Related papers: Essential sub-networks based on contact strength r…
According to the 'old view', proteins fold along well-defined sequential pathways, whereas the 'new view' sees protein folding as a highly parallel stochastic process on funnel-shaped energy landscapes. We have analyzed parallel and…
Stochastic simulations of coarse-grained protein models are used to investigate the propensity to form knots in early stages of protein folding. The study is carried out comparatively for two homologous carbamoyltransferases, a…
RNAs self-interact through hydrogen-bond base-pairing between nucleotides and fold into specific, stable structures that substantially govern their biochemical behaviour. Experimental characterization of these structures remains difficult,…
Entangled states are ubiquitous amongst fibrous materials, whether naturally occurring (keratin, collagen, DNA) or synthetic (nanotube assemblies, elastane). A key mechanical characteristic of these systems is their ability to reorganise in…
The Go model is extended to the case when the non-native contact energies may be either attractive or repulsive. The folding temperature is found to increase with the energy of non-native contacts. The repulsive non-native contact energies…
In cheminformatics, network representations of the space of compounds have been suggested extensively. Among these, the threshold-network consists of nodes representing molecules. In this network representation, two molecules are connected…
A large number of complex systems find a natural abstraction in the form of weighted networks whose nodes represent the elements of the system and the weighted edges identify the presence of an interaction and its relative strength. In…
Folding properties of a two-dimensional toy protein model containing only two amino-acid types, hydrophobic and hydrophilic, respectively, are analyzed. An efficient Monte Carlo procedure is employed to ensure that the ground states are…
Protein folding is a problem of large interest since it concerns the mechanism by which the genetic information is translated into proteins with well defined three-dimensional (3D) structures and functions. Recently theoretical models have…
Protein structure prediction and folding are fundamental to understanding biology, with recent deep learning advances reshaping the field. Diffusion-based generative models have revolutionized protein design, enabling the creation of novel…
Many protein systems fold in a two-state manner. Random models, however, rarely display two-state kinetics and thus such behavior should not be accepted as a default. To date, many theories for the prevalence of two-state kinetics have been…
Protein contacts provide key information for the understanding of protein structure and function, and therefore contact prediction from sequences is an important problem. Recent research shows that some correctly predicted long-range…
Networks of elastic fibers are ubiquitous in biological systems and often provide mechanical stability to cells and tissues. Fiber reinforced materials are also common in technology. An important characteristic of such materials is their…
Some dimeric proteins first fold and then dimerize (three--state dimers) while others first dimerize and then fold (two--state dimers). Within the framework of a minimal lattice model, we can distinguish between sequences obeying to one or…
In this study, we investigate how specific micro interaction structures (motifs) affect the occurrence of tipping cascades on networks of stylized tipping elements. We compare the properties of cascades in Erd\"os-R\'enyi networks and an…
Long, flexible physical filaments are naturally tangled and knotted, from macroscopic string down to long-chain molecules. The existence of knotting in a filament naturally affects its configuration and properties, and may be very stable or…
By means of contact dynamic simulations, we investigate the contact network topology and force chains in two-dimensional packings of elongated particles modeled by rounded-cap rectangles. The morphology of large packings of elongated…
Natural protein sequences contain a record of their history. A common constraint in a given protein family is the ability to fold to specific structures, and it has been shown possible to infer the main native ensemble by analyzing…
Within the frame of an effective, coarse-grained hydrophobic-polar protein model, we employ multicanonical Monte Carlo simulations to investigate free-energy landscapes and folding channels of exemplified heteropolymer sequences, which are…
Extensive Monte Carlo folding simulations for four proteins of various structural classes are carried out, using a single atomistic potential. In all cases, collapse occurs at a very early stage, and proteins fold into their native-like…