Final Model Project
Fibrin
PHYS 053-001
April 27, 2010
Jake Stringfield
Patrick Moseby
Michael Beben
Calvin Lewis Jr.
Part A:
Clot Formation in Human Blood
This project is focused on describing and modeling the overall process of hemostasis in
humans, with a particular focus on the role that the protein fibrinogen plays in the formation of
thrombi. Understanding this process is important for multiple reasons. This is a process that
occurs in a similar way in almost every mammal, so it is clear that this is a very essential process
for life: without clotting, blood would escape through holes worn in vessel walls, and oxygen
would not be delivered to the body, leading to death. While the process of coagulation is well
conserved in most mammals, the specifics of the human clotting are of most scientific interest,
because of the medical applications that a better knowledge of clotting could advance. It is
important that all processes involved in clot formation are functioning properly; a mutation
that inactivates a single clotting factor can lead to hemophilia, while overactive clotting
mechanisms can lead to heart attack, stroke, or other embolism. Besides the important medical
significance that this process has, an understanding of the mechanisms of clotting will be
valuable to pure science, with relevance to nanotechnology, biology, and the physics of protein
mechanics.
The blood is a very complex solution of ions, chemical messengers, cells, and proteins.
Blood carries oxygen, nutrients, and water to every cell in your body, sustaining their
metabolism, and keeping them alive. It helps to fight off infections, keeping the body healthy. It
removes waste and toxins from cells and safely disposing of them. All of these crucial functions
depend on blood being delivered, and this is why hemostasis is so important. The proteins
responsible for clotting, collectively referred to as clotting factors, are in constant circulation in
the blood, along with many other substances. However, all of these proteins are inactive in
normal blood. Certain proteins, called subendothelial proteins, contained behind the
endothelium, the one-cell-thick wall of blood vessels, enter the blood stream through an injury
to the endothelium. The other key component in blood clot formation are the platelets, cell
fragments to which, along with their role in clotting, produce growth factors, that speed healing
in regions where the blood vessels are damaged.
All of these components work together in a complex way to form clots. When
endothelial cells are ruptured, subendothelial proteins are exposed to the blood stream. These
proteins, including tissue factor and von Willebrand Factor, begin a cascade of conformational
changes in the clotting factors present in the blood stream, as well as activating nearby
platelets. The newly activated platelets, which begin as roughly spherical cell fragments, will
also change shape, growing protrusions that help facilitate their binding to each other, to the
area of the clot, and to clotting factors. Platelets then make up the primary hemostasis, a plug
formed from activated platelets at the site of the rupture, held together by various clotting
factors. At this point the secondary hemostasis, consisting mainly of clotting factor 1,
fibrinogen, will begin to form. The cascade of clotting factors will at this point lead to a surge of
thrombin, which activates the fibrinogen. Fibrinogen will then bind to itself, forming fibrin, a
network of strong and stretchy fiber that will seal the clot securely.
As with all proteins, the structure of fibrinogen is key to its function. Fibrinogen is a
fibrillar protein that polymerizes, as described above, to form a viscoelastic gel. Activation of
fibrin severs the ends of the BβN domain, exposing sticky knobs that can bind to adjacent
fibrinogen molecules at their holes in their D region. This results in a strong staggered
formation of fibrinogen molecules within the fiber they make up, and the lack of rigidity in the
BβN domain is likely one of the ways that fibrin stretches. The αC domain also plays a role in
binding and stretching, but it is less understood. The coiled coil domain that makes up most of
the length of the protein is also believed to be involved in stretching. All together, the structure
of the protein can, in some cases, allow stretching by a factor of six before breaking, making
fibrin the most flexible biological polymers yet.
Proteins stretch when strain uncoils them from their preferred, most stable state.
Shown above is the crystalline structure of fibrinogen, but under stress certain interactions
would be broken in order to accommodate the forces applied to the molecule. One of the main
interactions that will be broken is hydrogen bonds. These bonds are based upon magnetic
interactions between the hydrogen atoms bonded to nitrogen atoms, and oxygen atoms.
Because of the high electronegativity of both nitrogen and oxygen, the hydrogen atoms will
have most of their electron cloud stolen from them, giving them a slight positive charge.
Likewise the oxygen atoms will have slightly more electron density, and will have a slight
negative charge. The interactions between these atoms are analogous to natural magnets,
because they can be pulled apart and reformed if stress is applied and released. As the protein
is stretched, hydrogen bonds will break until eventually only the carbon-carbon-nitrogen
backbone resists, at which point it will take far more force to stretch the molecule any further.
In this way force will be distributed to adjacent fibrinogen molecules in the clot, allowing the
fibrin to have enough strength and flexibility to function in the highly dynamic environment of
pulsing blood.
Part B:
Model #1
What We Are Modeling
Our first model was of a blood clot, formed in a small vessel. We sought to represent the
function of fibrin and platelets in the process of forming a clot. Our model clot is different from
regular clots in that usually the clot forms on a small area of the vessel where a tear has
occurred. Our model shows a vessel that is completely occluded.(This is when a thrombus
occurs; if that thrombus breaks free, it forms an embolus.)
