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Protein Basics Maureen Hillenmeyer 02-04-02

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Protein Basics Maureen Hillenmeyer 02-04-02

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    1. Protein Basics Maureen Hillenmeyer 02-04-02 Protein function Protein structure Primary Amino acids Linkage Protein conformation framework Dihedral angles Ramachandran plots Sequence similarity and variation

    3. Protein Structure

    5. Model Molecule: Hemoglobin

    6. Hemoglobin: Background Protein in red blood cells

    7. Red Blood Cell (Erythrocyte)

    9. Heme Groups in Hemoglobin

    11. Hemoglobin Quaternary Structure

    13. Hemoglobin Secondary Structure

    14. Structure Stabilizing Interactions Noncovalent Van der Waals forces (transient, weak electrical attraction of one atom for another) Hydrophobic (clustering of nonpolar groups) Hydrogen bonding

    15. Hydrogen Bonding Involves three atoms: Donor electronegative atom (D) (Nitrogen or Oxygen in proteins) Hydrogen bound to donor (H) Acceptor electronegative atom (A) in close proximity

    16. D-H Interaction Polarization due to electron withdrawal from the hydrogen to D giving D partial negative charge and the H a partial positive charge Proximity of the Acceptor A causes further charge separation

    20. Disulfide Bonds Side chain of cysteine contains highly reactive thiol group Two thiol groups form a disulfide bond

    21. Disulfide Bridge

    23. Disulfide Bridge Linking Distant Amino Acids

    24. Hemoglobin Primary Structure

    26. Protein Structure - Primary Protein: chain of amino acids joined by peptide bonds Amino Acid Central carbon (Ca) attached to: Hydrogen (H) Amino group (-NH2) Carboxyl group (-COOH) Side chain (R)

    27. General Amino Acid Structure

    29. General Amino Acid Structure

    31. Chirality: Glyceraldehyde

    33. 20 Naturally-occurring Amino Acids

    38. Glycine Nonpolar (special case)

    40. Peptide Bond Formation

    41. Peptide Chain

    45. Peptide Bond Lengths

    47. Protein Conformation Framework Bond rotation determines protein folding, 3D structure

    48. Bond Rotation Determines Protein Folding

    52. Ethane Rotation

    54. Backbone Torsion Angles

    55. Backbone Torsion Angles Dihedral angle ? : rotation about the peptide bond, namely Ca1-{C-N}- Ca2

    61. Backbone Torsion Angles ? angle tends to be planar (0 - cis, or 180 - trans) due to delocalization of carbonyl p electrons and nitrogen lone pair

    66. Steric Hindrance Interference to rotation caused by spatial arrangement of atoms within molecule Atoms cannot overlap Atom size defined by van der Waals radii Electron clouds repel each other

    68. G.N. Ramachandran Used computer models of small polypeptides to systematically vary f and ? with the objective of finding stable conformations For each conformation, the structure was examined for close contacts between atoms Atoms were treated as hard spheres with dimensions corresponding to their van der Waals radii Therefore, f and ? angles which cause spheres to collide correspond to sterically disallowed conformations of the polypeptide backbone

    69. Ramachandran Plot Plot of f vs. ? The computed angles which are sterically allowed fall on certain regions of plot

    70. Computed Ramachandran Plot

    72. Experimental Ramachandran Plot

    77. Ramachandran Plot And Secondary Structure White = sterically disallowed conformations Red = sterically allowed regions if strict (greater) radii are used (namely right-handed alpha helix and beta sheet) Yellow = sterically allowed if shorter radii are used (i.e. atoms allowed closer together; brings out left-handed helix)

    80. Alanine Ramachandran Plot

    81. Arginine Ramachandran Plot

    85. f, ? and Secondary Structure

    86. Sequence Similarity Sequence similarity implies structural, functional, and evolutionary commonality

    87. Homologous Proteins: Enterotoxin and Cholera toxin

    89. Nonhomologous Proteins: Cytochrome and Barstar

    91. Sequence Similarity Exception Sickle-cell anemia resulting from one residue change in hemoglobin protein Replace highly polar (hydrophilic) glutamate with nonpolar (hydrophobic) valine

    92. Sickle-cell mutation in hemoglobin sequence

    93. Normal Trait Hemoglobin molecules exist as single, isolated units in RBC, whether oxygen bound or not Cells maintain basic disc shape, whether transporting oxygen or not

    95. Sickle-cell

    97. Hemoglobin Polymerization

    99. Capillary Blockage

    101. Protein: The Machinery of Life Life is the mode of existence of proteins, and this mode of existence essentially consists in the constant self-renewal of the chemical constituents of these substances. Friedrich Engles, 1878

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