Related papers: Facilitated diffusion of proteins on chromatin
The most common gene regulation mechanism is when a transcription factor protein binds to a regulatory sequence to increase or decrease RNA transcription. However, transcription factors face two main challenges when searching for these…
In this paper a lattice model for diffusional transport of particles in the interphase cell nucleus is proposed. Dense networks of chromatin fibers are created by three different methods: randomly distributed, non-interconnected obstacles,…
Cell spreading is investigated at various scales in order to understand motility of living cells which is essential for a range of physiological activities in higher organisms as well as in microbes. At a microscopic scale, it has been seen…
Protein dynamics is a fundamental element to comprehend their biological functions. However, a theoretical picture providing microscopic-detail explanation of its relevant features is still missing. One of the outmost relevant properties…
A theoretical framework for evaluating the approximate energy and dynamic properties associated with the folding of DNA into nucleosomes and chromatin is presented. For this purpose experimentally determined elastic constants of linear DNA…
Apart from being the gateway for all access to the eukaryotic genome, chromatin has in recent years been identified as carrying an epigenetic code regulating transcriptional activity. The detailed knowledge of this code contrasts the…
Chromatin is a complex of DNA and specific proteins forming an intermediary level of organization of eukaryotic genomes, between double-stranded DNA and chromosome. Within a generic modeling of the chromatin assembly, we investigate the…
The recently introduced method of excess collisions (MEC) is modified to estimate diffusion-controlled reaction times inside systems of arbitrary size. The resulting MEC-E equations contain a set of empirical parameters, which have to be…
Conformational fluctuations are believed to play an important role in the process by which transcription factor proteins locate and bind their target site on the genome of a bacterium. Using a simple model, we show that the binding time can…
The binding of proteins onto DNA contributes to the shaping and packaging of genome as well as to the expression of specific genetic messages. With a view to understanding the interplay between the presence of proteins and the deformation…
Molecular dynamics simulations of folding in an off-lattice protein model reveal a nucleation scenario, in which a few well-defined contacts are formed with high probability in the transition state ensemble of conformations. Their…
We use Brownian dynamics simulations to study the formation of chromatin loops through diffusive sliding of slip-link-like proteins, mimicking the behaviour of cohesin molecules. We recently proposed that diffusive sliding is sufficient to…
Dynamics of nucleosomes, the building blocks of the chromatin, has crucial effects on expression, replication and repair of genomes in eukaryotes. Beside constant movements of nucleosomes by thermal fluctuations, ATP-dependent chromatin…
The metazoan genome is replicated in precise cell lineage specific temporal order. However, the mechanism controlling this orchestrated process is poorly understood as no molecular mechanisms have been identified that actively regulate the…
Protein-mediated interactions are ubiquitous in the cellular environment, and particularly in the nucleus, where they are responsible for the structuring of chromatin. We show through molecular--dynamics simulations of a polymer surrounded…
We perform simulations of a system containing simple model proteins and a polymer representing chromatin. We study the interplay between protein-protein and protein-chromatin interactions, and the resulting condensates which arise due to…
The mean time required by a transcription factor (TF) or an enzyme to find a target in the nucleus is of prime importance for the initialization of transcription, gene activation or the start of DNA repair. We obtain new estimates for the…
Protein-DNA interactions are critical for the successful functioning of all natural systems. The key role in these interactions is played by processes of protein search for specific sites on DNA. Although it has been studied for many years,…
Measurements of lateral diffusion of proteins in a membrane typically assume that the movement of the protein occurs in a flat plane. Real membranes, however, are subject to thermal fluctuations, leading to movement of an inclusion into the…
Conditional diffusion models serve as the foundation of modern image synthesis and find extensive application in fields like computational biology and reinforcement learning. In these applications, conditional diffusion models incorporate…