidic bond of cellobiose is not completely rigid and exhibits low-level flexibility. The sources of this flexibility are discussed and evidence presented to support a hypothesis that it is associated with the ψ more than the φ angle.
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Affiliation(s)
- Nicholle G A Bell
- EastChem School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh, EH9 3JJ, UK.
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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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Schmidt C, Irausquin SJ, Valafar H. Advances in the REDCAT software package. BMC Bioinformatics 2013; 14:302. [PMID: 24098943 PMCID: PMC3840585 DOI: 10.1186/1471-2105-14-302] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Accepted: 09/13/2013] [Indexed: 12/24/2022] Open
Abstract
Background Residual Dipolar Couplings (RDCs) have emerged in the past two decades as an informative source of experimental restraints for the study of structure and dynamics of biological macromolecules and complexes. The REDCAT software package was previously introduced for the analysis of molecular structures using RDC data. Here we report additional features that have been included in this software package in order to expand the scope of its analyses. We first discuss the features that enhance REDCATs user-friendly nature, such as the integration of a number of analyses into one single operation and enabling convenient examination of a structural ensemble in order to identify the most suitable structure. We then describe the new features which expand the scope of RDC analyses, performing exercises that utilize both synthetic and experimental data to illustrate and evaluate different features with regard to structure refinement and structure validation. Results We establish the seamless interaction that takes place between REDCAT, VMD, and Xplor-NIH in demonstrations that utilize our newly developed REDCAT-VMD and XplorGUI interfaces. These modules enable visualization of RDC analysis results on the molecular structure displayed in VMD and refinement of structures with Xplor-NIH, respectively. We also highlight REDCAT’s Error-Analysis feature in reporting the localized fitness of a structure to RDC data, which provides a more effective means of recognizing local structural anomalies. This allows for structurally sound regions of a molecule to be identified, and for any refinement efforts to be focused solely on locally distorted regions. Conclusions The newly engineered REDCAT software package, which is available for download via the WWW from http://ifestos.cse.sc.edu, has been developed in the Object Oriented C++ environment. Our most recent enhancements to REDCAT serve to provide a more complete RDC analysis suite, while also accommodating a more user-friendly experience, and will be of great interest to the community of researchers and developers since it hides the complications of software development.
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Affiliation(s)
- Chris Schmidt
- Department of Computer Science & Engineering, University of South Carolina, Columbia, SC 29208, USA.
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Norrehed S, Erdélyi M, Light ME, Gogoll A. Protonation-triggered conformational modulation of an N,N′-dialkylbispidine: first observation of the elusive boat–boat conformer. Org Biomol Chem 2013; 11:6292-9. [DOI: 10.1039/c3ob41122b] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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