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DYNAMICS OF SINGLE-MOLECULE ROTATIONS ON SURFACES DEPEND ON SYMMETRY, INTERACTIONS AND MOLECULAR SIZES.

ABSTRACT: Rotating surface-mounted molecules have attracted attention of many research groups as a way to develop new nanoscale devices and materials. However, mechanisms of motion of these rotors at the single-molecule level are still not well understood. Theoretical and experimental studies on thioether molecular rotors on gold surfaces suggest that the size of the molecules, their flexibility and steric repulsions with the surface are important for dynamics of the system. A complex combination of these factors leads to the observation that the rotation speeds have not been hindered by increasing the length of the alkyl chains. However, experiments on diferrocene derivatives indicated that a significant increase in the rotational barriers for longer molecules. We present here a comprehensive theoretical study that combines molecular dynamics simulations and simple models to investigate what factors influence single-molecule rotations on the surfaces. Our results suggest that rotational dynamics is determined by the size and by the symmetry of the molecules and surfaces, and by interactions with surfaces. Our theoretical predictions are in excellent agreement with current experimental observations.

SUBMITTER: Akimov A

PROVIDER: S-EPMC3026388 | biostudies-literature | 2011 Jan

REPOSITORIES: biostudies-literature

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DYNAMICS OF SINGLE-MOLECULE ROTATIONS ON SURFACES DEPEND ON SYMMETRY, INTERACTIONS AND MOLECULAR SIZES.

Akimov Alexey A Kolomeisky Anatoly B AB

The journal of physical chemistry. C, Nanomaterials and interfaces 20110101 1

Rotating surface-mounted molecules have attracted attention of many research groups as a way to develop new nanoscale devices and materials. However, mechanisms of motion of these rotors at the single-molecule level are still not well understood. Theoretical and experimental studies on thioether molecular rotors on gold surfaces suggest that the size of the molecules, their flexibility and steric repulsions with the surface are important for dynamics of the system. A complex combination of these ...[more]

PMID: 21278909

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Project description:An important measure of the conformation of protein molecules is the degree of surface exposure of its specific segments. However, this is hard to measure at the level of individual molecules. Here, we combine single molecule photobleaching (smPB, which resolves individual photobleaching steps of single molecules) and fluorescence quenching techniques to measure the accessibility of individual fluorescently labeled protein molecules to quencher molecules in solution. A quencher can reduce the time a fluorophore spends in the excited state, increasing its photostability under continuous irradiation. Consequently, the photo-bleaching step length would increase, providing a measure for the accessibility of the fluorophore to the solvent. We demonstrate the method by measuring the bleaching step-length increase in a lipid, and also in a lipid-anchored peptide (both labelled with rhodamine-B and attached to supported lipid bilayers). The fluorophores in both molecules are expected to be solvent-exposed. They show a near two-fold increase in the step length upon incubation with 5 mM tryptophan (a quencher of rhodamine-B), validating our approach. A population distribution plot of step lengths before and after addition of tryptophan show that the increase is not always homogenous. Indeed there are different species present with differential levels of exposure. We then apply this technique to determine the solvent exposure of membrane-attached N-terminus labelled amylin (h-IAPP, an amyloid associated with Type II diabetes) whose interaction with lipid bilayers is poorly understood. hIAPP shows a much smaller increase of the step length, signifying a lower level of solvent exposure of its N-terminus. Analysis of results from individual molecules and step length distribution reveal that there are at least two different conformers of amylin in the lipid bilayer. Our results show that our method ("Q-SLIP", Quenching-induced Step Length increase in Photobleaching) provides a simple route to probe the conformational states of membrane proteins at a single molecule level.

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DYNAMICS OF SINGLE-MOLECULE ROTATIONS ON SURFACES DEPEND ON SYMMETRY, INTERACTIONS AND MOLECULAR SIZES.

Publications

DYNAMICS OF SINGLE-MOLECULE ROTATIONS ON SURFACES DEPEND ON SYMMETRY, INTERACTIONS AND MOLECULAR SIZES.

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