CLASS: Quaternary Structure of Proteins Scribe: Aynsley Girardeau

CLASS: Quaternary Structure of Proteins Scribe: Aynsley Girardeau

DATE: August 12, 2011 Proof: Sarah Erwin

PROFESSOR: Detloff Quaternary Structure of Proteins Page 1 of 5

I. QUATERNARY STRUCTURE OF PROTEINS [S1]

A.  Individual polypeptide chains fold into a tertiary structure and a bunch of secondary structures based on its primary structure.

a.  It can form a complex when it interacts with other subunits or other polypeptide chains that are not covalently linked or not coded on same gene. Either between two different subunits or 2 different polypeptides or a complex of same polypeptide but 2 different molecules that come together or more than two. (More rule than exception.)

b.  Proteins that carry out enzymatic activity or structural feature will stick together inside the cell in their normal state. (More the rule than exception.)

c.  Cell is not a bag of water with globular proteins floating, but little centers, places where things get done. This is dictated by protein-protein interactions that are classified as quaternary structures.

d.  There are non-covalent and covalent associations for globular proteins. The covalent associations are mostly disulfide bonds, but there are also other types of bonds between 2 polypeptide chains that make up this quaternary structure.

e.  Fibrous proteins have lots of covalent associations.

f.  There are some hydrophobic residues (R chains that don’t like to be in water), which create order in the water. Not good. Order is against the loss in free energy.

g.  Quaternary structures can bury large portions of hydrophobic surface areas. The invasion of water is what drives the tertiary structure.

II.  HOW DO PROTEIN SUBUNITS INTERACT AT THE QUATERNARY LEVEL OF STRUCTURE? [S2]

A. This slide is to show you that most proteins associate with one another (and themselves) to

create very large structures.

III. ADVANTAGES OF 4° ASSOCIATION [S3 & S4 continuation slide]

A.  Quaternary association can increase the stability of a protein.

B.  Its surface to volume ratio has changed such that less water has to interact with the molecules themselves. Usually when a tertiary structure is formed you have an exclusion of water. Hydrophobic chains go into the center of the molecule. Polar groups, the charged amino acids, orient on the outside of the molecule. On the outside, water goes around, with less water having to be organized.

C.  A hydrophobic patch on one side of a molecule will tend to stick to another hydrophobic face of another protein and form a stable structure.

D.  The cell has a way of disposing of abnormally structuring proteins. It is like a garbage disposal called the proteasome that chews up proteins that aren’t complexed correctly. When there has been a mistake in translation/transcription (i.e. mutated subunit) to give you an extra amino acid that is not supposed to be there, the normal folding of that protein and it’s ability to partner will be changed. That change would likely exclude it from becoming part of the quaternary structure. It would just be a polypeptide chain floating around. The cell would notice that as being abnormal and degrade it.

E.  Subunits: one unit that is repeated over and over. Another advantage is that you can build something very big using subunits, i.e. Subunits repeated over and over can create collagen fibrils, actin filaments, or other long, big structures. That subunit that is part of the unit that forms this tertiary structure, which then forms into a long polymer that would have a characteristic of being long, tough, or big. Could use this for tendon or bone that you need a structure for.

F.  Catalytic sites may not be formed until there is quaternary structure.

G.  There is also an idea that having coordinated activities is possible

Chemical Process Ex: A  B  C

B is the product of the chemical reaction, A, which then goes to C. We don’t want B to float free to become diluted and unavailable for the next reaction. We need it right there to be turned into C. We want it all combined together. There is an efficiency to this. There are enzyme complexes that have these enzymes together. It is based on localized concentration of the product of one being substrate of the other.

H. Cooperativity is another advantage. Ex. If you have one oxygen bound to hemoglobin, it

tends to make another oxygen bind more tightly.

