Related papers: Geometry of compact tubes and protein structures
Proteins are the common constituents of all living cells. They are molecular machines that interact with each other as well as with other cell products and carry out a dizzying array of functions with distinction. These interactions follow…
The shape of a polymer plays an important role in determining its interactions with other molecules and with the environment, and is in turn affected by both of them. As a consequence, in the literature the shape properties of a chain in…
The mechanisms by which a protein's 3D structure can be determined based on its amino acid sequence have long been one of the key mysteries of biophysics. Often simplistic models, such as those derived from geometric constraints, capture…
Proteins are the most important biomolecules for living organisms. The understanding of protein structure, function, dynamics and transport is one of most challenging tasks in biological science. In the present work, persistent homology is,…
Protein structures can be studied as complex networks of interacting amino acids. We study proteins of different structural classes from the network perspective. Our results indicate that proteins, regardless of their structural class, show…
It has recently been proposed that proteins embedded in lipidic bio-membranes can spontaneously self-organize into stable small clusters, or membrane nano-domains, due to the competition between short-range attractive and longer-range…
A typical protein structure is a compact packing of connected alpha-helices and/or beta-strands. We have developed a method for generating the ensemble of compact structures a given set of helices and strands can form. The method is tested…
Lattice-model simulations and experiments of some small proteins suggest that folding is essentially controlled by a few conserved contacts. Residues of these conserved contacts form the minimum set of native contacts needed to ensure…
There are many proteins or protein complexes which have multiple DNA binding domains. This allows them to bind to multiple points on a DNA molecule (or chromatin fibre) at the same time. There are also many proteins which have been found to…
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 biology, there are several processes in which unfolded protein chains are transported along narrow-tube channels. Normally, without such a severe configurational constraint, unfolded polypeptides would not bind to each other. However,…
Making use of a simplified model for protein folding, it can be shown that conformations which are particularly stable when their energy is minimized with respect to amino acid sequence (in the sense that they display a large energy gap to…
The control of biopolymer length is mediated by proteins that localize to polymer ends and regulate polymerization dynamics. Several mechanisms have been proposed to achieve end localization. Here, we propose a novel mechanism by which a…
Protein-protein binding enables orderly and lawful biological self-organization, and is therefore considered a miracle of nature. Protein-protein binding is steered by electrostatic forces, hydrogen bonding, van der Waals force, and…
A simple lattice model for proteins that allows for distinct sizes of the amino acids is presented. The model is found to lead to a significant number of conformations that are the unique ground state of one or more sequences or encodable.…
Understanding of the evolutionary origins of protein structures represents a key component of the understanding of molecular evolution as a whole. Here we seek to elucidate how the features of an underlying protein structural "space" might…
On the study of protein folding, our understanding about the protein structures is limited. In this paper we find one way to characterize the compact structures of lattice protein model. A quantity called Partnum is given to each compact…
Proteins populate a manifold in the high-dimensional sequence space whose geometrical structure guides their natural evolution. Leveraging recently-developed structure prediction tools based on transformer models, we first examine the…
Different aspects of protein folding are illustrated by simplified polymer models. Stressing the diversity of side chains (residues) leads one to view folding as the freezing transition of an heteropolymer. Technically, the most common…
Protein folding, peptide aggregation and crystallization, as well as adsorption of molecules on soft or solid substrates have an essential feature in common: In all these processes, structure formation is guided by a collective, cooperative…