Protein Structure and Folding PDF

Protein structure& folding  Prof / Ayman El Baz Professor of Medical Biochemistry & Molecular Biology Dr/ Sara El Derbaly Assistant Professor of Medical Biochemistry& Molecular Biology By the end of this lecture, the students should be able to: 1...

Protein structure& folding  Prof / Ayman El Baz Professor of Medical Biochemistry & Molecular Biology Dr/ Sara El Derbaly Assistant Professor of Medical Biochemistry& Molecular Biology By the end of this lecture, the students should be able to: 1. Describe the different levels of protein structure. 2. List the forces that stabilize the protein structure 3. Discuss protein denaturation 4. Identify protein misfolding 5. Correlate knowledge to clinical case  Protein Folding Definition:  Protein folding is a process by which a polypeptide chain folds to become a every protein specific shape (final 3D shape) biologically active protein in its native 3D structure. has a - If it's not 3D structure protein ; it won't work Importance  Protein structure is crucial to its function. ext enzymes hormones Stabilization of the folded protein  Folded proteins are held together by various bonds / forces. makes it stabalized Levels (Stages) of protein folding  The folding of a protein is a complex process  It involving four stages (Levels), arranged, from a primary to quaternary structure. All proteins have primary secondary tertiary Structure/Shapes , , but not quaternary all proteins have shapes med from more than one polypeptide chain  The wide variation in AAs sequences  different conformations (shapes) of proteins Levels of protein structure 1. Primary structure 2. Secondary structure 3. Tertiary structure 4. Quaternary structure Bonds related to protein structures: Protein structures are stabilized by the following bonds: I. Covalent (Strong) bonds: Peptide and Disulfide bonds a- Peptide bond  Peptide bond (-CO-NH-) is formed between COOH group of one amino acid and NH2 group of another with removing H2O S b- Disulfide bond (bridge):  It is formed between the SH groups of 2 cysteine residues by removal of 2 H atoms and formation of S-S bridge II- Non-covalent (Weak) bonds: Hydrogen, salt bridges bonds and hydrophobic interaction. a- Hydrogen Bonds (H bonds): H bonds are formed between the – CO group of one peptide bond and the –NH group of another nearby peptide bond Peptide bond b- Electrostatic interactions (Ionic bonds or salt bridges): Salt bridges are formed between oppositely charged side groups within or between biomolecules c- Hydrophobic interactions (van der Waals): These are formed between the non-polar side chains of neutral amino acids. Although no true bonds exist, these interactions play a significant role in maintaining the protein structure.  1. Primary structure ① Straight linear It is the number, type and sequence of AAs in the polypeptide chain. 3 Main bond: Peptide bond (-CO-HN-) Any change in 1 AA physiological defect.(ex : Sickle cell anemia) The free -NH2 group of the 1st AA is called as N-terminal end The free -COOH end of the last AA is called as C-terminal end counting proteins starting from N-terminal to N-terminal to Aterminals so we start terminal We count the AAs from the N terminal read it from. - we started diff type of protein because we're reading it in the opposite counting from C-terminal then - If we we will get a. way ,  10 20 1 15 5  2. Secondary structure 1ry structure (The polypeptide chain) will be folded by hydrogen bonds to give a specific shape /form which may be: α-Helix β- pleated sheets Shape Helix (coiled) Pleated (Zigzag) peptide chain peptide chain Right-handed helix is more but there's also abundant left-handed helix Arranged side by side Each turn contains 3.6 AA = Stabilized by: Hydrogen bond Hydrogen bonds between peptide bonds in the same - - between different segments of the chain(singleChain) same chain (Intrachain bond) (Intrachain H bond) within Within/Inside AA between adjacent 2 between O of 1st polypeptide chains Pr 1 2 peptide bond & H of in (Interchain H bond) between the next 4th peptide pepti 5 bond * Since hydrogen bond is weak we can break it by heat.. α-Helix β- pleated sheets  3. Tertiary structure  Definition: It is three-dimensional (3D) shape of a protein Circular or round shaped  Formed of :Secondary structures (α and β) are arranged to form final functional 3D structure of protein called domain (subunit). #f it has multiple domains it'll be graternary structure) 3ry structure is the final order of organization of protein. The function of a protein depend on its tertiary structure If it is disrupted  protein loses its activity  Bonds (Forces) stabilizing this 3ry structure Bonds occur due to interaction between side chains (R) group of AAs Both tertiary& guaternary depends on Several bonds (forces) like: the side chains (R) ; it stabilizes Covalent bond (U Strong 1. Disulfide bonds. : between Sulfur AA (Cysteine) 2. Hydrogen bonds : between polar (positive) side chains of AA 3. Hydrophobic forces : between Non-polar (negative) (R) groups of AAs Casis-Acidic 4. Electrostatic forces (Ionic bonds) : between oppositely Charged (R) of AAs 3ry structure  4. Quaternary Structure  Definition: It is the arrangement of several subunits into a closely packed arrangement. Each of the subunits has its own primary, secondary, and tertiary structure.  Bonds (Forces): The subunits are held together by (same as tertiaryg All bonds expect the peplide bond) 1. Hydrogen bonds 2. Hydrophobic interactions (van der Waals forces) between non-polar side chains. 3. Disulfide bond  Examples 4.Electrostatic bond (tonis bond) 1- Hemoglobin (Hb) and lactate dehydrogenase (LDH) enzyme: are tetramers (formed of 4 subunits) 2- Creatine kinase (CK) enzyme: is dimer(formed of 2 subunits) Hb tetramer Denaturation of proteins: Protein denaturation is the destruction of secondary, tertiary and quaternary structures of protein molecules. The peptide chains become unfolded, irregularly arranged, so: denaturation means unfolding. Causes of denaturation: Effects of protein denaturation: 1. High temperature 1. Loss of catalytic activity of 2. High pressure enzymes 3. Vigorous shaking 2. Loss of biological functions of 4. Strong acids and alkalis hormones 5. UV light and irradiation 3. Decreased solubility 6. X- ray 4. Increased viscosity 5.Increased digestibility e.g. cooking meat & eggs by boiling  Protein misfolding Definition Proteins that are not able to form stable 3D structure recognized as misfolded proteins The misfolded proteins form aggregates (large size, insoluble)  loss its structure and function Alzheimer's disease Characterized by dense plaques in the brain cause by misfolding of the secondary b- sheets (so no tertiary sequence forms) the proteins in the brain are not soluble anymore Caused by deposition of misfolded aggregates of amyloid β protein and formation of dense fibrous plaques in the brain and nervous system leading to neurodegeneration. Symptoms include: Memory loss, dementia and lack of recognition A 72-year-old male is suffering from forgetting recent events or conversations that started 2 years ago, recently he didn’t recognize his close relatives with sever memory impairment and lose the ability to carry out everyday tasks. 1-What is the diagnosis ? Alzheimer's disease 2-Mention the possible cause of this disease Amyloid β protein misfolding REFERENCES  Vasudevan's Textbook of Biochemistry For Medical Students, 7th Edition.  Chatterjea’s Textbook of Medical Biochemistry, 8th edition.  Lippincott’s Illustrated Reviews: Biochemistry, 8th edition.  https://www.youtube.com/watch?v=PPJ7C3hcnPw