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protein_structure_and_folding

protein_structure_and_folding - Ch Chemistry 237 237...

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Ch i t 237 Chemistry 237 Proteins 2: 3 dimensional Proteins 2: 3 dimensional structures of proteins
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Structure hierarchy Primary 1 ˚ : chemical structure S d 2 ˚ L l Secondary 2 : Local structural elements Tertiary 3 ˚ : long range interactions overall fold single polypeptide chain Quaternary 4 ˚ : Interactions between between polypeptide chains
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Peptide bond n-1 n
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Peptide bond The peptide bond exists as a resonance hybrid. The two structure contribute to the structural properties of the peptide Restricted rotation means that the atoms of the tid b d t b peptide bond must be co-planar .
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the peptide bond can be in the i t fi i cis or trans configuration: Figure 8-1 The trans-peptide group. Figure 8-2 The cis-peptide group. Bond angles at the C and N are close to those e pected for sp 2 h brid atoms Bond angles at the C and N are close to those expected for hybrid atoms
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the plane of each peptide bond shares one C α ith th t tid b d l with the next peptide bond plane Amino acid Figure 8-4 The torsional degrees of freedom in a peptide unit.
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Phi = psi = 0 phi = psi = 180
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Rotation of the angles Φ and Ψ changes the relative position of the amide planes. Some configurations are not possible. This causes steric hindrance BAD! N+1 N-1 n ramachandran animation Figure 8-6 Steric interference between adjacent residues.
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Ramachandran Plot (~1968): A plot of all of the possible configurations of Φ and Ψ . 7 The Ramachandran diagram. 8 Conformation angles in proteins. O l th h d d “ ll d” ( t i hi d ) Only the shaded areas are “allowed” (no steric hindrance) Most known protein structures fit into the allowed regions But peptide bonds to glycine or proline residues are sometimes found in un-allowed regions due to the small size of glycine side chain and the ring structure of proline.
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Secondary structure elements Alpha helix Beta sheet B t t Beta turns Loops The terms alpha helix and beta sheet were coined in 1930 by William Astbury l ki t l fib Th fi t t t b d ll d th l h looking at wool fibres. The first structure observed was celled the alpha helix and the second the beta sheet.
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The α -Helix Structure predicted by Linus Pauling (1951) i t t t t l f t C terminus important structural features: right handed helix with 3.6 residues per turn pitch of 5.4 Å (0.54 nm) per turn held together by H-bonds between C=0 residue n to NH of between C=0 residue n to NH of residue n+4 N terminus The right-handed helix. http://www.pnas.org/cgi/reprint/100/20/11207
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The amino acid side chains point outward from the i axis Not all sequences can form α -helices Not all sequences can form helices proline residues (why?) lots of (-) or (+) charged residues lots of bulky residues A f h li l Amount of α -helical structures in a protein can vary Phi -45 to -180 Psi -30 to -60
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Beta sheets Two separate sections of extended polypeptide interact via H-bonds Th t ibl i t ti ti ll l d There are two possible orientations: antiparallel and parallel Antiparallel strands: straight H-bonds:
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Beta sheets parallel strands: The H-bonds are not straight nc.
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  • Fall '10
  • ELISABETHDAUB
  • Chemistry, Proteins, SER GLU LEU ALA LEU LYS SER GLU LEU GLN ALA LEU LYS LYS GLU GLY PHE SER PRO GLU GLU LEU PHE SER PRO GLU GLU LEU ALA ALA ALA LEU GLU SER GLU LEU GLN ALA LEU GLU LYS LYS LEU GLU LYS LYS LEU, proteins Fibrous proteins

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