Lec16 Structure Of Proteins PDF

# Protein Structure ## Learning Objectives - Native Conformation - 4 levels of Structural Organization of proteins - Primary - Secondary - Tertiary - Quaternary - Abnormalities of Protein structure → Diseases ## Each Protein Usually Has One Native Conformation - Under physiologic...

# Protein Structure ## Learning Objectives - Native Conformation - 4 levels of Structural Organization of proteins - Primary - Secondary - Tertiary - Quaternary - Abnormalities of Protein structure → Diseases ## Each Protein Usually Has One Native Conformation - Under physiological conditions of solvent and temperature, each protein folds spontaneously into one 3D conformation, called the native conformation. - This conformation is usually the most stable thermodynamically, and usually only the native conformation is functional. ## Four Levels of Structural Organization A table showing the four levels of structural organization: | Level | Description | |---|---| | Primary | Amino acid sequence | | Secondary | Local folding patterns (α-helices and β-sheets) | | Tertiary | Three-dimensional structure of a polypeptide chain | | Quaternary | Arrangement of multiple polypeptide chains | ## Protein Structure - In nature, form follows function. - Thus, protein molecule must fold in a specific 3-D arrangement → specific chemical groups are positioned → functional efficiency appropriate for its biological function. ## Levels of Protein Structure - **(a) Primary structure:** - Amino acid sequence - Determined by genes - Held together by peptide bonds - **(b) Secondary structure:** - Localized folding patterns - Alpha (α) helix and beta (β) pleated sheet are the most common secondary structures - Held together by hydrogen bonds, ionic interactions, and hydrophobic interactions - **(c) Tertiary structure:** - Three-dimensional structure of a single polypeptide chain - Involves interactions between R groups - Held together by the same interactions as secondary structure, with the addition of disulfide bonds - **(d) Quaternary structure:** - Interaction of multiple polypeptide chains - Forms a functional protein - Held together by interactions between R groups and the same forces as tertiary structure ## Primary Structure of Protein ### **Characteristics** - Number & sequence of amino acids in a linear chain - Called the primary structure of proteins - Amino acids are linked by peptide bonds which are not broken by denaturation (heating) - Naming. E.g. Gly-Ala-Val = Glycyl Alanyl Valine. ### **Mutations** - Abnormal amino acid sequence → improper folding → loss of normal functions (genetic diseases) - Mutation → single A.A change → affects function - e.g. Hb-A (normal)→β chain → Glutamic acid (6th AA) - Hb-S (sickle cell) → β chain → Valine (6th AA) ### **Normal vs. Missense Mutation** | | Normal | Missense Mutation | |---|---|---| | **Partial DNA Sequence of Beta Globin Gene** | CCT GAG GAG GGA CTC CTC | CCT GTG GAG GGA CAC CTC | | **Partial RNA Sequence** | CCU GAG CTC | CCU GUG GAG | | **Partial Amino Acid Sequence for Beta Globin** | pro-Glu-Glu | pro-Val-Glu | ## Bonds in Primary Structure - **Peptide bonds** - strong covalent bonds, not broken by denaturation. - **Disulfide bonds** - (a) *inter chain* (b) *intra chain* ## Proinsulin - Pro Insulin (pro hormone) = 86 AA chain - →C peptide + Insulin {A chain(21AA) + B chain(30 AA)} ### **Diagram of Proinsulin** A diagram showing the structure of proinsulin with the following labels: *A-Chain*, *B-Chain*, *Connected by disulfide bonds*, *COOH terminal*, *NH2 terminal*, and *30 amino acids*. ## Insulin - **A - chain: ** Cys-Val-Glu-Gin-Cys-Cys-The-Ser-lle-Cys-Ser-Leu-Tyr-Gin-Leu-Glu-Asn-Tyr-Cys-Asn - **B - chain: ** Phe-Val-Asn-Gin-His-Leu-Cys-Gly-Ser-His-Leu-Val-Glu-Ala-Leu-Tyr-Leu-Val-Cys-Gly-Glu-Arg-Gly-Phe-Phe-Tyr-Thr-Pro-Lys-Ala ## Secondary Structure of Proteins - The polypeptide backbone generally forms a regular configurational arrangement of 3-30 amino acids that are located near each other in a linear sequence. - These arrangements are termed as the secondary structure of polypeptides. - Secondary structure can be present in many forms. - I. α helix - II. β pleated sheets - III. β bends (β turns) or loops ## Bonds in Secondary Structure - **Amino acids** are held together by non-covalent bonds - **Hydrogen bonds** - weak electrostatic attraction between (i) O/N (-ve) e.g. COO, CO, SS and (ii) H (covalently linked to another -ve ion) e.g. NH, OH, NH₂ - **Ionic bonds** - +ve AA (Lysine, Arginine, Histidine) bond with -ve AA (Aspartic acid, Glutamic acid) - **Hydrophobic interaction** - between hydrophobic side chains - **Van Der Waal’s forces** - weak but numerous, maximum contribution, short range attraction between polar and nonpolar molecules ## The Hydrogen Bonds in Protein Form - A diagram showing the formation of a hydrogen bond between an oxygen atom and a nitrogen atom. ## Secondary Structure of Proteins: α - Helix ### **Characteristics** - Most common & stable configuration - Polypeptide backbone. - R groups jut outward. - Spiral (tight) of 3.6 residues/turn. - H bonds between NH & C=O groups, 4 residues away. - All peptide bonds linked (except 1st & last). - Amino acids are L - right-handed helix. ### **Examples** - Keratin - fibrous protein e.g. hair, skin - Myoglobin - globular protein. Hemoglobin ## Direction of Helix - A diagram showing both a left-handed helix and a right-handed helix. ## Amino Acids That Disrupt An α – Helix - Proline (imino group) → kinks - Charged amino acids (Asp, Glu, His, Lys, Arg) → ionic bonds/repel - Glycine → bends in α - helix (small size) - Tryptophan, valine, isoleucine → interfere with formation of α helix. ## Amphipathic Helices - Hydrophilic "R" on one side and hydrophobic "R" on the other side - Cluster → Channel / Pore - Polar molecules to pass through the hydrophobic cell membrane. - A diagram showing a cell membrane with a transmembrane protein with a hydrophilic channel and hydrophobic regions embedded in the cell membrane. ## Bonds in β Pleated Sheets - Hydrogen Bonds formed between C=O & N-H (O-H), between adjacent segments of β sheets perpendicular to the polypeptide backbone. - Intra chain disulfide bridges stabilize bends ## Secondary Structure of Protein: β Pleated Sheets ### **Characteristics** - β sheets are composed of two or more peptide chains, or a single chain folded on itself. - (a) Parallel β sheets: N-C in the same direction - (b) Anti Parallel β sheets: N-C in opposite directions - Amino acid residues form zigzag pleated patterns. - Adjacent R groups point in opposite directions. - Form the core of many globular proteins - Hydrogen bonds are perpendicular to a polypeptide backbone. ### **Diagram of β Pleated Sheets** - A diagram showing a parallel β sheet and an antiparallel β sheet. ## Secondary Structure of Protein: β Bends ### **Characteristics** - Reverse direction of a polypeptide chain → forms compact, globular shape (e.g., connecting anti-parallel β sheets). - Composed of 4 amino acids, one of which may be Proline (which give kinks to a polypeptide chain). - Glycine, the amino acid with the smallest R-group, is also frequently found in them. - Stabilized by the formation of (a) hydrogen bonds between 1st and 4th AA = 180 bend (b) Ionic bonds ## Secondary Structure of Protein: Loops ### **Characteristics** - Irregular, many amino acid residues long - Bridge domains - Contain amino acid residues for catalysis - Loops & bends reside on the surface of proteins → recognition & binding of antibodies. ## Disordered Regions - At C / N terminal → flexibility - Become ordered on binding with ligand ## Secondary Structure of Protein: Super-Secondary Structure / Motifs ### **Characteristics** - Globular proteins are constructed by combining secondary structural elements → core connected by loops on the surface.. - *MOTIFS* are small 3D structures of amino acids ## Motifs - A diagram showing a β-α-β loop and a β-barrel ## Tertiary Structure of Protein ### **Characteristics** - Primary structure of a polypeptide chain determines its 3D tertiary structure - Amino acids far apart in the linear sequence are close in 3D - Secondary structural features (α-helix, β-sheets, bends, loops, turns) assemble into Domains - Domains are the structural and functional units (3D), performing specific chemical/physical tasks e.g., binding substrate. - Hydrophobic