Literature DB >> 29422120

Proper balance of solvent-solute and solute-solute interactions in the treatment of the diffusion of glucose using the Drude polarizable force field.

Mingjun Yang1, Asaminew H Aytenfisu2, Alexander D MacKerell3.   

Abstract

Motivated by underestimation of the diffusion constant of glucose in aqueous solution at high glucose concentrations we performed additional optimization of the Drude polarizable hexopyranose monosaccharide force field. This indicated aggregation of the glucose at higher concentrations, which is a concern for studies of complex glycan systems such as the HIV Envelope where high effective concentrations of sugars are present. High-level quantum mechanical calculations were undertaken on water monohydrate-glucose interactions, on water cluster-glucose interactions and on glucose-glucose dimers in stacked (parallel) and perpendicular orientations. Optimization of the nonbond and dihedral parameters targeting these data yielded a revised model that showed improved agreement with experimental aqueous diffusion data. However, limitations in the diffusion constants were still present. These were due to the SWM4-NDP inherently overestimating the diffusion constant of water, a problem that was validated by calculation of the aqueous diffusion constants using the SWM6-NDP water model. In addition, results show the water diffusion constant to be significantly overestimated at high glucose concentrations though the glucose diffusion is in satisfactory agreement with experiment. These results indicate the subtle balance of water-sugar, water-water and sugar-sugar interactions that needs to be properly modeled to account for the full range of aqueous behavior of sugars in aqueous solution.
Copyright © 2018 Elsevier Ltd. All rights reserved.

Entities:  

Keywords:  CHARMM; Carbohydrates; MD simulations; Molecular mechanics; Monosaccharides

Mesh:

Substances:

Year:  2018        PMID: 29422120      PMCID: PMC5809005          DOI: 10.1016/j.carres.2018.01.004

Source DB:  PubMed          Journal:  Carbohydr Res        ISSN: 0008-6215            Impact factor:   2.104


  36 in total

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Journal:  J Comput Chem       Date:  2009-07-30       Impact factor: 3.376

2.  Drude Polarizable Force Field for Molecular Dynamics Simulations of Saturated and Unsaturated Zwitterionic Lipids.

Authors:  Hui Li; Janamejaya Chowdhary; Lei Huang; Xibing He; Alexander D MacKerell; Benoît Roux
Journal:  J Chem Theory Comput       Date:  2017-08-08       Impact factor: 6.006

3.  Six-site polarizable model of water based on the classical Drude oscillator.

Authors:  Wenbo Yu; Pedro E M Lopes; Benoît Roux; Alexander D MacKerell
Journal:  J Chem Phys       Date:  2013-01-21       Impact factor: 3.488

4.  Polarizable empirical force field for nitrogen-containing heteroaromatic compounds based on the classical Drude oscillator.

Authors:  Pedro E M Lopes; Guillaume Lamoureux; Alexander D Mackerell
Journal:  J Comput Chem       Date:  2009-09       Impact factor: 3.376

5.  Additive empirical force field for hexopyranose monosaccharides.

Authors:  Olgun Guvench; Shannon N Greene; Ganesh Kamath; John W Brady; Richard M Venable; Richard W Pastor; Alexander D Mackerell
Journal:  J Comput Chem       Date:  2008-11-30       Impact factor: 3.376

6.  Microsecond Dynamics and Network Analysis of the HIV-1 SOSIP Env Trimer Reveal Collective Behavior and Conserved Microdomains of the Glycan Shield.

Authors:  Thomas Lemmin; Cinque Soto; Jonathan Stuckey; Peter D Kwong
Journal:  Structure       Date:  2017-09-07       Impact factor: 5.006

7.  GROMOS 53A6GLYC, an Improved GROMOS Force Field for Hexopyranose-Based Carbohydrates.

Authors:  Laercio Pol-Fachin; Victor H Rusu; Hugo Verli; Roberto D Lins
Journal:  J Chem Theory Comput       Date:  2012-09-18       Impact factor: 6.006

8.  A polarizable force field of dipalmitoylphosphatidylcholine based on the classical Drude model for molecular dynamics simulations of lipids.

