Related papers: Non-specific DNA-protein interaction: Why proteins…
DNA is an essential molecule central to the survival and propagation of life, it was imperative to investigate possible electromagnetic properties inherent to it, such as the existence of any non-trivial interactions of this molecule with…
We describe and solve a discrete persistent chain model of protein binding on DNA, involving an extra sigma_i s at a site i of the DNA. This variable takes the value 1 or 0 depending on whether the site is occupied by a protein or not. In…
We use nucleosome maps obtained by high-throughput sequencing to study sequence specificity of intrinsic histone-DNA interactions. In contrast with previous approaches, we employ an analogy between a classical one-dimensional fluid of…
An example of a nonspecific molecular bond is the affinity of any positive charge for any negative charge (like-unlike), or of nonpolar material for itself when in aqueous solution (like-like). This contrasts specific bonds such as the…
The encapsulation of polyanions, whether single-stranded RNAs or synthetic polymers, is primarily driven by attractive electrostatic interactions between the positively charged, structurally disordered RNA-binding domains of virus coat…
Conformation of a protein (CorA) is examined in a matrix with mobile solute constituents as a function of solute-residue interaction strength (f) by a coarse-grained model with a Monte Carlo simulation. Solute particles are found to reach…
Although mechanical properties of DNA are well characterized at the kilo base-pair range, a number of recent experiments have suggested that DNA is more flexible at shorter length scales, which correspond to the regime that is crucial for…
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…
Despite recent breakthroughs in understanding how protein sequence relates to structure and function, considerably less attention has been paid to the general features of protein surfaces beyond those regions involved in binding and…
Molecular networks guide the biochemistry of a living cell on multiple levels: its metabolic and signalling pathways are shaped by the network of interacting proteins, whose production, in turn, is controlled by the genetic regulatory…
The subject of this report is the dynamics of elastic system in conjunction with hydrogen bonds of the DNA. We draw attention to the draw-back of the familiar rod model of the DNA, and make a case of constructing models that could…
Small angle neutron scattering intensity distributions taken from cytochrome C and lysozyme protein solutions show a rising intensity at very small wave vector, Q, which can be interpreted in terms of the presence of a weak long-range…
Statistical analysis of protein-protein interactions shows anomalously high frequency of homodimers [Ispolatov, I., et al. (2005) Nucleic Acids Res 33, 3629-35]. Furthermore, recent findings [Wright, C.F., et al. (2005) Nature 438, 878-81]…
How do living cells achieve sufficient abundances of functional protein complexes while minimizing promiscuous non-functional interactions? Here we study this problem using a first-principle model of the cell whose phenotypic traits are…
The formation of DNA loops by proteins and protein complexes that bind at distal DNA sites plays a central role in many cellular processes, such as transcription, recombination, and replication. Here we review the basic thermodynamic…
DNA storage has emerged as an important area of research. The reliability of DNA storage system depends on designing the DNA strings (called DNA codes) that are sufficiently dissimilar. In this work, we introduce DNA codes that satisfy a…
We study the correlation between the codon usage bias of genetic sequences and the network features of protein-protein interaction (PPI) in bacterial species. We use PCA techniques in the space of codon bias indices to show that genes with…
We propose a DNA sequencing scheme based on silicene nanopores. Using first principles theory, we compute the electrical properties of such pores in the absence and presence of nucleobases. Within a two-terminal geometry, we analyze the…
It has recently been proposed that proteins embedded in lipidic bio-membranes can spontaneously self-organize into stable small clusters, or membrane nano-domains, due to the competition between short-range attractive and longer-range…
DNA nanocompartment is a typical DNA-based machine whose function is dependent of molecular collective effect. Fundamental properties of the device have been addressed via electrochemical analysis, fluorescent microscopy, and atomic force…