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Heine H, Zamyatina A. Therapeutic Targeting of TLR4 for Inflammation, Infection, and Cancer: A Perspective for Disaccharide Lipid A Mimetics. Pharmaceuticals (Basel) 2022; 16:23. [PMID: 36678520 PMCID: PMC9864529 DOI: 10.3390/ph16010023] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/13/2022] [Accepted: 12/14/2022] [Indexed: 12/28/2022] Open
Abstract
The Toll-like receptor 4 (TLR4) signaling pathway plays a central role in the prompt defense against infectious challenge and provides immediate response to Gram-negative bacterial infection. The TLR4/MD-2 complex can sense and respond to various pathogen-associated molecular patterns (PAMPs) with bacterial lipopolysaccharide (LPS) being the most potent and the most frequently occurring activator of the TLR4-mediated inflammation. TLR4 is believed to be both a friend and foe since improperly regulated TLR4 signaling can result in the overactivation of immune responses leading to sepsis, acute lung injury, or pathologic chronic inflammation involved in cancer and autoimmune disease. TLR4 is also considered a legitimate target for vaccine adjuvant development since its activation can boost the adaptive immune responses. The dual action of the TLR4 complex justifies the efforts in the development of both TLR4 antagonists as antisepsis drug candidates or remedies for chronic inflammatory diseases and TLR4 agonists as vaccine adjuvants or immunotherapeutics. In this review, we provide a brief overview of the biochemical evidences for possible pharmacologic applications of TLR4 ligands as therapeutics and report our systematic studies on the design, synthesis, and immunobiological evaluation of carbohydrate-based TLR4 antagonists with nanomolar affinity for MD-2 as well as disaccharide-based TLR4 agonists with picomolar affinity for the TLR4/MD-2 complex.
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Affiliation(s)
- Holger Heine
- Research Group Innate Immunity, Research Center Borstel—Leibniz Lung Center, Airway Research Center North (ARCN), German Center for Lung Research (DZL), Parkallee 22, 23845 Borstel, Germany
| | - Alla Zamyatina
- Department of Chemistry, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
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Strobl S, Hofbauer K, Heine H, Zamyatina A. Lipid A Mimetics Based on Unnatural Disaccharide Scaffold as Potent TLR4 Agonists for Prospective Immunotherapeutics and Adjuvants. Chemistry 2022; 28:e202200547. [PMID: 35439332 PMCID: PMC9325513 DOI: 10.1002/chem.202200547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Indexed: 11/11/2022]
Abstract
TLR4 is a key pattern recognition receptor that can sense pathogen- and danger- associated molecular patterns to activate the downstream signaling pathways which results in the upregulation of transcription factors and expression of interferons and cytokines to mediate protective pro-inflammatory responses involved in immune defense. Bacterial lipid A is the primary TLR4 ligand with very complex, species-specific, and barely predictable structure-activity relationships. Given that therapeutic targeting of TLR4 is an emerging tool for management of a variety of human diseases, the development of novel TLR4 activating biomolecules other than lipid A is of vast importance. We report on design, chemical synthesis and immunobiology of novel glycan-based lipid A-mimicking molecules that can activate human and murine TLR4-mediated signaling with picomolar affinity. Exploiting crystal structure - based design we have created novel disaccharide lipid A mimetics (DLAMs) where the inherently flexible β(1→6)-linked diglucosamine backbone of lipid A is exchanged with a conformationally restrained non-reducing βGlcN(1↔1')βGlcN scaffold. Excellent stereoselectivity in a challenging β,β-1,1' glycosylation was achieved by tuning the reactivities of donor and acceptor molecules using protective group manipulation strategy. Divergent streamlined synthesis of β,β-1,1'-linked diglucosamine-derived glycolipids entailing multiple long-chain (R)-3- acyloxyacyl residues and up two three phosphate groups was developed. Specific 3D-molecular shape and conformational rigidity of unnatural β,β-1,1'-linked diglucosamine combined with carefully optimized phosphorylation and acylation pattern ensured efficient induction of the TLR4-mediated signaling in a species-independent manner.
