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

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

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

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

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

Properties of proteins Molecular weights range from 10000-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.

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

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

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

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

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

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

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

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

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

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）

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

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.

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).

The a-helix

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

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

β-pleated sheet

Three-dimensional structure of proteins Tertiary structure Quaternary structure

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.

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)

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