Related papers: The network of stabilizing contacts in proteins st…
Intracellular protein patterns govern essential cellular functions by dynamically redistributing proteins between membrane-bound and cytosolic states, conserving their total numbers. This review presents a theoretical framework for…
Analyzing nonlinear conformational relaxation dynamics in elastic networks corresponding to two classical motor proteins, we find that they respond by well-defined internal mechanical motions to various initial deformations and that these…
The total conformational energy is assumed to consist of pairwise interaction energies between atoms or residues, each of which is expressed as a product of a conformation-dependent function (an element of a contact matrix, C-matrix) and a…
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…
Networks play a prominent role in the study of complex systems of interacting entities in biology, sociology, and economics. Despite this diversity, we demonstrate here that a statistical model decomposing networks into matching and…
Local and global inference methods have been developed to infer structural contacts from multiple sequence alignments of homologous proteins. They rely on correlations in amino-acid usage at contacting sites. Because homologous proteins…
Proteins are responsible for the most diverse set of functions in biology. The ability to extract information from protein sequences and to predict the effects of mutations is extremely valuable in many domains of biology and medicine.…
Increased ability to predict protein structures is moving research focus towards understanding protein dynamics. A promising approach is to represent protein dynamics through networks and take advantage of well-developed methods from…
Multicellular organisms comprise a diverse collection of stable tissues built from different cell types. It remains unclear how large numbers of interacting cells can precisely coordinate their gene expression during tissue…
Nowadays there is a multitude of measures designed to capture different aspects of network structure. To be able to say if the structure of certain network is expected or not, one needs a reference model (null model). One frequently used…
We are looking at local protein interaction networks from the perspective of directed, labeled graphs with quantitative values for monotonic changes in concentrations. These systems can be used to perform stability analysis for a stable…
Gene and protein networks are very important to model complex large-scale systems in molecular biology. Inferring or reverseengineering such networks can be defined as the process of identifying gene/protein interactions from experimental…
The time evolution of the formation probability of native bonds has been studied for designed sequences which fold fast into the native conformation. From this analysis a clear hierarchy of bonds emerge a) local, fast forming highly stable…
Entanglement generated by Ising model has been studied for several authors in order to understand the relation between it and magnetic properties of materials, principally using one or two dimensional models for two or more particles. In…
A protein structure is represented as a network of residues whereby edges are determined by intra-molecular contacts. We introduce inhomogeneity into these networks by assigning each edge a weight that is determined by amino-acid pair…
The dynamical characterization of proteins is crucial to understand protein function. From a microscopic point of view, protein dynamics is governed by the local atomic interactions that, in turn, trigger the functional conformational…
We present a simple model of protein folding dynamics that captures key qualitative elements recently seen in all-atom simulations. The goals of this theory are to serve as a simple formalism for gaining deeper insight into the physical…
In this work we employ various methods of analysis (unfolding simulations and comparative analysis of structures and sequences of proteomes of thermophilic organisms) to show that organisms can follow two major strategies of thermophilic…
The choice of structural resolution is a fundamental aspect of protein modelling, determining the balance between descriptive power and interpretability. Although atomistic simulations provide maximal detail, much of this information is…
The structure and function of a protein are determined by its amino acid sequence. While random mutations change a protein's sequence, evolutionary forces shape its structural fold and biological activity. Studies have shown that neutral…