IV.  HOW DO PROTEIN SUBUNITS INTERACT AT THE QUATERNARY LEVEL OF STRUCTURE? [S5]

A.  Classifications of the different interactions

a. 2 totally different proteins can interact and stick together

b. 2 same polypeptide can interact and stick together

c. 2 similar polypeptides can interact and stick together:

i.) Isologous associations: the same molecule is associating with itself in a way that it has symmetry to it. All of the associating groups are in the same plane. They will stick together. If you flip it around it will look identical. There is no polarity here. This forms a closed structure, so you will not have a polymer form.

ii.) Heterologous association: 2 different planes that associate with one another

and form open structures that you can continue to build on.

V.  HOW DO PROTEIN SUBUNITS INTERACT AT THE QUATERNARY LEVEL OF STRUCTURE? [S6, 7, 8, continuation]

A. An example of alcohol dehydrogenase (pictured) shows an isologous association. You could spin it around and notice it is the same plane. The beta pleated sheets need to be buried because of their hydrophobicity, which is what drives these two proteins together.

B. Tetramers can form and other ordered structures, dimer, trimer…dodecomer (12).

C. There is a symmetry that is formed even if the molecule is asymmetric beforehand. A structural symmetry can be formed with this.

VI.  ANTIBODY SLIDE: They do not work the same way without the quaternary structure. [S9]

a.  The area that binds to the antigen is highly variable. If you have 2 associations on 2 different molecules and it occurs over and over, then they will tend to aggregate that antigen. (The protein that that antigen is found in will tend to aggregate.) You will have a blob there.

b.  The effector region signals the immune system for what to do with these proteins. Cells will be sent in to chew up all of those proteins or the organism that the protein is on (example: bacteria).

c.  Light chain is coated by one gene

d.  Heavy chain is coated by a different gene

e.  The effector region won’t work unless those 2 sites are together

f.  The recognition site won’t work unless the heavy and light chain are together

g.  There are a bunch of hydrophobic interactions that bind these two together

h.  There are disulfide bonds to create a tertiary structure

i.  There are disulfide bonds that create a hinge to help to stabilize the tertiary structure

j.  Immune response cannot work without the quaternary structure put together correctly.

VII. OPEN QUATERNARY STRUCTURES CAN POLYMERIZE [S10]

A.  Multiple subunits with a heterologous, (open) system allows long polymers to be built

B.  Tubulin formed by having alpha and beta polypeptides

a.  From two different genes

b.  Get together to form an alpha beta dimer (shown)

c.  The beta sticks to the alpha because of a polarity between the two

d.  Forms a long polymer, called Tubulin, which carries out various reactions in the cell.

e.  If you have a mutation in one of the two, it would be hard to fit it into this polymer. Would be excluded and chewed up, destroyed. May not create a disease. The quaternary structure isn’t proper it is outside. Will get chewed up.

[S11 is a repeat from earlier in the lecture and was skipped over]

VII.  TOBACCO MOSAIC VIRUS [S12]

A. Viruses are very small; don’t have a lot of genetic material. They want to be efficient about what they have to code for. In order to form a whole protein coat, which may be very big, it would be evolutionarily disadvantageous to the virus to code for several proteins that make up that. It would be ideal if one small segment of DNA could code for the entire protein coat that’s around Tobacco Mosaic Virus. That would create this efficiency that is needed for the virus.

B. This efficiency is also needed to create large structures in human beings and eukaryotes.

Examples: Tubulin, Actin, Collagens are all repeated units that have this enormous

Quaternary structure.

C. The protein subunit is self-associating and it can wind around the DNA. Tobacco Mosaic Virus (RNA based virus) has about 2,100 identical protein subunits around a single RNA strand which is the genome of this virus.

VIII.  AN ENZYME COMPLEX [S13]

A  B  C

A. The entire reaction will go better if A, B, and C are localized in one place.

B. An example of the enzyme complex: Pyruvate dehydrogenase complex.

Pyruvate + CoA + NAD Acetyl-coA + CO2 + NADH

IX.  THE REACTION MECHANISM OF THE PYRUVATE DEHYDROGENASE COMPLEX [S14, 15]

A. Three enzymatic activities that are needed to carry out this reaction. Those three reactions are coded for by 3 different polypeptides, but they are all put together into one giant complex.

