protein_structure_and_folding

protein_structure_and_folding - Ch Chemistry 237 237...

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Chemistry 237 roteins 2: 3 dimensional Proteins 2: 3 dimensional structures of proteins
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Structure hierarchy Primary 1 ˚ : chemical structure Secondary 2 ˚ : Local structural elements Tertiary 3 ˚ : long range interactions overall fold single polypeptide chain Quaternary 4 ˚ : Interactions etween between polypeptide chains
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eptide bond Peptide bond n-1 n
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eptide bond Peptide bond The peptide bond exists as a resonance hybrid. The two structure contribute to the structural properties of the peptide n-1 Restricted rotation means that the atoms of the n peptide bond must be co-planar .
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the peptide bond can be in the 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 expected for sp 2 hybrid atoms
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the plane of each peptide bond shares one C α 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. pp Some configurations are not possible. This causes steric hindrance BAD! N+1 N-1 n machandran animation Figure 8-6 Steric interference between adjacent residues. ramachandran animation
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Ramachandran Plot (~1968): A plot of all of the possible configurations of Φ and Ψ . The Ramachandran diagram. Conformation angles in proteins. 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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econdary structure elements Secondary structure elements lpha helix Alpha helix Beta sheet Beta turns Loops The terms alpha helix and beta sheet were coined in 1930 by William Astbury 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 951) (1951) C terminus important structural features: right handed helix with 3.6 residues per turn itch of 5.4 Å (0.54 nm) per turn pitch of 5.4 Å (0.54 nm) per turn held together by H-bonds etween 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 axis ot all sequences can form α - elices Not all sequences can form helices proline residues (why?) lots of (-) or (+) charged residues lots of bulky residues Amount of α -helical structures in a protein can vary Phi -45 to -180 Psi - 0 to - 0 s 30 to 60
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eta sheets Beta sheets Two separate sections of extended polypeptide interact via H-bonds There are two possible orientations: antiparallel and parallel Antiparallel strands: straight H-bonds:
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eta sheets Beta sheets parallel strands: The H-bonds are not straight c.
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Beta sheet: Important Structural features Two or more strands of polypeptide H-bonded gether through peptide bond groups
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This note was uploaded on 07/07/2010 for the course CHEM 237 taught by Professor Elisabethdaub during the Fall '10 term at Waterloo.

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protein_structure_and_folding - Ch Chemistry 237 237...

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