Computational modeling of realistic cell membranes

SJ Marrink, V Corradi, PCT Souza, HI Ingolfsson… - Chemical …, 2019 - ACS Publications
Cell membranes contain a large variety of lipid types and are crowded with proteins,
endowing them with the plasticity needed to fulfill their key roles in cell functioning. The …

Characterization of lipid–protein interactions and lipid-mediated modulation of membrane protein function through molecular simulation

MP Muller, T Jiang, C Sun, M Lihan, S Pant… - Chemical …, 2019 - ACS Publications
The cellular membrane constitutes one of the most fundamental compartments of a living
cell, where key processes such as selective transport of material and exchange of …

Chimeric nanobody-decorated liposomes by self-assembly

MM Rahman, J Wang, G Wang, Z Su, Y Li… - Nature …, 2024 - nature.com
Liposomes as drug vehicles have advantages, such as payload protection, tunable carrying
capacity and improved biodistribution. However, due to the dysfunction of targeting moieties …

Perspective on the Martini model

SJ Marrink, DP Tieleman - Chemical Society Reviews, 2013 - pubs.rsc.org
The Martini model, a coarse-grained force field for biomolecular simulations, has found a
broad range of applications since its release a decade ago. Based on a building block …

Improved parameters for the martini coarse-grained protein force field

DH De Jong, G Singh, WFD Bennett… - Journal of chemical …, 2013 - ACS Publications
The Martini coarse-grained force field has been successfully used for simulating a wide
range of (bio) molecular systems. Recent progress in our ability to test the model against …

The multifaceted role of SNARE proteins in membrane fusion

J Han, K Pluhackova, RA Böckmann - Frontiers in physiology, 2017 - frontiersin.org
Membrane fusion is a key process in all living organisms that contributes to a variety of
biological processes including viral infection, cell fertilization, as well as intracellular …

CHARMM-GUI Membrane Builder: Past, Current, and Future Developments and Applications

S Feng, S Park, YK Choi, W Im - Journal of chemical theory and …, 2023 - ACS Publications
Molecular dynamics simulations of membranes and membrane proteins serve as
computational microscopes, revealing coordinated events at the membrane interface. As G …

Molecular machines governing exocytosis of synaptic vesicles

R Jahn, D Fasshauer - Nature, 2012 - nature.com
Calcium-dependent exocytosis of synaptic vesicles mediates the release of
neurotransmitters. Important proteins in this process have been identified such as the …

Free energies of membrane stalk formation from a lipidomics perspective

CS Poojari, KC Scherer, JS Hub - Nature communications, 2021 - nature.com
Many biological membranes are asymmetric and exhibit complex lipid composition,
comprising hundreds of distinct chemical species. Identifying the biological function and …

All-atom molecular dynamics simulations of Synaptotagmin-SNARE-complexin complexes bridging a vesicle and a flat lipid bilayer

J Rizo, L Sari, Y Qi, W Im, MM Lin - Elife, 2022 - elifesciences.org
Synaptic vesicles are primed into a state that is ready for fast neurotransmitter release upon
Ca 2+-binding to Synaptotagmin-1. This state likely includes trans-SNARE complexes …