[HTML][HTML] Computational modeling of membrane trafficking processes: From large molecular assemblies to chemical specificity

D Alvarez, J Sapia, S Vanni - Current Opinion in Cell Biology, 2023 - Elsevier
In the last decade, molecular dynamics (MD) simulations have become an essential tool to
investigate the molecular properties of membrane trafficking processes, often in conjunction …

Autophagosome biogenesis

Y Zhen, H Stenmark - Cells, 2023 - mdpi.com
Autophagy–the lysosomal degradation of cytoplasm–plays a central role in cellular
homeostasis and protects cells from potentially harmful agents that may accumulate in the …

TECPR1 is activated by damage‐induced sphingomyelin exposure to mediate noncanonical autophagy

N Kaur, LR de la Ballina, HS Haukaas… - The EMBO …, 2023 - embopress.org
Cells use noncanonical autophagy, also called conjugation of ATG8 to single membranes
(CASM), to label damaged intracellular compartments with ubiquitin‐like ATG8 family …

Three-step docking by WIPI2, ATG16L1, and ATG3 delivers LC3 to the phagophore

S Rao, M Skulsuppaisarn, LM Strong, X Ren… - Science …, 2024 - science.org
The covalent attachment of ubiquitin-like LC3 proteins (microtubule-associated proteins
1A/1B light chain 3) prepares the autophagic membrane for cargo recruitment. We resolve …

Unique amphipathic α helix drives membrane insertion and enzymatic activity of ATG3

T Nishimura, G Lazzeri, N Mizushima, R Covino… - Science …, 2023 - science.org
Autophagosome biogenesis requires a localized perturbation of lipid membrane dynamics
and a unique protein-lipid conjugate. Autophagy-related (ATG) proteins catalyze this …

Membrane curvature as a signal to ensure robustness of diverse cellular processes

RC Cail, DG Drubin - Trends in Cell Biology, 2023 - cell.com
An increasing corpus of research has demonstrated that membrane shape, generated either
by the external environment of the cell or by intrinsic mechanisms such as cytokinesis and …

WIPI2b recruitment to phagophores and ATG16L1 binding are regulated by ULK1 phosphorylation

A Gubas, E Attridge, HBJ Jefferies, T Nishimura… - EMBO …, 2024 - embopress.org
One of the key events in autophagy is the formation of a double-membrane phagophore,
and many regulatory mechanisms underpinning this remain under investigation. WIPI2b is …

Amphipathic helices can sense both positive and negative curvatures of lipid membranes

P Pajtinka, R Vácha - The Journal of Physical Chemistry Letters, 2023 - ACS Publications
Curvature sensing is an essential ability of biomolecules to preferentially localize to
membrane regions of a specific curvature. It has been shown that amphipathic helices …

Mesoscale simulation of biomembranes with FreeDTS

W Pezeshkian, JH Ipsen - Nature Communications, 2024 - nature.com
We present FreeDTS software for performing computational research on biomembranes at
the mesoscale. In this software, a membrane is represented by a dynamically triangulated …

SigmaR1 shapes rough endoplasmic reticulum membrane sheets

EM Sawyer, LE Jensen, JB Meehl, KP Larsen… - Developmental Cell, 2024 - cell.com
Rough endoplasmic reticulum (ER) sheets are a fundamental domain of the ER and the
gateway into the secretory pathway. Although reticulon proteins stabilize high-curvature ER …