Protein 3 dimensional structure and function
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This document discusses protein structure and function. It defines different levels of protein structure from primary to quaternary, and describes common secondary structures like alpha helices and beta sheets. Alpha helices are right-handed coils stabilized by hydrogen bonds between amino acids four positions apart in the sequence. Beta sheets consist of beta strands connected laterally by hydrogen bonds to form flat sheets, which can be arranged in parallel or anti-parallel configurations. Tertiary structure refers to the overall three-dimensional shape of a protein formed by the folding and interaction of secondary structures.
Protein 3 dimensional structure and function
- 1. PROTEIN 3- DIMENSIONAL STRUCTURE AND FUNCTION By- Dr. Armaan Singh
- 2. TERMINOLOGY Conformation – spatial arrangement of atoms in a protein Native conformation – conformation of functional protein
- 6. PROTEIN CLASSIFICATION Simple – composed only of amino acid residues Conjugated – contain prosthetic groups (metal ions, co-factors, lipids, carbohydrates) Example: Hemoglobin – Heme
- 7. PROTEIN CLASSIFICATION • One polypeptide chain - monomeric protein • More than one - multimeric protein • Homomultimer - one kind of chain • Heteromultimer - two or more different chains (e.g. Hemoglobin is a heterotetramer. It has two alpha chains and two beta chains.)
- 8. PROTEIN CLASSIFICATION Fibrous – 1) polypeptides arranged in long strands or sheets 2) water insoluble (lots of hydrophobic AA’s) 3) strong but flexible 4) Structural (keratin, collagen) Globular – 1) polypeptide chains folded into spherical or globular form 2) water soluble 3) contain several types of secondary structure 4) diverse functions (enzymes, regulatory proteins)
- 10. PROTEIN FUNCTION Catalysis – enzymes Structural – keratin Transport – hemoglobin Trans-membrane transport – Na+/K+ ATPases Toxins – rattle snake venom, ricin Contractile function – actin, myosin Hormones – insulin Storage Proteins – seeds and eggs Defensive proteins – antibodies
- 11. 4 LEVELS OF PROTEIN STRUCTURE
- 12. NON-COVALENT FORCES IMPORTANT IN DETERMINING PROTEIN STRUCTURE van der Waals: 0.4 - 4 kJ/mol hydrogen bonds: 12-30 kJ/mol ionic bonds: 20 kJ/mol hydrophobic interactions: <40 kJ/mol
- 13. 1O STRUCTURE DETERMINES 2O , 3O , 4O STRUCTURE Sickle Cell Anemia – single amino acid change in hemoglobin related to disease Osteoarthritis – single amino acid change in collagen protein causes joint damage
- 14. CLASSES OF 2O STRUCTURE Alpha helix B-sheet Loops and turns
- 15. 2O STRUCTURE RELATED TO PEPTIDE BACKBONE •Double bond nature of peptide bond cause planar geometry •Free rotation at N - αC and αC- carbonyl C bonds •Angle about the C(alpha)-N bond is denoted phi (φ) •Angle about the C(alpha)-C bond is denoted psi (ψ) •The entire path of the peptide backbone is known if all phi and psi angles are specified
- 16. NOT ALL Φ/Ψ ANGLES ARE POSSIBLE
- 17. RAMACHANDRAN PLOTS •Describes acceptable φ/ψ angles for individual AA’s in a polypeptide chain. •Helps determine what types of 2o structure are present
- 18. ALPHA-HELIX • First proposed by Linus Pauling and Robert Corey in 1951 • Identified in keratin by Max Perutz • A ubiquitous component of proteins • Stabilized by H-bonds
- 19. ALPHA-HELIX •Residues per turn: 3.6 •Rise per residue: 1.5 Angstroms •Rise per turn (pitch): 3.6 x 1.5A = 5.4 Angstroms •amino hydrogen H-bonds with carbonyl oxygen located 4 AA’s away forms 13 atom loop Right handed helix
- 20. ALPHA-HELIX All H-bonds in the alpha-helix are oriented in the same direction giving the helix a dipole with the N- terminus being positive and the C-terminus being negative
- 21. ALPHA-HELIX •Side chain groups point outwards from the helix •AA’s with bulky side chains less common in alpha-helix •Glycine and proline destabilizes alpha- helix
- 22. AMPHIPATHIC ALPHA-HELICES + One side of the helix (dark) has mostly hydrophobic AA’s Two amphipathic helices can associate through hydrophobic interactions
- 23. BETA-STRANDS AND BETA- SHEETS Also first postulated by Pauling and Corey, 1951 Strands may be parallel or antiparallel Rise per residue: 3.47 Angstroms for antiparallel strands 3.25 Angstroms for parallel strands Each strand of a beta sheet may be pictured as a helix with two residues per turn
- 24. BETA-SHEETS Beta-sheets formed from multiple side- by-side beta- strands. Can be in parallel or anti-parallel configuration Anti-parallel beta- sheets more stable
- 25. BETA-SHEETS Side chains point alternately above and below the plane of the beta-sheet 2- to 15 beta-strands/beta-sheet Each strand made of ~ 6 amino acids
- 26. LOOPS AND TURNS Loops Loops usually contain hydrophillic residues. Found on surfaces of proteins Connect alpha-helices and beta-sheets Turns Loops with < 5 AA’s are called turns Beta-turns are common
- 27. BETA-TURNS allows the peptide chain to reverse direction carbonyl C of one residue is H-bonded to the amide proton of a residue three residues away proline and glycine are prevalent in beta turns