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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: 107] [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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Ramadugu SK, Chung YH, Xia J, Margulis CJ. When sugars get wet. A comprehensive study of the behavior of water on the surface of oligosaccharides. J Phys Chem B 2009; 113:11003-15. [PMID: 19588947 DOI: 10.1021/jp904981v] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this article, we characterize the behavior of water on the surface of a diverse group of carbohydrates and attempt to determine the role of saccharide size, linkage, and branching as well as secondary structure on the dynamics and structure of water at the surface. In order to better understand the similarities and differences in the behavior of the solvent on the carbohydrate surface, we explore residence times, rotational correlation functions, local solvent occupancy numbers, and diffusivities. We find that due to the differences in secondary structure water residence times are longer and translational and rotational dynamics are retarded when in contact with wide helices and branched sugars. In the case of extended helices and smaller oligosaccharides, water dynamics is faster and less hindered. This indicates that branching, the type of linkage between monomers, and the anomeric configuration all play a major role in determining the structure and dynamics of water on the surface of carbohydrates.
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Bocchinfuso G, Palleschi A, Mazzuca C, Coviello T, Alhaique F, Marletta G. Theoretical and Experimental Study on a Self-Assembling Polysaccharide Forming Nanochannels: Static and Dynamic Effects Induced by a Soft Confinement. J Phys Chem B 2008; 112:6473-83. [DOI: 10.1021/jp076074f] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Gianfranco Bocchinfuso
- Dipartimento di Scienze e Tecnologie Chimiche, University of Roma “Tor Vergata”, via della Ricerca Scientifica, 00133 Roma, Italy, Dipartimento di Studi di Chimica e Tecnologia delle Sostanze Biologicamente Attive, Università di Roma “La Sapienza”, P.le Aldo Moro 5, 00185 Roma, Italy, and Dipartimento di Scienze Chimiche, Università di Catania, viale A. Doria, 95125 Catania, Italy
| | - Antonio Palleschi
- Dipartimento di Scienze e Tecnologie Chimiche, University of Roma “Tor Vergata”, via della Ricerca Scientifica, 00133 Roma, Italy, Dipartimento di Studi di Chimica e Tecnologia delle Sostanze Biologicamente Attive, Università di Roma “La Sapienza”, P.le Aldo Moro 5, 00185 Roma, Italy, and Dipartimento di Scienze Chimiche, Università di Catania, viale A. Doria, 95125 Catania, Italy
| | - Claudia Mazzuca
- Dipartimento di Scienze e Tecnologie Chimiche, University of Roma “Tor Vergata”, via della Ricerca Scientifica, 00133 Roma, Italy, Dipartimento di Studi di Chimica e Tecnologia delle Sostanze Biologicamente Attive, Università di Roma “La Sapienza”, P.le Aldo Moro 5, 00185 Roma, Italy, and Dipartimento di Scienze Chimiche, Università di Catania, viale A. Doria, 95125 Catania, Italy
| | - Tommasina Coviello
- Dipartimento di Scienze e Tecnologie Chimiche, University of Roma “Tor Vergata”, via della Ricerca Scientifica, 00133 Roma, Italy, Dipartimento di Studi di Chimica e Tecnologia delle Sostanze Biologicamente Attive, Università di Roma “La Sapienza”, P.le Aldo Moro 5, 00185 Roma, Italy, and Dipartimento di Scienze Chimiche, Università di Catania, viale A. Doria, 95125 Catania, Italy
| | - Franco Alhaique
- Dipartimento di Scienze e Tecnologie Chimiche, University of Roma “Tor Vergata”, via della Ricerca Scientifica, 00133 Roma, Italy, Dipartimento di Studi di Chimica e Tecnologia delle Sostanze Biologicamente Attive, Università di Roma “La Sapienza”, P.le Aldo Moro 5, 00185 Roma, Italy, and Dipartimento di Scienze Chimiche, Università di Catania, viale A. Doria, 95125 Catania, Italy
| | - Giovanni Marletta
- Dipartimento di Scienze e Tecnologie Chimiche, University of Roma “Tor Vergata”, via della Ricerca Scientifica, 00133 Roma, Italy, Dipartimento di Studi di Chimica e Tecnologia delle Sostanze Biologicamente Attive, Università di Roma “La Sapienza”, P.le Aldo Moro 5, 00185 Roma, Italy, and Dipartimento di Scienze Chimiche, Università di Catania, viale A. Doria, 95125 Catania, Italy
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Umemura M, Yuguchi Y, Hirotsu T. Interaction between Cellooligosaccharides in Aqueous Solution from Molecular Dynamics Simulation: Comparison of Cellotetraose, Cellopentaose, and Cellohexaose. J Phys Chem A 2004. [DOI: 10.1021/jp049044a] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Myco Umemura
- National Institute of Advanced Industrial Science & Technology, AIST, 2217-14 Hayashi-cho, Takamatsu-shi, Kagawa 761-0395, Japan
| | - Yoshiaki Yuguchi
- National Institute of Advanced Industrial Science & Technology, AIST, 2217-14 Hayashi-cho, Takamatsu-shi, Kagawa 761-0395, Japan
| | - Takahiro Hirotsu
- National Institute of Advanced Industrial Science & Technology, AIST, 2217-14 Hayashi-cho, Takamatsu-shi, Kagawa 761-0395, Japan
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