Biology subjects

Marrink, S. J.

Publications and source records attributed to Marrink, S. J..

7 recordsLinked to original sources

bioRxiv2026

Actin and AnkJ reciprocally regulate the catalytic state of the Legionella effector Ceg14

Ceg14 is a Legionella pneumophila effector whose enzymatic activity is activated by host actin and inhibited by the cognate metaeffector AnkJ. Recent studies established that Ceg14 cleaves ATP to AMP and pyrophosphate and can transfer AMP to 3-phosphoglycerate, but how actin and AnkJ regulate these catalytic states remained unclear. Here, we show that Ceg14 is selectively activated by G-actin and determine the cryo-EM structure of the Ceg14-actin-AnkJ complex. Structure-guided mutagenesis identifies two actin-binding elements, a C-terminal anchor and an extended sensor region, that are required for Ceg14 activation and toxicity. Structural modelling and molecular dynamics simulations reveal that the catalytic center is assembled from three spatially distinct components: an N-terminal nucleoside-binding region, a phosphate-coordinating region within the actin sensor, and the catalytic triad. G-actin constrains the sensor and thereby organizes the phosphate-binding component of the active site. AnkJ binds at a distinct surface and allosterically repositions the N-terminal domain, disrupting nucleoside coordination while leaving part of the catalytic machinery intact. Consistent with this mechanism, AnkJ strongly suppresses AMP production and 3-phosphoglycerate-stimulated activity, yet the ternary complex retains weak Ceg14-dependent ATP-to-ADP activity. Thus, our results show that actin and AnkJ do not simply switch Ceg14 on and off, but reciprocally remodel its multipart catalytic center to determine its catalytic state and reaction output.

biochemistry↗

bioRxiv2024

Oxygen partitioning into biomolecular condensates is governed by excluded volume

Biomolecular condensates form through the self-assembly of proteins and nucleic acids to create dynamic compartments in cells. By concentrating specific molecules, condensates establish distinct microenvironments that regulate biochemical reactions in time and space. Macromolecules and metabolites partition into condensates depending on their interactions with the macromolecular constituents, however, the partitioning of gases has not been explored. We investigated oxygen partitioning into condensates formed by intrinsically disordered repeat proteins with systematic sequence variations using microelectrodes and phosphorescence lifetime imaging microscopy (PLIM). Unlike other hydrophobic metabolites, oxygen is partially excluded from the condensate with partitioning constants more strongly modulated by changes in protein length than hydrophobicity. For repeat proteins, the dense phase protein concentration drops with chain length resulting in a looser condensate. We found that oxygen partitioning is anti-correlated with dense phase protein concentration. Several mechanisms could explain such an anti-correlation including excluded volume or salting out effects. Molecular dynamics simulations suggest that oxygen does not form strong and specific interactions with the scaffold and is dynamic on the nanosecond timescale. Biomolecular condensates thus result in variation of oxygen concentrations on nanometer length-scales, which may tune the oxygen concentration available for biochemical reactions within the cell.

biophysics↗

bioRxiv2024

GoMartini 3: From large conformational changes in proteins to environmental bias corrections

Coarse-grained modeling has become an important tool to supplement experimental measurements, allowing access to spatio-temporal scales beyond all-atom based approaches. The G[o]Martini model combines structure- and physics-based coarse-grained approaches, balancing computational efficiency and accurate representation of protein dynamics with the capabilities of studying proteins in different biological environments. This paper introduces an enhanced G[o]Martini model, which combines a virtual-site implementation of G[o] models with Martini 3. The implementation has been extensively tested by the community since the release of the new version of Martini. This work demonstrates the capabilities of the model in diverse case studies, ranging from protein-membrane binding to protein-ligand interactions and AFM force profile calculations. The model is also versatile, as it can address recent inaccuracies reported in the Martini protein model. Lastly, the paper discusses the advantages, limitations, and future perspectives of the Martini 3 protein model and its combination with G[o] models.

biophysics↗

bioRxiv2023

Probing the stability and interdomain interactions in the ABC transporter OpuA, using single-molecule optical tweezers

Transmembrane transporter proteins are essential for the maintenance of cellular homeostasis and, as such, are key drug targets. Many transmembrane transporter proteins are known to undergo large structural rearrangements during their functional cycles. Despite the large amount of detailed structural and functional data available for these systems, our understanding of their dynamics and therefore how they function is generally limited. We introduce an innovative approach which enables us to directly measure the dynamics and stabilities of inter-domain interactions of transmembrane proteins using optical tweezers. Focusing on the osmoregulatory ABC transporter OpuA from Lactococcus lactis, we examine the mechanical properties and potential interactions of its substrate-binding domains. Our measurements are performed in lipid nanodiscs, providing a native-mimicking environment for the transmembrane protein. The technique provides high spatial and temporal resolution and allows us to study the functionally-relevant motions and inter-domain interactions of individual transmembrane transporter proteins in real-time in a lipid bilayer.

biophysics↗

bioRxiv2022

Coarse-graining made easy with the MArtini Database Server

The MArtini Database (MAD - www.mad.ibcp.fr) is a web server designed for the sharing structures and topologies of molecules parameterized with the Martini coarse-grained (CG) force field. MAD can also convert atomistic structures into CG structures and prepare complex systems (including proteins, lipids etc.) for molecular dynamics (MD) simulations at the CG level. It is dedicated to the generation of input files for Martini 3, the most recent version of this popular CG force field. Specifically, the MAD server currently includes tools to submit or retrieve CG models of a wide range of molecules (lipids, carbohydrates, nanoparticles, etc.), transform atomistic protein structures into CG structures and topologies, with fine control on the process and assemble biomolecules into large systems and deliver all files necessary to start simulations in the GROMACS MD engine.

biophysics↗

bioRxiv2021

Membrane thickness, lipid phase and sterol type are determining factors in the permeability of membranes to small solutes

Cell membranes provide a selective semi-permeable barrier to the passive transport of molecules. This property differs greatly between organisms. While the cytoplasmic membrane of bacterial cells is highly permeable for weak acids and glycerol, yeasts can maintain large concentration gradients. Here we show that such differences can arise from the physical state of the plasma membrane. By combining stopped-flow kinetic measurements with molecular dynamics simulations, we performed a systematic analysis of the permeability through synthetic lipid membranes to obtain detailed molecular insight into the permeation mechanisms. While membrane thickness is an important parameter for the permeability through fluid membranes, the largest differences occur when the membranes transit from the liquid-disordered to liquid-ordered and/or to gel state. By comparing our results with in vivo measurements from yeast, we conclude that the yeast membrane exists in a highly ordered and rigid state, which is comparable to synthetic saturated DPPC-sterol membranes.

biochemistry↗

bioRxiv2017

Lipid-protein interactions are unique fingerprints for membrane proteins

Cell membranes contain hundreds of different proteins and lipids in an asymmetric arrangement. Understanding the lateral organization principles of these complex mixtures is essential for life and health. However, our current understanding of the detailed organization of cell membranes remains rather elusive, owing to the lack of experimental methods suitable for studying these fluctuating nanoscale assemblies of lipids and proteins with the required spatiotemporal resolution. Here, we use molecular dynamics simulations to characterize the lipid environment of ten membrane proteins. To provide a realistic lipid environment, the proteins are embedded in a model plasma membrane, where more than 60 lipid species are represented, asymmetrically distributed between leaflets. The simulations detail how each protein modulates its local lipid environment through local lipid composition, thickness, curvature and lipid dynamics. Our results provide a molecular glimpse of the complexity of lipid-protein interactions, with potentially far reaching implications for the overall organization of the cell membrane.

biophysics↗