1. Fundamentals of Protein Structure
Dr. Saba Abdi
Assistant professor
Depatrment Of Biochemistry
King Saud University

2. Proteins play key roles in a living system
examples of protein functions
Transport: Some proteins transports various substances, such as oxygen, ions, and so on.
Information transfer: For example, hormones.
Catalysis: Almost all chemical reactions in a living cell are catalyzed by protein enzymes.
Physical cell support and shape (tubulin, actin, collagen)
Mechanical movement (flagella, mitosis, muscles)
Alcohol dehydrogenase oxidizes alcohols to aldehydes or ketones
Haemoglobin carries oxygen
Insulin controls the amount of sugar in the blood

3. Protein classification
Classification based of structure:
Globular Proteins:
Usually water soluble, compact, roughly spherical
Hydrophobic interior, hydrophilic surface
Globular proteins include enzymes,carrier and regulatory proteins

4. Protein classification
Classification based of structure:
2. Fibrous Protein:
Provide mechanical support
Often assembled into large cables or threads
a-Keratins: major components of hair and nails
Collagen: major component of tendons, skin, bones and teeth

5. Protein classification
Classification based of composition:
Simple proteins: albumin, lysozyme
Conjugated proteins: haemoglobin, myoglobin, cytochromes,
immunoglobins.

6. Properties of proteins
Molecular weights range from several hundred thousand
•Generally proteins are soluble in water, except the membrane proteins which are hydrophobic
•Absorb light in the UV range. Maximum absorption at 280nm due to aromatic a.a
•Have a specific Isoelectric pH [pI]. Positively charged below PI, and negatively charged above pI
•Proteins are charged molecules, but the charge depend on the pH of the buffer.
•Move under an electric field and can be separated by electrophoresis
•Give color reactions; e.g blue color with Ninhydrin reagent.

7. Amino acid: Basic unit of protein
COO-
NH3+ C R H
Different side chains, R, determin the properties of 20 amino acids.
Amino group
Carboxylic acid group
An amino acid

8. White: Hydrophobic, Green: Hydrophilic, Red: Acidic, Blue: Basic
20 Amino acids
Glycine (G)
Alanine (A)
Valine (V)
Isoleucine (I)
Leucine (L)
Proline (P)
Methionine (M)
Phenylalanine (F)
Tryptophan (W)
Asparagine (N)
Glutamine (Q)
Serine (S)
Threonine (T)
Tyrosine (Y)
Cysteine (C)
Asparatic acid (D)
Glutamic acid (E)
Lysine (K)
Arginine (R)
Histidine (H)
White: Hydrophobic, Green: Hydrophilic, Red: Acidic, Blue: Basic

9. zwitterions
Under normal cellular conditions amino acids are zwitterions (dipolar ions):
Amino group = -NH3+
Carboxyl group = -COO-

10. Proteins are linear polymers of amino acids
NH3＋ C
COOー ＋
NH3＋ C
COOー ＋ H H
A carboxylic acid condenses with an amino group with the release of a water
H2O
H2O R1 R2 R3
NH3＋ C CO NH C CO NH C CO H
Peptide bond H
Peptide bond H
The amino acid sequence is called as primary structure F T D A G S K A N G S

11. Peptide bond
Peptide bond - linkage between amino acids is a secondary amide bond
Formed by condensation of the a-carboxyl of one amino acid with the a-amino of another amino acid (loss of H2O molecule)
Primary structure - linear sequence of amino acids in a polypeptide or protein

12. Planar peptide groups in a polypeptide chain
Rotation around C-N bond is restricted due to the double-bond nature of the resonance hybrid form
Peptide groups (blue planes) are therefore planar

13. Trans and cis conformations of a peptide group
Nearly all peptide groups in proteins are in the trans conformation

14. Amino acid sequence is encoded by DNA base sequence in a gene
DNA molecule
DNA base sequence ・ C G A T ＝

15. Each Protein has a unique structure
Amino acid sequence
NLKTEWPELVGKSVEEAKKVILQDKPEAQIIVLPVGTIVTMEYRIDRVRLFVDKLDNIAEVPRVG
Folding!

16. Hierarchical nature of protein structure
Primary structure (Amino acid sequence) ↓
Secondary structure （α-helix, β-sheet）
Tertiary structure （Three-dimensional structure formed by assembly of secondary structures）
Quaternary structure （Structure formed by more than one polypeptide chains）

17. Basic structural units of proteins: Secondary structure
α-helix
β-sheet
Secondary structures, α-helix and β-sheet, have regular hydrogen-bonding patterns.

18. α-helix α-helix:(is composed of one polypeptide chain)
•It is spiral structure;
•consisting of a tightly packed, coiled polypeptide backbone core with the side chains of the component amino acids extending outward from the central axis in order to avoid interfering sterically with each other.

19. α-helix
•Right handed α-helix is stabilized by intra-chain hydrogen bond.
•Counting from the N-terminal end, the C=O group of each amino acid residue is hydrogen bonded to the N-H group of the amino acid four residues away from it in the covalently bonded sequence.
•(each C ) of one a.a. is hydrogen bonded to the (-NH) of the next fourth amino acid in the chain (1 →4).
•There are 3.6 residuesfor each turn of the helix.
•The pitch (complete turn distance) is 0.54 nm (5.4 A0).

20. The a-helix

21. Examples of α-helix
Some proteins are entirely α-helix eg α-keratin fibrous protein in hair.
•Other proteins have different amount of α-helix e.g. hemoglobin has 80% α-helix
•Some proteins have no α-helices eg β–keratin in silk

22. β-pleated sheet
The surface of β-sheet appear pleated and these structures are called β-pleated sheet
•β-sheet are composed of two or more separate peptide chains. (β-strands) or segments of polypeptide chains that are almost fully extended.
•The peptide backbone is almost completely extended.
•It is stabilized by:
•Interchain hydrogen bonds(between the polypeptide backbone of separate polypeptide chains)(It is formed between (-NH) group of one chain or one segment and (C=O) of the adjacent chain (or segment)
•Intrachain hydrogen bonds(between the polypeptide backbone of single polypeptide chain folding back on itself)
•There are two types of β-pleated sheet:•Parallel β-sheet •Antiparallel β-sheet

23. β-pleated sheet

24. Three-dimensional structure of proteins
Tertiary structure
Quaternary structure

25. TertairyStructure
•It is spatial arrangement of amino acids that are far apart in the linear sequence.
•The polypeptide chain is folded in three of dimension. Bonds responsible for its stability:
(1)Hydrogen bonds (between side chains)
(2)Hydrophobic bonds (between the non-polar side chain of a.a.)
(3)Electrostatic bonds (salt bonds)(Formed between oppositely charged group in the side chains of amino acids)e.g. epsilon-amino group of lysine and carboxyl group of aspartate, interact electrostatically to stabilize the protein structure.

26. Quarternary Structure
•This structure for proteins that have more than one polypeptide chains.
Refers to the organization of subunits in a protein with multiple subunits (an “oligomer”)
Subunits (may be identical or different) have a defined stoichiometry and arrangement
Subunits are held together by many weak, noncovalent interactions (hydrophobic, electrostatic)
•The interaction between subunits are stabilized by:
•hydrogen bonds
•electrostatic bonds
•hydrophobic bonds
e.g. of proteins having quaternary structure:•Insulin (2 subunits), Lactate dehydrogenase enzyme: (4 subunits), hemoglobin (4 subunits)

27. Close relationship between protein structure and its function
Example of enzyme reaction
Hormone receptor
Antibody
substrates A
enzyme
enzyme B
Matching the shape to A
Digestion of A!
enzyme A
Binding to A