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Affiliation(s)
- Sebastian Strobl
- Department of ChemistryUniversity of Natural Resources and Life SciencesMuthgasse 18Vienna1190Austria
| | - Karin Hofbauer
- Department of ChemistryUniversity of Natural Resources and Life SciencesMuthgasse 18Vienna1190Austria
| | - Holger Heine
- Research Group Innate ImmunityResearch Center Borstel-Leibniz Lung Center, Airway Research Center North (ARCN), German Center for Lung Disease (DZL)Parkallee 22Borstel23845Germany
| | - Alla Zamyatina
- Department of ChemistryUniversity of Natural Resources and Life SciencesMuthgasse 18Vienna1190Austria
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French AD. Combining Computational Chemistry and Crystallography for a Better Understanding of the Structure of Cellulose. Adv Carbohydr Chem Biochem 2021; 80:15-93. [PMID: 34872656 DOI: 10.1016/bs.accb.2021.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The approaches in this article seek to enhance understanding of cellulose at the molecular level, independent of the source and the particular crystalline form of cellulose. Four main areas of structure research are reviewed. Initially, the molecular shape is inferred from the crystal structures of many small molecules that have β-(1→4) linkages. Then, conformational analyses with potential energy calculations of cellobiose are covered, followed by the use of Atoms-In-Molecules theory to learn about interactions in experimental and theoretical structures. The last section covers models of cellulose nanoparticles. Controversies addressed include the stability of twofold screw-axis conformations, the influence of different computational methods, the predictability of crystalline conformations by studies of isolated molecules, and the twisting of model cellulose crystals.
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Affiliation(s)
- Alfred D French
- Southern Regional Research Center, U.S. Department of Agriculture, New Orleans, Louisiana, USA
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French AD, Montgomery DW, Prevost NT, Edwards JV, Woods RJ. Comparison of cellooligosaccharide conformations in complexes with proteins with energy maps for cellobiose. Carbohydr Polym 2021; 264:118004. [PMID: 33910736 DOI: 10.1016/j.carbpol.2021.118004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 03/24/2021] [Accepted: 03/25/2021] [Indexed: 01/24/2023]
Abstract
Shapes (conformations) of cellulose molecules are described by their glycosidic linkage torsion angles ϕ and ψ. Although the torsions are known for cellulose in crystals, amorphous shapes are also interesting for understanding reactivity and physical properties. ϕ and ψ determination for unorganized matter is difficult; one approach is to study their range in many related molecules. For example, linkage torsions of cellulose should be similar to those in cellobiose. Herein, torsions were measured for cellooligosaccharides and lactose moieties complexed with proteins in the Protein Data Bank (PDB). These torsions were compared with ϕ/ψ maps based on quantum mechanics energies for solvated cellobiose and analogs lacking hydroxyl groups. Most PDB conformations corresponded to low map energies. Amorphous cellulose should be generally extended with individual linkages that would give 2- to 3-fold helices. The map for an analog lacking hydrogen bonding ability was more predictive for PDB linkages than the cellobiose map.
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Affiliation(s)
- Alfred D French
- Southern Regional Research Center, U. S. Department of Agriculture, 1100 Robert E. Lee Blvd., New Orleans, LA, 70124, USA.
| | - David W Montgomery
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA, 30602, USA.
| | - Nicolette T Prevost
- Southern Regional Research Center, U. S. Department of Agriculture, 1100 Robert E. Lee Blvd., New Orleans, LA, 70124, USA.
| | - J Vincent Edwards
- Southern Regional Research Center, U. S. Department of Agriculture, 1100 Robert E. Lee Blvd., New Orleans, LA, 70124, USA.
| | - Robert J Woods
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA, 30602, USA.
