Bioinformatics approaches to discovering food-derived bioactive peptides: Reviews and perspectives

Z Du, J Comer, Y Li - TrAC Trends in Analytical Chemistry, 2023 - Elsevier
Food-derived bioactive peptides (FBPs) are gaining interest due to their great potential in
agricultural byproduct valorization and high-activity peptide screening. The introduction of …

Unconventional production strategies, action mechanisms, and structure-functional attributes of food-derived peptides

TD Le, I Suttikhana, TJ Ashaolu - Food Hydrocolloids, 2023 - Elsevier
Food-derived peptides (FDPs) are constantly increasing in popularity due to their health-
promoting potential. However, using the lens of conventional techniques to study FDPs is …

Protein assembly and crowding simulations

L Heo, Y Sugita, M Feig - Current opinion in structural biology, 2022 - Elsevier
Proteins encounter frequent molecular interactions in biological environments. Computer
simulations have become an increasingly important tool in providing mechanistic insights …

Toward a general neural network force field for protein simulations: refining the intramolecular interaction in protein

P Zhang, W Yang - The Journal of Chemical Physics, 2023 - pubs.aip.org
Molecular dynamics (MD) is an extremely powerful, highly effective, and widely used
approach to understanding the nature of chemical processes in atomic details for proteins …

Preferential Solvation Phenomena as Solute-Induced Structure-Making/Breaking Processes: Linking Thermodynamic Preferential Interaction Parameters to …

AA Chialvo - The Journal of Physical Chemistry B, 2024 - ACS Publications
In this work, we identify the explicit macroscopic-to-microscopic rigorous links between
existing thermodynamic preferential interaction parameters Γ Q α Q β (χ i) and …

Trifluoroethanol direct interactions with protein backbones destabilize α-helices

AF Pereira, V Piccoli, L Martínez - Journal of Molecular Liquids, 2022 - Elsevier
Abstract 2, 2, 2-Trifluoroethanol (TFE) is a well-known protein α-helix stabilizer;
nevertheless, after much investigation, no consensus has been reached on TFE's stabilizing …

Ion–Ion Association in Bulk Mixed Electrolytes Using Global and Local Electroneutrality Constraints

EA Ploetz, ND Smyers, PE Smith - The Journal of Physical …, 2025 - ACS Publications
Ion atmospheres play a critical role in modulating the interactions between charged
components in solutions. However, a detailed description of the nature of ion atmospheres …

Structural Study of Aqueous Electrolyte Solution by MeV Liquid Electron Scattering

B Huang, L Yun, Y Yang, R Han, K Chen… - The Journal of …, 2024 - ACS Publications
The impact of ions on water has long been a subject of great interest, as it is closely tied to
the hydration structure, dynamics, and properties of electrolyte solutions. Over centuries of …

Simulating polyproline ii-helix-rich peptides with the latest kirkwood–buff force field: A direct comparison with amber and charmm

JAP McIvor, DS Larsen… - The Journal of Physical …, 2022 - ACS Publications
We simulated the dynamics of a set of peptides characterized by ensembles rich in PPII-
helical content, to assess the ability of the most recent Kirkwood–Buff force field (KBFF20) to …

[HTML][HTML] Linking Solution Microstructure and Solvation Thermodynamics of Mixed-Solvent Systems: Formal Results, Critical Observations, and Modeling Pitfalls

AA Chialvo - Thermo, 2024 - mdpi.com
This review provides a critical assessment of the current state of affairs regarding the
solvation thermodynamics involving mixed-solvent systems. It focuses specifically on (i) its …