1. Levels of Protein Structure
Primary to Quaternary Structure

2. Learning Objectives After today you should be able to:
Define the structural levels of proteins.
Identify the structural units of the protein backbone.
Explain why some backbone conformations are “forbidden”, i.e. not found in natural proteins.
Name properties on which the amino acids can be grouped.
Name more amino acids than you could before
One and three letter codes

3. Amino Acids Proteins are built from amino acids
Amino group and acid group
Side chain at Ca
Chiral, only one enantiomer found in proteins (L-amino acids)
20 natural amino acids Ce Sd Cg Cb C Ca N O
Methionine

4. L-amino acids in Living organisms

5. How to Group Them? Many features Charge +/- Polarity (polar/non-polar)
Acidic vs. basic (pKa)
Polarity (polar/non-polar)
Type, distribution
Size
Length, weight, volume, surface area
Type (Aromatic/aliphatic) 5

6. The Amino Acids Thr (T) Phe (F) Val (V) Ala (A) His (H) Arg (R)
Ser (S)
Leu (L)
Cys (C)
Met (M)
Asp (D)
Lys (K)
Asn (N)
Ile (I)
Trp (W)
Gln (Q)
Glu (E)
Tyr (Y)
Pro (P)
Gly (G)

7. Amino Acids A – Ala M – Met C – Cys N – Asn D – Asp P – Pro E – Glu
F – Phe
G – Gly
H – His
I – Ile
K – Lys
L – Leu
M – Met
N – Asn
P – Pro
Q – Gln
R – Arg
S – Ser
T – Thr
V – Val
W – Trp
Y - Tyr
Livingstone & Barton, CABIOS, 9, , 1993

8. Blosum62 substitution matrix

9. The Evolution Way Based on Blosum62 matrix
Measure of evolutionary substitution probability

10. The Simple Aliphatic
Val (V)
Ala (A)
Leu (L)
Met (M)
Ile (I)

11. The Small Polar
Ser (S)
Cys (C)
Thr (T)
Cystin

12. The Unusual P, G Also aliphatic Structural impact
Strictly speaking, proline is an imino acid
Gly (G)
Pro (P)

13. The Acidic and Their Derivatives
Asp (D)
Asn (N)
Glu (E)
Gln (Q)

14. The Basic
Arg (R)
Lys (K)
His (H)

15. The Aromatic
Phe (F)
His (H)
Trp (W)
Tyr (Y)

16. Proteins Are Polypeptides
The peptide bond
A polypeptide chain

17. Ramachandran Plot
Allowed backbone torsion angles in proteins N H

18. Small Exercise (5 minutes)
For the polypeptide on the left discuss the following with your neighbour:
Why is the lower right quadrant a ”forbidden” region in the Ramachandran plot?
What makes Gly a special amino acid when it comes to Ramachandran plots?
What about Pro?

19. Structure Levels Primary structure = Sequence (of amino acids)
Secondary Structure = Helix, sheets/strands, bends, loops & turns (all defined by H-bond pattern in backbone)
Structural Motif = Small, recurrent arrangement of secondary structure, e.g.
Helix-loop-helix
Beta hairpins
EF hand (calcium binding motif)
Many others…
Tertiary structure = Arrangement of Secondary structure elements within one protein chain
MSSVLLGHIKKLEMGHS…

20. Quaternary Structure
Assembly of monomers/subunits into protein complex
Backbone-backbone, backbone-side-chain & side-chain-side-chain interactions:
Intramolecular vs. intermolecular contacts.
For ligand binding side chains may or may not contribute. For the latter, mutations have little effect.
Myoglobin
Haemoglobin a a b

21. Hydrophobic Core
Hydrophobic side chains go into the core of the molecule – but the main chain is highly polar.
The polar groups (C=O and NH) are neutralized through formation of H-bonds.
Myoglobin
Surface
Interior

22. Hydrophobic vs. Hydrophilic
Globular protein (in solution)
Membrane protein (in membrane)
Myoglobin
Aquaporin

23. Hydrophobic vs. Hydrophilic
Globular protein (in solution)
Membrane protein (in membrane)
Cross-section
Cross-section
Myoglobin
Aquaporin

24. Characteristics of Helices
Aligned peptide units  Dipolar moment
Ion/ligand binding
Secondary and quaternary structure packing
Capping residues
The a helix (i→i+4)
Other helix types! (310, p) C N

25. Helix Types

26. b-Sheets Multiple strands  sheet Parallel vs. antiparallel Twist
Coil regions between the secondary structure elements
Thioredoxin

27. b-Sheets
Multiple strands  sheet
Parallel vs. antiparallel
Twist

28. b-Sheets
Multiple strands  sheet
Parallel vs. antiparallel
Twist

29. b-Sheets
Multiple strands  sheet
Parallel vs. antiparallel
Twist

30. b-Sheets Multiple strands  sheet Strand interactions are non-local
Parallel vs. antiparallel
Twist
Strand interactions are non-local
Flexibility
Vs. helices
Folding
Antiparallel
Parallel

31. Summary Amino acids in Living organisms have L-configuration
One & three letter codes
Groups of amino acids: hydrophobic ...
The backbone of polypeptides form regular secondary structures.
Helices, sheets & loops.

32. Building Blocks Ca Peptide unit (amide) COOH OH C/CH/CH2/CH3 Amide
Indole N
S/SH
H-bond
Phenyl
Imidazole
Guanidine
NH2/NH3+

33. Building Blocks Ce Sd c3 Cg c2 Cb c1 Ca y N f C O O On-1 Nn+1 Ca Ca O
Cn-1 c2 O Cb O c1 Ca y
Single amino acid N
Residue f C O O
Methionine

34. Procedure Build backbone in extended conformation (strand).
Twist to align all peptide units (look at the C=O groups).
Add H-bonds (i+4) to construct an ideal a-helix.
Add side chains along the way (pointing “down”). C N