Fundamentals of Fundamentals of Protein StructureProtein Structure

Dr. Saba Abdi

Assistant professor

Depatrment Of Biochemistry

King Saud University

Proteins play key roles in a living Proteins play key roles in a living systemsystem

• 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 classificationClassification based of structure:

1.Globular Proteins:

• Usually water soluble, compact, roughly spherical

• Hydrophobic interior, hydrophilic surface

• Globular proteins include enzymes,carrier and regulatory proteins

Protein classificationClassification based of structure:

2. Fibrous Protein:

• Provide mechanical support

• Often assembled into large cables or threads

• -Keratins: major components of hair and nails

• Collagen: major component of tendons, skin, bones and teeth

Protein classificationClassification based of composition:

1.Simple proteins: albumin, lysozyme

1.Conjugated proteins: haemoglobin, myoglobin, cytochromes,

immunoglobins.

Properties of proteinsMolecular 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 Amino acid: Basic unit of proteinprotein

COO-NH3+ C

R

HAn amino

acid

Different side chains, R, determin the properties of 20 amino acids.

Amino group Carboxylic acid group

20 20 Amino acidsAmino acidsGlycine

(G)

Glutamic acid (E)Asparatic acid (D)

Methionine (M)

Threonine (T)

Serine (S)

Glutamine (Q)

Asparagine (N)

Tryptophan (W)Phenylalanine (F)

Cysteine (C)

Proline (P)

Leucine (L)Isoleucine (I)Valine (V)

Alanine (A)

Histidine (H)Lysine (K)

Tyrosine (Y)

Arginine (R)

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 Proteins are linear polymers of amino acidsof amino acids

R1

NH3＋

C CO

H

R2

NH C CO

H

R3

NH C CO

H

R2

NH3＋

C COOー

H＋

R1

NH3＋

C COOー

H＋

H2OH2O

Peptide bond

Peptide bond

The amino acid sequence is called

as primary structure A AF

NGG

S TS

DK

A carboxylic acid condenses with an amino group with the release of a water

Peptide bond• Peptide bond - linkage between amino

acids is a secondary amide bond

• Formed by condensation of the -carboxyl of one amino acid with the -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 Amino acid sequence is encoded by DNA base encoded by DNA base sequence in a genesequence in a gene

・CGCGAATTCGCG・

・GCGCTTAAGCGC・

DNA molecule

＝

DNA base sequence

Each Protein has a unique Each Protein has a unique structurestructure

Amino acid sequence

NLKTEWPELVGKSVEEAKKVILQDKPEAQIIVLPVGTIVTMEYRIDRVRLFVDKLDNIAE

VPRVGFolding!

Hierarchical nature of Hierarchical nature of protein structureprotein 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 Basic structural units of proteins: Secondary structureproteins: Secondary structure

α-helix β-sheet

Secondary structures, α-helix and β-sheet, have regular hydrogen-bonding patterns.

α-helixα-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 -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 sheetThe 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 Three-dimensional structure of proteinsstructure 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 Close relationship between protein structure and its protein structure and its

functionfunction

enzyme

A

B

A

Binding to A

Digestion of A!

enzyme

Matching the shape to A

Hormone receptor AntibodyExample of enzyme reaction

enzyme

substrates