side chains are in the core, and hydrophilic side chains are on the surface ## Tertiary Structure of Protein: Domain ### **Characteristics** - A domain is a section of protein structure that is sufficient to perform a particular chemical or physical task. - e.g. (a) Myoglobin (has 1 domain), - (b) Protein kinase (has 2 domains) → catalyze the transfer of phosphate from ATP to protein - Terminal N → binds ATP - Terminal C → binds protein ## 2 Domains of Protein Kinase - a diagram showing two domains of a protein kinase ## Motifs to Domains - β-α-β Loop - α/β Barrel ## Tertiary Structure of Proteins: Bonds - Non-covalent interactions: - Hydrophobic interactions - Hydrogen bonds (with side chains) - Electrostatic interaction - Di-sulfide bonds (intra polypeptide chain) - Van Der Waals forces ## Tertiary Structure of Proteins: Bonds Diagram - A diagram showing an electrostatic interaction and hydrogen bonding between Lysine and Glutamic acid, a disulfide bond between the two cysteine residues, and hydrophobic interactions between amino acids. ## Quaternary Structure of Protein ### **Characteristics** - Protomer/Oligomer = Protein made up of > 1 polypeptide chains (>1monomer) - The spatial arrangement of polypeptide (PP) subunits of protomers of an Oligomeric protein is called the quaternary structure of a protein - Monomer = 1 polypeptide chain - Protomer = more than 1 polypeptide chain. - Dimers = 2 PP chains, Tetramer = 4 PP chains. - Homo-dimer = 2 copies of the same PP chain. - Hetero-dimer = different PP chains (α, β) - Subscript :- α₂= homodimer, α₂β₂ = heterotetramer of 4 polypeptide chains of 2 types each ## Quaternary Structure - The quaternary structure describes the arrangement and position of each of the subunits in a multiunit protein. - Only those proteins containing more than one polypeptide chain. - Subunits may be identical or different. - Only then it is a functional protein. - Subunits are held together by many weak, noncovalent interactions (hydrophobic, electrostatic) ## Quaternary Structure Diagram - a diagram showing the quaternary structures of collagen and hemoglobin. ## Quaternary Structure of Protein ### **Characteristics** - All polypeptide chains together form 1 functional protein. - Protein loses function if subunits dissociate. - Subunits may function cooperatively. - Example: hemoglobin (α₂,β₂), immunoglobulin (2 heavy, 2 light chains) ## Quaternary Structure of Protein: Bonds - Interactions: - Hydrogen bonds - Ionic bonds - Hydrophobic interactions - Van Der Waals forces ## Protein Folding - Proteins are conformationally dynamic molecules - Fold into their functionally competent conformation in milliseconds even if denatured. - Folding into the native state does not involve a haphazard search of all possible structures. This would require billions of years. - Native conformation is thermodynamically favored. - Native conformation is specified in the primary sequence. - Protein folding is orderly and guided. - Secondary structures are formed at translation. ## Chaperones in Protein Folding - Guide protein folding - Provide shelter for folding polypeptides. - Keep the new protein segregated from cytoplasmic influences. ### **Diagram of Chaperones in Protein Folding** - A diagram showing the three steps of a chaperone assisting a polypeptide to fold into a correctly folded protein. ## Steps of Protein Folding - Orderly but not a rigid process = Flexibility. - Modular folding: in steps: - Stage 1: Secondary structures are formed at translation. - Stage 2: Hydrophobic regions cluster in the core assisted by Chaperones (doughnut-shaped proteins which fold over and shield the protein). ## Diseases of Impaired Protein Structure - Mad Cow Disease: Conformational transformation of protein - Insoluble protein deposits aggregate in nerve cells. - Psychiatric and behavior disorders. - Fatal neurodegenerative disease. - Alzheimer’s disease: Misfolding of brain tissue protein, β amyloid → aggregates → senile plaques. - Scurvy: Vitamin C deficiency - ↓ hydroxy proline and hydroxy lysine residue. - ↓ conformational stability of collagen fibers. - Bleeding gums, swollen joints, poor wound healing. - Death.