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It is shown that a small subset of modes which are likely to be involved in protein functional motions of large amplitude can be determined by retaining the most robust normal modes obtained using different protein models. This result…
The self-organization of proteins into enriched compartments and the formation of complex patterns are crucial processes for life on the cellular level. Liquid-liquid phase separation is one mechanism for forming such enriched compartments.…
The understanding of protein structure, folding, and interaction with other proteins remains one of the grand challenges of modern biology. Tremendous progress has been made thanks to X-ray- or electron-based techniques that have provided…
A remarkable property of nastic, shape changing plants is their complete fusion between actuators and structure. This is achieved by combining a large number of cells whose geometry, internal pressures and material properties are optimized…
As protein informatics advances rapidly, the demand for enhanced predictive accuracy, structural analysis, and functional understanding has intensified. Transformer models, as powerful deep learning architectures, have demonstrated…
Proteins are sequences of amino acids that serve as the basic building blocks of living organisms. Despite rapidly growing databases documenting structural and functional information for various protein sequences, our understanding of…
Exchanges between the blood compartment and the surrounding tissues require a tight regulation by the endothelial barrier. Recent reports inferred that VE-cadherin, an endothelial specific cell-cell adhesion molecule, plays a pivotal role…
As I compress on the canvas of a few pages here major results of my research on the retinoblastoma tumor suppressor protein (RB) spreading over the past 15 years, an exciting picture emerges on this unique host molecule which surpasses in…
Many pressing medical challenges - such as diagnosing disease, enhancing directed stem cell differentiation, and classifying cancers - have long been hindered by limitations in our ability to quantify proteins in single cells.…
Optimal characterization of the mechanical properties of both cells and their surrounding is an issue of major interest. Indeed, cell function and development are strongly influenced by external stimuli. Furthermore, a change in cell…
The native state structures of globular proteins are stable and well-packed indicating that self-interactions are favored over protein-solvent interactions under folding conditions. We use this as a guiding principle to derive the geometry…
Understanding protein self-assembly is important for many biological and industrial processes. Proteins can self-assemble into crystals, filaments, gels, and other amorphous aggregates. The final forms include virus capsids and condensed…
Cell division is an essential biological process, and regulation of cell division is of relevance for many important fields of biology and medicine. Introducing exogenous substances, such as nanoparticles, into the nucleus, has been…
Using analytical calculations and computer simulations we consider both the lateral diffusion of a membrane protein and the fluctuation spectrum of the membrane in which the protein is embedded. The membrane protein interacts with the…
A reduced model, which can fold both helix and sheet structures, is proposed to study the problem of protein folding. The goal of this model is to find an unbiased effective potential that has included the effects of water and at the same…
Given an algorithm the quality of the output largely depends on a proper specification of the input parameters. A lot of work has been done to analyze tasks related to using a fixed model [25] and finding a good set of inputs. In this paper…
Cell adhesion proteins are transmembrane proteins that bind cells to their environment. These proteins typically cluster into disk-shaped or linear structures. Here we show that such clustering patterns spontaneously emerge when the protein…
As the only thiol-bearing amino acid, cysteine (Cys) residues in proteins have the reactive thiol side chain, which is susceptible to a series of post-translational modifications (PTMs). These PTMs participate in a wide range of biological…
Complexes of physically interacting proteins constitute fundamental functional units responsible for driving biological processes within cells. A faithful reconstruction of the entire set of complexes is therefore essential to understand…
Biological condensates are assemblies of proteins and nucleic acids that form membraneless compartments in cells and play essential roles in cellular functions. In many cases they exhibit the physical properties of liquid droplets that…