Related papers: DNA-Protein Cooperative Binding through Long-Range…
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…
Increasing evidence suggests that chromosome folding and genetic expression are intimately connected. For example, the co-expression of a large number of genes can benefit from their spatial co-localization in the cellular space.…
The presence of knots has been observed in a small fraction of single-domain proteins and related to their thermodynamic and kinetic properties. The exchanging of identical structural elements, typical of domain-swapped proteins, make such…
The similarity in the three-dimensional structures of homologous proteins imposes strong constraints on their sequence variability. It has long been suggested that the resulting correlations among amino acid compositions at different…
The theory of elastic rods can be used to describe certain geometric and topological properties of the DNA molecules. A similar effective field theory approach was previously suggested to describe the conformations and dynamics of proteins.…
It has long been asserted that proteins like transcription factors may locate their target in DNA sequences at rates that surpass by several orders of magnitude the three-dimensional diffusion limit thank to facilitated diffusion, that 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…
DNA-coated particles are promising as building blocks for functional and finite-sized assemblies because they can be programmed with orthogonal interactions owing to the sequence-specific hybridization of DNA strands. To fully exploit this…
Cotranslational folding depends on the folding speed and stability of the nascent protein. It remains difficult, however, to predict which proteins cotranslationally fold. Here, we simulate evolution of model proteins to investigate how…
This paper introduces the use of cable dynamics models as a means to explore the mechanics of DNA on long-length scales. It is on these length scales that DNA forms twisted and curved three-dimensional shapes known as supercoils and loops.…
We explore in detail the structural, mechanical and thermodynamic properties of a coarse-grained model of DNA similar to that introduced in Thomas E. Ouldridge, Ard A. Louis, Jonathan P.K. Doye, Phys. Rev. Lett. 104 178101 (2010). Effective…
A DNA-protein complex modelled by a semiflexible chain and an attractive spherical core is studied in the situation when an external stretching force is acting on one end monomer of the chain while the other end monomer is kept fixed in…
We investigate the folding behavior of protein sequences by numerically studying all sequences with maximally compact lattice model through exhaustive enumeration. We get the prion-like behavior of protein folding. Individual proteins…
Current experimental and theoretical studies on the effect of intermolecular interactions on molecular conduction appear to be in conflict with each other. In particular, some experimental results, e.g., the observation of 2-dimensional…
The respective roles of local and nonlocal interactions in the thermodynamic cooperativity of proteins are investigated using continuum (off-lattice) native-centric G\=o-like models with a coarse-grained C$_\alpha$ chain representation. We…
We present a self-contained theory for the mechanical response of DNA in single molecule experiments. Our model is based on a 1D continuum description of the DNA molecule and accounts both for its elasticity and for DNA-DNA electrostatic…
Bacterial genomes have been shown to be partitioned into several kilobases long chromosomal domains that are topologically independent from each other, meaning that change of DNA superhelicity in one domain does not propagate to neighbors.…
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…
Integral membrane proteins deform the surrounding bilayer creating long-ranged forces that influence distant proteins. These forces can be attractive or repulsive, depending on the proteins' shape, height, contact angle with the bilayer, as…
The structure of molecular networks derives from dynamical processes on evolutionary time scales. For protein interaction networks, global statistical features of their structure can now be inferred consistently from several…