Biological molecular machines From Wikipedia, the free encyclopedia
This article is about biological molecular motors. For man-made molecular motors, see Synthetic molecular motor.
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.
Dynamin is responsible for the separation of clathrin buds from the plasma membrane. GTP is used.
Rotary motors:
FoF1-ATP synthase family of proteins convert the chemical energy in ATP to the electrochemical potential energy of a proton gradient across a membrane or the other way around. The catalysis of the chemical reaction and the movement of protons are coupled to each other via the mechanical rotation of parts of the complex. This is involved in ATP synthesis in the mitochondria and chloroplasts as well as in pumping of protons across the vacuolar membrane.[3]
The bacterial flagellum responsible for the swimming and tumbling of E. coli and other bacteria acts as a rigid propeller that is powered by a rotary motor. This motor is driven by the flow of protons across a membrane, possibly using a similar mechanism to that found in the Fo motor in ATP synthase.
Molecular dynamics simulation of a synthetic molecular motor composed of three molecules in a nanopore (outer diameter 6.7 nm) at 250 K.[4]
Viral DNA packaging motors inject viral genomic DNA into capsids as part of their replication cycle, packing it very tightly.[8] Several models have been put forward to explain how the protein generates the force required to drive the DNA into the capsid. An alternative proposal is that, in contrast with all other biological motors, the force is not generated directly by the protein, but by the DNA itself.[9] In this model, ATP hydrolysis is used to drive protein conformational changes that alternatively dehydrate and rehydrate the DNA, cyclically driving it from B-DNA to A-DNA and back again. A-DNA is 23% shorter than B-DNA, and the DNA shrink/expand cycle is coupled to a protein-DNA grip/release cycle to generate the forward motion that propels DNA into the capsid.
Enzymatic motors: The enzymes below have been shown to diffuse faster in the presence of their catalytic substrates, known as enhanced diffusion. They also have been shown to move directionally in a gradient of their substrates, known as chemotaxis. Their mechanisms of diffusion and chemotaxis are still debated. Possible mechanisms include solutal buoyancy, phoresis or conformational changes leading to change in effective diffusivity[10][11][12] and kinetic asymmetry.[13]
Catalase
Urease
Aldolase
Hexokinase
Phosphoglucose isomerase
Phosphofructokinase
Glucose Oxidase
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.[14]
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.[16]
Kinesin– These molecular motors always move towards the positive end of the cell
The "foot" of the motor binds using ATP, the "foot" proceeds a step, and then ADP comes off. This repeats itself until the destination has been reached
The kinesin family consists of a multitude of different motor types
Intermediate/light chains that will attach to the dynactin bonding region
A Head
A Stalk
With a domain that will bind to the microtubule
These molecular motors tend to take the path of the microtubules. This is most likely due to the facts that the microtubules spring forth out of the centrosome and surround the entire volume of the cell. This in turn creates a "Rail system" of the whole cell and paths leading to its organelles.
In experimental biophysics, the activity of molecular motors is observed with many different experimental approaches, among them:
Fluorescent methods: fluorescence resonance energy transfer (FRET), fluorescence correlation spectroscopy (FCS), total internal reflection fluorescence (TIRF).
Magnetic tweezers can also be useful for analysis of motors that operate on long pieces of DNA.
Neutron spin echo spectroscopy can be used to observe motion on nanosecond timescales.
Optical tweezers (not to be confused with molecular tweezers in context) are well-suited for studying molecular motors because of their low spring constants.
Single-molecule electrophysiology can be used to measure the dynamics of individual ion channels.
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.
Recently, chemists and those involved in nanotechnology have begun to explore the possibility of creating molecular motors de novo.[17] 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.[18] 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.[19] 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.[20]
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. PMID11607035. S2CID4424168.
Lodish H, Berk A, Kaiser CA, Krieger M, Bretscher A, Ploegh H, Amon A, Martin KC (2014). Molecular Cell Biology (8thed.). New York, NY: w.h.freeman, Macmillan Learning. ISBN978-1-4641-8339-3.
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. PMID29064685.
