Abstract Visual proteomics attempts to build atlases of the molecular content cells but automated annotation cryo electron tomograms remains challenging. Template matching (TM) and methods based on machine learning detect structural signatures macromolecules. However, their applicability limited in terms both abundance size targets. Here we show that performance TM is greatly improved by using template-specific search parameter optimization including higher-resolution information. We...

Magnesium ions play an essential role in many vital processes. To correctly describe their interactions molecular dynamics simulations, accurate parametrization is crucial. Despite the importance and considerable scientific effort, current force fields based on commonly used 12–6 Lennard-Jones interaction potential fail to reproduce a variety of experimental solution properties. In particular, no exists so far that simultaneously reproduces solvation free energy distance water oxygens first...

Abstract The structure and properties of DNA depend on the environment, in particular ion atmosphere. Here, we investigate how twist -one central DNA- changes with concentration identity surrounding ions. To resolve cations influence twist, combine single-molecule magnetic tweezer experiments extensive all-atom molecular dynamics simulations. Two interconnected trends are observed for monovalent alkali divalent alkaline earth cations. First, increases monotonously increasing all ions...

Cryo-electron tomography (cryo-ET) is a powerful method to elucidate subcellular architecture and structurally analyze biomolecules in situ by subtomogram averaging, yet data quality critically depends on specimen thickness. Cells that are too thick for transmission imaging can be thinned into lamellae cryo-focused ion beam (cryo-FIB) milling. Despite being crucial parameter directly affecting attainable resolution, optimal lamella thickness has not been systematically investigated nor the...

Summary Upon infection, human immunodeficiency virus (HIV-1) releases its cone-shaped capsid into the cytoplasm of infected T-cells and macrophages. As largest known cargo, enters nuclear pore complex (NPC), driven by interactions with numerous FG-repeat nucleoporins (FG-Nups). Whether NPCs structurally adapt to passage whether capsids are modified during remains unknown, however. Here, we combined super-resolution correlative microscopy cryo electron tomography molecular simulations study...

Abstract Changing environmental conditions necessitate an immediate cellular adaptation to ensure survival. Dictyostelium discoideum , a bacteriovore slime mold present in the soil of most terrestrial ecosystems, is known for its ability tolerate drastic changes osmolarity. How cells cope with resulting mechanical stress remains understudied. Here we show that D. has extraordinarily elaborate and resilient nuclear pores serve as conduits massive fluid exchange between cytosol nucleus. We...

A large variety of physicochemical properties involving RNA depends on the type metal cation present in solution. In order to gain microscopic insight into origin these ion specific effects, we apply molecular dynamics simulations describe interactions cations and RNA. For three most common binding sites RNA, calculate affinities exchange rates eight different mono- divalent cations. Our results reveal that phosphate groups preferentially bind with high charge density (such as Mg2+)...

Magnesium and calcium play an essential role in the folding function of nucleic acids. To correctly describe their interactions with DNA RNA biomolecular simulations, accurate parameterization is crucial. In most cases, ion parameters are optimized based on a set experimental solution properties such as solvation free energies, radial distribution functions, water exchange rates, activity coefficient derivatives. However, transferability bulk-optimized to quantitatively systems limited....

The distribution of cations around nucleic acids is essential for a broad variety processes ranging from DNA condensation and RNA folding to the detection biomolecules in biosensors. Predicting exact ions remains challenging since and, hence, acid properties depend on salt concentration, valency ions, ion type. Despite importance, general theory quantify ion-specific effects highly charged still lacking. Moreover, recent experiments reveal that despite their similar building blocks, duplexes...

Abstract Cryo-electron tomography (CryoET) resolves individual macromolecules inside living cells. However, the complex composition and high density of cells challenge faithful identification features in tomograms. Here, we capitalize on recent advances electron demonstrate that 3D template matching (TM) localizes a wide range structures crowded eukaryotic with confidence 10 to 100-fold above noise level. We establish TM pipeline systematically tuned parameters for automated, objective...

Changing environmental conditions necessitate rapid adaptation of cytoplasmic and nuclear volumes. We use the slime mold Dictyostelium discoideum, known for its ability to tolerate extreme changes in osmolarity, assess which role pore complexes (NPCs) play achieving volume relieving mechanical stress. capitalize on unique properties D. discoideum quantify fluid flow across NPCs. has an elaborate NPC structure situ. Its dilation state affects permeability nucleocytosolic flow. Based...

In eukaryotes, meters of DNA are packaged into micrometer scale nuclei. Nucleosomes, as the major organizational unit, have been extensively studied in vitro, yet elaborate 3D structure chromatin inside cells and its distinct multi-nucleosome arrangements remain poorly resolved. Here, we combine cryo-electron tomography with template matching, subtomogram averaging molecular simulations to visualize nucleosomes human cells. We confidently assign individual report their in-situ at secondary...

A coarse-grained model for simulating structural properties of double-stranded RNA is developed with parameters obtained from quantum-mechanical calculations. This follows previous parametrization DNA, which based on mapping the all-atom picture to a four-bead scheme. Chemical and differences between DNA have been taken into account development. The simulations using density functional theory (DFT) separate units molecule without implementing experimental data. total energy decomposed four...

MolecularWebXR is our new website for education, science communication and scientific peer discussion in chemistry biology built on WebXR. It democratizes multi-user, inclusive virtual reality (VR) experiences that are deeply immersive users wearing high-end headsets, yet allow participation by with consumer devices such as smartphones, possibly inserted into cardboard goggles immersivity, or even computers tablets. With no installs it all web-served, enables multiple to simultaneously...

Abstract Multiscale simulations have broadened our understanding of RNA structure and function. Various methodologies enabled the quantification electrostatic mechanical interactions at nanometer scale. Atom-by-atom simulations, coarse-grained strategies, continuum models its environment provide physical insight allow to interpret diverse experiments in a systematic way. In this chapter, we present discuss recent advances set methods study nucleic acids different scales. particular,...

Abstract MolecularWebXR is a new website for education, science communication and scientific peer discussion in chemistry biology, based on modern web-based Virtual Reality (VR) Augmented (AR). With no installs as it all web-served, enables multiple users to simultaneously explore, communicate discuss concepts about biology immersive 3D environments, by manipulating passing around objects with their bare hands pointing at different elements natural hand gestures. User may either be present...

Cryo-electron tomography enables the visualization of macromolecular complexes within native cellular environments, but is limited by incomplete angular sampling and maximal electron dose that biological specimen can be exposed to. Here, we developed cryoTIGER (Tilt Interpolation Generator for Enhanced Reconstruction), a computational workflow leveraging deep learning-based frame interpolation to generate intermediate tilt images. By interpolating between series projections, improves...

Abstract The structure and properties of DNA depend on the environment, in particular ion atmosphere. Here, we investigate how twist -one central DNA- changes with concentration identity surrounding ions. To resolve cations influence helical twist, combine single-molecule magnetic tweezer experiments extensive all- atom molecular dynamics simulations. Two interconnected trends are observed for monovalent alkali divalent alkaline earth cations. First, increases monotonously increasing all...

MolecularWebXR is our new website for education, science communication and scientific peer discussion in chemistry biology built on WebXR. It democratizes multi-user, inclusive virtual reality (VR) experiences that are deeply immersive users wearing high-end headsets, yet allow participation by with consumer devices such as smartphones, possibly inserted into cardboard goggles immersivity, or even computers tablets. With no installs it all web-served, enables multiple to simultaneously...