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Di Pietro ME, Sternberg U, Luy B. Molecular Dynamics with Orientational Tensorial Constraints: A New Approach to Probe the Torsional Angle Distributions of Small Rotationally Flexible Molecules. J Phys Chem B 2019; 123:8480-8491. [PMID: 31502838 DOI: 10.1021/acs.jpcb.9b07008] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The potential of residual dipolar couplings (RDCs) in conformational studies of small molecules is now widely recognized, but current theoretical approaches for their interpretation have several limitations and there is still the need for a general method to probe the torsional angle distributions applicable to any rotationally flexible molecule. Molecular dynamics simulations with RDC-based orientational tensorial constraints (MDOC), implemented in the software COSMOS, are presented here as a conceptually new strategy. For the cases of the fluorinated anti-inflammatory drug diflunisal and the disaccharide cellobiose, we demonstrate that MDOC simulations with one-bond RDCs as tensorial constraints unveil torsion distributions and allow the determination of relative configuration in the presence of rotational flexibility. The independence of the initial structure or any a priori assumption as well as the possibility to combine different experimental constraints represent features, which make the COSMOS software a promising tool for the investigation of torsional angle distributions of flexible molecules, regardless of their size and degree of freedom.
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Affiliation(s)
- Maria E Di Pietro
- Institute of Organic Chemistry , Karlsruhe Institute of Technology (KIT) , Karlsruhe 76131 , Germany
| | - Ulrich Sternberg
- COSMOS GbR , Jena 07743 , Germany.,Research Partner , Karlsruhe Institute of Technology (KIT) , Karlsruhe 76131 , Germany
| | - Burkhard Luy
- Institute of Organic Chemistry , Karlsruhe Institute of Technology (KIT) , Karlsruhe 76131 , Germany.,Institute for Biological Interfaces 4-Magnetic Resonance , Karlsruhe Institute of Technology (KIT) , Eggenstein-Leopoldshafen 76021 , Germany
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Abstract
Complex carbohydrates are ubiquitous in nature, and together with proteins and nucleic acids they comprise the building blocks of life. But unlike proteins and nucleic acids, carbohydrates form nonlinear polymers, and they are not characterized by robust secondary or tertiary structures but rather by distributions of well-defined conformational states. Their molecular flexibility means that oligosaccharides are often refractory to crystallization, and nuclear magnetic resonance (NMR) spectroscopy augmented by molecular dynamics (MD) simulation is the leading method for their characterization in solution. The biological importance of carbohydrate-protein interactions, in organismal development as well as in disease, places urgency on the creation of innovative experimental and theoretical methods that can predict the specificity of such interactions and quantify their strengths. Additionally, the emerging realization that protein glycosylation impacts protein function and immunogenicity places the ability to define the mechanisms by which glycosylation impacts these features at the forefront of carbohydrate modeling. This review will discuss the relevant theoretical approaches to studying the three-dimensional structures of this fascinating class of molecules and interactions, with reference to the relevant experimental data and techniques that are key for validation of the theoretical predictions.
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Affiliation(s)
- Robert J Woods
- Complex Carbohydrate Research Center and Department of Biochemistry and Molecular Biology , University of Georgia , 315 Riverbend Road , Athens , Georgia 30602 , United States
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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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Berglund J, Angles d'Ortoli T, Vilaplana F, Widmalm G, Bergenstråhle-Wohlert M, Lawoko M, Henriksson G, Lindström M, Wohlert J. A molecular dynamics study of the effect of glycosidic linkage type in the hemicellulose backbone on the molecular chain flexibility. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 88:56-70. [PMID: 27385537 DOI: 10.1111/tpj.13259] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 06/16/2016] [Accepted: 06/28/2016] [Indexed: 06/06/2023]
Abstract
The macromolecular conformation of the constituent polysaccharides in lignocellulosic biomass influences their supramolecular interactions, and therefore their function in plants and their performance in technical products. The flexibility of glycosidic linkages from the backbone of hemicelluloses was studied by evaluating the conformational freedom of the φ and ψ dihedral angles using molecular dynamic simulations, additionally selected molecules were correlated with experimental data by nuclear magnetic resonance spectroscopy. Three types of β-(1→4) glycosidic linkages involving the monosaccharides (Glcp, Xylp and Manp) present in the backbone of hemicelluloses were defined. Different di- and tetrasaccharides with combinations of such sugar monomers from hemicelluloses were simulated, and free energy maps of the φ - ψ space and hydrogen-bonding patterns were obtained. The glycosidic linkage between Glc-Glc or Glc-Man (C-type) was the stiffest with mainly one probable conformation; the linkage from Man-Man or Man-Glc (M-type) was similar but with an increased probability for an alternative conformation making it more flexible, and the linkage between two Xyl-units (X-type) was the most flexible with two almost equally populated conformations. Glycosidic linkages of the same type showed essentially the same conformational space in both disaccharides and in the central region of tetrasaccharides. Different probabilities of glycosidic linkage conformations in the backbone of hemicelluloses can be directly estimated from the free energy maps, which to a large degree affect the overall macromolecular conformations of these polymers. The information gained contributes to an increased understanding of the function of hemicelluloses both in the cell wall and in technical products.
