Literature DB >> 29471634

Force fields for monovalent and divalent metal cations in TIP3P water based on thermodynamic and kinetic properties.

Shavkat Mamatkulov1, Nadine Schwierz2.   

Abstract

Metal cations are essential in many vital processes. In order to capture the role of different cations in all-atom molecular dynamics simulations of biological processes, an accurate parametrization is crucial. Here, we develop force field parameters for the metal cations Li+, Na+, K+, Cs+, Mg2+, Ca2+, Sr2+, and Ba2+ in combination with the TIP3P water model that is frequently used in biomolecular simulations. In progressing toward improved force fields, the approach presented here is an extension of previous efforts and allows us to simultaneously reproduce thermodynamic and kinetic properties of aqueous solutions. We systematically derive the parameters of the 12-6 Lennard-Jones potential which accurately reproduces the experimental solvation free energy, the activity derivative, and the characteristics of water exchange from the first hydration shell of the metal cations. In order to reproduce all experimental properties, a modification of the Lorentz-Berthelot combination rule is required for Mg2+. Using a balanced set of solution properties, the optimized force field parameters aim to capture the fine differences between distinct metal cations including specific ion binding affinities and the kinetics of cation binding to biologically important anionic groups.

Entities:  

Year:  2018        PMID: 29471634     DOI: 10.1063/1.5017694

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


  10 in total

1.  A multiscale approach to predict the binding mode of metallo beta-lactamase inhibitors.

Authors:  Silvia Gervasoni; James Spencer; Philip Hinchliffe; Alessandro Pedretti; Franco Vairoletti; Graciela Mahler; Adrian J Mulholland
Journal:  Proteins       Date:  2021-09-20

2.  Twisting DNA by salt.

Authors:  Sergio Cruz-León; Willem Vanderlinden; Peter Müller; Tobias Forster; Georgina Staudt; Yi-Yun Lin; Jan Lipfert; Nadine Schwierz
Journal:  Nucleic Acids Res       Date:  2022-06-10       Impact factor: 19.160

3.  Novel eGZ-motif formed by regularly extruded guanine bases in a left-handed Z-DNA helix as a major motif behind CGG trinucleotide repeats.

Authors:  Ashkan Fakharzadeh; Jiahui Zhang; Christopher Roland; Celeste Sagui
Journal:  Nucleic Acids Res       Date:  2022-05-20       Impact factor: 19.160

4.  Tuning the Sensitivity of Genetically Encoded Fluorescent Potassium Indicators through Structure-Guided and Genome Mining Strategies.

Authors:  Cristina C Torres Cabán; Minghan Yang; Cuixin Lai; Lina Yang; Fedor V Subach; Brian O Smith; Kiryl D Piatkevich; Edward S Boyden
Journal:  ACS Sens       Date:  2022-04-15       Impact factor: 9.618

5.  Ion-Specific and pH-Dependent Hydration of Mica-Electrolyte Interfaces.

Authors:  Simone R van Lin; Kara K Grotz; Igor Siretanu; Nadine Schwierz; Frieder Mugele
Journal:  Langmuir       Date:  2019-04-22       Impact factor: 3.882

6.  Desmosome architecture derived from molecular dynamics simulations and cryo-electron tomography.

Authors:  Mateusz Sikora; Utz H Ermel; Anna Seybold; Michael Kunz; Giulia Calloni; Julian Reitz; R Martin Vabulas; Gerhard Hummer; Achilleas S Frangakis
Journal:  Proc Natl Acad Sci U S A       Date:  2020-10-16       Impact factor: 11.205

7.  Cryo-EM demonstrates the in vitro proliferation of an ex vivo amyloid fibril morphology by seeding.

Authors:  Thomas Heerde; Matthies Rennegarbe; Alexander Biedermann; Dilan Savran; Peter B Pfeiffer; Manuel Hitzenberger; Julian Baur; Ioana Puscalau-Girtu; Martin Zacharias; Nadine Schwierz; Christian Haupt; Matthias Schmidt; Marcus Fändrich
Journal:  Nat Commun       Date:  2022-01-10       Impact factor: 14.919

8.  Optimized Magnesium Force Field Parameters for Biomolecular Simulations with Accurate Solvation, Ion-Binding, and Water-Exchange Properties in SPC/E, TIP3P-fb, TIP4P/2005, TIP4P-Ew, and TIP4P-D.

Authors:  Kara K Grotz; Nadine Schwierz
Journal:  J Chem Theory Comput       Date:  2021-12-09       Impact factor: 6.006

9.  Artificial Intelligence Resolves Kinetic Pathways of Magnesium Binding to RNA.

Authors:  Jan Neumann; Nadine Schwierz
Journal:  J Chem Theory Comput       Date:  2022-01-27       Impact factor: 6.006

10.  SAA fibrils involved in AA amyloidosis are similar in bulk and by single particle reconstitution: A MAS solid-state NMR study.

Authors:  Arpita Sundaria; Falk Liberta; Dilan Savran; Riddhiman Sarkar; Natalia Rodina; Carsten Peters; Nadine Schwierz; Christian Haupt; Matthias Schmidt; Bernd Reif
Journal:  J Struct Biol X       Date:  2022-07-19
  10 in total

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