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Heine H, Adanitsch F, Peternelj TT, Haegman M, Kasper C, Ittig S, Beyaert R, Jerala R, Zamyatina A. Tailored Modulation of Cellular Pro-inflammatory Responses With Disaccharide Lipid A Mimetics. Front Immunol 2021; 12:631797. [PMID: 33815382 PMCID: PMC8012497 DOI: 10.3389/fimmu.2021.631797] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 02/17/2021] [Indexed: 01/08/2023] Open
Abstract
Pro-inflammatory signaling mediated by Toll-like receptor 4 (TLR4)/myeloid differentiation-2 (MD-2) complex plays a crucial role in the instantaneous protection against infectious challenge and largely contributes to recovery from Gram-negative infection. Activation of TLR4 also boosts the adaptive immunity which is implemented in the development of vaccine adjuvants by application of minimally toxic TLR4 activating ligands. The modulation of pro-inflammatory responses via the TLR4 signaling pathway was found beneficial for management of acute and chronic inflammatory disorders including asthma, allergy, arthritis, Alzheimer disease pathology, sepsis, and cancer. The TLR4/MD-2 complex can recognize the terminal motif of Gram-negative bacterial lipopolysaccharide (LPS)—a glycophospholipid lipid A. Although immense progress in understanding the molecular basis of LPS-induced TLR4-mediated signaling has been achieved, gradual, and predictable TLR4 activation by structurally defined ligands has not yet been attained. We report on controllable modulation of cellular pro-inflammatory responses by application of novel synthetic glycolipids—disaccharide-based lipid A mimetics (DLAMs) having picomolar affinity for TLR4/MD-2. Using crystal structure inspired design we have developed endotoxin mimetics where the inherently flexible β(1 → 6)-linked diglucosamine backbone of lipid A is replaced by a conformationally restricted α,α-(1↔1)-linked disaccharide scaffold. The tertiary structure of the disaccharide skeleton of DLAMs mirrors the 3-dimensional shape of TLR4/MD-2 bound E. coli lipid A. Due to exceptional conformational rigidity of the sugar scaffold, the specific 3D organization of DLAM must be preserved upon interaction with proteins. These structural factors along with specific acylation and phosphorylation pattern can ensure picomolar affinity for TLR4 and permit efficient dimerization of TLR4/MD-2/DLAM complexes. Since the binding pose of lipid A in the binding pocket of MD-2 (±180°) is crucial for the expression of biological activity, the chemical structure of DLAMs was designed to permit a predefined binding orientation in the binding groove of MD-2, which ensured tailored and species-independent (human and mice) TLR4 activation. Manipulating phosphorylation and acylation pattern at the sugar moiety facing the secondary dimerization interface allowed for adjustable modulation of the TLR4-mediated signaling. Tailored modulation of cellular pro-inflammatory responses by distinct modifications of the molecular structure of DLAMs was attained in primary human and mouse immune cells, lung epithelial cells and TLR4 transfected HEK293 cells.
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Affiliation(s)
- Holger Heine
- Research Group Innate Immunity, Research Center Borstel - Leibniz Lung Center, Airway Research Center North (ARCN), German Center for Lung Research (DZL), Borstel, Germany
| | - Florian Adanitsch
- Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Tina Tinkara Peternelj
- Department of Biotechnology, National Institute of Chemistry, University of Ljubljana, Ljubljana, Slovenia
| | - Mira Haegman
- Unit of Molecular Signal Transduction in Inflammation, Department of Biomedical Molecular Biology, Ghent University, Center for Inflammation Research, VIB, Ghent, Belgium
| | | | - Simon Ittig
- Biozentrum University of Basel, Basel, Switzerland
| | - Rudi Beyaert
- Unit of Molecular Signal Transduction in Inflammation, Department of Biomedical Molecular Biology, Ghent University, Center for Inflammation Research, VIB, Ghent, Belgium
| | - Roman Jerala
- Department of Biotechnology, National Institute of Chemistry, University of Ljubljana, Ljubljana, Slovenia
| | - Alla Zamyatina
- Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Austria
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Scherbinina SI, Toukach PV. Three-Dimensional Structures of Carbohydrates and Where to Find Them. Int J Mol Sci 2020; 21:E7702. [PMID: 33081008 PMCID: PMC7593929 DOI: 10.3390/ijms21207702] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 10/15/2020] [Accepted: 10/16/2020] [Indexed: 02/06/2023] Open
Abstract
Analysis and systematization of accumulated data on carbohydrate structural diversity is a subject of great interest for structural glycobiology. Despite being a challenging task, development of computational methods for efficient treatment and management of spatial (3D) structural features of carbohydrates breaks new ground in modern glycoscience. This review is dedicated to approaches of chemo- and glyco-informatics towards 3D structural data generation, deposition and processing in regard to carbohydrates and their derivatives. Databases, molecular modeling and experimental data validation services, and structure visualization facilities developed for last five years are reviewed.