Materials and Reasons
We built the “vessel wall” by making a geometrically approximate topless and bottomless
cylinder out of plastic building beams (they are like K-Nex). The primary reason we chose to use
this material for the vessel wall was that it was strong enough to withhold the tension of the
bands (our fibrin) while still providing a basically cylindrical shape, which is supposed to be
analogous to a cylindrical blood vessel. Then, to represent the fibrin, we used our “vessel wall”
as a loom to weave rubber bands randomly throughout the cylinder, creating a misshapen
web. We chose to use rubber band because of their stretchiness, which is analogous to the
stretchiness of fibrin. Because of this stretchiness, Fibrin is able to form a powerful net that
slows/prevents bleeding. To represent the platelets, we inadvertently used the same plastic
building balls that function as the joint stabilizers in our vessel wall (the small building balls
perfect for the representation of platelets). To construct clusters which represent the cell
fragments that make up platelets, we poke toothpicks through the holes in these building balls
to represent the pseudopods that extend from the platelets. We chose these mainly for their
scale relative to the blood cells. Finally to represent the red blood cells, we carved Styrofoam
spheres into the shape of blood cells, spray-painted them red, and tangled them into the web
of fibrin that represents the clot.
Model #2
What We Are Modeling
Our second model is a very basic model of fibrin. It shows the mirror-like structure of fibrin and
includes coiled coils. We sought to demonstrate a larger view of fibrin while simply showing
how the components of fibrin come together.
Materials and Reasons
We have three different colors of telephone wire (one which we spray-painted) to represent
the intertwining regions of fibrin. The components of Fibrin make it highly elastic and capable
of stretching to double or even triple in size. On either end of the the Fibrin molecule, there are
alpha helices. The ends of the alpha helices can be seen at the end of each colored telephone
wire. Fibrinogen molecules form elastic fibers which are essential in blood clots. When a blood
vessel breaks, it causes fibrin to be created from fibrinogen. It is the active form that is able to
polymerize with itself. Fibrin molecules link together in somewhat of a net which then catches
the flow of the bloodstream. Cells in the blood, such as red blood cells, fill the gaps. Our model
shows the fibrin components linking together forming the strands which would eventually
cause blod clots. We wrapped the telephone wire around a pole to make it coil, in order to
represent the coiled coil region. Then we combined the different wires together in order to
create the complete fibrin strand. We chose telephone wire because of its ability to hold a
shape, and yet remain flexible. To ensure it sprung back to its original crystalline structure,
rubber bands were used to simulate the forces that facilitate folding, such as hydrogen bonding
and hydrophobic interactions. Although they are not exactly analogous to these forces, the
combined entropic forces, in effect, act like a rubber band, to eventually pull the molecule back
to its ideal configuration.
Model #3
What We Are Modeling
Our third model is a model of the alpha helix region- a key part of any protein. It shows the
molecular makeup with the correct sequence and structure. Alpha helices are important
structural motifs of most proteins. As a crystalline structure the alpha helix is the most regular
and rigid, helping to give proteins their definite shape. Alpha helices relate to our project
because the central region of fibrinogen, the main clotting factor, is made up of a coil made of
three alpha helices. The model demonstrates not only the structure of this protein formation,
but also its ability to break its hydrogen bonds, uncoil, and stretch.
Materials and Reasons
The model is made up of wooden balls color coded to represent the 4 atoms that are necessary
in a alpha helix. The red ones represent oxygen, the white ones hydrogen, the black ones
represent carbon, and the blue ones Nitrogen. The wooden balls have holes drilled at the
appropriate angles at which each of the atoms would form a covalent bond to its neighbor.
Through these holes, fishing line attaches the balls, representing the covalent bonds that are
fairly rigid, but with some rotational flexibility. Attached to every hydrogen that is bonded to a
highly electronegative nitrogen atom, is a positively oriented magnet. Similarly attached to each
oxygen is a negatively oriented magnet. The attractive force between these two magnets is
representative of hydrogen bonding between the two atoms, which is essentially magnetic in
nature. This detail was included so that the model could demonstrate protein unfolding. When
the hydrogen bonds are broken, the molecule is able to stretch out to just its covalent
backbone, and become significantly longer. This helps to explain how fibrin can be so flexible,
and yet still strong enough to remain stable.
Referenced Works
Coagulation. (2010, April 25). In Wikipedia, The Free Encyclopedia. Retrieved 11:15, April 27, 2010,
from http://en.wikipedia.org/w/index.php?title=Coagulation&oldid=358137239
Fibrin. (2010, April 22). In Wikipedia, The Free Encyclopedia. Retrieved 11:16, April 27, 2010,
from http://en.wikipedia.org/w/index.php?title=Fibrin&oldid=357694502
Platelet. (2010, April 25). In Wikipedia, The Free Encyclopedia. Retrieved 11:16, April 27, 2010,
from http://en.wikipedia.org/w/index.php?title=Platelet&oldid=358268063
Medved, L, and J Weisel. "Recommendations for nomenclature on fibrinogen and fibrin." Journal of Thrombosis
and Hemostasis (2008): n. pag. Web. 27 Apr 2010.
Weisel, J. "Enigmas of Blood Clot Elasticity." Science 320. (2008): n. pag. Web. 27 Apr 2010.
http://www.pdb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb83_1.html
http://serpins.med.unc.edu/~fcc/ResearchPicts2006/Thrombin.html
http://www.jci.org/articles/view/26987/version/1
http://www3.interscience.wiley.com/journal/118717136/abstract