相关论文: 3D pattern formation of a protein-membrane suspens…
While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learned how to extract this information to predict the three--dimensional, biologically active, native conformation of…
A fundamental goal of research in molecular biology is to understand protein structure. Protein crystallography is currently the most successful method for determining the three-dimensional (3D) conformation of a protein, yet it remains…
Proteins perform critical processes in all living systems: converting solar energy into chemical energy, replicating DNA, as the basis of highly performant materials, sensing and much more. While an incredible range of functionality has…
A physical scenario accounting for the existence of size-limited submicrometric domains in cell membranes is proposed. It is based on the numerical investigation of the counterpart, in lipidic membranes where proteins are diffusing, of the…
In recent years, there has been a surge in the development of 3D structure-based pre-trained protein models, representing a significant advancement over pre-trained protein language models in various downstream tasks. However, most existing…
Lipid rafts are heterogeneous dynamic lipid domains of the cell membranes that are involved in several biological processes, like protein and lipids specific transport and signaling. Our understanding of lipid raft formation is still…
Membrane proteins often form dimers and higher-order oligomers whose stability and spatial organization depend sensitively on their lipid environment. To investigate the physical principles underlying this coupling, we employ a lattice…
The interaction of a protein with its environment can be understood and controlled via its 3D structure. Experimental methods for protein structure determination, such as X-ray crystallography or cryogenic electron microscopy, shed light on…
We describe simulations of Proteins and artificial pseudo-molecules interacting and shaping lipid bilayer membranes. We extract protein diffusion Parameters, membrane deformation profiles and the elastic properties of the used membrane…
Many cell functions require a concerted effort from multiple membrane proteins, for example, for signaling, cell division, and endocytosis. One contribution to their successful self-organization stems from the membrane deformations that…
Proteins are the fundamental macromolecules that play diverse and crucial roles in all living matter and have tremendous implications in healthcare, manufacturing, and biotechnology. Their functions are largely determined by the sequences…
We propose a PDE-constrained shape registration algorithm that captures the deformation and growth of biological tissue from imaging data. Shape registration is the process of evaluating optimum alignment between pairs of geometries through…
The patterns observed on the body surface of living organisms have traditionally been attributed solely to ecological strategies. However, this study investigates a fascinating phenomenon in Pelodiscus sinensis, where patterns formed on the…
Biomolecular condensates composed of intrinsically disordered proteins (IDPs) are vital for proper cellular function, and their dysfunction is associated with diseases including neurodegeneration and cancer. Despite their biological…
Pattern formation often occurs in confined systems, yet how boundaries shape patterning dynamics is unclear. We develop techniques to analyze confinement effects in nonlocal advection-diffusion equations, which generically capture the…
A complete time-parameterized statistical model quantifying the divergent evolution of protein structures in terms of the patterns of conservation of their secondary structures is inferred from a large collection of protein 3D structure…
Membrane proteins and lipids can self-assemble into membrane protein polyhedral nanoparticles (MPPNs). MPPNs have a closed spherical surface and a polyhedral protein arrangement, and may offer a new route for structure determination of…
Proteins perform their biological functions through three-dimensional structures encoded by amino acid sequences, and ligand-binding protein co-design requires models that generate sequence-structure compatible proteins under explicit…
Pattern formation and the mechanics of a mixture of actin filaments and myosin motors that is confined by a rigid membrane is investigated. By using a coarse-grained molecular dynamics model, we demonstrate that the competition between the…
Proteins are large biomolecules that regulate all living organisms and consist of one or several chains. The primary structure of a protein chain is a sequence of amino acid residues whose three main atoms (alpha-carbon, nitrogen, and…