Related papers: Sequence Heterogeneity Accelerates Protein Search …
Strong experimental and theoretical evidence shows that transcription factors and other specific DNA-binding proteins find their sites using a two-mode search: alternating between 3D diffusion through the cell and 1D sliding along the DNA.…
Molecular search phenomena are observed in a variety of chemical and biological systems. During the search the participating particles frequently move in complex inhomogeneous environments with random transitions between different dynamic…
DNA-interacting proteins have roles multiple processes, many operating as molecular machines which undergo dynamic metastable transitions to bring about their biological function. To fully understand this molecular heterogeneity, DNA and…
The structure of DNA Binding Proteins enables a strong interaction with their specific target site on DNA. However, recent single molecule experiment reported that proteins can diffuse on DNA. This suggests that the interactions between…
The effect of sequence heterogeneity on the dynamics of molecular motors is reviewed and analyzed using a set of recently introduced lattice models. First, we review results for the influence of heterogenous tracks such as a single-strand…
Efficient search acts as a strong selective force in biological systems ranging from cellular populations to predator-prey systems. The search processes commonly involve finding a stationary or mobile target within a heterogeneously…
We present Brownian dynamics simulations of the facilitated diffusion of a protein, modelled as a sphere with a binding site on its surface, along DNA, modelled as a semi-flexible polymer. We consider both the effect of DNA organisation in…
The mechanism allowing a protein to search of a target sequence on DNA is currently described as an intermittent process composed of 3D diffusion in bulk and 1D diffusion along the DNA molecule. Due to the relevant charge of protein and…
The most common gene regulation mechanism is when a protein binds to a regulatory sequence to change RNA transcription. However, these sequences are short relative to the genome length, so finding them poses a challenging search problem.…
We study the target searching on the DNA for proteins in the presence of non-constant drift and non-Gaussian $\alpha$-stable L\'evy fluctuations. The target searching is realized by the facilitated diffusion process. The existing works are…
This commentary discusses a recently proposed measure of heterogeneity of DNA sequences and compares with the measures of complexity.
The detection of similarities between long DNA and protein sequences is studied using concepts of statistical physics. It is shown that mutual similarities can be detected by sequence alignment methods only if their amount exceeds a…
With the continued improvement of sequencing technologies, the prospect of genome-based medicine is now at the forefront of scientific research. To realize this potential, however, we need a revolutionary sequencing method for the…
Protein complexes involved in DNA mismatch repair appear to diffuse along dsDNA in order to locate a hemimethylated incision site via a dissociative mechanism. Here, we study the probability that these complexes locate a given target site…
Complex DNA topological structures, including polymer loops, are frequently observed in biological processes when protein molecules simultaneously bind to several distant sites on DNA. However, the molecular mechanisms of formation of these…
In gene expression, various kinds of proteins need to bind to specific locus of DNA. It is still not clear how these proteins find their target locus. In this study, the mean first-passage time (FPT) of protein binding to its target locus…
In the course of evolution, proteins undergo important changes in their amino acid sequences, while their three-dimensional folded structure and their biological function remain remarkably conserved. Thanks to modern sequencing techniques,…
DNA sequence alignment is important today as it is usually the first step in finding gene mutation, evolutionary similarities, protein structure, drug development and cancer treatment. Covid-19 is one recent example. There are many…
Genetic algorithms have been used in recent decades to solve a broad variety of search problems. These algorithms simulate natural selection to explore a parameter space in search of solutions for a broad variety of problems. In this paper,…
Proteins, by virtue of their central role in most biological processes, represent one of the key subjects of the study of molecular evolution. Inherent to the indispensability of proteins for living cells is the fact that a given protein…