Two decades of Martini: Better beads, broader scope

SJ Marrink, L Monticelli, MN Melo… - Wiley …, 2023 - Wiley Online Library
The Martini model, a coarse‐grained force field for molecular dynamics simulations, has
been around for nearly two decades. Originally developed for lipid‐based systems by the …

[HTML][HTML] Simulating realistic membrane shapes

W Pezeshkian, SJ Marrink - Current opinion in cell biology, 2021 - Elsevier
Biological membranes exhibit diversity in their shapes and complexity in chemical
compositions that are linked to many cellular functions. These two central features of …

Effects of weak nonspecific interactions with ATP on proteins

M Nishizawa, E Walinda, D Morimoto… - Journal of the …, 2021 - ACS Publications
Adenosine triphosphate (ATP) is an immensely well-studied metabolite serving multiple key
biochemical roles as the major chemical energy currency in living systems, a building block …

Actin remodeling defects leading to autoinflammation and immune dysregulation

R Papa, F Penco, S Volpi, M Gattorno - Frontiers in Immunology, 2021 - frontiersin.org
A growing number of monogenic immune-mediated diseases have been related to genes
involved in pathways of actin cytoskeleton remodeling. Increasing evidences associate …

Assessing the Martini 3 protein model: A review of its path and potential

L Borges-Araújo, GP Pereira, M Valério… - Biochimica et Biophysica …, 2024 - Elsevier
Coarse-grained (CG) protein models have become indispensable tools for studying many
biological protein details, from conformational dynamics to the organization of protein macro …

Protein reconstitution inside giant unilamellar vesicles

T Litschel, P Schwille - Annual Review of Biophysics, 2021 - annualreviews.org
Giant unilamellar vesicles (GUVs) have gained great popularity as mimicries for cellular
membranes. As their sizes are comfortably above the optical resolution limit, and their lipid …

[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 …

Actomyosin-driven division of a synthetic cell

L Baldauf, L Van Buren, F Fanalista… - ACS Synthetic …, 2022 - ACS Publications
One of the major challenges of bottom-up synthetic biology is rebuilding a minimal cell
division machinery. From a reconstitution perspective, the animal cell division apparatus is …

Unbreaking Assemblies in Molecular Simulations with Periodic Boundaries

BMH Bruininks, TA Wassenaar… - Journal of chemical …, 2023 - ACS Publications
In molecular simulations, periodic boundary conditions are typically used to avoid surface
effects occurring at the boundaries of the simulation box. A consequence of this is that …

Active surface flows accelerate the coarsening of lipid membrane domains

DP Arnold, A Gubbala, SC Takatori - Physical Review Letters, 2023 - APS
Phase separation of multicomponent lipid membranes is characterized by the nucleation
and coarsening of circular membrane domains that grow slowly in time as∼ t 1/3, following …