From structure and dynamics to biomolecular functions: The ubiquitous role of solvent in biology

S Mondal, B Bagchi - Current Opinion in Structural Biology, 2022 - Elsevier
Biological activity requires a solvent that can provide a suitable environment, which satisfies
the twin need for stability and the ability to change. Among all the solvents water plays the …

[HTML][HTML] Conformational stability and denaturation processes of proteins investigated by electrophoresis under extreme conditions

P Masson, S Lushchekina - Molecules, 2022 - mdpi.com
The functional structure of proteins results from marginally stable folded conformations.
Reversible unfolding, irreversible denaturation, and deterioration can be caused by …

[HTML][HTML] Thermodynamic forces from protein and water govern condensate formation of an intrinsically disordered protein domain

S Mukherjee, LV Schäfer - Nature Communications, 2023 - nature.com
Liquid-liquid phase separation (LLPS) can drive a multitude of cellular processes by
compartmentalizing biological cells via the formation of dense liquid biomolecular …

Entropy tug-of-war determines solvent effects in the liquid–liquid phase separation of a globular protein

S Mukherjee, S Ramos, S Pezzotti… - The Journal of …, 2024 - ACS Publications
Liquid–liquid phase separation (LLPS) plays a key role in the compartmentalization of cells
via the formation of biomolecular condensates. Here, we combined atomistic molecular …

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 …

[HTML][HTML] Protein 3D Hydration: A Case of Bovine Pancreatic Trypsin Inhibitor

SE Kruchinin, EE Kislinskaya, GN Chuev… - International Journal of …, 2022 - mdpi.com
Characterization of the hydrated state of a protein is crucial for understanding its structural
stability and function. In the present study, we have investigated the 3D hydration structure of …

Fortification of thermal and structural stability of hemoglobin using choline chloride-based deep eutectic solvents

H Arora, D Dhiman, K Kumar… - Physical Chemistry …, 2022 - pubs.rsc.org
Of late, DESs have occupied the centre stage due to their eco-friendly and resource-efficient
nature and their low toxicity. In this work, we have investigated the structural and thermal …

Free Energy Density of a Fluid and Its Role in Solvation and Binding

MK Gilson, T Kurtzman - Journal of Chemical Theory and …, 2024 - ACS Publications
The concept that a fluid has a position-dependent free energy density appears in the
literature but has not been fully developed or accepted. We set this concept on an …

Fluorinated Protein–Ligand Complexes: A Computational Perspective

L Wehrhan, BG Keller - The Journal of Physical Chemistry B, 2024 - ACS Publications
Fluorine is an element renowned for its unique properties. Its powerful capability to modulate
molecular properties makes it an attractive substituent for protein binding ligands; however …

Thermodynamic consequences of stapling side‐chains on a peptide ligand using a lactam‐bridge: A theoretical study on anti‐angiogenic peptides targeting VEGF

M Kalathingal, YM Rhee - Proteins: Structure, Function, and …, 2024 - Wiley Online Library
Peptides are promising therapeutic agents for various biological targets due to their high
efficacy and low toxicity, and the design of peptide ligands with high binding affinity to the …