B. Pictured is the enormously large complex

C. The enzymatic activities are E1, E2, and E3. (E3 is not shown)

D. All of the substrates stay together. The down stream reactions can be driven here.

E. A more efficient system for making acetyl-CoA

X.  RIBOSOME [S16]

A.  70% is ribosomal RNA, the RNA has catalytic activities, which is odd, because normally a protein would carry out catalytic activities, not RNA

B.  Review: think of an activity as being separate from a protein. You can in a laboratory have an activity that happens. An activity can be: “How much penicillin kills bacteria?” Give 1000 units of penicillin. How much bacteria can be killed? The penicillin itself could be of different structural forms, could be impure, and could need more to carry out same activity because some of your penicillin is impure. You really care about your patients not having a bacterial infection. You care about the activity of this.

C.  It’s the same for proteins. Biochemists would go in and crack open a bunch of cells. They are following a chemical reaction to see how much activity is in this particular sample. They would see how much of that one particular chemical reaction went on. That would be the activity. You can purify the proteins or activity following where the activity goes over different steps of purifications. You can get down to a point where you have such a pure protein that you can have it sequenced so you would know that this enzyme carries out this activity. Your isolated protein catalyzes this protein reaction. But the activity is a separate concept from the actual protein. It is all about how you measure what that protein is doing. The amount of protein that you have is somewhat different that the activity. The activity of a ribosome all together is to synthesize the polypeptides from RNA.

XI.  DISTRIBUTION OF RNA AND PROTEIN ON THE CHLORO-RIBOSOME WITH POSITIONS OF PSRPs AND PRP EXTENSIONS HIGHLIGHTED [S17]

A.  There are 50-60 different proteins stuck to this RNA that are absolutely essential for this to work.

B. Don’t worry about all the details to this slide, just to show you all the different proteins that are present and in a particular structure and order to give the ribosome it’s shape so it can carry out it’s activity.

XII.  HEMOGLOBIN [S18]

A.  A protein and its structural components as helping catalyze a chemical reaction in its simple form.

B.  He drew a free energy diagram depicting that an enzyme decreases the transition state energy for any process. A process may be thermodynamically favorable but not kinetically favorable.

C.  A concrete example that explains, “Structure is function”: The enzymatic activity you have is that you have to break a bond. Pull on the R groups and cause the structure to create a stress on the bond that would make it more likely to be broken. The structure actually creates this decrease in free energy of the transition state. This can help drive the reaction forward. You still need the thermodynamic difference in order for the reaction to go forward but it is much more likely to go forward if you can provide those structural elements around that bond.

D.  Hemoglobin is the greatest example of quaternary structure altering the properties such that you have a biological necessary property of coopertivity.

E.  Hemoglobin binds and carries oxygen around. If one oxygen molecule binds to a heme group it increases the likelihood that another oxygen will bind to another heme group. It allosterically alters the protein structure slightly so that oxygen is more likely to bind to the remaining heme groups. When going through an oxygen rich environment (the lungs), the heme groups will be full. Then will travel to the tissue to dump off the attached oxygen all at once. The coopertivity gives hemoglobin the property it needs to be an efficient oxygen picker upper in the lungs and dumper offer in the tissues!

XIII. THE STRUCTURE OF MYOGLOBIN IS SIMILAR TO THAT OF THE Hb MONOMER [S19]

A. Myoglobin also binds oxygen but is not cooperative because it doesn’t have 4 heme groups that bind the oxygen. It holds onto oxygen and keeps on holding. Myoglobin is present where the oxygen needs to be dumped. Doesn’t let go unless your body really needs oxygen, like during strenuous exercise.