[HTML][HTML] Modeling membranes in situ

CM Brown, SJ Marrink - Current Opinion in Structural Biology, 2024 - Elsevier
Molecular dynamics simulations of cellular membranes have come a long way—from simple
model lipid bilayers to multicomponent systems capturing the crowded and complex nature …

Pathways to a shiny future: Building the foundation for computational physical chemistry and biophysics in 2050

D Biriukov, R Vácha - ACS Physical Chemistry Au, 2024 - ACS Publications
In the last quarter-century, the field of molecular dynamics (MD) has undergone a
remarkable transformation, propelled by substantial enhancements in software, hardware …

Interaction of MRI Contrast Agent [Gd(DOTA)] with Lipid Membranes: A Molecular Dynamics Study

AC Oliveira, HAL Filipe, CFGC Geraldes… - Inorganic …, 2024 - ACS Publications
Contrast agents are important imaging probes in clinical MRI, allowing the identification of
anatomic changes that otherwise would not be possible. Intensive research on the …

Solid-state NMR validation of OPLS4: Structure of pc-lipid bilayers and its modulation by dehydration

M Kurki, AM Nesterenko, NE Alsaker… - The Journal of …, 2024 - ACS Publications
Atomistic molecular dynamics (MD) simulations are a much-used tool for investigating the
structure and dynamics of biomembranes with atomic resolution. The validity of the …

Probing the dynamic landscape of peptides in molecular assemblies by synergized NMR experiments and MD simulations

R Nencini, MLG Regnier, SM Backlund… - Communications …, 2024 - nature.com
Peptides or proteins containing small biomolecular aggregates, such as micelles, bicelles,
droplets and nanodiscs, are pivotal in many fields ranging from structural biology to …

Evaluating polarizable biomembrane simulations against experiments

HS Antila, S Dixit, B Kav, JJ Madsen… - Journal of chemical …, 2024 - ACS Publications
Owing to the increase of available computational capabilities and the potential for providing
a more accurate description, polarizable molecular dynamics force fields are gaining …

Free Energy of Membrane Pore Formation and Stability from Molecular Dynamics Simulations

T Rivel, D Biriukov, I Kabelka… - Journal of Chemical …, 2025 - ACS Publications
Understanding the molecular mechanisms of pore formation is crucial for elucidating
fundamental biological processes and develo** therapeutic strategies, such as the design …

[HTML][HTML] Membrane binding and lipid-protein interaction of the C2 domain from coagulation factor V

YZ Ohkubo, PW Radulovic, AN Kahira… - Current Research In …, 2024 - Elsevier
Anchoring of coagulation factors to anionic regions of the membrane involves the C2
domain as a key player. The rate of enzymatic reactions of the coagulation factors is …

Meta-Analysis of Permeability Literature Data Shows Possibilities and Limitations of Popular Methods

K Storchmannová, M Balouch, J Juračka… - Molecular …, 2024 - ACS Publications
Permeability is an important molecular property in drug discovery, as it co-determines
pharmacokinetics whenever a drug crosses the phospholipid bilayer, eg, into the cell, in the …

Signal peptidase SpsB coordinates staphylococcal cell cycle, surface protein septal trafficking, and LTA synthesis

R Zhang, Y Jia, SJ Scaffidi, JJ Madsen, W Yu - mBio, 2025 - journals.asm.org
Cell wall-anchored surface proteins of Gram-positive bacteria, harboring a highly conserved
YSIRK/GS signal peptide (SPYSIRK+), are deposited at cell division septum and anchored …