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Affiliation(s)
- Sofya I. Scherbinina
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Science, Leninsky prospect 47, 119991 Moscow, Russia
- Higher Chemical College, D. Mendeleev University of Chemical Technology of Russia, Miusskaya Square 9, 125047 Moscow, Russia
| | - Philip V. Toukach
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Science, Leninsky prospect 47, 119991 Moscow, Russia
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Abstract
Glycosidic linkage conformations are the main factors in determining the shapes of disaccharide, oligosaccharide, and polysaccharide molecules. The conformations are expressed in terms of the torsion angles about the bonds from each ring of the disaccharide moiety to its glycosidic oxygen atom, and the probability of a given conformation is often expressed in terms of its free or potential energy. The energy surface or map for a disaccharide is a display of the energy plotted against the two torsion angles. Successful mapping allows a particular kind of energy calculation to provide the energy values for each conformation and avoids possible pitfalls. Although different methods are discussed, the main emphasis of this chapter is on the technical production of the maps and their exploitation in further understanding the shape of the molecule in question.
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Plazinski W, Lonardi A, Hünenberger PH. Revision of the GROMOS 56A6(CARBO) force field: Improving the description of ring-conformational equilibria in hexopyranose-based carbohydrates chains. J Comput Chem 2015; 37:354-65. [PMID: 26525424 DOI: 10.1002/jcc.24229] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 10/03/2015] [Accepted: 10/06/2015] [Indexed: 01/19/2023]
Abstract
This article describes a revised version 56A6(CARBO_R) of the GROMOS 56A6(CARBO) force field for hexopyranose-based carbohydrates. The simulated properties of unfunctionalized hexopyranoses are unaltered with respect to 56A6CARBO . In the context of both O1 -alkylated hexopyranoses and oligosaccharides, the revision stabilizes the regular (4) C1 chair for α-anomers, with the opposite effect for β-anomers. As a result, spurious ring inversions observed in α(1→4)-linked chains when using the original 56A6(CARBO) force field are alleviated. The (4) C1 chair is now the most stable conformation for all d-hexopyranose residues, irrespective of the linkage type and anomery, and of the position of the residue along the chain. The methylation of a d-hexopyranose leads to a systematic shift in the ring-inversion free energy ((4) C1 to (1) C4 ) by 7-8 kJ mol(-1), positive for the α-anomers and negative for the β-anomers, which is qualitatively compatible with the expected enhancement of the anomeric effect upon methylation at O1. The ring-inversion free energies for residues within chains are typically smaller in magnitude compared to those of the monomers, and correlate rather poorly with the latter. This suggests that the crowding of ring substituents upon chain formation alters the ring flexibility in a nonsystematic fashion. In general, the description of carbohydrate chains afforded by 56A6(CARBO_R) suggests a significant extent of ring flexibility, i.e., small but often non-negligible equilibrium populations of inverted chairs, and challenges the "textbook" picture of conformationally locked carbohydrate rings.
