Ratchets, power strokes, and molecular motors

Wang, H.; Oster, George

doi:10.1007/s003390201340

Cited by 146 publications

(173 citation statements)

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“…There are two basic proposals for how translocation occurs: the ''powerstroke'' mechanism makes use of the energy released during phosphodiester bond formation to drive translocation between states 0 and ϩ1 (24,25); whereas in the ''Brownian ratchet'' mechanism bidirectional translocational steps occur stochastically as a result of reversible thermal (Brownian) motion of the polymerase along DNA (22,(26)(27)(28). In the latter case the phosphodiester bond formation rectifies the motion and resets the system into a state with a longer transcript length, poised to incorporate the next NTP.…”

Section: Model Of Transcription Elongationmentioning

confidence: 99%

Thermodynamic and kinetic modeling of transcriptional pausing

Tadigotla

Maoiléidigh

Sengupta

et al. 2006

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

106

185

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We present a statistical mechanics approach for the prediction of backtracked pauses in bacterial transcription elongation derived from structural models of the transcription elongation complex (EC). Our algorithm is based on the thermodynamic stability of the EC along the DNA template calculated from the sequence-dependent free energy of DNA–DNA, DNA–RNA, and RNA–RNA base pairing associated with ( i ) the translocational and size fluctuations of the transcription bubble; ( ii ) changes in the associated DNA–RNA hybrid; and ( iii ) changes in the cotranscriptional RNA secondary structure upstream of the RNA exit channel. The calculations involve no adjustable parameters except for a cutoff used to discriminate paused from nonpaused complexes. When applied to 100 experimental pauses in transcription elongation by Escherichia coli RNA polymerase on 10 DNA templates, the approach produces statistically significant results. We also present a kinetic model for the rate of recovery of backtracked paused complexes. A crucial ingredient of our model is the incorporation of kinetic barriers to backtracking resulting from steric clashes of EC with the cotranscriptionally generated RNA secondary structure, an aspect not included explicitly in previous attempts at modeling the transcription elongation process.

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Section: Model Of Transcription Elongationmentioning

confidence: 99%

Thermodynamic and kinetic modeling of transcriptional pausing

Tadigotla

Maoiléidigh

Sengupta

et al. 2006

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

106

185

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“…Remarkably, a proper approach to quantify the rotational dynamics and efficiency of synthetic rotational motors is lacking. This is in contrast to the situation for biological molecular motors, generally defined as Brownian motors (28)(29)(30)(31)(32)(33)(34) or steppers (35)(36)(37)(38), which have been the inspiration of numerous studies.…”

mentioning

confidence: 87%

Optimizing rotary processes in synthetic molecular motors

Geertsema

Molen

Martens

et al. 2009

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

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We deal with the issue of quantifying and optimizing the rotation dynamics of synthetic molecular motors. For this purpose, the continuous four-stage rotation behavior of a typical light-activated molecular motor was measured in detail. All reaction constants were determined empirically. Next, we developed a Markov model that describes the full motor dynamics mathematically. We derived expressions for a set of characteristic quantities, i.e., the average rate of quarter rotations or ''velocity,'' V, the spread in the average number of quarter rotations, D, and the dimensionless Pé clet number, Pe ‫؍‬ V/D. Furthermore, we determined the rate of full, four-step rotations (⍀ eff), from which we derived another dimensionless quantity, the ''rotational excess,'' r.e. This quantity, defined as the relative difference between total forward (⍀ ؉) and backward (⍀؊) full rotations, is a good measure of the unidirectionality of the rotation process. Our model provides a pragmatic tool to optimize motor performance. We demonstrate this by calculating V, D, Pe, ⍀ eff, and r.e. for different rates of thermal versus photochemical energy input. We find that for a given light intensity, an optimal temperature range exists in which the motor exhibits excellent efficiency and unidirectional behavior, above or below which motor performance decreases. Markov model ͉ unidirectional rotation

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“…Likewise, the notion of a Brownian or thermal ratchet is reserved for the operating principle of protein translocation processes. The latter term was introduced by Simon et al ͑1992͒ to describe isothermal trapping of Brownian particles to drive protein translocation; see also Wang and Oster ͑2002͒. has become one of the most promising techniques for powering microdevices and nanodevices.…”

Section: Single-particle Transportmentioning

confidence: 99%

“…As emphasized in the Introduction, the field of Brownian motors has its roots in the study and applications of intracelluar transport in terms of molecular motors ͑Jülicher et al, 1997; Astumian and Hänggi, 2002;Reimann, 2002;Wang and Oster, 2002;Lipowsky and Klumpp, 2005͒. These molecular motors function in terms of structure and motility by use of specialized proteins in living systems.…”

Section: B Synthetic Molecular Motors and Machinesmentioning

confidence: 99%

Artificial Brownian motors: Controlling transport on the nanoscale

2009

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In systems possessing spatial or dynamical symmetry breaking, Brownian motion combined with unbiased external input signals, deterministic and random alike, can assist directed motion of particles at submicron scales. In such cases, one speaks of "Brownian motors." In this review the constructive role of Brownian motion is exemplified for various physical and technological setups, which are inspired by the cellular molecular machinery: the working principles and characteristics of stylized devices are discussed to show how fluctuations, either thermal or extrinsic, can be used to control diffusive particle transport. Recent experimental demonstrations of this concept are surveyed with particular attention to transport in artificial, i.e., nonbiological, nanopores, lithographic tracks, and optical traps, where single-particle currents were first measured. Much emphasis is given to two-and three-dimensional devices containing many interacting particles of one or more species; for this class of artificial motors, noise rectification results also from the interplay of particle Brownian motion and geometric constraints. Recently, selective control and optimization of the transport of interacting colloidal particles and magnetic vortices have been successfully achieved, thus leading to the new generation of microfluidic and superconducting devices presented here. The field has recently been enriched with impressive experimental achievements in building artificial Brownian motor devices that even operate within the quantum domain by harvesting quantum Brownian motion. Sundry akin topics include activities aimed at noise-assisted shuttling other degrees of freedom such as charge, spin, or even heat and the assembly of chemical synthetic molecular motors. This review ends with a perspective for future pathways and potential new applications.

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Ratchets, power strokes, and molecular motors

Cited by 146 publications

References 0 publications

Thermodynamic and kinetic modeling of transcriptional pausing

Thermodynamic and kinetic modeling of transcriptional pausing

Optimizing rotary processes in synthetic molecular motors

Artificial Brownian motors: Controlling transport on the nanoscale

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