Related papers: Modelling Protein Target-Search in Human Chromosom…
It is widely recognized that the cleaving rate of a restriction enzyme on target DNA sequences is several orders of magnitude faster than the maximal one calculated from the diffusion--limited theory. It was therefore commonly assumed that…
The interaction between proteins and DNA is a key driving force in a significant number of biological processes such as transcriptional regulation, repair, recombination, splicing, and DNA modification. The identification of DNA-binding…
To better understand DNA's 3D folding in cell nuclei, researchers developed chromosome capture methods such as Hi-C that measure the contact frequencies between all DNA segment pairs across the genome. As Hi-C data sets often are massive,…
We present a novel framework for understanding node target search in systems organized as hierarchical networks-within-networks. Our work generalizes traditional search models on complex networks, where the mean-first passage time is…
DNA-binding proteins are a class of proteins which have a specific or general affinity to DNA and include three important components: transcription factors; nucleases, and histones. DNA-binding proteins also perform important roles in many…
The spatial organization of the DNA in the cell nucleus plays an important role for gene regulation, DNA replication, and genomic integrity. Through the development of chromosome conformation capture experiments (such as 3C, 4C, Hi-C) it is…
Eukaryotic DNA is packaged into chromatin: one-dimensional arrays of nucleosomes separated by stretches of linker DNA are folded into 30-nm chromatin fibers which in turn form higher-order structures. Each nucleosome, the fundamental unit…
In living cells, proteins combine 3D bulk diffusion and 1D sliding along the DNA to reach a target faster. This process is known as facilitated diffusion, and we investigate its dynamics in the physiologically relevant case of confined DNA.…
Researchers developed chromosome capture methods such as Hi-C to better understand DNA's 3D folding in nuclei. The Hi-C method captures contact frequencies between DNA segment pairs across the genome. When analyzing Hi-C data sets, it is…
Computer experiments are performed to investigate why protein contact networks (networks induced by spatial contacts between amino acid residues of a protein) do not have shorter average shortest path lengths in spite of their importance to…
Protein motifs are conserved fragments occurred frequently in protein sequences. They have significant functions, such as active site of an enzyme. Search and clustering protein sequence motifs are computational intensive. Most existing…
Generating molecules that bind to specific proteins is an important but challenging task in drug discovery. Previous works usually generate atoms in an auto-regressive way, where element types and 3D coordinates of atoms are generated one…
Protein contacts contain important information for protein structure and functional study, but contact prediction from sequence information remains very challenging. Recently evolutionary coupling (EC) analysis, which predicts contacts by…
The mechanical model based on beads and springs, which we recently proposed to study non-specific DNA-protein interactions [J. Chem. Phys. 130, 015103 (2009)], was improved by describing proteins as sets of interconnected beads instead of…
When analyzing the genome, researchers have discovered that proteins bind to DNA based on certain patterns of the DNA sequence known as "motifs". However, it is difficult to manually construct motifs due to their complexity. Recently,…
DNA sequence alignment involves assigning short DNA reads to the most probable locations on an extensive reference genome. This process is crucial for various genomic analyses, including variant calling, transcriptomics, and epigenomics.…
Under dilute in vitro conditions transcription factors rapidly locate their target sequence on DNA by using the facilitated diffusion mechanism. However, whether this strategy of alternating between three-dimensional bulk diffusion and…
The evolutionary trajectory of a protein through sequence space is constrained by function and three-dimensional (3D) structure. Residues in spatial proximity tend to co-evolve, yet attempts to invert the evolutionary record to identify…
Surviving in a diverse environment requires corresponding organism responses. At the cellular level, such adjustment relies on the transcription factors (TFs) which must rapidly find their target sequences amidst a vast amount of…
The eukaryotic cell nucleus harbors the DNA genome that is organized in a dynamic chromatin network and embedded in a viscous crowded fluid. This environment directly affects enzymatic reactions and target search processes that access the…