Building asymmetric lipid bilayers for molecular dynamics simulations: What methods exist and how to choose one?

EH Chaisson, FA Heberle, M Doktorova - Membranes, 2023‏ - mdpi.com
The compositional asymmetry of biological membranes has attracted significant attention
over the last decade. Harboring more differences from symmetric membranes than …

[HTML][HTML] Model membrane systems used to study plasma membrane lipid asymmetry

HL Scott, KB Kennison, TA Enoki, M Doktorova… - Symmetry, 2021‏ - mdpi.com
It is well known that the lipid distribution in the bilayer leaflets of mammalian plasma
membranes (PMs) is not symmetric. Despite this, model membrane studies have largely …

[HTML][HTML] Molecular dynamics simulations of drug-conjugated cell-penetrating peptides

M Ivánczi, B Balogh, L Kis, I Mándity - Pharmaceuticals, 2023‏ - mdpi.com
Cell-penetrating peptides (CPPs) are small peptides capable of translocating through
biological membranes carrying various attached cargo into cells and even into the nucleus …

Unraveling the molecular mechanisms of membrane rupture: Insights from all-atom simulations and theoretical modeling

P Zhu, J Lin, Y Fu, C Shen, H Zhou, S Qu… - Journal of the Mechanics …, 2025‏ - Elsevier
Cell membrane rupture occurs universally and is long thought to be the terminal event of cell
death; however, there is an inadequate understanding of the microscopic mechanisms of …

[HTML][HTML] Exploring membrane binding targets of disordered human tau aggregates on lipid rafts using multiscale molecular dynamics simulations

KH Cheng, A Graf, A Lewis, T Pham, A Acharya - Membranes, 2022‏ - mdpi.com
The self-aggregation of tau, a microtubule-binding protein, has been linked to the onset of
Alzheimer's Disease. Recent studies indicate that the disordered tau aggregates, or …

[HTML][HTML] The Influence of Cholesterol on Membrane Targeted Bioactive Peptides: Modulating Peptide Activity Through Changes in Bilayer Biophysical Properties

JM Giraldo-Lorza, C Leidy, M Manrique-Moreno - Membranes, 2024‏ - mdpi.com
Cholesterol is a biological molecule that is essential for cellular life. It has unique features in
terms of molecular structure and function, and plays an important role in determining the …

Effects of gastrointestinal digestion on the cell bioavailability of sodium alginate coated liposomes containing DPP-IV inhibition active collagen peptides

P Wu, Y Yuan, L Chen, M Chen, BS Chiou, F Liu… - Food Bioscience, 2023‏ - Elsevier
Delivery matrices in foods need to be carefully designed for optimal delivery and to ensure
that beneficial compounds are subsequently absorbed in the gut. It has been found that …

Lipid domain boundary triggers membrane damage and protein folding of human islet amyloid polypeptide in the early pathogenesis of amyloid diseases

A Lewis, T Pham, N Nguyen, A Graf, KH Cheng - Biophysical Chemistry, 2023‏ - Elsevier
The misfolding and self-aggregation of human Islet Amyloid Polypeptide (hIAPP) are linked
to the onset of type 2 diabetes (T2D). However, the mechanism of how the disordered hIAPP …

Impact of increased membrane realism on conformational sampling of proteins

AT Weigle, M Carr, D Shukla - Journal of Chemical Theory and …, 2021‏ - ACS Publications
The realism and accuracy of lipid bilayer simulations through molecular dynamics (MD) are
heavily dependent on the lipid composition. While the field is pushing toward implementing …

Multiscale modeling of macromolecular interactions between tau-amylin oligomers and asymmetric lipid nanodomains that link Alzheimer's and diabetic diseases

N Santos, L Segura, A Lewis, T Pham, KH Cheng - Molecules, 2024‏ - mdpi.com
The molecular events of protein misfolding and self-aggregation of tau and amylin are
associated with the progression of Alzheimer's and diabetes, respectively. Recent studies …