chapter 4 students - Chapter 4: Protein Structure MCDB310...

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Chapter 4: Protein Structure 1 MCDB310 – Chapter 4: Protein Structure
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Primary Structure (= Amino Acid Sequence) 2 MCDB310 – Chapter 4: Protein Structure
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The Peptide Bond 3 MCDB310 – Chapter 4: Protein Structure
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The Peptide Bond Has a Partial Double Bond Character peptide bond is planar and rigid peptide bond resonance energy (derives from partial electron sharing between carbonyl- oxygen and amide-nitrogen) C—N bond is 0.14 Å shorter than normal 4 MCDB310 – Chapter 4: Protein Structure
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Trans Configuration of Peptide Bonds R1 R2 Partial double bond character restricts free rotation around the peptide bond ( cis/trans configuration) 5 MCDB310 – Chapter 4: Protein Structure Due to steric clashes of side-chains, trans is favored
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Cis-Configuration is Only Observed in Peptide Bonds Preceding Proline Proline Normally: cis :trans ~ 1:1000 Xaa-Pro: cis :trans ~ 1:3 6 MCDB310 – Chapter 4: Protein Structure
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The Polypeptide Backbone Conformation Can Be Described by Bond Angles 7 MCDB310 – Chapter 4: Protein Structure Dihedral angles between N and C α [ φ (phi)] C α and C [ ψ (psi)]
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Proteins Can Adopt a Huge Number of Conformations (Theoretically) Assumption: Each peptide bond can adopt 3 different conformations N(AA) N(possible conformations) 2 3 3 3 2 (9) 4 3 3 (27) 100 3 = 1.7·10 8 MCDB310 – Chapter 4: Protein Structure
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2D-Ramachandran Plot (L-Ala peptide) Not all φ / ψ -Combinations are Allowed ~ 3/4 of possible combinations are excluded because of steric hindrances (e.g. interatomic distances smaller than van der Waals radii) φ (phi) [degree] ψ (psi) [degree] no steric overlap: allowed conformations steric overlap: not allowed 9 MCDB310 – Chapter 4: Protein Structure
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Secondary Structure 10 MCDB310 – Chapter 4: Protein Structure Repetitive local backbone conformations conferred by short-range interactions α -helix , β -sheet , loops
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The α -Helix 11 MCDB310 – Chapter 4: Protein Structure
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12 MCDB310 – Chapter 4: Protein Structure predominantly right handed (counter-clockwise) twist in proteins The α -Helix
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Basic Features of α -Helices tightly coiled backbone, side-chains protrude outwards each amino acid is related to next by a rise of 1.5 Å and a rotation of 100 o each helical turn includes 3.6 amino acids 13 MCDB310 – Chapter 4: Protein Structure
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Side-chains 14 MCDB310 – Chapter 4: Protein Structure Top and Side-Views of an α -Helix
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1 2 3 4 5 15 MCDB310 – Chapter 4: Protein Structure stabilized by H-bonds between carbonyl oxygen of n th AA and amino group of (n + 4) th AA peptide bond dipoles are in parallel alignment helix dipole Interactions Within the α -Helix
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16 MCDB310 – Chapter 4: Protein Structure additional stabilization by interacting side-chains that are 3-4 residues apart (i.e., are located above each other ) Interactions Within the α -Helix Arg 103 Asp 100
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Summary: Energetics of α -Helices Stabilizing: hydrogen bonds
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chapter 4 students - Chapter 4: Protein Structure MCDB310...

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