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Krivdin LB. Computational NMR of Carbohydrates: Theoretical Background, Applications, and Perspectives. Molecules 2021; 26:molecules26092450. [PMID: 33922318 PMCID: PMC8122784 DOI: 10.3390/molecules26092450] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/19/2021] [Accepted: 04/19/2021] [Indexed: 12/11/2022] Open
Abstract
This review is written amid a marked progress in the calculation of NMR parameters of carbohydrates substantiated by a vast amount of experimental data coming from several laboratories worldwide. By no means are we trying to cover in the present compilation a huge amount of all available data. The main idea of the present review was only to outline general trends and perspectives in this dynamically developing area on the background of a marked progress in theoretical and computational NMR. Presented material is arranged in three basic sections: (1)-a brief theoretical introduction; (2)-applications and perspectives in computational NMR of monosaccharides; and (3)-calculation of NMR chemical shifts and spin-spin coupling constants of di- and polysaccharides.
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Affiliation(s)
- Leonid B Krivdin
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, 664033 Irkutsk, Russia
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Bestaoui-Berrekhchi-Berrahma N, Springborg M, Berrekhchi-Berrahma C, Sekkal-Rahal M. DFT and MP2 conformational study of 3,6-anhydro-α-d-galactose in gas phase and in aqueous solvent. COMPUT THEOR CHEM 2018. [DOI: 10.1016/j.comptc.2018.01.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Lee SB, Lee SY, Lim HS. Aldehydic nature and conformation of 3,6-anhydro-L-galactose monomer. BIOTECHNOL BIOPROC E 2015. [DOI: 10.1007/s12257-015-0520-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Abstract
The article reviews the significant contributions to, and the present status of, applications of computational methods for the characterization and prediction of protein-carbohydrate interactions. After a presentation of the specific features of carbohydrate modeling, along with a brief description of the experimental data and general features of carbohydrate-protein interactions, the survey provides a thorough coverage of the available computational methods and tools. At the quantum-mechanical level, the use of both molecular orbitals and density-functional theory is critically assessed. These are followed by a presentation and critical evaluation of the applications of semiempirical and empirical methods: QM/MM, molecular dynamics, free-energy calculations, metadynamics, molecular robotics, and others. The usefulness of molecular docking in structural glycobiology is evaluated by considering recent docking- validation studies on a range of protein targets. The range of applications of these theoretical methods provides insights into the structural, energetic, and mechanistic facets that occur in the course of the recognition processes. Selected examples are provided to exemplify the usefulness and the present limitations of these computational methods in their ability to assist in elucidation of the structural basis underlying the diverse function and biological roles of carbohydrates in their dialogue with proteins. These test cases cover the field of both carbohydrate biosynthesis and glycosyltransferases, as well as glycoside hydrolases. The phenomenon of (macro)molecular recognition is illustrated for the interactions of carbohydrates with such proteins as lectins, monoclonal antibodies, GAG-binding proteins, porins, and viruses.
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Affiliation(s)
- Serge Pérez
- Department of Molecular Pharmacochemistry, CNRS, University Grenoble-Alpes, Grenoble, France.
| | - Igor Tvaroška
- Department of Chemistry, Slovak Academy of Sciences, Bratislava, Slovak Republic; Department of Chemistry, Faculty of Natural Sciences, Constantine The Philosopher University, Nitra, Slovak Republic.
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Toukach FV, Ananikov VP. Recent advances in computational predictions of NMR parameters for the structure elucidation of carbohydrates: methods and limitations. Chem Soc Rev 2013; 42:8376-415. [DOI: 10.1039/c3cs60073d] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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Bestaoui-Berrekhchi-Berrahma N, Derreumaux P, Sekkal-Rahal M, Springborg M, Sayede A, Yousfi N, Kadoun AED. Density functional conformational study of 2-O-sulfated 3,6 anhydro-α-D-galactose and of neo-κ- and ι-carrabiose molecules in gas phase and water. J Mol Model 2012; 19:893-904. [PMID: 23086461 DOI: 10.1007/s00894-012-1621-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Accepted: 10/01/2012] [Indexed: 10/27/2022]
Abstract
We examined the conformational preferences of the 2-O-sulfated-3,6-α-D-anhydrogalactose (compound I) and two 1,3 linked disaccharides constituting-κ or ι-carrageenans using density functional and ab initio methods in gas phase and aqueous solution. Systematic modifications of two torsion angles leading to 324 and 144 starting geometries for the compound I and each disaccharide were used to generate adiabatic maps using B3LYP/6-31G(d). The lower energy conformers were then fully optimized using B3LYP, B3PW91 and MP2 with several basis sets. Overall, we discuss the impact of full relaxation on the energy and structure of the dominant conformations, present the performance comparison with previous molecular mechanics calculations if available, and determine whether our results are impacted, when polarization and diffuse functions are added to the 6-31G(d) basis set, or when the MP2 level of theory is used.
