Polymer Chains in Confined Spaces and Flow-Injection Problems:  Some Remarks

Sakaue, Takahiro; Raphaël, Élie

doi:10.1021/ma0514424

Cited by 147 publications

(226 citation statements)

References 30 publications

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“…The confinement part of the free energy barrier is discussed extensively in literature [36][37][38] and it depends on the pore characteristics, such as the diameter, interaction energy between the polymer and pore surface, and polymer chain statistics reflecting the solvent quality and chain stiffness. The free energy barrier for localizing a chain end at the pore mouth is difficult to estimate.…”

Section: Barriermentioning

confidence: 99%

Theory of capture rate in polymer translocation

Muthukumar

2010

The Journal of Chemical Physics

152

186

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The translocation of macromolecules through a nanopore requires the impingement of the molecules at the pore followed by threading through the pore. While most of the discussion on the translocation phenomenon focused so far on the threading process, the phenomenology on the frequency of encounters between the polymer and the pore exhibits diverse features in terms of polymer length, solution conditions, driving force, and pore geometry. We derive a general theory for the capture rate of polyelectrolyte molecules and the probability of successful translocation through a nanopore, under an externally imposed electric field. By considering the roles of entropic barrier at the pore entrance and drift of the polyelectrolyte under the electric field, we delineate two regimes: ͑a͒ entropic barrier regime and ͑b͒ drift regime. In the first regime dominated by the entropic barrier for the polyelectrolyte, the capture rate is an increasing nonlinear function in the electric field and chain length. In the drift regime, where the electric field dwarfs the role of entropic barriers, the capture rate is independent of chain length and linear in electric field. An analytical formula is derived for the crossover behavior between these regimes, and the general results are consistent with various experimentally observed trends.

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Section: Barriermentioning

confidence: 99%

Theory of capture rate in polymer translocation

Muthukumar

2010

The Journal of Chemical Physics

152

186

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“…The much lower probability at such a separation amounts to an entropy barrier. For a Gaussian chain, the diffusion-controlled rate of contact formation at a separation σ is [29] k f = 3(6 / π) 1/2 Dσ / R s 3 (17) where D is the relative diffusion constant of the chain ends.…”

Section: Speed Up Of Contact Formation and Protein Folding By Confinementioning

confidence: 99%

Protein folding in confined and crowded environments

Zhou

2008

Archives of Biochemistry and Biophysics

152

137

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Confinement and crowding are two major factors that can potentially impact protein folding in cellular environments. Theories based on considerations of excluded volumes predict disparate effects on protein folding stability for confinement and crowding: confinement can stabilize proteins by over 10k B T but crowding has a very modest effect on stability. On the other hand, confinement and crowding are both predicted to favor conformations of the unfolded state which are compact, and consequently may increase the folding rate. These predictions are largely borne out by experimental studies of protein folding under confined and crowded conditions in the test tube. Protein folding in cellular environments is further complicated by interactions with surrounding surfaces and other factors. Concerted theoretical modeling and test-tube and in vivo experiments promise to elucidate the complexity of protein folding in cellular environments.The complexity of the cellular environments in which proteins function is increasingly been appreciated [1]. Potential impacts of two related, but distinct factors, confinement and macromolecular crowding, on protein folding are receiving extensive attention [2][3][4][5]. Confinement arises from encapsulation of proteins in compartments with dimensions on the scales of 10's to 100's Å, which are only moderately larger than the sizes of the proteins themselves. Examples of such compartments include the Anfinsen cage of chaperonins and the exit tunnel of ribosomes. Crowding refers to the exclusion of volumes to proteins of interest by the presence of other macromolecules. The aims of this paper are to discuss potential impacts of confinement and crowding on protein folding and to review the progress made by recent studies on protein folding in confined and crowded conditions and in cellular environments.

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“…This effect can be quantified based on the theory of polymers with excluded volume (33). From the scaling arguments, the conformational entropy cost reads (10,(33)(34)(35) 15/4 , where S u denotes the unfolded states, S c is the conformational entropy, N is the number of residues (or beads) with size a of the beads in a chain, and L the size of the confined space. The exponent 15/4 is more generally equal to 3/(3 Ϫ 1) where ϭ 3/5 is the Flory exponent.…”

Section: Free-energy Profiles Of Folding and Bindingmentioning

confidence: 99%

Confinement effects on the kinetics and thermodynamics of protein dimerization

Wang

Levy

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

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In the cell, protein complexes form by relying on specific interactions between their monomers. Excluded volume effects due to molecular crowding would lead to correlations between molecules even without specific interactions. What is the interplay of these effects in the crowded cellular environment? We study dimerization of a model homodimer when the mondimers are free and when they are tethered to each other. We consider a structured environment: Two monomers first diffuse into a cavity of size L and then fold and bind within the cavity. The folding and binding are simulated by using molecular dynamics based on a simplified topology based model. The confinement in the cell is described by an effective molecular concentration C ϳ L ؊3 . A two-state coupled folding and binding behavior is found. We show the maximal rate of dimerization occurred at an effective molecular concentration C op Ӎ 1 mM, which is a relevant cellular concentration. In contrast, for tethered chains the rate keeps at a plateau when C < C op but then decreases sharply when C > C op . For both the free and tethered cases, the simulated variation of the rate of dimerization and thermodynamic stability with effective molecular concentration agrees well with experimental observations. In addition, a theoretical argument for the effects of confinement on dimerization is also made. molecular crowding ͉ folding and binding ͉ effective molecular concentration ͉ Arc homodimer monolayer ͉ native topology-based models

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Polymer Chains in Confined Spaces and Flow-Injection Problems: Some Remarks

Cited by 147 publications

References 30 publications

Theory of capture rate in polymer translocation

Theory of capture rate in polymer translocation

Protein folding in confined and crowded environments

Confinement effects on the kinetics and thermodynamics of protein dimerization

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