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We consider multi-chain protein native structures and propose a criterion that determines whether two chains in the system are entangled or not. The criterion is based on the behavior observed by pulling at both temini of each chain simultaneously in the two chains. We have identified about 900 entangled systems in the Protein Data Bank and provided a more detailed analysis for several of them. We argue that entanglement enhances the thermodynamic stability of the system but it may have other functions: burying the hydrophobic residues at the interface, and increasing the DNA or RNA binding area. We also study the folding and stretching properties of the knotted dimeric proteins MJ0366, YibK and bacteriophytochrome. These proteins have been studied theoretically in their monomer
Normal mode analysis offers an efficient way of modeling the conformational flexibility of protein structures. Simple models defined by contact topology, known as elastic network models, have been used to model a variety of systems, but the validatio
We use a coarse-grained model to study the conformational changes in two barley proteins, LTP1 and its ligand adduct isoform LTP1b, that result from their adsorption to the air-water interface. The model introduces the interface through hydropathy in
Motivation: Bridging the exponentially growing gap between the number of unlabeled and labeled proteins, a couple of works have adopted semi-supervised learning for protein sequence modeling. They pre-train a model with a substantial amount of unlabe
Recent computational advances in the accurate prediction of protein three-dimensional (3D) structures from amino acid sequences now present a unique opportunity to decipher the interrelationships between proteins. This task entails--but is not equiva
Dense packing of hydrophobic residues in the cores of globular proteins determines their stability. Recently, we have shown that protein cores possess packing fraction $phi approx 0.56$, which is the same as dense, random packing of amino acid-shaped