Biological Machines

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Paramecium beating cilia

And

Biflagellate Breaststroke Swimming

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 Prof. Ben Feringa, University of Groningen,
Nobel Prize in Chemistry, 2016
“Go beyond our current horizon”

At IIT-Delhi

Asteroid named after Ben????

Looking for Ben? Maybe try 2.8 AU from the
sun! Main belt asteroid 12655 has recently
been named 'Benferinga' by the International
Astronomical Union. (Posted on 12-4-2019)
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• A machine is an apparatus using mechanical power and
having several parts, each with a definite function and
together performing a particular task.
• Living organisms are made up of numerous such
biological machines (or “nanomachines”). Such
biological machines are necessary for performing life
functions.
• Proteins that hydrolyze ATP perform mechanical work in
the cells. ATP is analogous to the fuel required by engines
to perform work.
• Biological processes are performed by protein machines
those interact reversibly.

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 Motor Proteins
• All motor proteins transduce chemical energy from nucleotide
hydrolysis to movement.
• Motors are encoded by multigene families.
• Individual gene is highly conserved in organisms as diverse as
yeast to human.
• Motors , structurally divided into two domains: a head which
contains the motor and a tail which interacts with its cargo.
• Head domain: highly conserved within members of a super family;
Tails: highly divergent.
• In multi-subunit complexes, a single type of motor could be used in
several different machines by virtue of its association with
functionally diverse tails.

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 Types of molecular motor proteins

• Myosin: Contraction. (relaxation).

• Kinesin: Cargo movement.
• Dynein: Cargo movement and beating of cilia and
flagella.
Myosin is an actin based motor
Kinesin and Dynein are microtubule (tubulin) based
motors.

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MICROTUBULES: The Tubulins

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 Actin
• Monomeric subunit of microfilaments
• Highly conserved through evolution
• Binds to ATP or ADP
• Two forms:
– G-actin: globular monomeric actin
– F-actin: filamentous polymeric actin; called Thin Filament.

Polymerization

• Actin cytoskeleton is dynamic (microfilaments grow and shrink)

• G-actin polymerizes to F-actin
• ATP influences polymerization rate

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Polymerization

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 Myosin
• Contractile force of muscle generated by the interaction of two
proteins, myosin and actin.
• Together, actin and myosin make up more than 80% of the protein
mass of muscle.
• Molecules of myosin aggregate to form structures called thick
filaments. (F-actin: filamentous polymeric actin; called thin
filament)
• The thick and thin filaments that undergo transient interactions
and slide pass each other to bring about contraction.

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 Myosin structure
• Two heavy chains, two essential light chains, and two regulatory
light chains
• Heavy chain has head domain, neck region, and tail domain.
• Head domain contains actin-binding site and ATP-binding site
• Tail domain is a dimeric coiled-coil

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 Myosin
• Skeletal muscle consists of parallel bundles of muscle fibers, each
fiber a single, very large, multinucleated cell, (20 to 100 µm in
diameter), formed from many cells fused together. Each fiber
contains about 1,000 myofibrils, (2 µm in diameter), each
consisting of a vast number of regularly arrayed thick and thin
filaments complexed to other proteins.

Muscle fibers consist of

single, elongated,
multinucleated cells that
arise from the fusion of
many cells. The fibers
are made up of many
myofibrils surrounded
by the membranous
sarcoplasmic reticulum,
the source of calcium.
The organization of
thick and thin filaments
in a myofibril gives it a
striated appearance. 13
Sarcomere: where the cycles of contraction and relaxation takes place
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 Myosin movement
• Myosin head attached to
actin filament (rigor)
• Calcium from
sarcoplasmic reticulum
comes and stimulates.
• ATP binds head and actin
released
• ATP hydrolyzed,
conformational change
occurs, head moves closer
to (+) end and reattaches
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 Myosin movement
• “Power stroke:”
phosphate released and
second conformational
change moves actin
filament
• ADP released.
• Cross bridge cycle.
• Calcium, Troponin,
Tropomyosin plays
important roles.