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Affiliation(s)
- Wojciech Plazinski
- Laboratory of Physical Chemistry, ETH Hönggerberg, HCI, Zürich, CH-8093, Switzerland.,J. Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Ul. Niezapominajek 8, Cracow, 30-239, Poland
| | - Alice Lonardi
- Laboratory of Physical Chemistry, ETH Hönggerberg, HCI, Zürich, CH-8093, Switzerland
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Plazinski W, Drach M. The influence of the hexopyranose ring geometry on the conformation of glycosidic linkages investigated using molecular dynamics simulations. Carbohydr Res 2015; 415:17-27. [DOI: 10.1016/j.carres.2015.07.018] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 07/20/2015] [Accepted: 07/29/2015] [Indexed: 11/29/2022]
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Khodabandeh MH, Rezaeianpour S, Davari MD, Sakhaee N, Zare K, Anary M, Naderi F. Quantum chemical study of the equatorial/axial exchange of different substituents in nitrogen and phosphorous-containing 6-membered rings: Role of charge transfer interactions. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2014. [DOI: 10.1142/s0219633614500473] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Understanding the nature of equatorial/axial conversion in six-membered rings is important because of involvement of these motifs in some biological systems. In this work we have studied the equatorial/axial exchange of nitrogen and phosphorous bearing six-membered rings with different representative substituents by using quantum chemistry methods. Three possible routes, i.e. heteroatom inversion and two ring flipping modes were considered. The feasibility of equatorial/axial conversion (based on ΔE#) for the substituted piperidine rings with substituents was in the following order; H > CH 3> Cl ~ OH ~ F , whereas for the phosphorous bearing six-membered rings it was H ~ F > OH > Cl ~ CH 3. In the piperidine system hydrogen and methyl substituents preferred the atom inversion route while the other substituents ( Cl , F , OH ) favored C4 site ring flipping in equatorial/axial conversion. For the phosphorous bearing rings, however, phosphorous retards the atom inversion mechanism and heteroatom site ring flipping is the preferred route for all substituents. We demonstrate that charge transfer effect is one of the key factors that determines the favored route in the presence of various substituents. We show how wave function analysis by natural bond orbital (NBO) method can be used as a straightforward technique to explain the most favored route in the equatorial/axial conversion of substituted 6-membered rings.
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Affiliation(s)
- M. Hassan Khodabandeh
- Department of Chemistry, Faculty of Sciences, Shahid Beheshti University, G.C., Evin 19839-6313, Tehran, Iran
| | - Sedigheh Rezaeianpour
- Department of Chemistry, North Tehran Branch Islamic Azad University, 19585/936 Tehran, Iran
| | - Mehdi D. Davari
- Department of Chemistry, Faculty of Sciences, Shahid Beheshti University, G.C., Evin 19839-6313, Tehran, Iran
- Institute of Biotechnology, RWTH Aachen University, Worringer Weg 3, D-52074 Aachen, Germany
| | - Nader Sakhaee
- Department of Chemistry, Khajeh Nasir Toosi University of Technology, Shariati St., Tehran, Iran
| | - Karim Zare
- Department of Chemistry, Faculty of Sciences, Shahid Beheshti University, G.C., Evin 19839-6313, Tehran, Iran
| | - Mohammad Anary
- Department of Chemistry, Rafsanjan Valie-e-Asr University, P. O. Box 77176, Rafsanjan, Iran
| | - Fereshteh Naderi
- Department of Chemistry, Shahr-e-Qods Branch, Islamic Azad University, Tehran, Iran
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Yamane C, Miyamoto H, Hayakawa D, Ueda K. Folded-chain structure of cellulose II suggested by molecular dynamics simulation. Carbohydr Res 2013; 379:30-7. [DOI: 10.1016/j.carres.2013.06.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2013] [Revised: 05/21/2013] [Accepted: 06/15/2013] [Indexed: 10/26/2022]
