Lecture 4 Flashcards
(48 cards)
What is the secondary Structure
The local conformation of the polypeptide backbone (mainchain), without regard to the conformation of the side chains.
What angles/network define the conformations of the secondary structure?
The ϕ/ψ angles and the mainchain hydrogen-bonding network define these conformations
What are the 3 types of secondary structure?
- a-helices
- b-sheets
- turns
Why do proteins form secondary structure?
Hydrogen bonds neutralize the dipoles of the mainchain, this helps drives the formation of regular secondary structure.
What is the most common and stable helix?
Alpha helix
What is the christmas tree effect
If put alpha-helix on its head with N terminus down, all R groups are pointed down like branches of pine tree. Carbonyl also all pointing in same direction
What are the bonds in alpha helices? List in order of increasing distance
- Covalent i.e. H-O
- H bond i.e. H ——- O
- vdW-bond i.e. HO
Where is the alpha helix region on the Ramachandran plot
-60, -45
Upper right hand corner of lower left quadrant
For a-helix, how many:
1) residues/turn
2) A/residue (How far along the α-helix one residues will take you)
3) A/turn (pitch of the α-helix, distance for a repeat of the pattern, 1 full turn)
4) degree/residue
1) 3.6 residues/turn
2) 1.5 A/residue (How far along the α-helix one residues will take you)
3) 5.4 A/turn (pitch of the α-helix, distance for a repeat of the pattern, 1 full turn)
4) 100 degree/residue
How many residues does it take to travel 30 Å, assuming the residues are in a α-helical conformation?
20
A α-helix is 36 amino acids, how many turns are in the helix?
10
What is the length of a α-helix with ## residues?
N/A
Why 3.6 residues/turn?
- Notice the residue backbone atoms can be thought of as having three parts:
- NH 2. Ca 3. CO.
Look at one turn of the helix (using the molecular graphics or a model).
You can see the first residue in the helix contributes 0.3 of that residue (CO) to the turn, the last residue in the helical turn also contributed 0.3 of a residue (NH) and there are 3 full residue in between.
What is the handedness of the α-helix? (what direction does the helix turns?)
Right-handed vs. left-handed: all α-helices are right handed.
What is the right hand rule?
The THUMBS indicate the direction of TRANSLATION and the FINGERS indicate the direction of ROTATION or propagation of the CHAIN.
Role of proline in alpha helix?
- Secondary amine so no H to contribute to H bonding
- good at beginning or end or helix, or give kink/bend
Why do you think that Ser, Asn and Asp may disrupt α-helices?
H-bonding side chains compete directly with backbone H-bonds
What is the average length of helix?
~10 residues (~3 turns)
What is the normal range of helices?
4 residues (~1 turn) to >40 residues (~10 turns).
What is the extreme range of helices? Example?
they can be as long as 150 residues in length, as seen in the coiled-coil of tropomyosin (residues 147-301). Tropomyocin is part of cytoskeleton structure and muscle fibers (bind actin).
Example of heptad-repeats?
(Leu-zipper- tropomyosin, PDB: 1ic2) every seventh amino acid is Leu.
Describes a-helix dipole moment
All C=O groups point in the same direction and all N-H groups point the other way. This leads to a build up of charge (or dipole moment) along α-helices.
Are the ends of helices common found buried or at the surface of proteins?
ends of helices are commonly found at the surface of proteins.
What are helix capping residues and capping ligands?
Often a positively charge side chain (Arg/Lys) is found at the C-terminal (-) end of a α-helix or a negatively charged side chain is found at the N-terminal (+) end of a helix. These are called capping residues and they are thought to play a stabilizing role in protein structure. Negatively charged ligands such as Phosphates often bind near the positively charged N-termini of α-helices.
