Role of hydration water in the onset of protein structural dynamics

G Schirò, M Weik - Journal of Physics: Condensed Matter, 2019 - iopscience.iop.org
Proteins are the molecular workhorses in a living organism. Their 3D structures are
animated by a multitude of equilibrium fluctuations and specific out-of-equilibrium motions …

Different force fields give rise to different amyloid aggregation pathways in molecular dynamics simulations

S Samantray, F Yin, B Kav… - Journal of chemical …, 2020 - ACS Publications
The progress toward understanding the molecular basis of Alzheimers's disease is strongly
connected to elucidating the early aggregation events of the amyloid-β (Aβ) peptide …

[HTML][HTML] The geometry of protein hydration

F Persson, P Söderhjelm, B Halle - The Journal of chemical physics, 2018 - pubs.aip.org
Based on molecular dynamics simulations of four globular proteins in dilute aqueous
solution, with three different water models, we examine several, essentially geometrical …

[HTML][HTML] The spatial range of protein hydration

F Persson, P Söderhjelm, B Halle - The Journal of Chemical Physics, 2018 - pubs.aip.org
Proteins interact with their aqueous surroundings, thereby modifying the physical properties
of the solvent. The extent of this perturbation has been investigated by numerous methods in …

[HTML][HTML] Excess entropy and crystallization in Stillinger-Weber and Lennard-Jones fluids

D Dhabal, AH Nguyen, M Singh, P Khatua… - The Journal of …, 2015 - pubs.aip.org
Molecular dynamics simulations are used to contrast the supercooling and crystallization
behaviour of monatomic liquids that exemplify the transition from simple to anomalous …

On the coupling between the dynamics of protein and water

Y Gavrilov, JD Leuchter, Y Levy - Physical Chemistry Chemical Physics, 2017 - pubs.rsc.org
Interactions between water and biomolecules can significantly change the former's
structural, dynamic, and thermodynamic properties relative to the bulk. Experimental …

Total free energy analysis of fully hydrated proteins

J Kalayan, A Chakravorty, J Warwicker… - Proteins: Structure …, 2023 - Wiley Online Library
The total free energy of a hydrated biomolecule and its corresponding decomposition of
energy and entropy provides detailed information about regions of thermodynamic stability …

Dynamic heterogeneity at the interface of an intrinsically disordered peptide

S Mondal, KP Ghanta… - Journal of Chemical …, 2022 - ACS Publications
It is believed that water around an intrinsically disordered protein or peptide (IDP) in an
aqueous environment plays an important role in guiding its conformational properties and …

Exploring Heterogeneous Dynamical Environment around an Ensemble of Aβ42 Peptide Monomer Conformations

P Khatua, M Gupta… - Journal of Chemical …, 2022 - ACS Publications
Exploring the conformational properties of amyloid β (Aβ) peptides and the role of solvent
(water) in guiding the dynamical environment at their interfaces is crucial for microscopic …

Hydration water distribution around intrinsically disordered proteins

L Aggarwal, P Biswas - The Journal of Physical Chemistry B, 2018 - ACS Publications
The distribution and local structural order of hydration water in the proximity of intrinsically
disordered proteins/regions are investigated within the frame work of three-dimensional (3D) …