1. Protein Architecture and Biological Function
General principles of protein design
Elements of secondary structure
Protein tertiary structure
Protein quaternary structure
Protein structure and biological function

2. General principles of protein design
All proteins have the same covalent backbone.
Primary structure.
Polymer unit of amino acids.
H O
| ||
H2N - C - C | R H
NH - C - COOH
R’’’
| ||
- NH - C - C - R’
R’’

3. General principles of protein design
Since there is a wide range of protein shapes, other factors must play a role.
Type of linkage between amino acids.
cis or trans linkages
Sidechain interactions.
Hydrogen bonding
Ionic linkages
Metal ion coordination
Hydrophobic interactions
Covalent bonds

4. Elements of secondary structure
Long chains of amino acids will commonly fold or curl into a regular repeating structure.
Structure is a result of hydrogen bonding between amino acids within the protein.
Common secondary structures are:
 - helix
 - pleated sheet
Secondary structure adds new properties to a protein like strength, flexibility, ...

5. -Helix One common type of secondary structure.
Properties of an -helix include strength and low solubility in water.
Originally proposed by
Pauling and Corey in 1951.

6. -Helix
Every amide hydrogen and carbonyl oxygen is involved in a hydrogen bond.
Multiple strands may entwine to make a
protofibril.

7. -Pleated sheets Another secondary structure for protein.
Held together by hydrogen bonding between adjacent sheets of protein. C | R N H O ||

8. -Pleated sheets Silk fibroin - main protein of silk is an example
of a  pleated sheet structure.
Composed primarily of
glycine and alanine.
Stack like
corrugated
cardboard for extra strength.

9. Comparison of  and  linkages in glycine
Note - in  form, all carbonyls point in the same
direction - they alternate in .

10. Alpha helix

11. Beta sheet

12. Bends and Loops Bend - 4 residues.
Reverse direction of the main polypeptide chain.
Connect regions of more regular secondary structure (-helix, -sheet)
Loop residues.
Continuous segment of a polypeptide chain.
Both have no secondary structure. They serve to tie together other units.

13. Structural Motifs
Often the individual elements of secondary structure combine into stable arrangements - supersecondary structure or motifs
Some examples
 motif  helix - loop -  helix
 motif  sheet - loop -  sheet
 motif  sheet - loop -  helix -
loop -  sheet.

14. Structural Motifs
 motif
 motif
 motif

15. Structural Motifs
Triose phosphate isomerase

16. Collagen Family of related proteins.
About one third of all protein in humans.
Structural protein
Provides strength to bones, tendon, skin, blood vessels.
Forms triple helix - tropocollagen.

17. Collagen
Tropocollagen

18. Collagen and Vitamin C Major use of vitamin C is for making collagen.
Vitamin C ascorbic acid
Proline and lysine in collagen are converted to 4-hydroxyproline and 5-hydroxylysine using this vitamin.
Scurvy - disease from lack of Vitamin C results in skin lesions, bleeding gums and fragile blood vessels. O HO OH
CH-CH2OH

19. Protein Tertiary Structure
Interactions between amino acid residues results in a protein taking on a stable, compact arrangement.
Central dogma of protein folding
“The primary structure determines the tertiary structure”
Proteins with a unique primary structure tend to fold spontaneously into a distinct tertiary structure.

20. Protein Tertiary Structure
Folding occurs as a stepwise process.
Only the final form is ‘biologically active.’
Molecular chaperones
catalysts that assist in the folding process.

21. Tertiary structure of proteins
Fibrous proteins
insoluble in water
form used by connective tissues
silk, collagen, -keratins
Globular proteins
soluble in water
form used by cell proteins
3-D structure - tertiary

22. Tertiary structure of proteins
Results from interaction of side chains.
The protein folds into a tertiary structure.
Possible side chain interactions:
- Similar solubilities
- Ionic attractions
- Attraction between + and - sidechains
- Covalent bonding

23. Tertiary structure of proteins
- S - S -
Salt bridge
Sulfide
Crosslink
Hydrogen
bonding
Hydrophobic
interaction
-COO- H3N+- -O \ H

24. Tertiary structure of proteins
Side chain interactions
Help maintain specific structure.
Oxidation of cysteine - crosslink formation. O ||
HO-C-CH-CH2-SH |
NH2
HS-CH2-CH-C-OH
covalent
disulfide
bond + O ||
HO-C-CH-CH2-S - |
NH2
S-CH2-CH-C-OH +H2O
oxidation
[O]

25. How -S-S- cross link can effect structure
In this example -
20 glycines - cysteine
40 glycines
crosslink
 - helix structure

26. Tertiary structure of proteins
Hydrophobic attractions
Attractions between R groups of non-polar amino acids.
Hydrogen bonding
Interaction between polar amino acid
R groups.
Ionic bonding
Bonding between + and - charged amino acid R groups.

