Lecture 4 Flashcards
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.
How are the side chains of a-helices angled?
The side chains point outward from the α-helical axis and are angled towards the N-terminal end of the helix. This gives a look of a Christmas tree, if you stand the helix on its N-terminus.
The helical wheel plot calculates ______
the hydrophobic moment
The helical wheel projection plot is used to calculate the hydrophobic moment in order to distinguish between what 3 types of helices?
- Membranous helices (high hydrophobicity, but low hydrophobic moment)
- Surface helices (amphipathic, high hydrophobic moment)
- Soluble helices (low hydrophobicity, low hydrophobic moment)
Draw a helical wheel projection plot of
LEEVFSQLMTIVETLI
N/A Lecture 4 Slide 27
Describe the helical wheel projection plot of the signal-peptide for import into mitochondria.
Build up of pos residues on one side (signal for mta import)
What are 2 other types of helices
- 310-helix
2. pi helix
What is the 310-helix? Describe its stability in comparison to alpha-helices
N + 3 helices, 3 residues per turn, more tightly coiled than the α-helix. There are 10 atoms between the H-bond donor and acceptor, thus its name (note the hydrogen atom is included in this count).
- The dipoles of the 310-helix are not so well aligned as in the α-helix, i.e. it is a less stable structure and side chain packing is less favorable. It is more tightly packed.
- The 310-helix occurs close to the upper right of the α-helical region within the Φ/Ψ plot, on the edge of the allowed region, indicating lower stability.
What is the pi-helix? Describe its stability in comparison to alpha-helices
(¼ helix (i+5,i), 4.316) 4.3 residues per turn, 16 atoms in a hydrogen-bonded ring. More loosely coiled than the α-helix. There’s a hole in the middle.
What is the numerical naming system for helices based on?
H bonding pattern
What is the base number?
The base number corresponds to the number of residues in one turn of the helix.
What is the subscript #?
The subscript number represents the number of atoms in the hydrogen bond connection/network (including the H).
Where are left handed a-helices?
(small allowed region in the upper-right quadrant of the Φ/Ψ plot
Which individual residues can adopt the left handed a-helices conformation
Gly, Asp, Asn
The β-strand Φ/Ψ values (Ramachandron plot) ?
-135, 135
____: residues per repeat unit in a β-strand (up and down and then up)
____: distance of the advance along the β-strand, per residue
____: the pitch of a β-strand (distance for a repeat of the pattern, 2 residues)
2: residues per repeat unit in a β-strand (up and down and then up)
3.5 Å: distance of the advance along the β-strand, per residue
7 Å: the pitch of a β-strand (distance for a repeat of the pattern, 2 residues)
What are the 3 types of beta sheets
- Antiparallel β-sheets: The neighboring strands run anti-parallel to each other.
- Parallel β-sheets: The neighboring strands run parallel to each other.
- Mixed β-sheets: The neighboring strands run both anti-parallel and parallel to each other.
Draw the HB in antiparallel B-sheets
N/A Lecture 4 Slide 36
What is hairpin connection? Example of what type of B sheet?
When the backbone enters the same end of the sheet that it left. Requires a shorter piece of peptide (turn) to connect the strands.
- antiparallel
What is crossover connection? Example of what type of B sheet?
required in parallel β-sheets. Requires a longer piece of peptide (loop) to connect the strands. Crossover connections can be thought of as a type of helical connection of the strand ends
Fxn of turns (reverse turns or B-turns)?
Reverse the direction of secondary structure
What way do turns face?
Normally face the surface
What AA’s do turns contain?
Often contain polar residues, Proline, Glycine
Describe the 4 types of B-turns
Type I and II:
Each containing a H-bond between the C=O of residue i and the N-H of i+3. (Involves 4 residues).
Type I turns occur most frequently 2-3 times more frequently than type II
Type III: is simply a single turn of a 310 helix.
Gamma turns: tightest turn, involving just 3 residues.
How to tell apart type I and type II B-turn?
Type 1 carbonyl points away (into page), type 2 points toward you
