Related papers: Integrative dynamic structural biology unveils con…
GTPases are molecular switches that regulate a wide range of cellular processes, such as organelle biogenesis, position, shape, and signal transduction. These enzymes operate by toggling between an active ("ON") guanosine triphosphate…
While G-protein coupled receptors (GPCRs) constitute the largest class of membrane proteins, structures and endogenous ligands of a large portion of GPCRs remain unknown. Due to the involvement of GPCRs in various signaling pathways and…
We present an extended structural study of globular complexes made by mixing a positively charge protein (lysozyme) and a negatively charged polyelectrolyte (PSS). We study the influence of all the parameters that may act on the structure…
Biased bilayer graphene (BBG) is an important system for studies of excitonic effects in graphene--based systems, with its easily tunable bandgap. This bandgap is governed by an external gate voltage, allowing one to tune the optical…
The $\alpha$ and $\beta$ subunits comprising the hexameric assembly of F1-ATPase share a high degree of structural identity, though low primary identity. Each subunit binds nucleotide in similar pockets, yet only $\beta$ subunits are…
Phagocytosis is the fundamental cellular process by which eukaryotic cells bind and engulf particles by their cell membrane. Particle engulfment involves particle recognition by cell-surface receptors, signaling and remodeling of the actin…
Bacteria produce a range of proteolytic enzymes, for which a number human equivalent or structurally similar examples exist and the primary focus of this study was to analyse the published literature to find proteolytic enzymes,…
Intrinsically disordered proteins (IDPs) constitute a broad set of proteins with few uniting and many diverging properties. IDPs-and intrinsically disordered regions (IDRs) interspersed between folded domains-are generally characterized as…
Nonequilibrium dynamics of biomembranes with active inclusions is considered. The inclusions represent protein molecules which perform cyclic internal conformational motions driven by the energy brought with ATP ligands. As protein…
This paper reports the analysis of the dynamics of a model of pulse-coupled oscillators with global inhibitory coupling. The model is inspired by experiments on colonies of bacteria-embedded synthetic genetic circuits. The total population…
The response of lipid bilayers to osmotic stress is an important part of cellular function. Previously, in [Oglecka et al. 2014], we reported that cell-sized giant unilamellar vesicles (GUVs) exposed to hypotonic media, respond to the…
ATP-binding cassette (ABC) transporters are integral membrane proteins that mediate the exchange of diverse substrates across membranes powered by ATP hydrolysis. We report results of coarse-grained dynamical simulations performed for the…
We introduce a new class of machine learning interatomic potentials - fast General Two- and Three-body Potential (GTTP), which is as fast as conventional empirical potentials and require computational time that remains constant with…
Foundation models (FMs) have exhibited remarkable performance across a wide range of downstream tasks in many domains. Nevertheless, general-purpose FMs often face challenges when confronted with domain-specific problems, due to their…
The cornerstone of structural biology is the unique relationship between protein sequence and the 3D structure at equilibrium. Although intrinsically disordered proteins (IDPs) do not fold into a specific 3D structure, breaking this…
The spatiotemporal organisation of proteins and lipids on the cell surface has direct functional consequences for signaling, sorting and endocytosis. Earlier studies have shown that multiple types of membrane proteins including…
Interfaces formed by correlated oxides offer a critical avenue for discovering emergent phenomena and quantum states. However, the fabrication of oxide interfaces with variable crystallographic orientations and strain states integrated…
Recent advances in geometric deep learning and generative modeling have enabled the design of novel proteins with a wide range of desired properties. However, current state-of-the-art approaches are typically restricted to generating…
Novel numerical techniques, validated by an analysis of barnase and chymotrypsin inhibitor, are used to elucidate the paramount role played by the geometry of the protein backbone in steering the folding to the correct native state. It is…
G protein-coupled receptors (GPCRs) are a large superfamily of membrane proteins that are activated by extracellular small molecules or photons. Neurotensin receptor 1 (NTSR1) is a GPCR that is activated by neurotensin, i.e. a 13 amino acid…