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Csonka GI, Kaminsky J. Accurate Conformational Energy Differences of Carbohydrates: A Complete Basis Set Extrapolation. J Chem Theory Comput 2011; 7:988-97. [DOI: 10.1021/ct200007x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Gábor I. Csonka
- Department of Inorganic and Analytical Chemistry, Budapest University of Technology, Szent Gellért tér 4, Budapest, H-1521 Hungary
| | - Jakub Kaminsky
- Department of Molecular Spectroscopy, Institute of Organic Chemistry and Biochemistry, Flemingovo nam. 2, 166 10 Prague, Czech Republic
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Baldoni L, Stortz CA, Marino C. Synthesis and conformational analysis of 1,2-cis fused bicyclic α-d-galactofuranosyl thiocarbamate from per-O-tert-butyldimethylsilyl-β-d-galactofuranosyl isothiocyanate. Carbohydr Res 2011; 346:191-6. [PMID: 21168127 DOI: 10.1016/j.carres.2010.11.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2010] [Revised: 11/04/2010] [Accepted: 11/15/2010] [Indexed: 11/19/2022]
Affiliation(s)
- Luciana Baldoni
- CIHIDECAR-CONICET, Departamento de Química Orgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires. Pabellón II, Ciudad Universitaria, 1428 Buenos Aires, Argentina
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Yousfi N, Sekkal-Rahal M, Sayede A, Springborg M. Relaxed energetic maps of kappa-carrabiose: a DFT study. J Comput Chem 2010; 31:1312-20. [PMID: 20127880 DOI: 10.1002/jcc.21497] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The B3LYP density function was used with the 6-31G(d) basis set to perform relaxed energetic contour maps of the charged form of kappa-carrabiose in the gas phase and for the neutral form first in the gas phase and then by simulating the presence of water as solvent using the Onsager model. Only one starting conformation has been considered to perform all the calculations. Rigid energetic maps have been then constructed either by addition of diffuse or polarization functions to the basis set obtaining in that way 6-31+G(d)//6-31G(d), 6-31+G(d,p)//6-31G(d), and 6-311++G(d,p)//6-31G(d) energetic maps that have been carefully examined. The obtained structures corresponding to the lower energy conformers have been then fully optimized using different basis sets with the B3LYP method, a reversion in term of energy has been observed for the two first minima in the case of the charged disaccharide in the gas phase, this was attributed to the large grid of 30 degrees that could lead to the exclusion of an intermediate value corresponding to the real minimum of energy. We thus suggest that after establishing potential energy maps it is essential to proceed to full optimizations of the lower energy conformers. Calculations using the more accurate correlated method MP2 with the 6-31G(d) basis set have also been performed for conformers of the two disaccharides in the gas phase.
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Affiliation(s)
- N Yousfi
- Faculté des Sciences, Laboratoire L2MSM, Université Djillali Liabes de Sidi Bel Abbes, B.P. 89, Sidi Bel Abbes 22000, Algeria
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Schnupf U, Willett JL, Momany FA. 27 ps DFT molecular dynamics simulation of α-maltose: A reduced basis set study. J Comput Chem 2010; 31:2087-97. [DOI: 10.1002/jcc.21495] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Csonka GI, French AD, Johnson GP, Stortz CA. Evaluation of Density Functionals and Basis Sets for Carbohydrates. J Chem Theory Comput 2009; 5:679-92. [DOI: 10.1021/ct8004479] [Citation(s) in RCA: 165] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Gábor I. Csonka
- Department of Inorganic and Analytical Chemistry, Budapest University of Technology, Szent Gellért tér 4, Budapest, H-1521 Hungary, Southern Regional Research Center, U.S. Department of Agriculture, 1100 Robert E. Lee Boulevard, New Orleans, Louisiana 70124, and Departamento de Química Orgánica-CIHIDECAR, Universidad de Buenos Aires, Ciudad Universitaria, 1428 Buenos Aires, Argentina
| | - Alfred D. French
- Department of Inorganic and Analytical Chemistry, Budapest University of Technology, Szent Gellért tér 4, Budapest, H-1521 Hungary, Southern Regional Research Center, U.S. Department of Agriculture, 1100 Robert E. Lee Boulevard, New Orleans, Louisiana 70124, and Departamento de Química Orgánica-CIHIDECAR, Universidad de Buenos Aires, Ciudad Universitaria, 1428 Buenos Aires, Argentina
| | - Glenn P. Johnson
- Department of Inorganic and Analytical Chemistry, Budapest University of Technology, Szent Gellért tér 4, Budapest, H-1521 Hungary, Southern Regional Research Center, U.S. Department of Agriculture, 1100 Robert E. Lee Boulevard, New Orleans, Louisiana 70124, and Departamento de Química Orgánica-CIHIDECAR, Universidad de Buenos Aires, Ciudad Universitaria, 1428 Buenos Aires, Argentina
| | - Carlos A. Stortz
- Department of Inorganic and Analytical Chemistry, Budapest University of Technology, Szent Gellért tér 4, Budapest, H-1521 Hungary, Southern Regional Research Center, U.S. Department of Agriculture, 1100 Robert E. Lee Boulevard, New Orleans, Louisiana 70124, and Departamento de Química Orgánica-CIHIDECAR, Universidad de Buenos Aires, Ciudad Universitaria, 1428 Buenos Aires, Argentina
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