Literature DB >> 20831339

Puckering free energy of pyranoses: A NMR and metadynamics-umbrella sampling investigation.

E Autieri1, M Sega, F Pederiva, G Guella.   

Abstract

We present the results of a combined metadynamics-umbrella sampling investigation of the puckered conformers of pyranoses described using the GROMOS 45a4 force field. The free energy landscape of Cremer-Pople puckering coordinates has been calculated for the whole series of α and β aldohexoses, showing that the current force field parameters fail in reproducing proper puckering free energy differences between chair conformers. We suggest a modification to the GROMOS 45a4 parameter set which improves considerably the agreement of simulation results with theoretical and experimental estimates of puckering free energies. We also report on the experimental measurement of altrose conformer populations by means of NMR spectroscopy, which show good agreement with the predictions of current theoretical models.

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Year:  2010        PMID: 20831339     DOI: 10.1063/1.3476466

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  9 in total

1.  Effects of varying the 6-position oxidation state of hexopyranoses: a systematic comparative computational analysis of 48 monosaccharide stereoisomers.

Authors:  Alison E Vickman; Daniel C Ashley; Mu-Hyun Baik; Nicola L B Pohl
Journal:  J Mol Model       Date:  2017-06-27       Impact factor: 1.810

2.  Perspective on computational simulations of glycosaminoglycans.

Authors:  Balaji Nagarajan; Nehru Viji Sankaranarayanan; Umesh R Desai
Journal:  Wiley Interdiscip Rev Comput Mol Sci       Date:  2018-09-10

3.  Conformational sampling of oligosaccharides using Hamiltonian replica exchange with two-dimensional dihedral biasing potentials and the weighted histogram analysis method (WHAM).

Authors:  Mingjun Yang; Alexander D MacKerell
Journal:  J Chem Theory Comput       Date:  2015-02-10       Impact factor: 6.006

4.  String method for calculation of minimum free-energy paths in Cartesian space in freely-tumbling systems.

Authors:  Davide Branduardi; José D Faraldo-Gómez
Journal:  J Chem Theory Comput       Date:  2013-09-10       Impact factor: 6.006

5.  Dependence of pyranose ring puckering on anomeric configuration: methyl idopyranosides.

Authors:  Benedict M Sattelle; Bidisha Bose-Basu; Matthew Tessier; Robert J Woods; Anthony S Serianni; Andrew Almond
Journal:  J Phys Chem B       Date:  2012-05-23       Impact factor: 2.991

6.  Testing of the GROMOS Force-Field Parameter Set 54A8: Structural Properties of Electrolyte Solutions, Lipid Bilayers, and Proteins.

Authors:  Maria M Reif; Moritz Winger; Chris Oostenbrink
Journal:  J Chem Theory Comput       Date:  2013-01-02       Impact factor: 6.006

7.  The complete conformational free energy landscape of β-xylose reveals a two-fold catalytic itinerary for β-xylanases.

Authors:  Javier Iglesias-Fernández; Lluís Raich; Albert Ardèvol; Carme Rovira
Journal:  Chem Sci       Date:  2014-10-27       Impact factor: 9.825

8.  Pyranose Ring Puckering Thermodynamics for Glycan Monosaccharides Associated with Vertebrate Proteins.

Authors:  Olgun Guvench; Devon Martin; Megan Greene
Journal:  Int J Mol Sci       Date:  2021-12-31       Impact factor: 5.923

9.  Conformational properties of α- or β-(1→6)-linked oligosaccharides: Hamiltonian replica exchange MD simulations and NMR experiments.

Authors:  Dhilon S Patel; Robert Pendrill; Sairam S Mallajosyula; Göran Widmalm; Alexander D MacKerell
Journal:  J Phys Chem B       Date:  2014-03-05       Impact factor: 2.991

  9 in total

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