Siewert Jan Marrink

Accurate simulation of protein–ligand interactions remains a central challenge in drug discovery. Coarse-grained (CG) molecular dynamics offers a route to broader system coverage and efficient sampling by reducing molecular resolution. Here, we examine the potential of Martini 3 for drug discovery, reviewing methodological advances in simulation setup and addressing persistent challenges in sampling, model parameterization, and the reliable estimation of binding thermodynamics. Finally, we discuss priorities for translating CG simulations into robust, scalable drug discovery workflows.

Biomolecular condensates are multicomponent organelles that orchestrate diverse cellular functions, yet their emergent internal structures remain poorly understood. Here we use the recently developed coarse-grained Martini3-IDP model to perform a molecular dynamics simulation of a multicomponent P-body condensate with a realistic composition, comprising six different scaffold proteins and both short and long client RNA mimics. We reveal the interior structure and dynamics of this condensate to be highly heterogeneous, featuring local solvent cavities with enhanced mobility. Furthermore, we uncover component-specific differences in conformation behavior. Whereas the terminal intrinsically disordered regions (IDRs) of Xrn1 display limited conformation sampling due to strong interactions with the scaffold proteins, the Dhh1 C-terminal IDR and Pat1 N-terminal IDR retain substantially greater flexibility. For client dynamics, length-dependent client partitioning is observed, arising from increased interaction valency of the long RNA mimic compared to the short one. For the latter, two client states were identified, characterized by distinct exchange behavior between the dilute and condensate phase. Together, this study establishes a heterogeneous picture of multicomponent condensate internal architecture and dynamics, advancing our understanding of how complex condensate architectures emerge from intricate molecular interactions in realistic condensates.

Bridging the gap between atomistic detail and continuum mechanics is a central challenge in modeling biological membranes, particularly for mesoscopic phenomena spanning large length and time scales. In this work, we introduce a new, solvent-free, one-particle-thick, coarse-grained model for lipid bilayers, governed by an additive potential. Our approach treats orientational elasticity through distinct additive energy terms for tilt and splay, offering an unbiased potential form. The model is implemented in the molecular-dynamics engine. Our simulations show spontaneous self-assembly of lamellar structures and stable vesicles from disordered states. We map the dynamical phase diagram of the system, identifying distinct gel-like, fluid, and gas regimes, controlled by temperature and the steepness of the isotropic attraction. The model accurately reproduces the theoretical 1 / q 4 fluctuation spectrum for tensionless membranes and exhibits tunable mechanical properties, including biologically relevant bending rigidities. We show how we can include osmotic pressure and spontaneous curvature in our model. Finally, we demonstrate the model's applicability to complex membrane remodeling by simulating the adhesive wrapping of colloidal nanoparticles, recovering the predicted dependency on particle size and adhesion strength.

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.

Minimal cells offer a platform to uncover the fundamental physicochemical principles of cellular life. While genomes, proteomes, and metabolic networks of cells have been elucidated, the lipidome, which determines the physicochemical identity of the membrane, remains only partially characterized. Yet, the membrane is a central determinant of cellular viability, regulating solute permeability, mechanical stability, and environmental cues. Here, we investigate membranes that recapitulate the lipid composition of the minimal cell JCVI-syn3A, which is distinguished by an unusually high cholesterol content and simple composition. Combining cryo-electron microscopy, Langmuir monolayer experiments, permeability assays, and coarse-grained molecular dynamics simulations, we demonstrate that cholesterol and sphingomyelin act as dominant condensing agents that stabilize the membrane while preserving an ordered yet fluid state. These lipids enhance lipid packing and acyl-chain order, whereas cardiolipin, POPC, and DOPG counterbalance condensation by promoting fluidity and compressibility. Cholesterol–sphingomyelin interactions emerge as a key thermodynamic driver that fine-tunes membrane order, fluidity, and permeability. Remarkably, membranes containing up to 60 mol% of cholesterol remain permeable to water and physiologically relevant osmolytes at rates compatible with growth of JCVI-syn3A. Together, our results define the physicochemical principles underlying minimal cell membranes and reveal how lipid composition enables passive permeation while maintaining membrane integrity.

Mitochondrial cristae are essential for respiration, yet the molecular basis of how the high curvature of these membrane folds is maintained remains unclear. Using structure prediction tools and multiscale simulations, we examined the role of the MIC10 subcomplex of the mitochondrial contact site and cristae organizing system (MICOS). We found that the MIC10 proteins Mic10, Mic26, and Mic27 strongly recruit cardiolipin at conserved positive loop motifs, driving oligomerization of these subunits and resulting in the stabilization of curvature in model membranes. Reconstruction of the full MIC10 complex in a realistic crista junction setup shows its capability to maintain membrane bending, while intrinsically disordered regions may form a permeability barrier between cristae and the intermembrane space. These findings provide a mechanistic model for cristae curvature formation and suggest how MICOS components cooperate with cardiolipins to maintain mitochondrial architecture.

Coarse-grained molecular dynamics simulations of bio- and macromolecular systems offer a method of accessing otherwise unobtainable time and length scales, compared to atomistic simulation techniques. However, a limiting step is often the generation and validation of the coarse-grained models. Here, we describe a new software package, Fast-Forward, which aids parametrization of models for the widely used Martini coarse-grained force field. In comparison to other similar packages, Fast-Forward offers a system-agnostic suite of tools to parametrize molecules of any size, existing in any environment. It achieves this while maintaining ease of use and the use of interoperable file formats from the Martini software ecosystem. Through its three subprograms, the package offers tools for trajectory mapping, parameter generation, and model validation. We demonstrate the potential of the package for several different use cases, from small biological molecules (glutathione and glutathione disulfide) to models of synthetic polymers (poly(methyl methacrylate), PMMA).

Cells grow their boundaries by incorporating newly synthesized lipids into their membranes as well as through fusion of intracellular vesicles. As these processes yield trans-bilayer imbalances in lipid numbers, cells must redistribute lipids across the bilayer to enable sustained growth. Using giant and large unilamellar vesicles (GUVs and LUVs, respectively), we here recapitulate cellular growth and division under various conditions of transmembrane ‘flip flop’ of lipids. By dynamically monitoring the changes in reduced volume, spontaneous curvature, and area difference of GUVs that grow by fusion of many small LUVs, the morphology of these growing ‘synthetic cells’ is quantified. We demonstrate, for membranes containing various flip flop-capable molecules, that curvature stresses are relieved, generating more symmetrically sized buds, without significantly compromising the membrane integrity. Further increasing the neck curvature is shown to lead to bud scission. The mechanisms presented here offer insights into cell growth and division, which are important for understanding early protocells and designing synthetic cells that are able to grow and divide.