Concepts in Bionanomachines: Translocators

Baumgaertner, A.

doi:10.1166/jctn.2008.903

Cited by 3 publications

(1 citation statement)

References 112 publications

(136 reference statements)

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“…In this section we review the generic models of "translocators" [544], i.e., motors that translocate linear polymers across a narrow passage on a surface. The process of macromolecule translocation can be divided into two steps.…”

Section: Pull Of De-polymerization: Generic Model Of a Nanohookmentioning

confidence: 99%

Stochastic mechano-chemical kinetics of molecular motors: a multidisciplinary enterprise from a physicist's perspective

Chowdhury

2012

Preprint

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A molecular motor is made of either a single macromolecule or a macromolecular complex. Just like their macroscopic counterparts, molecular motors "transduce" input energy into mechanical work. All the nanomotors considered here operate under isothermal conditions far from equilibrium. Moreover, one of the possible mechanisms of energy transduction, called Brownian ratchet, does not even have any macroscopic counterpart. But, molecular motor is not synonymous with Brownian ratchet; a large number of molecular motors execute a noisy power stroke, rather than operating as Brownian ratchet. We review not only the structural design and stochastic kinetics of individual single motors, but also their coordination, cooperation and competition as well as the assembly of multimodule motors in various intracellular kinetic processes. Although all the motors considered here execute mechanical movements, efficiency and power output are not necessarily good measures of performance of some motors. Among the intracellular nano-motors, we consider the porters, sliders and rowers, pistons and hooks, exporters, importers, packers and movers as well as those that also synthesize, manipulate and degrade "macromolecules of life". We review mostly the quantitative models for the kinetics of these motors. We also describe several of those motordriven intracellular stochastic processes for which quantitative models are yet to be developed. In part I, we discuss mainly the methodology and the generic models of various important classes of molecular motors. In part II, we review many specific examples emphasizing the unity of the basic mechanisms as well as diversity of operations arising from the differences in their detailed structure and kinetics. Multi-disciplinary research is presented here from the perspective of physicists.

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Section: Pull Of De-polymerization: Generic Model Of a Nanohookmentioning

confidence: 99%

Stochastic mechano-chemical kinetics of molecular motors: a multidisciplinary enterprise from a physicist's perspective

Chowdhury

2012

Preprint

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Fast-ion transport in peptide nanochannels

Baumgaertner

2009

Materials Science and Engineering: B

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Peptide aggregation and solvent electrostriction in a simple zwitterionic dipeptide via molecular dynamics simulations

Tulip

Bates

2009

The Journal of Chemical Physics

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We investigate the structure of the glycyl-l-alanine dipeptide in aqueous solution at a 1:20 peptide:water concentration via classical, atomistic molecular dynamics simulations using the CHARMM22 force field, and compare to recent neutron diffraction data [S. E. McLain, A. K. Soper, and A. Watts, Eur. Biophys. J. 37, 647 (2008); S. E. McLain, A. K. Soper, I. Diadone, J. C. Smith, and A. Watts, Angew. Chem. Int. Ed. 47, 9059 (2008)]. Comparison between simulations and experiments is made using the static structure factor S(Q). The effect of water model (TIP3P, TIP4P, and SPC/E) upon the solution structure is investigated. Agreement between experiment and simulation is generally good across the entire Q range, although some model-dependent variation is observed, particularly in the predicted intensities of features in S(Q). Peptide aggregation is found to be driven by "hydrophilic" (often bifurcated) hydrogen bonds formed between carboxy and amine functional groups, although simulations suggest that the degree of aggregation is less than that observed experimentally. It is found that hydrophobic association is not significant, with hydrophobic hydration being preferred to association. Detailed examination of the solute structural motifs reveals the existence of bifurcated motifs that are suggested to be an artifact of the CHARMM force field, and may imply that classical force fields provide a flawed structural and dynamical description of such molecular fluids. Investigation of the water structure reveals the presence of an electrostrictive effect which manifests itself as an increase in the number of interstitial molecules in the water second coordination shell, in contradiction to suggestions that this phenomenon arises owing to hydrogen bond bending. Detailed analysis based upon two-dimensional distribution functions suggests an intimate link between the phenomenon of electrostriction and the behavior of water under high-pressure compression. We find the magnitude of the electrostrictive effect inferred from the neutron diffraction data to be greater than that found in the simulations. Investigation of the solvation structure suggests that the CHARMM force field overhydrates the terminal carboxy group, and that this overhydration is accompanied by the presence of bifurcated hydrogen bonds.

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Concepts in Bionanomachines: Translocators

Cited by 3 publications

References 112 publications

Stochastic mechano-chemical kinetics of molecular motors: a multidisciplinary enterprise from a physicist's perspective

Stochastic mechano-chemical kinetics of molecular motors: a multidisciplinary enterprise from a physicist's perspective

Fast-ion transport in peptide nanochannels

Peptide aggregation and solvent electrostriction in a simple zwitterionic dipeptide via molecular dynamics simulations

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