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Gubica T, Bukowicki J, Stępień DK, Ostrowski A, Pisklak DM, Cyrański MK. Solid-state structure of methyl 2,4,6-tri-O-acetyl-3-O-(2,3,4,6-tetra-O-acetyl-β-d-glucopyranosyl)-β-d-galactopyranoside and methyl 3,4,6-tri-O-acetyl-2-O-(2,3,4,6-tetra-O-acetyl-β-d-glucopyranosyl)-β-d-galactopyranoside. J Mol Struct 2013. [DOI: 10.1016/j.molstruc.2012.12.027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Pincu M, Brauer B, Gerber RB. When a proton attacks cellobiose in the gas phase: ab initio molecular dynamics simulations. Phys Chem Chem Phys 2013; 15:15382-91. [DOI: 10.1039/c3cp52220b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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French AD. Combining computational chemistry and crystallography for a better understanding of the structure of cellulose. Adv Carbohydr Chem Biochem 2012; 67:19-93. [PMID: 22794182 DOI: 10.1016/b978-0-12-396527-1.00002-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Potential of mean force for separation of the repeating units in cellulose and hemicellulose. Carbohydr Res 2011; 346:867-71. [DOI: 10.1016/j.carres.2011.01.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2010] [Revised: 01/05/2011] [Accepted: 01/07/2011] [Indexed: 11/20/2022]
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Perić-Hassler L, Hansen HS, Baron R, Hünenberger PH. Conformational properties of glucose-based disaccharides investigated using molecular dynamics simulations with local elevation umbrella sampling. Carbohydr Res 2010; 345:1781-801. [PMID: 20576257 DOI: 10.1016/j.carres.2010.05.026] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2010] [Revised: 05/20/2010] [Accepted: 05/22/2010] [Indexed: 10/19/2022]
Abstract
Explicit-solvent molecular dynamics (MD) simulations of the 11 glucose-based disaccharides in water at 300K and 1bar are reported. The simulations were carried out with the GROMOS 45A4 force-field and the sampling along the glycosidic dihedral angles phi and psi was artificially enhanced using the local elevation umbrella sampling (LEUS) method. The trajectories are analyzed in terms of free-energy maps, stable and metastable conformational states (relative free energies and estimated transition timescales), intramolecular H-bonds, single molecule configurational entropies, and agreement with experimental data. All disaccharides considered are found to be characterized either by a single stable (overwhelmingly populated) state ((1-->n)-linked disaccharides with n=1, 2, 3, or 4) or by two stable (comparably populated and differing in the third glycosidic dihedral angle omega ; gg or gt) states with a low interconversion barrier ((1-->6)-linked disaccharides). Metastable (anti-phi or anti-psi) states are also identified with relative free energies in the range of 8-22 kJ mol(-1). The 11 compounds can be classified into four families: (i) the alpha(1-->1)alpha-linked disaccharide trehalose (axial-axial linkage) presents no metastable state, the lowest configurational entropy, and no intramolecular H-bonds; (ii) the four alpha(1-->n)-linked disaccharides (n=1, 2, 3, or 4; axial-equatorial linkage) present one metastable (anti-psi) state, an intermediate configurational entropy, and two alternative intramolecular H-bonds; (iii) the four beta(1-->n)-linked disaccharides (n=1, 2, 3, or 4; equatorial-equatorial linkage) present two metastable (anti-phi and anti-psi) states, an intermediate configurational entropy, and one intramolecular H-bond; (iv) the two (1-->6)-linked disaccharides (additional glycosidic dihedral angle) present no (isomaltose) or a pair of (gentiobiose) metastable (anti-phi) states, the highest configurational entropy, and no intramolecular H-bonds. The observed conformational preferences appear to be dictated by four main driving forces (ring conformational preferences, exo-anomeric effect, steric constraints, and possible presence of a third glycosidic dihedral angle), leaving a secondary role to intramolecular H-bonding and specific solvation effects. In spite of the weak conformational driving force attributed to solvent-exposed H-bonds in water (highly polar protic solvent), intramolecular H-bonds may still have a significant influence on the physico-chemical properties of the disaccharide by decreasing its hydrophilicity. Along with previous work, the results also complete the suggestion of a spectrum of approximate transition timescales for carbohydrates up to the disaccharide level, namely: approximately 30 ps (hydroxyl groups), approximately 1 ns (free lactol group, free hydroxymethyl groups, glycosidic dihedral angleomega in (1-->6)-linked disaccharides), approximately 10 ns to 2 micros (ring conformation, glycosidic dihedral angles phi and psi). The calculated average values of the glycosidic torsional angles agree well with the available experimental data, providing validation for the force-field and simulation methodology employed.