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Affiliation(s)
- Jennie Berglund
- Wallenberg Wood Science Centre (WWSC), Department of Fiber and Polymer Technology, School of Chemical Engineering, Royal Institute of Technology KTH, SE-100 44, Stockholm, Sweden
| | - Thibault Angles d'Ortoli
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Francisco Vilaplana
- Wallenberg Wood Science Centre (WWSC), Department of Fiber and Polymer Technology, School of Chemical Engineering, Royal Institute of Technology KTH, SE-100 44, Stockholm, Sweden
- Division of Glycoscience, School of Biotechnology, Royal Institute of Technology KTH, AlbaNova University Centre, SE-106 91, Stockholm, Sweden
| | - Göran Widmalm
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Malin Bergenstråhle-Wohlert
- Wallenberg Wood Science Centre (WWSC), Department of Fiber and Polymer Technology, School of Chemical Engineering, Royal Institute of Technology KTH, SE-100 44, Stockholm, Sweden
| | - Martin Lawoko
- Wallenberg Wood Science Centre (WWSC), Department of Fiber and Polymer Technology, School of Chemical Engineering, Royal Institute of Technology KTH, SE-100 44, Stockholm, Sweden
| | - Gunnar Henriksson
- Wallenberg Wood Science Centre (WWSC), Department of Fiber and Polymer Technology, School of Chemical Engineering, Royal Institute of Technology KTH, SE-100 44, Stockholm, Sweden
| | - Mikael Lindström
- Wallenberg Wood Science Centre (WWSC), Department of Fiber and Polymer Technology, School of Chemical Engineering, Royal Institute of Technology KTH, SE-100 44, Stockholm, Sweden
| | - Jakob Wohlert
- Wallenberg Wood Science Centre (WWSC), Department of Fiber and Polymer Technology, School of Chemical Engineering, Royal Institute of Technology KTH, SE-100 44, Stockholm, Sweden.
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Blaum BS, Frank M, Walker RC, Neu U, Stehle T. Complement Factor H and Simian Virus 40 bind the GM1 ganglioside in distinct conformations. Glycobiology 2015; 26:532-9. [PMID: 26715202 DOI: 10.1093/glycob/cwv170] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 12/22/2015] [Indexed: 11/13/2022] Open
Abstract
Mammalian cell surfaces are decorated with a variety of glycan chains that orchestrate development and defense and are exploited by pathogens for cellular attachment and entry. While glycosidic linkages are, in principle, flexible, the conformational space that a given glycan can sample is subject to spatial and electrostatic restrictions imposed by its overall chemical structure. Here, we show how the glycan moiety of the GM1 ganglioside, a branched, monosialylated pentasaccharide that serves as a ligand for various proteins, undergoes differential conformational selection in its interactions with different lectins. Using STD NMR and X-ray crystallography, we found that the innate immune regulator complement Factor H (FH) binds a previously not reported GM1 conformation that is not compatible with the GM1-binding sites of other structurally characterized GM1-binding lectins such as the Simian Virus 40 (SV40) capsid. Molecular dynamics simulations of the free glycan in explicit solvent on the 10 μs timescale reveal that the FH-bound conformation nevertheless corresponds to a minimum in the Gibbs free energy plot. In contrast to the GM1 conformation recognized by SV40, the FH-bound GM1 conformation is associated with poor NOE restraints, explaining how it escaped(1)H-(1)H NOE-restrained modeling in the past and highlighting the necessity for ensemble representations of glycan structures.
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Affiliation(s)
- Bärbel S Blaum
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen 72076, Germany
| | - Martin Frank
- Biognos AB, Generatorsgatan 1, Gothenburg 41705, Sweden
| | - Ross C Walker
- San Diego Supercomputer Center and Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ursula Neu
- Max-Planck-Institute of Colloids and Interfaces, Potsdam 14476, Germany
| | - Thilo Stehle
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen 72076, Germany Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, TN 37212, USA
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Kapla J, Engström O, Stevensson B, Wohlert J, Widmalm G, Maliniak A. Molecular dynamics simulations and NMR spectroscopy studies of trehalose-lipid bilayer systems. Phys Chem Chem Phys 2015; 17:22438-47. [PMID: 26252429 DOI: 10.1039/c5cp02472b] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The disaccharide trehalose (TRH) strongly affects the physical properties of lipid bilayers. We investigate interactions between lipid membranes formed by 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and TRH using NMR spectroscopy and molecular dynamics (MD) computer simulations. We compare dipolar couplings derived from DMPC/TRH trajectories with those determined (i) experimentally in TRH using conventional high-resolution NMR in a weakly ordered solvent (bicelles), and (ii) by solid-state NMR in multilamellar vesicles (MLV) formed by DMPC. Analysis of the experimental and MD-derived couplings in DMPC indicated that the force field used in the simulations reasonably well describes the experimental results with the exception for the glycerol fragment that exhibits significant deviations. The signs of dipolar couplings, not available from the experiments on highly ordered systems, were determined from the trajectory analysis. The crucial step in the analysis of residual dipolar couplings (RDCs) in TRH determined in a bicelle-environment was access to the conformational distributions derived from the MD trajectory. Furthermore, the conformational behavior of TRH, investigated by J-couplings, in the ordered and isotropic phases is essentially identical, indicating that the general assumptions in the analyses of RDCs are well founded.
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Affiliation(s)
- Jon Kapla
- Department of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden.
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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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