Overcoming the limitations of the MARTINI force field in simulations of polysaccharides

PS Schmalhorst, F Deluweit, R Scherrers… - Journal of Chemical …, 2017 - ACS Publications
Polysaccharides (carbohydrates) are key regulators of a large number of cell biological
processes. However, precise biochemical or genetic manipulation of these often complex …

Hydrotropy: Monomer–Micelle equilibrium and minimum hydrotrope concentration

S Shimizu, N Matubayasi - The Journal of Physical Chemistry B, 2014 - ACS Publications
Drug molecules with low aqueous solubility can be solubilized by a class of cosolvents,
known as hydrotropes. Their action has often been explained by an analogy with micelle …

Preferential solvation: Dividing surface vs excess numbers

S Shimizu, N Matubayasi - The Journal of Physical Chemistry B, 2014 - ACS Publications
How do osmolytes affect the conformation and configuration of supramolecular assembly,
such as ion channel opening and actin polymerization? The key to the answer lies in the …

The origin of cooperative solubilisation by hydrotropes

S Shimizu, N Matubayasi - Physical Chemistry Chemical Physics, 2016 - pubs.rsc.org
The signature of hydrotropic solubilisation is the sigmoidal solubility curve; when plotted
against hydrotrope concentration, solubility increases suddenly after the minimum …

Optimizing solute–solute interactions in the GLYCAM06 and CHARMM36 carbohydrate force fields using osmotic pressure measurements

WK Lay, MS Miller, AH Elcock - Journal of chemical theory and …, 2016 - ACS Publications
GLYCAM06 and CHARMM36 are successful force fields for modeling carbohydrates. To
correct recently identified deficiencies with both force fields, we adjusted intersolute …

Predicting the chemical potential and osmotic pressure of polysaccharide solutions by molecular simulations

J Sauter, A Grafmüller - Journal of chemical theory and …, 2016 - ACS Publications
Differences in the chemical potential of water and the resulting osmotic pressure across
semipermeable membranes are of fundamental importance for many biological systems …

Reparametrization of protein force field nonbonded interactions guided by osmotic coefficient measurements from molecular dynamics simulations

MS Miller, WK Lay, S Li, WC Hacker, J An… - Journal of chemical …, 2017 - ACS Publications
There is a small, but growing, body of literature describing the use of osmotic coefficient
measurements to validate and reparametrize simulation force fields. Here we have …

Kirkwood–Buff-derived force field for peptides and proteins: philosophy and development of KBFF20

EA Ploetz, S Karunaweera, N Bentenitis… - Journal of Chemical …, 2021 - ACS Publications
A new classical nonpolarizable force field, KBFF20, for the simulation of peptides and
proteins is presented. The force field relies heavily on the use of Kirkwood–Buff theory to …

Molecular dynamics simulations of highly crowded amino acid solutions: comparisons of eight different force field combinations with experiment and with each other

CT Andrews, AH Elcock - Journal of chemical theory and …, 2013 - ACS Publications
Although it is now commonly accepted that the highly crowded conditions encountered
inside biological cells have the potential to significantly alter the thermodynamic properties …

[HTML][HTML] Linking Solution Microstructure and Solvation Thermodynamics of Mixed-Solvent Systems: Formal Results, Critical Observations, and Modeling Pitfalls

AA Chialvo - Thermo, 2024 - mdpi.com
This review provides a critical assessment of the current state of affairs regarding the
solvation thermodynamics involving mixed-solvent systems. It focuses specifically on (i) its …