Secondary, tertiary, and quaternary structure

What is mad cow disease a result of?

It is a protein misfolding disease that is incurable, fatal, and has a months to decades long incubation period

What are proteins defined as?

Polypeptide chains longer than 50 residues (5 000 Da or 5 kDa)

What if it is less than 50 residues?

Then it is called a peptide

What does primary structure determine?

All higher order structure (conformation). Secondary-quaternary structure can be predicted

What are four ways to look at proteins? What do they include?

1. Backbone- shows the backbone of the peptide (no R groups, only the amino and carbonyl)

2. Wireframe- full representation and is very complex

3. Ribbon- highlights secondary structure (alpha-helix and beta sheets)

4. Spacefill- Shows the surface and shape of molecule

What does a peptide bond limit? Why?

Conformational flexibility due to its partial (40%) double bond character (can be shown through peptide bond resonance), restricting rotation around the bond.

Where is rotation permitted in a peptide?

Only around phi and psi which are the angles around the alpha carbon (connected to R group)

What are the peptides like?

A series of playing cards

Are some dihedral angles preferred in a peptide?

Yes they are. There is constained rotation around psi/phi to make sure there is no clashing. They also allow for hydrogen bonding (C double bonded to O or N-H) to stabilize the secondary structure

What do the psi and phi dihedral angles define?

The direction/shape of the peptide chain

What stabilizes an alpha helix?

Hydrogen bonds between I and I+4

How many residues per turn in a right handed alpha helix? What would the approximate angstroms be?

3.6 residues or 5.4 angstroms per turn

Where do the R-groups point in an alpha helix? What determines the surface properties of the alpha helix?

They point out. The R groups of the amino acids determine the surface properties

Do some R groups destabilize the helix?

Yes if they are very bulky

Describe the structure of a beta sheet

The beta sheet is an extended zig zag conformation. Several alternating strands give us this secondary structure. The hydrogen bonds are between the beta strands and R groups extend from both sides

What are the two conformations of beta sheets?

They can be parallel or anti-parallel

What are parallel beta sheets?

It is when all strands are in the same orientation (all C terminus are on the same side and N-terminus is on the same side). The EN atoms (O-H) are also not in a straight line

What are anti-parallel beta sheets?

It is when the strands are in alternating orientation and the EN atoms are linear which makes them stronger and the H-bonds are more stable

What are protein motifs? Are they a super secondary structure? What is an example?

They are small regions with defined sequence or structure that often serve a common function in different proteins. Yes. EF hand Ca²⁺ binding motif (purpose is to bind calcium)

What are protein domains? Are they a super secondary structure? What is an example?

They are sub-regions of single polypeptide chains that can fold and function independently (sometimes correlated with exons). Yes. Pyruvate kinase has 3 domains

What are forces that stabilize the tertiary structure of a protein?

1. Hydrophobic effect

2. Hydrogen bonding

3. Metal ion coordination

4. Van der Waals

5. Disulfide bonds

6. Ion-ion/salt bridge

What was the anfinsen experiment trying to determine?

If proteins are able to fold on their own

What is native proteins structure encoded by?

Its sequence

Describe what happened in the Anfinsen experiment

1. Have native RNAse A that is catalytically active with proper disulfide bonds

2. Reduce with mercaptoethanol and denature with urea

3. RNAse A is now unfolded and has no disulfide bonds

4. If you oxidize first and then renature you end up with a misfolded protein aggregate due to improper disulfide bond pattern (can’t refold correctly)

5. If you renature by removing urea via dialysis you get a folded protein but no disulfide bonds

6. Then oxidize to return to the original refolded protein with disulfide bonds

What did the Anfinsen experiment conclude?

That most but not all proteins can refold on their own

Do proteins fold much faster than random chance would allow? What guides/restricts protein folding?

Yes and initial secondary structure elements

Do some intermediates promote misfiling or aggregation?

Yes

Is protein folding always guaranteed?

No it is not and misfolding can be irreversible with serious physiological consequences

Describe what can happen in protein folding and misfolding

1. Have a newly synthesized polypeptide

2. It misfolds and can either aggregate or be degraded by a proteasome or refold via a chaperone or on their own

3. Then you have the native structure

4. Newly synthesized protein can just skip straight to folding into the native structure

What do misfolded proteins cause?

Many neurological diseases