Biology subjects

Koefinger, J.

Publications and source records attributed to Koefinger, J..

4 recordsLinked to original sources

bioRxiv2025

RNA at Lipid/Water Interfaces: Molecular Insights from Coarse-Grained Simulations and Reflectivity Data Predictions

Interactions between RNA and lipids are fundamental for biological processes and are increasingly exploited for RNA delivery by lipid nanoparticles. However, RNA-lipid interactions remain challenging to characterize at the molecular level. Here, we address the modeling of RNA at lipid/water interfaces using coarse-grained (CG) simulations, experimental validation using scattering data and prediction of neutron (NR) and X-ray reflectivity (XRR) profiles from the simulations. Using neutral DOPC and cationic DOTAP bilayers, we show that lipid-RNA interactions depend strongly on RNA secondary structure, with single-stranded regions exhibiting higher interfacial affinity than double-stranded segments. We validate the CG lipid simulations, showing that while they reproduce experimental X-ray scattering data only qualitatively, the agreement improves markedly after backmap-ping to atomistic resolution followed by energy minimization and short all-atom molecular dynamics simulations. We further simulated distinct tRNA conformations and analyzed the influence of RNA secondary structure, concentration, solvent contrast, and lipid deuteration on NR and XRR signals identifying the conditions under which such experiments probe RNA adsorption and discriminate between different RNA conformations. Together, these results demonstrate that CG simulations combined with reflectivity data provide a powerful approach to probe RNA adsorption and structure at lipid/water interfaces and support the design and interpretation of scattering experiments. TOC Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=109 SRC="FIGDIR/small/689668v2_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@9a1297org.highwire.dtl.DTLVardef@13aa90dorg.highwire.dtl.DTLVardef@30a68corg.highwire.dtl.DTLVardef@662aa_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2025

Mechanical forces drive mitochondrial matrix extrusion and apoptotic pore growth

Apoptotic pore opening by BAX and BAK at the mitochondrial outer membrane is a key step in the cell commitment to death. The subsequent inner membrane extrusion and permeabilization releases mitochondrial DNA into the cytosol, which can trigger inflammatory signaling. However, the underlying mechanisms have not been elucidated. Here we developed CLOSE microscopy, a multi-correlative approach that enabled the simultaneous analysis of BAK stoichiometry and nanoscale organization in individual apoptotic pore complexes in relation to mitochondrial ultrastructure. We find that the outer membrane opening at the apoptotic pore defines the spatial arrangement of BAK nanoassemblies. We identify mechanical stress as a driver of inner membrane extrusion, which can be perturbed by osmoregulation. The extruded inner membrane in turn exerts forces on the outer membrane that promote apoptotic pore growth, in line with membrane dynamics simulations. Our study reveals a tight interplay between the inner and outer membranes during mitochondrial permeabilization in apoptosis and establishes a biophysical mechanism for inner membrane extrusion that defines the structural organization of the apoptotic pore.

cell biology↗

bioRxiv2024

Passage of the HIV capsid cracks the nuclear pore

Upon infection, human immunodeficiency virus (HIV-1) releases its cone-shaped capsid into the cytoplasm of infected T-cells and macrophages. As its largest known cargo, the capsid enters the nuclear pore complex (NPC), driven by interactions with numerous FG-repeat nucleoporins (FG-Nups). Whether NPCs structurally adapt to capsid passage and whether capsids are modified during passage remains unknown, however. Here, we combined super-resolution and correlative microscopy with cryo electron tomography and molecular simulations to study nuclear entry of HIV-1 capsids in primary human macrophages. We found that cytosolically bound cyclophilin A is stripped off capsids entering the NPC, and the capsid hexagonal lattice remains largely intact inside and beyond the central channel. Strikingly, the NPC scaffold rings frequently crack during capsid passage, consistent with computer simulations indicating the need for NPC widening. The unique cone shape of the HIV-1 capsid facilitates its entry into NPCs and helps to crack their rings.

biophysics↗

bioRxiv2022

TriMem: A Parallelized Hybrid Monte Carlo Software for Efficient Simulations of Lipid Membranes

Lipid membranes are integral building blocks of living cells and perform a multitude of biological functions. Currently, molecular simulations of cellular-scale membrane structures at atomic resolution are nearly impossible, due to their size, complexity, and the large times-scales required. Instead, elastic membrane models are used to simulate membrane topologies and transitions between them, and to infer their properties and functions. Unfortunately, efficiently parallelized open-source simulation code to do so has been lacking. Here, we present TriMem, a parallel hybrid Monte Carlo simulation engine for triangulated lipid membranes. The kernels are efficiently coded in C++ and wrapped with Python for ease-of-use. The parallel implementation of the energy and gradient calculations and of Monte Carlo flip moves of edges in the triangulated membrane enable us to simulate also large and highly curved sub-cellular structures. For validation, we reproduce phase diagrams of vesicles with varying surface-to-volume ratios and area difference. The software can tackle a range of membrane remodelling processes on sub-cellular and cellular scales. Additionally, extensive documentation make the software accessible to the broad biophysics and computational cell biology communities.

biophysics↗