27. Protein unfolding
Denaturation - the unraveling of a protein’s structure. The disorganized protein will no longer act as intended.
When this occurs, protein strands will clump together - coagulate.
Examples - frying an egg
reason for HCl in stomach
Temperature or pH outside the normal range can both cause denaturation.

28. Denaturing of a protein
denatured coagulated
heat or
acid
heat or
acid

29. Hydrolysis
Will result in protein being reduced to simpler peptides and amino acids.
Amount of hydrolysis depends on pH, time and temperature. O ||
H2N - CH - C - OH | R O ||
H2N - CH - C - | R
NH - CH - C - OH + H2O R’
H+ or
OH- O ||
H2N - CH - C - OH | R’ +

30. Effect of pH on proteins
+H3N-
NH2 | /
H2N
-NH3+
COOH
-COOH
-COO-
-OOC-
charge
+H3N-
NH2 | /
H2N
-NH3+
COOH
-COOH
HOOC-
charge +2
lower pH
raise pH
Changing pH will alter
charge on protein.
This alters their
solubility and may
change their shape.
H2N-
NH3+ | /
H2N
-NH2
COO-
-COOH
-OOC-
charge -2
-COO-

31. Quaternary structure of proteins
Many proteins are not single peptide strands.
They are combinations of several proteins
- aggregate of smaller globular proteins.
Conjugated protein - incorporate another type of group that performs a specific function.
prosthetic group

32. Quaternary structure of proteins
Aggregate structure
This example
shows four
different proteins
and two prosthetic
groups.

33. Hemoglobin and myoglobin
oxygen transport protein of red blood cells.
Myoglobin
oxygen storage protein of skeletal muscles.
Both proteins rely on the heme group as the binding site for oxygen.

34. Heme
myoglobin
1 heme group
hemoglobin
4 heme groups

35. Myoglobin
Heme

36. Hemoglobin
2  chains
4 heme
2  chains

37. Hemoglobin and oxygen transport
In the lungs, there is an abundance of O2 so oxygen is picked up by the hemoglobin.
When blood reaches the cells, there is a lack of O2 so oxygen is given up by the hemoglobin.
Hb + 4 O Hb(O2)4
Hb + 4 O Hb(O2)4

38. Oxygen transport mother to fetus
Fetus takes oxygen from mother by diffusion across the placenta.
Fetus has a different, more efficient type of hemoglobin than mother.
Fetal hemoglobin - Hb F
Results in more efficient transfer of oxygen.
Hb F production stops shortly before birth.

39. Sickle cell anemia
Defective gene results in production of mutant hemoglobin - one misplaced amino acid.
Still transports oxygen but results in deformed blood cells - elongated, sickle shaped.
Difficult to pass through capillaries. Causes organ damage, reduced circulation.
Affects 0.4 % of American blacks.

40. Comparison of normal and sickle cell hemoglobin

41. Summary of protein structure
primary
secondary
H O
| ||
H2N - C - C | R H
NH - C - COOH
R’’
- NH - C - C - R’
tertiary
quaternary

42. Protein example myosin/actin structure Proteins used in muscle
myosin head
myosin tail
ATP and actin
binding sites
thick filament
thin filament
actin
myosin/actin structure
Proteins used in muscle
troponin

43. Protein example
Permease
Assists in cell transport.

44. Protein example
Human Insulin
51 residues
3 S-S crosslinks

45. Protein example Human growth hormone 596 residues Originally obtained
from human cadavers.
It would cost $20,000
per year to treat one
child.
Now produced by
genetically engineered
bacteria.

46. Protein example Immunoglobin FC - 262 residues
A ‘Y” shaped protein actually composed of 4 protein chains linked by disulfide bonds.
antigen-binding
site

47. Protein example
Lipoprotein
116 residues
2 helical strands

48. Protein example
Protein coating
of the Bushy
Tomato Virus.