Related papers: Geometry of compact tubes and protein structures
The response of low-dimensional solid objects combines geometry and physics in unusual ways, exemplified in structures of great utility such as a thin-walled tube that is ubiquitous in nature and technology. Here we provide a particularly…
A phenomenological model hamiltonian to describe the folding of a protein with any given sequence is proposed. The protein is thought of as a collection of pieces of helices; as a consequence its configuration space increases with the…
The structures of proteins exhibit secondary elements composed of helices and loops. Comparison of several water-only hydrophobicity scales with the functionalities of two repeat proteins shows that these secondary elements possess…
Protein chains of the (FG)$_n$ ($n \simeq$ 300) type cap the cytoplasmatic side of the nucleopore complex, which connects the nucleus to the remainder of an eukaryotic cell. We study the properties of three fundamental polymer models that…
In this work we present the general phase behavior of short tubelike flexible polymers. The geometric thickness constraint is implemented through the concept of the global radius of curvature. We use sophisticated Monte Carlo sampling…
Using a simple three-dimensional lattice copolymer model and Monte Carlo dynamics, we study the collapse and folding of protein-like heteropolymers. The polymers are 27 monomers long and consist of two monomer types. Although these chains…
Protein aggregation in cell membrane is vital for the majority of biological functions. Recent experimental results suggest that transmembrane domains of proteins such as $\alpha$-helices and $\beta$-sheets have different structural…
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…
How proteins fold remains a central unsolved problem in biology. While the idea of a folding code embedded in the amino acid sequence was introduced more than 6 decades ago, this code remains undefined. While we now have powerful predictive…
The endoplasmic reticulum (ER), a cellular organelle that forms a cell-spanning network of tubes and sheets, is an important location of protein synthesis and folding. When the ER experiences sustained unfolded protein stress, IRE1 proteins…
The prediction of the three-dimensional native structure of proteins from the knowledge of their amino acid sequence, known as the protein folding problem, is one of the most important yet unsolved issues of modern science. Since the…
Rigid particles pack into structures, such as sand dunes on the beach, whose overall stability is determined by the average number of contacts between particles. However, when packing spatially extended objects with flexible shapes,…
Natural protein molecules are exceptional polymers. Encoded in apparently random strings of amino-acids, these objects perform clear physical tasks that are rare to find by simple chance. Accurate folding, specific binding, powerful…
Chiral heteropolymers such as larger globular proteins can simultaneously support multiple length scales. The interplay between different scales brings about conformational diversity, and governs the structure of the energy landscape.…
In living cells, proteins self-assemble into large functional structures based on specific interactions between molecularly complex patches. Due to this complexity, protein self-assembly results from a competition between a large number of…
The three dimensional structure of a protein is an outcome of the interactions of its constituent amino acids in 3D space. Considering the amino acids as nodes and the interactions among them as edges we have constructed and analyzed…
Proteins must fold quickly to acquire their biologically functional three-dimensional native structures. Hence, these are mainly stabilized by local contacts, while intricate topologies such as knots are rare. Here, we reveal the existence…
This work reports a new methodology aimed at describing characteristics of protein structural shapes, and suggests a framework in which to resolve or classify automatically such structures into known families. This new approach to protein…
It is widely accepted that (1) the natural or folded state of proteins is a global energy minimum, and (2) in most cases proteins fold to a unique state determined by their amino acid sequence. The H-P (hydrophobic-hydrophilic) model is a…
We examine the phase transition of polymer adsorption as well as the underlying kinetics of polymer binding from dilute solutions on a structureless solid surface. The emphasis is put on the properties of regular multiblock copolymers,…