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09 - 2 Ψ C-C α Torsional Angle(Clockwise rotational...

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11/19/09 Amino Acids Amino Acids Monomeric Units of Proteins At physiological pH, Zwitterionic form : compound that carries a net charge of zero, but carries formal charges on different atoms The Peptide Bond AA 1 + AA 2  AA 1 —AA 2 + H 2 O What is a protein? Proteins consist of 1 or more polypeptides Polypeptides range from ~40-4,000 AA residues Protein molecular weights range from 4-400 kiloDaltons Four Levels of Protein Structure 1) Primary (1 o ) Structure-All sequence 2) Secondary (2 o ) Structure-Local spatial arrangement of polypeptide backbone without regard to its side chains 3) Tertiary (3 o ) Structure- 3 Dimensional structure of polypeptide 4) Quaternary (4 o ) Structure- 3 Dimensional arrangement of the protein’s subunits Secondary Structure Pauling/Corey (1930-1940) Find that the peptide bond is planar Planarity of the peptide bond places important constraints on peptide conformations Remains Degrees of Freedom 1) Φ N-C α Torsional Angle (Clockwise rotational)
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Unformatted text preview: 2) Ψ C-C α Torsional Angle (Clockwise rotational) Definitions: Vander-Waals radius radius of an imaginary hard sphere that corresponds to the volume of a particular atom Two atoms cannot occupy positions in space where their separation distance corresponds to a value less than the sum of their Vander Waals radii Two atoms cannot exist in a space where their Vander Waals radii overlap G.N. Ramachandran Built space-filling models to determine the ranges of allowed values of Φ and Ψ Ala-Ala-Ala Helical structures proposed by Pauling in 1951 Form when polypeptides are twisted the same amount about each C α 11/19/09 α-helix 1) Φ = -57 , Ψ = =47 2) 3.6 peptides/turn 3)C=O of residue “n” points directly at NH of residue n+4 4) Van der Waals contact in the helix interior 5) R-groups point outward β-pleated sheets β-pleated sheets...
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