Authors:  Janamejaya Chowdhary; Edward Harder; Pedro E M Lopes; Lei Huang; Alexander D MacKerell; Benoît Roux
Journal:  J Phys Chem B       Date:  2013-07-30       Impact factor: 2.991

9.  Polarizable empirical force field for hexopyranose monosaccharides based on the classical Drude oscillator.

Authors:  Dhilon S Patel; Xibing He; Alexander D MacKerell
Journal:  J Phys Chem B       Date:  2014-02-24       Impact factor: 2.991

10.  Differential Impact of the Monovalent Ions Li⁺, Na⁺, K⁺, and Rb⁺ on DNA Conformational Properties.

Authors:  Alexey Savelyev; Alexander D MacKerell
Journal:  J Phys Chem Lett       Date:  2015-01-02       Impact factor: 6.475

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  10 in total

1.  Polarizable force field for RNA based on the classical drude oscillator.

Authors:  Justin A Lemkul; Alexander D MacKerell
Journal:  J Comput Chem       Date:  2018-12-15       Impact factor: 3.376

2.  Polarizable Force Field for Molecular Ions Based on the Classical Drude Oscillator.

Authors:  Fang-Yu Lin; Pedro E M Lopes; Edward Harder; Benoît Roux; Alexander D MacKerell
Journal:  J Chem Inf Model       Date:  2018-04-17       Impact factor: 4.956

3.  Balanced polarizable Drude force field parameters for molecular anions: phosphates, sulfates, sulfamates, and oxides.

Authors:  Abhishek A Kognole; Asaminew H Aytenfisu; Alexander D MacKerell
Journal:  J Mol Model       Date:  2020-05-24       Impact factor: 1.810

4.  Drude Polarizable Force Field Parametrization of Carboxylate and N-Acetyl Amine Carbohydrate Derivatives.

Authors:  Poonam Pandey; Asaminew H Aytenfisu; Alexander D MacKerell; Sairam S Mallajosyula
Journal:  J Chem Theory Comput       Date:  2019-08-29       Impact factor: 6.006

5.  Force Fields for Small Molecules.

Authors:  Fang-Yu Lin; Alexander D MacKerell
Journal:  Methods Mol Biol       Date:  2019

6.  Extension of the CHARMM Classical Drude Polarizable Force Field to N- and O-Linked Glycopeptides and Glycoproteins.

Authors:  Abhishek A Kognole; Asaminew H Aytenfisu; Alexander D MacKerell
Journal:  J Phys Chem B       Date:  2022-08-25       Impact factor: 3.466

7.  Further Optimization and Validation of the Classical Drude Polarizable Protein Force Field.

Authors:  Fang-Yu Lin; Jing Huang; Poonam Pandey; Chetan Rupakheti; Jing Li; Benoı T Roux; Alexander D MacKerell
Journal:  J Chem Theory Comput       Date:  2020-04-27       Impact factor: 6.006

8.  CHARMM Drude Polarizable Force Field for Glycosidic Linkages Involving Pyranoses and Furanoses.

Authors:  Asaminew H Aytenfisu; Mingjun Yang; Alexander D MacKerell
Journal:  J Chem Theory Comput       Date:  2018-05-04       Impact factor: 6.006

9.  CHARMM-GUI Drude prepper for molecular dynamics simulation using the classical Drude polarizable force field.

Authors:  Abhishek A Kognole; Jumin Lee; Sang-Jun Park; Sunhwan Jo; Payal Chatterjee; Justin A Lemkul; Jing Huang; Alexander D MacKerell; Wonpil Im
Journal:  J Comput Chem       Date:  2021-12-07       Impact factor: 3.376

Review 10.  Three-Dimensional Structures of Carbohydrates and Where to Find Them.

Authors:  Sofya I Scherbinina; Philip V Toukach
Journal:  Int J Mol Sci       Date:  2020-10-18       Impact factor: 5.923

  10 in total

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