A ribosome is a biological machine that utilizes protein dynamics

Molecular motors are natural (biological) or artificial molecular machines that are the essential agents of movement in living organisms. In general terms, a motor is a device that consumes energy in one form and converts it into motion or mechanical work; for example, many protein-based molecular motors harness the chemical free energy released by the hydrolysis of ATP in order to perform mechanical work.[1] In terms of energetic efficiency, this type of motor can be superior to currently available man-made motors. One important difference between molecular motors and macroscopic motors is that molecular motors operate in the thermal bath, an environment in which the fluctuations due to thermal noise are significant.

Examples

Kinesin  uses protein domain dynamics on nanoscales to walk along a microtubule.

Some examples of biologically important molecular motors:[2]

Molecular dynamics simulation of a synthetic molecular motor composed of three molecules in a nanopore (outer diameter 6.7 nm) at 250 K.[4]
Molecular dynamics simulation of a synthetic molecular motor composed of three molecules in a nanopore (outer diameter 6.7 nm) at 250 K.[4]

A recent study has also shown that certain enzymes, such as Hexokinase and Glucose Oxidase, are aggregating or fragmenting during catalysis. This changes their hydrodynamic size that can affect enhanced diffusion measurements.[13]

Organelle and vesicle transport

There are two major families of molecular motors that transport organelles throughout the cell. These families include the dynein family and the kinesin family. Both have very different structures from one another and different ways of achieving a similar goal of moving organelles around the cell. These distances, though only few micrometers, are all preplanned out using microtubules.[15]

Theoretical considerations

Because the motor events are stochastic, molecular motors are often modeled with the Fokker–Planck equation or with Monte Carlo methods. These theoretical models are especially useful when treating the molecular motor as a Brownian motor.

Experimental observation

In experimental biophysics, the activity of molecular motors is observed with many different experimental approaches, among them:

Many more techniques are also used. As new technologies and methods are developed, it is expected that knowledge of naturally occurring molecular motors will be helpful in constructing synthetic nanoscale motors.

Non-biological

Main article: Synthetic molecular motor

Recently, chemists and those involved in nanotechnology have begun to explore the possibility of creating molecular motors de novo. These synthetic molecular motors currently suffer many limitations that confine their use to the research laboratory. However, many of these limitations may be overcome as our understanding of chemistry and physics at the nanoscale increases. One step toward understanding nanoscale dynamics was made with the study of catalyst diffusion in the Grubb's catalyst system.[16] Other systems like the nanocars, while not technically motors, are also illustrative of recent efforts towards synthetic nanoscale motors.

Other non-reacting molecules can also behave as motors. This has been demonstrated by using dye molecules that move directionally in gradients of polymer solution through favorable hydrophobic interactions.[17] Another recent study has shown that dye molecules, hard and soft colloidal particles are able to move through gradient of polymer solution through excluded volume effects.[18]

