Biomolecules
Evidence accumulated over the past decade provides support for liquid-liquid phase separation as the mechanism underlying the formation of biomolecular condensates, which include not only membraneless organelles such as nucleoli and RNA…
The inapplicability of amino acid covariation methods to small protein families has limited their use for structural annotation of whole genomes. Recently, deep learning has shown promise in allowing accurate residue-residue contact…
The theory of elastic rods can be used to describe certain geometric and topological properties of the DNA molecules. A similar effective field theory approach was previously suggested to describe the conformations and dynamics of proteins.…
Proteins are a matter of dual nature. As a physical object, a protein molecule is a folded chain of amino acids with multifarious biochemistry. But it is also an instantiation along an evolutionary trajectory determined by the function…
Studying evolutionary correlations in alignments of homologous sequences by means of an inverse Potts model has proven useful to obtain residue-residue contact energies and to predict contacts in proteins. The quality of the results depend…
Open-source 3D data processing libraries originally developed for computer vision and pattern recognition are used to align and compare molecular shapes and sub-shapes. Here, a shape is represented by a set of points distributed on the van…
Ligands entering a protein binding pocket essentially compete with water molecules for binding to the protein. Hence, the location and thermodynamic properties of water molecules in protein structures have gained increased attention in the…
To understand the effects of fluctuations on achieving homochirality, we employ a Monte-Carlo method where autocatalysis and enantiomeric cross-inhibition, as well as racemization and deracemization reactions are included. The results of…
We present the assembly category assessment in the 13th edition of the CASP community-wide experiment. For the second time, protein assemblies constitute an independent assessment category. Compared to the last edition we see a clear uptake…
Solutions of manually purified gastric mucins have been shown to be promising lubricants for biomedical purposes, where they can efficiently reduce friction and wear. However, so far, such mucin solutions have been mostly tested in specific…
Cryo-Electron Microscopy (cryo-EM) has become an extremely powerful method for resolving structural details of large biomolecular complexes. However, challenging problems in single-particle methods remain open because of (1) the low…
We report that protein confinement within nanoscopic vesicular compartments corresponds to a liquid-liquid phase transition with the protein/water within vesicle lumen interacting very differently than in bulk. We show this effect leads to…
By combining analytical and numerical calculations, we investigate the minimal-energy shape of short DNA loops of approximately $100$ base pairs (bp). We show that in these loops the excess twist density oscillates as a response to an…
According to implicit ligand theory, the standard binding free energy is an exponential average of the binding potential of mean force (BPMF), an exponential average of the interaction energy between the ligand apo ensemble and a rigid…
The output of molecular dynamics simulations is high-dimensional, and the degrees of freedom among the atoms are related in intricate ways. Therefore, a variety of analysis frameworks have been introduced in order to distill complex motions…
The recurrent geometric network (RGN), the first end-to-end differentiable neural architecture for protein structure prediction, is a competitive alternative to existing models. However, the RGN's use of recurrent neural networks (RNNs) as…
Recent years have witnessed a trend that advanced mathematical tools, such as algebraic topology, differential geometry, graph theory, and partial differential equations, have been developed for describing biological macromolecules. These…
Significant progress in computer hardware and software have enabled molecular dynamics (MD) simulations to model complex biological phenomena such as protein folding. However, enabling MD simulations to access biologically relevant…
The primary building block of the body is collagen, which is found in the extracellular matrix and in many stress-bearing tissues such as tendon and cartilage. It provides elasticity and support to cells and tissues while influencing…
Estrogen receptors (ERs) are a group of proteins activated by 17$\beta$-estradiol. The endocrine-disrupting chemicals (EDCs) mimic estrogen action by bind directly to the ligand binding domain of ER. From this perspective, ER represent a…