Entropic release of a big sphere from a cylindrical vessel

Mishima, Hirokazu; Oshima, Hiraku; Yasuda, Satoshi; Amano, Ken-ichi; Kinoshita, Masahiro

doi:10.1016/j.cplett.2013.01.045

Cited by 9 publications

(10 citation statements)

References 31 publications

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“…The transport process has wide implications towards understanding the multidrug efflux function of TolC and its homologues, which contributes to resistance against organic solvent, dyes, detergents, and lipophilic antibiotics such as novobiocin, erythromycin, fusidic acid, and cloxacillin. Using rigid body models, Mishima and colleagues have investigated the insertion and release of a solute into and from a cylindrical vessel, a process that mimics the behavior of TolC and its homologues [65]. They proposed that the insertion/release process can be described by solvent-entropy effect arising from the displacement of solvent molecules [65].…”

Section: Discussionmentioning

confidence: 99%

“…Using rigid body models, Mishima and colleagues have investigated the insertion and release of a solute into and from a cylindrical vessel, a process that mimics the behavior of TolC and its homologues [65]. They proposed that the insertion/release process can be described by solvent-entropy effect arising from the displacement of solvent molecules [65]. A more realistic view of the transport process can be obtained by evaluating the potential of mean force (PMF) with umbrella sampling and related approaches.…”

Section: Discussionmentioning

confidence: 99%

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Assembly and stability of Salmonella enterica ser. Typhi TolC protein in POPE and DMPE

et al. 2014

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In this work we assessed the suitability of two different lipid membranes for the simulation of a TolC protein from Salmonella enterica serovar Typhi. The TolC protein family is found in many pathogenic Gram-negative bacteria including Vibrio cholera and Pseudomonas aeruginosa and acts as an outer membrane channel for expulsion of drug and toxin from the cell. In S. typhi, the causative agent for typhoid fever, the TolC outer membrane protein is an antigen for the pathogen. The lipid environment is an important modulator of membrane protein structure and function. We evaluated the conformation of the TolC protein in the presence of DMPE and POPE bilayers using molecular dynamics simulation. The S. typhi TolC protein exhibited similar conformational dynamics to TolC and its homologues. Conformational flexibility of the protein is seen in the C-terminal, extracellular loops, and α-helical region. Despite differences in the two lipids, significant similarities in the motion of the protein in POPE and DMPE were observed, including the rotational motion of the C-terminal residues and the partially open extracellular loops. However, analysis of the trajectories demonstrated effects of hydrophobic matching of the TolC protein in the membrane, particularly in the lengthening of the lipids and subtle movements of the protein's β-barrel towards the lower leaflet in DMPE. The study exhibited the use of molecular dynamics simulation in revealing the differential effect of membrane proteins and lipids on each other. In this study, POPE is potentially a more suitable model for future simulation of the S. typhi TolC protein.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Assembly and stability of Salmonella enterica ser. Typhi TolC protein in POPE and DMPE

et al. 2014

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“…A brief report has already been published by us in a Letter, 17 but much more extensive parametric studies are carried out with detailed arguments in the present article. In particular, we show for the first time that solutes with a wide range of sizes can be handled, thus developing a sounder physical basis of the multidrug efflux.…”

Section: Introductionmentioning

confidence: 94%

“…Though the model, basic equations, numerical solution strategy were described in our earlier brief report, 17 they are reinterpreted here.…”

Section: A Three-dimensional Integral Equation Theory Applied To Rigmentioning

confidence: 99%

“…It is quite interesting that the two apparently opposite events, insertion and release, successively occur in a system. In earlier works, [14][15][16][17] we showed that the spatial distribution of the solute-vessel potential of mean force (PMF denoted by ) formed by the solvent plays imperative roles for the insertion/release process. The PMF represents "the free energy of the solvent for a fixed configuration of the solute-vessel pair" minus "that for the configuration where the solute is infinitely far from the vessel."…”

Section: Introductionmentioning

confidence: 99%

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On the physics of multidrug efflux through a biomolecular complex

Mishima

Oshima

Yasuda

et al. 2013

The Journal of Chemical Physics

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Insertion and release of a solute into and from a vessel comprising biopolymers is a fundamental function in a biological system. A typical example is found in a multidrug efflux transporter. "Multidrug efflux" signifies that solutes such as drug molecules with diverse properties can be handled. In our view, the mechanism of the multidrug efflux is not chemically specific but rather has to be based on a physical factor. In earlier works, we showed that the spatial distribution of the solute-vessel potential of mean force (PMF) induced by the solvent plays imperative roles in the insertion∕release process. The PMF can be decomposed into the energetic and entropic components. The entropic component, which originates from the translational displacement of solvent molecules, is rather insensitive to the solute-solvent and vessel inner surface-solvent affinities. This feature is not shared with the energetic component. When the vessel inner surface is neither solvophobic nor solvophilic, the solvents within the vessel cavity and in the bulk offer almost the same environment to any solute with solvophobicity or solvophilicity, and the energetic component becomes much smaller than the entropic component (i.e., the latter predominates over the former). Our idea is that the multidrug efflux can be realized if the insertion/release process is accomplished by the entropic component exhibiting the insensitivity to the solute properties. However, we have recently argued that the entropic release of the solute is not feasible as long as the vessel geometry is fixed. Here we consider a model of TolC, a cylindrical vessel possessing an entrance at one end and an exit at the other end for the solute. The spatial distribution of the PMF is calculated by employing the three-dimensional integral equation theory with rigid-body models in which the constituents interact only through hard-body potentials. Since the behavior of these models is purely entropic in origin, our analysis is focused on the entropic component. We show that the entropically inserted solute can be released by a continuous variation of the vessel geometry which forms a time-dependent entropic force continuing to accelerate the solute motion to the exit. Solutes with a wide range of sizes are entropically released using the same vessel-geometry variation. The results obtained are fairly general and also applicable to the efflux pump protein AcrB and ATP-binding cassette transporter.

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A New View on Mechanism of Functional Expression of an ATP-Driven Molecular Motor

Kinoshita

2020

SpringerBriefs in Molecular Science

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Entropic release of a big sphere from a cylindrical vessel

Cited by 9 publications

References 31 publications

Assembly and stability of Salmonella enterica ser. Typhi TolC protein in POPE and DMPE

Assembly and stability of Salmonella enterica ser. Typhi TolC protein in POPE and DMPE

On the physics of multidrug efflux through a biomolecular complex

A New View on Mechanism of Functional Expression of an ATP-Driven Molecular Motor

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