See also

References

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  2. ^ Nelson P, Radosavljevic M, Bromberg S (2004). Biological physics. Freeman.
  3. ^ Tsunoda SP, Aggeler R, Yoshida M, Capaldi RA (January 2001). "Rotation of the c subunit oligomer in fully functional F1Fo ATP synthase". Proceedings of the National Academy of Sciences of the United States of America. 98 (3): 898–902. Bibcode:2001PNAS...98..898T. doi:10.1073/pnas.031564198. PMC 14681. PMID 11158567.
  4. ^ Palma CA, Björk J, Rao F, Kühne D, Klappenberger F, Barth JV (August 2014). "Topological dynamics in supramolecular rotors". Nano Letters. 14 (8): 4461–8. Bibcode:2014NanoL..14.4461P. doi:10.1021/nl5014162. PMID 25078022.
  5. ^ Dworkin J, Losick R (October 2002). "Does RNA polymerase help drive chromosome segregation in bacteria?". Proceedings of the National Academy of Sciences of the United States of America. 99 (22): 14089–94. Bibcode:2002PNAS...9914089D. doi:10.1073/pnas.182539899. PMC 137841. PMID 12384568.
  6. ^ Hubscher U, Maga G, Spadari S (2002). "Eukaryotic DNA polymerases". Annual Review of Biochemistry. 71: 133–63. doi:10.1146/annurev.biochem.71.090501.150041. PMID 12045093. S2CID 26171993.
  7. ^ Peterson CL (November 1994). "The SMC family: novel motor proteins for chromosome condensation?". Cell. 79 (3): 389–92. doi:10.1016/0092-8674(94)90247-X. PMID 7954805. S2CID 28364947.
  8. ^ Smith DE, Tans SJ, Smith SB, Grimes S, Anderson DL, Bustamante C (October 2001). "The bacteriophage straight phi29 portal motor can package DNA against a large internal force". Nature. 413 (6857): 748–52. Bibcode:2001Natur.413..748S. doi:10.1038/35099581. PMID 11607035. S2CID 4424168.
  9. ^ Harvey SC (January 2015). "The scrunchworm hypothesis: transitions between A-DNA and B-DNA provide the driving force for genome packaging in double-stranded DNA bacteriophages". Journal of Structural Biology. 189 (1): 1–8. doi:10.1016/j.jsb.2014.11.012. PMC 4357361. PMID 25486612.
  10. ^ Zhao X, Gentile K, Mohajerani F, Sen A (October 2018). "Powering Motion with Enzymes". Accounts of Chemical Research. 51 (10): 2373–2381. doi:10.1021/acs.accounts.8b00286. PMID 30256612. S2CID 52845451.
  11. ^ Ghosh S, Somasundar A, Sen A (2021-03-10). "Enzymes as Active Matter". Annual Review of Condensed Matter Physics. 12 (1): 177–200. doi:10.1146/annurev-conmatphys-061020-053036. S2CID 229411011.
  12. ^ Zhang Y, Hess H (June 2019). "Enhanced Diffusion of Catalytically Active Enzymes". ACS Central Science. 5 (6): 939–948. doi:10.1021/acscentsci.9b00228. PMC 6598160. PMID 31263753.
  13. ^ Gentile, Kayla; Bhide, Ashlesha; Kauffman, Joshua; Ghosh, Subhadip; Maiti, Subhabrata; Adair, James; Lee, Tae-Hee; Sen, Ayusman (2021-09-22). "Enzyme aggregation and fragmentation induced by catalysis relevant species". Physical Chemistry Chemical Physics. 23 (36): 20709–20717. doi:10.1039/D1CP02966E. ISSN 1463-9084.
  14. ^ Kay, Euan R.; Leigh, David A.; Zerbetto, Francesco (January 2007). "Synthetic Molecular Motors and Mechanical Machines". Angewandte Chemie International Edition. 46 (1–2): 72–191. doi:10.1002/anie.200504313.
  15. ^ Lodish H, Berk A, Kaiser CA, Krieger M, Bretscher A, Ploegh H, Amon A, Martin KC (2014). Molecular Cell Biology (8th ed.). New York, NY: w.h.freeman, Macmillan Learning. ISBN 978-1-4641-8339-3.
  16. ^ Dey KK, Pong FY, Breffke J, Pavlick R, Hatzakis E, Pacheco C, Sen A (January 2016). "Dynamic Coupling at the Ångström Scale". Angewandte Chemie. 55 (3): 1113–7. Bibcode:2016AngCh.128.1125D. doi:10.1002/ange.201509237. PMID 26636667.
  17. ^ Guha R, Mohajerani F, Collins M, Ghosh S, Sen A, Velegol D (November 2017). "Chemotaxis of Molecular Dyes in Polymer Gradients in Solution". Journal of the American Chemical Society. 139 (44): 15588–15591. doi:10.1021/jacs.7b08783. PMID 29064685.
  18. ^ Collins M, Mohajerani F, Ghosh S, Guha R, Lee TH, Butler PJ, et al. (August 2019). "Nonuniform Crowding Enhances Transport". ACS Nano. 13 (8): 8946–8956. doi:10.1021/acsnano.9b02811. PMID 31291087. S2CID 195879481.