1. From: Protein Data Bank PDB ID: 1B0E
Protein Structure
Protein Structure
From: Protein Data Bank PDB ID: 1B0E
Kalus, W., Zweckstetter, M., Renner, C., Sanchez, Y., Georgescu, J., Grol, M., Demuth, D., Schumacher, R., Dony, C., Lang, K., Holak, T. A.: structure of the IGF-binding domain of the insulin-like growth factor-binding protein-5 (IGFBP-5): implications for IGF and IGF-I receptor interactions. EMBO J 17 pp (1998)

2. Functions Diverse functions related to structure
Structural components of cells
Motor proteins
Enzymes
Antibodies
Hormones
Hemoglobin/myoglobin
Transport proteins in blood

3. Structure Amino acids Amino group (NH2) Carboxyl group (COOH)
Proline has imino group rather than amino group

4. Amino acids 20 amino acids make up protein
8 essential amino acids (must be eaten in diet)
9 in infant (histidine)
Zwitterion = double ion – when both NH3+ and COO- are ionised
COO- can accept a proton, NH3+ can accept electron, so can act as acid and base (amphoteric)

5. Protein structure - bonding
5 bonds or forces determine structure
Peptide bond
Hydrogen bond
Disulfide bond
Ionic bond
Hydrophobic force

6. Peptide bond Peptide bond joins amino acids Bond at both ends
Increases range of possible proteins
1.0 x 1026 peptides can be formed from 20 amino acids
Ability to form peptide bonds at both ends increases diversity of protein structure:
3 amino acids can make 6 possible peptides if only used once, but can make 27 if used more than once
20 different amino acids make up 1 x 1026 different arrangements if each used more than once
Bonding in peptide chain blocks dissociable groups (NH2 and COOH). Ionized state of a protein therefore dependent on R groups.

7. condensation reaction

8. Primary protein structure
Linear sequence of amino acids forms primary structure (long chain of amino acids)
Sequence essential for proper physiological function

9. Sickle cell anemia
Replacement of a single glutamine amino acid with valine in one chain of hemoglobin alters the structure and function of the protein
Oxytocin and ADH only differ in primary structure by 2 amino acids, but Oxytocin induces contraction of uterus and milk ejection from mammary glands and ADH increases water reabsorption in the kidney and plays a role in the regulation of blood pressure.

10. Secondary protein structure
Peptide chains fold into secondary structures to become more compact:
 - helix
 - pleated sheet

11. Alpha helix is a virtual solid cylinder
Alpha helix is a virtual solid cylinder. There is almost no space along the axis, which makes it a very stable structure.

12. Alpha Helix

13.  - pleated sheet
The term ‘ form’ came from the fact that it was first recognised in -keratin.

14. Beta Helix

15. Tertiary protein structure
Secondary structures fold and pack together to form tertiary structure
Usually globular shape
Tertiary structure stabilized by bonds between R groups (i.e. sidechains)
Bonds that stabilise tertiary structure are: hydrogen, disulfide, ionic and hydrophobic bonds
Intracellular protein tertiary structures mostly held together by weak forces. Extracellular tertiary structures stabilised by disulfide (covalent) bonds.

16. Amino acid r-groups
All amino acids contain a carboxyl group and an amino group. R-Groups distinguish between individual amino acids. R-Groups make them different from one another.

18. Tertiary structure - H bond
Hydrogen bonds are weak electrical attractions between positively and negatively charged atoms of different molecules.

19. Tertiary structure - disulfide bond
Covalent bond between sulfur atoms on two cysteine amino acids

20. Tertiary structure - ionic bond
Ions on R groups form bridges through ionic bonds
Ionic bonds form from the exchange of electrons between atoms
Example: NaCl (table salt)

21. Tertiary structure - hydrophobic forces
Close attraction of non-polar R groups in the chains
Very weak but collective interactions over large areas help stabilize the protein structure

22. All bonds shown together

23. Quaternary protein structure
The arrangement of many tertiary structures into one large protein molecule
Not all proteins have or need a quaternary structure
Allows for changes in structure/function in response to chemical stimuli