Literature DB >> 28437100

Reparameterization of Solute-Solute Interactions for Amino Acid-Sugar Systems Using Isopiestic Osmotic Pressure Molecular Dynamics Simulations.

Wesley K Lay1, Mark S Miller1, Adrian H Elcock1.   

Abstract

AMBER/GLYCAM and CHARMM are popular force fields for simulations of amino acids and sugars. Here we report excessively attractive amino acid-sugar interactions in both force fields, and corrections to nonbonded interactions that match experimental osmotic pressures of mixed aqueous solutions of diglycine and sucrose. The modified parameters also improve the ΔGtrans of diglycine from water to aqueous sucrose and, with AMBERff99SB/GLYCAM06, eliminate a caging effect seen in previous simulations of the protein ubiquitin with glucose.

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Year:  2017        PMID： 28437100      PMCID： PMC5844349          DOI： 10.1021/acs.jctc.7b00194

Source DB:  PubMed          Journal:  J Chem Theory Comput        ISSN： 1549-9618            Impact factor:   6.006


  42 in total

1.  CHARMM additive all-atom force field for carbohydrate derivatives and its utility in polysaccharide and carbohydrate-protein modeling.

Authors:  Olgun Guvench; Sairam S Mallajosyula; E Prabhu Raman; Elizabeth Hatcher; Kenno Vanommeslaeghe; Theresa J Foster; Francis W Jamison; Alexander D Mackerell
Journal:  J Chem Theory Comput       Date:  2011-10-11       Impact factor: 6.006

2.  Comparison of multiple Amber force fields and development of improved protein backbone parameters.

Authors:  Viktor Hornak; Robert Abel; Asim Okur; Bentley Strockbine; Adrian Roitberg; Carlos Simmerling
Journal:  Proteins       Date:  2006-11-15

3.  A GROMOS-Compatible Force Field for Small Organic Molecules in the Condensed Phase: The 2016H66 Parameter Set.

Authors:  Bruno A C Horta; Pascal T Merz; Patrick F J Fuchs; Jozica Dolenc; Sereina Riniker; Philippe H Hünenberger
Journal:  J Chem Theory Comput       Date:  2016-07-08       Impact factor: 6.006

4.  Are Protein Force Fields Getting Better? A Systematic Benchmark on 524 Diverse NMR Measurements.

Authors:  Kyle A Beauchamp; Yu-Shan Lin; Rhiju Das; Vijay S Pande
Journal:  J Chem Theory Comput       Date:  2012-03-12       Impact factor: 6.006

5.  Investigation of the effect of glycosylation on human prion protein by molecular dynamics.

Authors:  Linghao Zhong; Jimin Xie
Journal:  J Biomol Struct Dyn       Date:  2009-04

6.  Solution Properties of Hemicellulose Polysaccharides with Four Common Carbohydrate Force Fields.

Authors:  Jörg Sauter; Andrea Grafmüller
Journal:  J Chem Theory Comput       Date:  2015-03-23       Impact factor: 6.006

7.  The stabilization of proteins by sucrose.

Authors:  J C Lee; S N Timasheff
Journal:  J Biol Chem       Date:  1981-07-25       Impact factor: 5.157

Review 8.  Murein (peptidoglycan) structure, architecture and biosynthesis in Escherichia coli.

Authors:  Waldemar Vollmer; Ute Bertsche
Journal:  Biochim Biophys Acta       Date:  2007-06-16

9.  Improved side-chain torsion potentials for the Amber ff99SB protein force field.

Authors:  Kresten Lindorff-Larsen; Stefano Piana; Kim Palmo; Paul Maragakis; John L Klepeis; Ron O Dror; David E Shaw
Journal:  Proteins       Date:  2010-06

10.  Multisite ion model in concentrated solutions of divalent cations (MgCl2 and CaCl2): osmotic pressure calculations.

Authors:  Akansha Saxena; Angel E García
Journal:  J Phys Chem B       Date:  2014-12-22       Impact factor: 2.991
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  5 in total

Review 1.  Predicting the Structures of Glycans, Glycoproteins, and Their Complexes.

Authors:  Robert J Woods
Journal:  Chem Rev       Date:  2018-08-09       Impact factor: 60.622

2.  Reparametrization of Protein Force Field Nonbonded Interactions Guided by Osmotic Coefficient Measurements from Molecular Dynamics Simulations.

Authors:  Mark S Miller; Wesley K Lay; Shuxiang Li; William C Hacker; Jiadi An; Jianlan Ren; Adrian H Elcock
Journal:  J Chem Theory Comput       Date:  2017-03-27       Impact factor: 6.006

Review 3.  New tricks for old dogs: improving the accuracy of biomolecular force fields by pair-specific corrections to non-bonded interactions.

Authors:  Jejoong Yoo; Aleksei Aksimentiev
Journal:  Phys Chem Chem Phys       Date:  2018-03-28       Impact factor: 3.676

4.  Optimizing Nonbonded Interactions of the OPLS Force Field for Aqueous Solutions of Carbohydrates: How to Capture Both Thermodynamics and Dynamics.

Authors:  Seyed Hossein Jamali; Thijs van Westen; Othonas A Moultos; Thijs J H Vlugt
Journal:  J Chem Theory Comput       Date:  2018-11-20       Impact factor: 6.006

5.  Insight into the Dual Inhibition Mechanism of Corilagin against MRSA Serine/Threonine Phosphatase (Stp1) by Molecular Modeling.

Authors:  Yanan Yang; Xiyan Wang; Yawen Gao; Xiaodi Niu
Journal:  ACS Omega       Date:  2020-12-15
  5 in total

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