Lecture 4

Question 1

What is the secondary Structure

Answer 1

The local conformation of the polypeptide backbone (mainchain), without regard to the conformation of the side chains.

Question 2

What angles/network define the conformations of the secondary structure?

Answer 2

The ϕ/ψ angles and the mainchain hydrogen-bonding network define these conformations

Question 3

What are the 3 types of secondary structure?

Answer 3

1. a-helices
2. b-sheets
3. turns

Question 4

Why do proteins form secondary structure?

Answer 4

Hydrogen bonds neutralize the dipoles of the mainchain, this helps drives the formation of regular secondary structure.

Question 5

What is the most common and stable helix?

Answer 5

Alpha helix

Question 6

What is the christmas tree effect

Answer 6

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

Question 7

What are the bonds in alpha helices? List in order of increasing distance

Answer 7

1. Covalent i.e. H-O
2. H bond i.e. H ——- O
3. vdW-bond i.e. HO

Question 8

Where is the alpha helix region on the Ramachandran plot

Answer 8

-60, -45

Upper right hand corner of lower left quadrant

Question 9

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

Answer 9

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

Question 10

How many residues does it take to travel 30 Å, assuming the residues are in a α-helical conformation?

Answer 10

20

Question 11

A α-helix is 36 amino acids, how many turns are in the helix?

Answer 11

10

Question 12

What is the length of a α-helix with ## residues?

Answer 12

N/A

Question 13

Why 3.6 residues/turn?

Answer 13

1. Notice the residue backbone atoms can be thought of as having three parts:
2. 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.

Question 14

What is the handedness of the α-helix? (what direction does the helix turns?)

Answer 14

Right-handed vs. left-handed: all α-helices are right handed.

Question 15

What is the right hand rule?

Answer 15

The THUMBS indicate the direction of TRANSLATION and the FINGERS indicate the direction of ROTATION or propagation of the CHAIN.

Question 16

Role of proline in alpha helix?

Answer 16

• Secondary amine so no H to contribute to H bonding

- good at beginning or end or helix, or give kink/bend

Question 17

Why do you think that Ser, Asn and Asp may disrupt α-helices?

Answer 17

H-bonding side chains compete directly with backbone H-bonds

Question 18

What is the average length of helix?

Answer 18

~10 residues (~3 turns)

Question 19

What is the normal range of helices?

Answer 19

4 residues (~1 turn) to >40 residues (~10 turns).

Question 20

What is the extreme range of helices? Example?

Answer 20

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).

Question 21

Example of heptad-repeats?

Answer 21

(Leu-zipper- tropomyosin, PDB: 1ic2) every seventh amino acid is Leu.

Question 22

Describes a-helix dipole moment

Answer 22

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.

Question 23

Are the ends of helices common found buried or at the surface of proteins?

Answer 23

ends of helices are commonly found at the surface of proteins.

Question 24

What are helix capping residues and capping ligands?

Answer 24

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.

Question 25

How are the side chains of a-helices angled?

Answer 25

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.

Question 26

The helical wheel plot calculates ______

Answer 26

the hydrophobic moment

Question 27

The helical wheel projection plot is used to calculate the hydrophobic moment in order to distinguish between what 3 types of helices?

Answer 27

1. Membranous helices (high hydrophobicity, but low hydrophobic moment)
2. Surface helices (amphipathic, high hydrophobic moment)
3. Soluble helices (low hydrophobicity, low hydrophobic moment)

Question 28

Draw a helical wheel projection plot of

LEEVFSQLMTIVETLI

Answer 28

N/A Lecture 4 Slide 27

Question 29

Describe the helical wheel projection plot of the signal-peptide for import into mitochondria.

Answer 29

Build up of pos residues on one side (signal for mta import)

Question 30

What are 2 other types of helices

Answer 30

1. 310-helix

2. pi helix

Question 31

What is the 310-helix? Describe its stability in comparison to alpha-helices

Answer 31

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.

Question 32

What is the pi-helix? Describe its stability in comparison to alpha-helices

Answer 32

(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.

Question 33

What is the numerical naming system for helices based on?

Answer 33

H bonding pattern

Question 34

What is the base number?

Answer 34

The base number corresponds to the number of residues in one turn of the helix.

Question 35

What is the subscript #?

Answer 35

The subscript number represents the number of atoms in the hydrogen bond connection/network (including the H).

Question 36

Where are left handed a-helices?

Answer 36

(small allowed region in the upper-right quadrant of the Φ/Ψ plot

Question 37

Which individual residues can adopt the left handed a-helices conformation

Answer 37

Gly, Asp, Asn

Question 38

The β-strand Φ/Ψ values (Ramachandron plot) ?

Answer 38

-135, 135

Question 39

____: 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)

Answer 39

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)

Question 40

What are the 3 types of beta sheets

Answer 40

1. Antiparallel β-sheets: The neighboring strands run anti-parallel to each other.
2. Parallel β-sheets: The neighboring strands run parallel to each other.
3. Mixed β-sheets: The neighboring strands run both anti-parallel and parallel to each other.

Question 41

Draw the HB in antiparallel B-sheets

Answer 41

N/A Lecture 4 Slide 36

Question 42

What is hairpin connection? Example of what type of B sheet?

Answer 42

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

Question 43

What is crossover connection? Example of what type of B sheet?

Answer 43

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

Question 44

Fxn of turns (reverse turns or B-turns)?

Answer 44

Reverse the direction of secondary structure

Question 45

What way do turns face?

Answer 45

Normally face the surface

Question 46

What AA’s do turns contain?

Answer 46

Often contain polar residues, Proline, Glycine

Question 47

Describe the 4 types of B-turns

Answer 47

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.

Question 48

How to tell apart type I and type II B-turn?

Answer 48

Type 1 carbonyl points away (into page), type 2 points toward you