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Cross bridge cycle

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 Kinesin
• Within cells, proteins, organelles, and vesicles move many micrometers along well-
defined routes in the cytosol and delivered to particular addresses.
• In Nerve cells microtubules function as tracks in the intracellular transport of various
types of “cargo.”
• To date, approximately 10 different kinesin subfamilies identified. All contain a globular
head (motor) domain, but differ in their tail domains and several other properties.
• Two broad functional groups— cytosolic and mitotic kinesins.
Cytosolic kinesins: vesicle and organelle transport.
Mitotic kinesins: spindle assembly and chromosome segregation in cell
division.

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 Kinesin moves in 8 nm steps corresponding to the distance between successive alpha- and
beta-Tubulin monomers in a protofilament. Moves from –ve to +ve direction of
microtubules.

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Molecular Cell Biology. 5th Edition. 2004.
Kinesin delivering cargo in brain through neuron

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 Dynein
• A microtubule-based molecular motor involved in axonal transport, mitosis, and
cilia/flagella movement.
• Two types: Cytoplasmic and Axonemal
• Unlike kinesin and myosin dynein form large molecular complexes. E.g.,: one
axonemal dynein molecule of Clamidomonous composed of three dynein heavy
chains, two intermediate chains, and more than ten light chains.
• Cargoes: lysosomes, endosomes, phagosomes, golgi complex.
• Dynein mediates transport to the (-) end of MTs (opposite to Kinesin)

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• Dynein present in cilia and flagella are termed axonemal dyneins.
• Cilia and flagella: found on a variety of cell types, from single cell protozoa and
“sperm” to the ciliated surface of respiratory and reproductive tracts.
• Ciliary motility is generated by the dynein-driven sliding of doublet
microtubules.
• Defects in the dynein motors or components that regulate their activity can have
profound consequences; in vertebrates, these include infertility, respiratory
disease, and defects in the determination of the left–right axis during
embryonic development. These defects are called “Ciliopathies”.
• No medicine.

Cilia. 2012. 1:1-16

Cell Motil Cytoskel. 2009. 66:220-336
Cilia of Paramecium 22
Flagella of sperm
17.75Hz-10fps

And

100 fps

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Video 1: Bacterial Infection and microtubule

Video 2: A Day in the Life of a Motor Protein :

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 References
• Lehninger Principles of Biochemistry. 5th Edition. 2008. David L. Nelson and
Michael M. Cox.
• Molecular Cell Biology. 5th Edition. 2004. Lodish, Berk, Matsudaira, Kaiser,
Krieger, Scott,Zipursky and Darnell.
• Alberts B and Lye RM (1992) Unscrambling the puzzle of biological machines:
The importance of the details. Cell 68:415-420.
• Howard J (1997) Molecular motors: Structural adaptations to cellular functions.
Nature 389:561-567.
• Kikkawa M (2013) Big steps toward understanding dynein. J Cell Biol 202:15-23.
• Porter ME and Sale WS (2000) The 9+2 axoneme anchor multiple inner arm
dyneins and a network of kinases and phosphatases that control motility. J Cell Biol
151: F37-42.
• Sowa Y and Berry RM (2008) Bacterial flagellar motor. Quarterly Rev Biophy
41:103-132.
• Vallee RB, Williams JC, Varma D, Barnhart LE (2004) Dynein: An ancient motor
protein involved in multiple modes of transport. J Neurobiol 58:189–200.

• Acknowledgement: Mr. Aakash Gautam Mukhopadhyay

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 Videos
• https://www.youtube.com/watch?v=Ct8AbZn_A8A
• https://www.youtube.com/watch?v=y‐uuk4Pr2i8
• https://www.youtube.com/watch?v=tMKlPDBRJ1E
• https://www.youtube.com/watch?v=BbI47l2nbDQ
• https://www.youtube.com/watch?v=mu72Qoy1xq0

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