Helicase activity on DNA as a propagating front

Bhattacharjee, Somendra M.

doi:10.1209/epl/i2003-10107-2

Cited by 15 publications

(14 citation statements)

References 24 publications

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“…In contrast to Davydov's model, Yomosa [37] and very recently Sataric et al [38] studied soliton excitations in protein by considering the molecule as a toda lattice chain. The recent results on the statistical mechanics of protein-DNA system through coarse-grain and worm-like chain models describe unzipping of the DNA chain [39,40,41,42]. Normally, protein molecule interacts with DNA either through non-specific interaction (sequence-independent) which is mainly driven by the electrostatic attractive force between positively charged amino acids and negatively charged phosphate groups of the DNA back bone or through specific interactions (sequence-dependent) including hydrogen bonds, van der Waals force and water mediated bonds between the protein molecule and specific site of DNA [43].…”

Section: Introductionmentioning

confidence: 99%

Base-pair opening and bubble transport in a DNA double helix induced by a protein molecule in a viscous medium

Vasumathi

Daniel

2009

Phys. Rev. E

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The protein-DNA interaction dynamics is studied by modeling the DNA bases as classical spins in a coupled spin system, which are bosonized and coupled to thermal phonons and longitudinal motion of the protein molecule in the nonviscous limit. The nonlinear dynamics of this protein-DNA complex molecular system is governed by the completely integrable nonlinear Schrödinger (NLS) equation which admits N -soliton solutions. The soliton excitations of the DNA bases in the two strands make localized base-pair opening and travel along the DNA chain in the form of a bubble. This may characterize the bubble generated during the transcription process, when an RNA polymerase binds to a promoter site in the DNA double helical chain. When the protein-DNA molecular system interacts with the surrounding viscous solvating water medium, the dynamics is governed by a perturbed NLS equation. This equation is solved using a multiple scale perturbation analysis, by treating the viscous effect as a weak perturbation, and the results show that the viscosity of the solvent medium damps out the soliton as time progresses.

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Section: Introductionmentioning

confidence: 99%

Base-pair opening and bubble transport in a DNA double helix induced by a protein molecule in a viscous medium

Vasumathi

Daniel

2009

Phys. Rev. E

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“…Helicases like dnaB work in the fixed distance ensemble, but PcrA type helicases have both the fixed-distance and the fixed-force character (see, e.g., the references in Ref. [18,19]). Consequently, these explore or take advantage of the various features of the phase diagrams.…”

Section: Introductionmentioning

confidence: 99%

Unzipping DNA by force: thermodynamics and finite size behaviour

Kapri

Bhattacharjee

2006

J. Phys.: Condens. Matter

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We discuss the thermodynamic behaviour near the force induced unzipping transition of a double stranded DNA in two different ensembles. The Y-fork is identified as the coexisting phases in the fixed distance ensemble. From finite size scaling of thermodynamic quantities like the extensibility, the length of the unzipped segment of a Y-fork, the phase diagram can be recovered. We suggest that such procedures could be used to obtain the thermodynamic phase diagram from experiments on finite length DNA.

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“…We define β = 1/k B T and denote the time of relaxation of the long wave length oscillations of the string by τ = ζ/k. A model with similar structure has been studied in the context of DNA replication by Bhattacharjee [19].…”

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confidence: 99%

Diffusion in an elastic medium: A model for macromolecule transport across the nuclear pore complex

Chakrabarti

Debnath

Sebastian

2014

Physica A: Statistical Mechanics and its Applications

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Nuclear pore complexes (NPCs) are very selective filters that monitor the transport between the cytoplasm and the nucleoplasm. Two models have been suggested for the plug of the NPC. They are (i) it is a reversible hydrogel or (ii) it is a polymer brush. We propose a mesoscopic model for the transport of a protein through the plug, that is general enough to cover both. The protein stretches the plug and creates a local deformation. The bubble so created (prtoein+deformation) executes random walk in the plug. We find that for faster relaxation of the gel, the diffusion of the bubble is greater. Further, on using parameters appropriate for the brush, we find that the diffusion coefficient is much lower. Hence the gel model seems to be more likely explanation for the workings of the plug.The nuclear envelope in all eucaryotes is perforated with nuclear pores [1,2,3,4,5,6]. Each pore has a selective filter, referred to as the nuclear pore complex (NPC). The NPC is a self-assembled, eightfold symmetric ringlike structure consisting of eight copies each of 30-50 different proteins, connecting the inner and outer nuclear membranes. It regulates the import and export traffic of proteins and has two distinct modes of transport: passive and facilitated. Passive transport is nonspecific and takes place by ordinary diffusion. Colloidal gold particles with radii up to 4 nm, and generic proteins up to 50 kDa in mass, pass efficiently through the NPC in this way [7]. In contrast, facilitated translocation allows the passage of objects as large as several megadaltons. Proteins having a short amino acid sequence known as nuclear localization signal (NLS) form a complex with transportin [5] (a transporter protein rich in hydrophobic units) and are transported in this mode.The transport requires specific interactions between the translocating species and constituents of the NPC and consequently is highly selective. Gold particles of up to 32-36 nm in diameter are able to pass through some NPC if they are coated with nucleoplasmin-importin complexes [3].This suggests that the interaction of the protein-transportin complex with NPC is essential for transport. Passage of proteins through the NPC has attracted considerable experimental and theoretical attention [8,9,10,11]. According to Ribbeck and Görlich (RG) [8] the central plug of the nuclear pore is made of long diblock copolymers rich in hydrophobic phenylalanine-glycine (FG) units forming a meshwork. Only the macromolecules which can form hydrophobic contacts with the FG units are incorporated into this network and get transported. In an interesting paper,

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Helicase activity on DNA as a propagating front

Cited by 15 publications

References 24 publications

Base-pair opening and bubble transport in a DNA double helix induced by a protein molecule in a viscous medium

Base-pair opening and bubble transport in a DNA double helix induced by a protein molecule in a viscous medium

Unzipping DNA by force: thermodynamics and finite size behaviour

Diffusion in an elastic medium: A model for macromolecule transport across the nuclear pore complex

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