Comparative Conformational Analysis of Acyclic Sugar Alcohols Ribitol, Xylitol and <span style="font-variant: small-caps">d</span>-Arabitol by Solution NMR and Molecular Dynamics Simulations
Ribitol (C<sub>5</sub>H<sub>12</sub>O<sub>5</sub>) is an acyclic sugar alcohol that was recently identified in <i>O</i>-mannose glycan on mammalian <inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline...
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MDPI AG
2024-02-01
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| Series: | Molecules |
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| Online Access: | https://www.mdpi.com/1420-3049/29/5/1072 |
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| author | Shiho Ohno Noriyoshi Manabe Jun Uzawa Yoshiki Yamaguchi |
| author_facet | Shiho Ohno Noriyoshi Manabe Jun Uzawa Yoshiki Yamaguchi |
| author_sort | Shiho Ohno |
| collection | DOAJ |
| description | Ribitol (C<sub>5</sub>H<sub>12</sub>O<sub>5</sub>) is an acyclic sugar alcohol that was recently identified in <i>O</i>-mannose glycan on mammalian <inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mi mathvariant="sans-serif">α</mi></semantics></math></inline-formula>-dystroglycan. The conformation and dynamics of acyclic sugar alcohols such as ribitol are dependent on the stereochemistry of the hydroxyl groups; however, the dynamics are not fully understood. To gain insights into the conformation and dynamics of sugar alcohols, we carried out comparative analyses of ribitol, <span style="font-variant: small-caps;">d</span>-arabitol and xylitol by a crystal structure database search, solution NMR analysis and molecular dynamics (MD) simulations. The crystal structures of the sugar alcohols showed a limited number of conformations, suggesting that only certain stable conformations are prevalent among all possible conformations. The three-bond scholar coupling constants and exchange rates of hydroxyl protons were measured to obtain information on the backbone torsion angle and possible hydrogen bonding of each hydroxyl group. The 100 ns MD simulations indicate that the ribitol backbone has frequent conformational transitions with torsion angles between 180<inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><msup><mrow></mrow><mo>∘</mo></msup></semantics></math></inline-formula> and ±60<inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><msup><mrow></mrow><mo>∘</mo></msup></semantics></math></inline-formula>, while <span style="font-variant: small-caps;">d</span>-arabitol and xylitol showed fewer conformational transitions. Taking our experimental and computational data together, it can be concluded that ribitol is more flexible than <span style="font-variant: small-caps;">d</span>-arabitol or xylitol, and the flexibility is at least in part defined by the configuration of the OH groups, which may form intramolecular hydrogen bonds. |
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| language | English |
| last_indexed | 2024-04-25T00:23:24Z |
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| spelling | doaj.art-7f3bbad34ee44ac3918caab5343774552024-03-12T16:50:58ZengMDPI AGMolecules1420-30492024-02-01295107210.3390/molecules29051072Comparative Conformational Analysis of Acyclic Sugar Alcohols Ribitol, Xylitol and <span style="font-variant: small-caps">d</span>-Arabitol by Solution NMR and Molecular Dynamics SimulationsShiho Ohno0Noriyoshi Manabe1Jun Uzawa2Yoshiki Yamaguchi3Division of Structural Biology, Institute of Molecular Biomembrane and Glycobiology, Tohoku Medical and Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai 981-8558, Miyagi, JapanDivision of Structural Biology, Institute of Molecular Biomembrane and Glycobiology, Tohoku Medical and Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai 981-8558, Miyagi, JapanStructural Glycobiology Team, RIKEN (The Institute of Physical and Chemical Research), 2-1 Hirosawa, Wako 351-0198, Saitama, JapanDivision of Structural Biology, Institute of Molecular Biomembrane and Glycobiology, Tohoku Medical and Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai 981-8558, Miyagi, JapanRibitol (C<sub>5</sub>H<sub>12</sub>O<sub>5</sub>) is an acyclic sugar alcohol that was recently identified in <i>O</i>-mannose glycan on mammalian <inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mi mathvariant="sans-serif">α</mi></semantics></math></inline-formula>-dystroglycan. The conformation and dynamics of acyclic sugar alcohols such as ribitol are dependent on the stereochemistry of the hydroxyl groups; however, the dynamics are not fully understood. To gain insights into the conformation and dynamics of sugar alcohols, we carried out comparative analyses of ribitol, <span style="font-variant: small-caps;">d</span>-arabitol and xylitol by a crystal structure database search, solution NMR analysis and molecular dynamics (MD) simulations. The crystal structures of the sugar alcohols showed a limited number of conformations, suggesting that only certain stable conformations are prevalent among all possible conformations. The three-bond scholar coupling constants and exchange rates of hydroxyl protons were measured to obtain information on the backbone torsion angle and possible hydrogen bonding of each hydroxyl group. The 100 ns MD simulations indicate that the ribitol backbone has frequent conformational transitions with torsion angles between 180<inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><msup><mrow></mrow><mo>∘</mo></msup></semantics></math></inline-formula> and ±60<inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><msup><mrow></mrow><mo>∘</mo></msup></semantics></math></inline-formula>, while <span style="font-variant: small-caps;">d</span>-arabitol and xylitol showed fewer conformational transitions. Taking our experimental and computational data together, it can be concluded that ribitol is more flexible than <span style="font-variant: small-caps;">d</span>-arabitol or xylitol, and the flexibility is at least in part defined by the configuration of the OH groups, which may form intramolecular hydrogen bonds.https://www.mdpi.com/1420-3049/29/5/1072ribitolxylitolarabitolconformationdynamicsNMR |
| spellingShingle | Shiho Ohno Noriyoshi Manabe Jun Uzawa Yoshiki Yamaguchi Comparative Conformational Analysis of Acyclic Sugar Alcohols Ribitol, Xylitol and <span style="font-variant: small-caps">d</span>-Arabitol by Solution NMR and Molecular Dynamics Simulations Molecules ribitol xylitol arabitol conformation dynamics NMR |
| title | Comparative Conformational Analysis of Acyclic Sugar Alcohols Ribitol, Xylitol and <span style="font-variant: small-caps">d</span>-Arabitol by Solution NMR and Molecular Dynamics Simulations |
| title_full | Comparative Conformational Analysis of Acyclic Sugar Alcohols Ribitol, Xylitol and <span style="font-variant: small-caps">d</span>-Arabitol by Solution NMR and Molecular Dynamics Simulations |
| title_fullStr | Comparative Conformational Analysis of Acyclic Sugar Alcohols Ribitol, Xylitol and <span style="font-variant: small-caps">d</span>-Arabitol by Solution NMR and Molecular Dynamics Simulations |
| title_full_unstemmed | Comparative Conformational Analysis of Acyclic Sugar Alcohols Ribitol, Xylitol and <span style="font-variant: small-caps">d</span>-Arabitol by Solution NMR and Molecular Dynamics Simulations |
| title_short | Comparative Conformational Analysis of Acyclic Sugar Alcohols Ribitol, Xylitol and <span style="font-variant: small-caps">d</span>-Arabitol by Solution NMR and Molecular Dynamics Simulations |
| title_sort | comparative conformational analysis of acyclic sugar alcohols ribitol xylitol and span style font variant small caps d span arabitol by solution nmr and molecular dynamics simulations |
| topic | ribitol xylitol arabitol conformation dynamics NMR |
| url | https://www.mdpi.com/1420-3049/29/5/1072 |
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