Related papers: RSC remodeling of oligo-nucleosomes: an atomic for…
Coarse-grained models can be of great help to address the problem of structure prediction in nucleic acids. On one hand they can make the prediction more efficient, while on the other hand, they can also help to identify the essential…
Eukaryotic DNA is packaged into chromatin: one-dimensional arrays of nucleosomes separated by stretches of linker DNA are folded into 30-nm chromatin fibers which in turn form higher-order structures. Each nucleosome, the fundamental unit…
Atomic force microscopy (AFM) is one of the most promising methods for investigating the structure of materials at the micro and nanoscale levels, as well as their local physical-mechanical properties. The experimental data obtained with…
To gain a deeper insight into cellular processes such as transcription and translation, one needs to uncover the mechanisms controlling the configurational changes of nucleic acids. As a step toward this aim, we present here a novel…
Topology affects physical and biological properties of DNA and impacts fundamental cellular processes, such as gene expression, genome replication, chromosome structure and segregation. In all organisms DNA topology is carefully modulated…
We developed the models and algorithms to describe two main artefacts of AFM: (i) broadening effect and (ii) decreased heights of profiles for individual objects adsorbed on a hard substrate. It was shown how to measure elastic properties…
The ribosome is a macromolecular complex which is responsible for protein synthesis in all living cells according to their transcribed genetic information. Using X-ray crystallography and, more recently, cryo-electron microscopy (cryo-EM),…
The chromatin folding and the spatial arrangement of chromosomes in the cell play a crucial role in DNA replication and genes expression. An improper chromatin folding could lead to malfunctions and, over time, diseases. For eukaryotes,…
In eukaryotic genomes, nucleosomes function to compact DNA and to regulate access to it both by simple physical occlusion and by providing the substrate for numerous covalent epigenetic tags. While nucleosome positions in vitro are…
Post-transcriptional modifications are crucial for RNA function, with roles ranging from the stabilization of functional RNA structures to modulation of RNA--protein interactions. Additionally, artificially modified RNAs have been suggested…
Well-ordered stepped semiconductor surfaces attract intense attention owing to the regular arrangements of their atomic steps that makes them perfect templates for the growth of one- dimensional systems, e.g. nanowires. Here, we report on…
Using the perturbation-response scanning (PRS) technique, we study a set of 23 proteins that display a variety of conformational motions upon ligand binding (e.g. shear, hinge, allosteric). In most cases, PRS determines residues that may be…
Real-space refinement of atomic models in macromolecular crystallography or in cryo electron microscopy fits a model to a map obtained experimentally. This requires generating model maps of a limited resolution which moreover may vary from…
Performing full-resolution atomistic simulations of nucleic acid folding has remained a challenge for biomolecular modeling. Understanding how nucleic acids fold and how they transition between different folded structures as they unfold and…
Understanding chromatin dynamics across multiple spatiotemporal scales requires models that reconcile biological specificity with physics-based interactions and computational tractability. We present a modular, recognition-enabled…
The centrosomal aster is a mobile cellular organelle that exerts and transmits forces necessary for nuclear migration and spindle positioning. Recent experimental and theoretical studies of nematode and human cells demonstrate that pulling…
Atomic-scale characteristics of surfaces dictate the principles governing numerous scientific phenomena ranging from catalysis to friction. Despite this fact, our ability to visualize and alter surfaces on the atomic scale is severely…
Analytical expressions for the elastic and dynamic form factors (FFs) are derived in the shell model (SM) with a potential well of finite depth. The consideration takes into account the motion of the target-nucleus center of mass (CM).…
A novel assay based on micropatterning and time-lapse microscopy has been developed for the study of nuclear migration dynamics in cultured mammalian cells. When cultured on 10-20 um wide adhesive stripes, the motility of C6 glioma and…
Increasing evidence suggests that chromosome folding and genetic expression are intimately connected. For example, the co-expression of a large number of genes can benefit from their spatial co-localization in the cellular space.…