Residue-Specific Structural and Dynamical Coupling of Protein and Hydration Water Revealed by Molecular Dynamics Simulations DOI Creative Commons
Shuai Wang, Jun Gao, Xiakun Chu

et al.

Biomolecules, Journal Year: 2025, Volume and Issue: 15(5), P. 660 - 660

Published: May 2, 2025

Proteins and their surrounding hydration water engage in a dynamic interplay that is critical for maintaining structural stability functional integrity. However, the intricate coupling between protein dynamics order of remains poorly understood. Here, we employ all-atom molecular simulations to investigate this relationship across four representative proteins. Our results reveal residues with greater flexibility or solvent exposure are surrounded by more disordered water, akin bulk whereas rigid buried non-polar associated structurally ordered shells. Due strong hydrogen bonding electrostatic interactions, charged exhibit most while water. We further uncovered positive correlation relaxation water: slower (faster) coupled Notably, weakens increasing residue exposure, displaying strongest coupling, weakest. To uncover mechanism, elucidate residue-specific fluctuations generating scatter plots. These findings provide comprehensive understanding mechanisms underlying protein–water offering valuable insights into role stability, dynamics, function.

Language: Английский

Exploring the influence of water micro assemblies on protein folding, enzyme catalysis and membrane dynamics DOI
Arturo Tozzi

European Biophysics Journal, Journal Year: 2025, Volume and Issue: unknown

Published: April 14, 2025

Language: Английский

Citations

0
Surface activity of optically-trapped single subpollen particle interacting with atmospheric water DOI Creative Commons
Yukai Ai,

Chuji Wang,

Yong‐Le Pan

et al.

Journal of Aerosol Science, Journal Year: 2025, Volume and Issue: unknown, P. 106609 - 106609

Published: May 1, 2025

Language: Английский

Citations

0
Accurate Determination of Isotope Effects on the Dynamics of H-Bond Breaking and Making in Liquid Water DOI
Ravi Malik, Nore Stolte, Harald Forbert

et al.

The Journal of Physical Chemistry Letters, Journal Year: 2025, Volume and Issue: unknown, P. 3727 - 3733

Published: April 5, 2025

Isotopic substitution of light hydrogen atoms with heavier deuterium in liquid water renders the resulting liquid, heavy (D2O), poisonous to most organisms when it replaces a critical fraction living organisms. The mechanisms through which disrupts biological function are challenging disentangle experimentally. has long been known affect H-bond dynamics water, but experiments have yet quantify extent differences time scales breaking and making processes between H2O D2O. In this work, we analyze extensive coupled cluster-quality path integral simulations D2O under ambient conditions that grant access unambiguous molecular analyses. We find substantial isotope effects on rates formation breaking, lifetimes, ∼25% slower than H2O. toxicity can thus be ascribed, at least part, effect slowed biochemical reactions.

Language: Английский

Citations

0
Residue-Specific Structural and Dynamical Coupling of Protein and Hydration Water Revealed by Molecular Dynamics Simulations DOI Creative Commons
Shuai Wang, Jun Gao, Xiakun Chu

et al.

Biomolecules, Journal Year: 2025, Volume and Issue: 15(5), P. 660 - 660

Published: May 2, 2025

Proteins and their surrounding hydration water engage in a dynamic interplay that is critical for maintaining structural stability functional integrity. However, the intricate coupling between protein dynamics order of remains poorly understood. Here, we employ all-atom molecular simulations to investigate this relationship across four representative proteins. Our results reveal residues with greater flexibility or solvent exposure are surrounded by more disordered water, akin bulk whereas rigid buried non-polar associated structurally ordered shells. Due strong hydrogen bonding electrostatic interactions, charged exhibit most while water. We further uncovered positive correlation relaxation water: slower (faster) coupled Notably, weakens increasing residue exposure, displaying strongest coupling, weakest. To uncover mechanism, elucidate residue-specific fluctuations generating scatter plots. These findings provide comprehensive understanding mechanisms underlying protein–water offering valuable insights into role stability, dynamics, function.

Language: Английский

Citations

0