Local water bridges and protein conformational stability

M Petukhov, D Cregut, CM Soares, L Serrano - Protein Science, 1999 - cambridge.org
Recent studies have pointed out the important role of local water structures in protein
conformational stability. Here, we present an accurate and computationally effective way to …

Buried water molecules contribute to the conformational stability of a protein

K Takano, Y Yamagata, K Yutani - Protein engineering, 2003 - academic.oup.com
This study sought to attain a better understanding of the contribution of buried water
molecules to protein stability. The 3SS human lysozyme lacks one disulfide bond between …

Thermodynamic analysis of water molecules at the surface of proteins and applications to binding site prediction and characterization

T Beuming, Y Che, R Abel, B Kim… - Proteins: Structure …, 2012 - Wiley Online Library
Water plays an essential role in determining the structure and function of all biological
systems. Recent methodological advances allow for an accurate and efficient estimation of …

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 of hydration water in proteins: a comparison of molecular dynamics simulations and database analysis

N Bhattacharjee, P Biswas - Biophysical Chemistry, 2011 - Elsevier
Hydration layer water molecules play important structural and functional roles in proteins.
Despite being a critical component in biomolecular systems, characterizing the properties of …

How the stability of a folded protein depends on interfacial water properties and residue-residue interactions

V Bianco, N Pages-Gelabert, I Coluzza… - Journal of Molecular …, 2017 - Elsevier
Proteins tend to adopt a single or a reduced ensemble of configurations at natural conditions
[1], but changes in temperature T and pressure P induce their unfolding. Therefore for each …

Water‐mediated interactions destabilize proteins

T Sumi, H Imamura - Protein Science, 2021 - Wiley Online Library
Proteins are folded to avoid exposure of the nonpolar groups to water because water‐
mediated interactions between nonpolar groups are a promising factor in the …

Statistical and molecular dynamics studies of buried waters in globular proteins

S Park, JG Saven - Proteins: Structure, Function, and …, 2005 - Wiley Online Library
Buried solvent molecules are common in the core of globular proteins and contribute to
structural stability. Folding necessitates the burial of polar backbone atoms in the protein …

A “solvated rotamer” approach to modeling water‐mediated hydrogen bonds at protein–protein interfaces

L Jiang, B Kuhlman, T Kortemme… - … : structure, function, and …, 2005 - Wiley Online Library
Water‐mediated hydrogen bonds play critical roles at protein–protein and protein–nucleic
acid interfaces, and the interactions formed by discrete water molecules cannot be captured …

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 …