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Affiliation(s)
- Lovorka Perić-Hassler
- Laboratory of Physical Chemistry, ETH Zürich, ETH Hönggerberg, HCI, CH-8093 Zürich, Switzerland
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Chapter 16 Pyrolysis of Carbohydrates. PYROLYSIS OF ORGANIC MOLECULES WITH APPLICATIONS TO HEALTH AND ENVIRONMENTAL ISSUES 2010. [DOI: 10.1016/s0167-9244(09)02816-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Cocinero EJ, Gamblin DP, Davis BG, Simons JP. The building blocks of cellulose: the intrinsic conformational structures of cellobiose, its epimer, lactose, and their singly hydrated complexes. J Am Chem Soc 2009; 131:11117-23. [PMID: 19722675 DOI: 10.1021/ja903322w] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A combination of vibrational spectroscopy conducted under molecular beam conditions and quantum chemical calculation has established the intrinsic three-dimensional structures of the cellulose disaccharide and, focusing on the critical beta1,4-linkage at the nonreducing end of the growing cellulose polymer, its C-4' epimer. Left to their own devices they both adopt a cis (anti-phi/syn-psi) glycosidic configuration, supported in the epimer by strong, cooperative inter-ring hydrogen bonding. In the cellulose disaccharide, however, where the OH-4'(Glc) group is equatorial, the cooperativity is reduced and the corresponding inter-ring hydrogen bonding is relatively weak. The cis conformational preference is still retained in their singly hydrated complexes. In the cellulose disaccharide insertion of the water molecule at the favored binding site between OH-4' and the neighboring hydroxyl group OH-6' promotes a structural reorganization to create a configuration that parallels that of its unhydrated epimer and greatly strengthens the inter-ring hydrogen bonding. In the C-4' epimer, the axial orientation of OH-4' blocks this binding site and the bound water molecule simply adds on at the end of the (OH-O)(n) chain, which has a negligible effect on the (already strong) inter-ring bonding. The implications of these results are discussed with respect to the structure and insolubility of native cellulose polymers.
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Affiliation(s)
- Emilio J Cocinero
- Department of Chemistry, University of Oxford, Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford OX1 3QZ, United Kingdom
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Shen T, Langan P, French AD, Johnson GP, Gnanakaran S. Conformational Flexibility of Soluble Cellulose Oligomers: Chain Length and Temperature Dependence. J Am Chem Soc 2009; 131:14786-94. [DOI: 10.1021/ja9034158] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tongye Shen
- Theoretical Biology & Biophysics Group, Center for Nonlinear Studies, and Biosciences, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, and Cotton Structure and Quality Research Unit, USDA, ARS, SRRC, New Orleans, Louisiana 70124
| | - Paul Langan
- Theoretical Biology & Biophysics Group, Center for Nonlinear Studies, and Biosciences, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, and Cotton Structure and Quality Research Unit, USDA, ARS, SRRC, New Orleans, Louisiana 70124
| | - Alfred D. French
- Theoretical Biology & Biophysics Group, Center for Nonlinear Studies, and Biosciences, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, and Cotton Structure and Quality Research Unit, USDA, ARS, SRRC, New Orleans, Louisiana 70124
| | - Glenn P. Johnson
- Theoretical Biology & Biophysics Group, Center for Nonlinear Studies, and Biosciences, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, and Cotton Structure and Quality Research Unit, USDA, ARS, SRRC, New Orleans, Louisiana 70124
| | - S. Gnanakaran
- Theoretical Biology & Biophysics Group, Center for Nonlinear Studies, and Biosciences, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, and Cotton Structure and Quality Research Unit, USDA, ARS, SRRC, New Orleans, Louisiana 70124
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French A, Johnson G. Roles of starting geometries in quantum mechanics studies of cellobiose. MOLECULAR SIMULATION 2008. [DOI: 10.1080/08927020701663347] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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