Solvent effects on the energy landscapes and folding kinetics of polyalanine
Y Levy, J Jortner, OM Becker - Proceedings of the National …, 2001 - National Acad Sciences
The effect of a solvation on the thermodynamics and kinetics of polyalanine (Ala12) is
explored on the basis of its energy landscapes in vacuum and in an aqueous solution. Both …
explored on the basis of its energy landscapes in vacuum and in an aqueous solution. Both …
Helix folding of an alanine-based peptide in explicit water
X Wu, S Wang - The Journal of Physical Chemistry B, 2001 - ACS Publications
Computer simulations using full atomic representations for both the peptide and water
molecules were performed to study the folding of a 16-residue alanine-based helical peptide …
molecules were performed to study the folding of a 16-residue alanine-based helical peptide …
ABSINTH: a new continuum solvation model for simulations of polypeptides in aqueous solutions
A new implicit solvation model for use in Monte Carlo simulations of polypeptides is
introduced. The model is termed ABSINTH for self‐Assembly of Biomolecules Studied by an …
introduced. The model is termed ABSINTH for self‐Assembly of Biomolecules Studied by an …
Water and proteins: A love–hate relationship
Y Levy, JN Onuchic - … of the National Academy of Sciences, 2004 - National Acad Sciences
It is widely appreciated that water molecules play an invaluable role in governing the
structure, stability, dynamics, and function of biomolecules. The hydration forces are …
structure, stability, dynamics, and function of biomolecules. The hydration forces are …
A test on peptide stability of AMBER force fields with implicit solvation
We used replica exchange molecular dynamics (REMD) simulations to evaluate four
different AMBER force fields and three different implicit solvent models. Our aim was to …
different AMBER force fields and three different implicit solvent models. Our aim was to …
Protein simulations with an optimized water model: cooperative helix formation and temperature-induced unfolded state collapse
A recognized shortcoming in current protein simulations is that most force fields are
parametrized with relatively primitive three-site water models. Since the deficiencies of the …
parametrized with relatively primitive three-site water models. Since the deficiencies of the …
Discrimination between native and intentionally misfolded conformations of proteins: ES/IS, a new method for calculating conformational free energy that uses both …
YN Vorobjev, JC Almagro… - … : Structure, Function, and …, 1998 - Wiley Online Library
A new method for calculating the total conformational free energy of proteins in water solvent
is presented. The method consists of a relatively brief simulation by molecular dynamics with …
is presented. The method consists of a relatively brief simulation by molecular dynamics with …
Osmotic pressure simulations of amino acids and peptides highlight potential routes to protein force field parameterization
Recent molecular dynamics (MD) simulations of proteins have suggested that common force
fields overestimate the strength of amino acid interactions in aqueous solution. In an attempt …
fields overestimate the strength of amino acid interactions in aqueous solution. In an attempt …
Toward a coarse-grained protein model coupled with a coarse-grained solvent model: Solvation free energies of amino acid side chains
W Han, CK Wan, YD Wu - Journal of chemical theory and …, 2008 - ACS Publications
Recently, we reported that molecular dynamics (MD) simulations using a coarse-grained
(CG) peptide model coupled with a CG water model are able to reproduce many of the …
(CG) peptide model coupled with a CG water model are able to reproduce many of the …
On the coupling between the dynamics of protein and water
Interactions between water and biomolecules can significantly change the former's
structural, dynamic, and thermodynamic properties relative to the bulk. Experimental …
structural, dynamic, and thermodynamic properties relative to the bulk. Experimental …