The 3Dimensional Structure of Proteins

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Chapter 4

• The 3-Dimensional Structure of Proteins

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• Three-dimensional, functional structure is called
  native
• Folded shape is called conformation
• There are thousands of possible conformations,
  but not an infinite amount
• Conformations are restrained by allowed angles

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There are 4 levels of protein stucture

• Primary Linear amino acid sequence
• Bonds Covalent
• Secondary Local structure certain motifs are
  common
• Bonds Mostly H-bonds
• Tertiary Complete 3-D shape
• Bonds H-bonds, hydrophobic interactions, ionic
  bonds, van der Waals interactions, disulfide
  bonds
• Quaternary gt1 peptide chains
• Mostly H-bonds

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Thermodynamics of protein folding
Entropy is driving force for
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Secondary Structure

• The alpha helix
• Tightly wound, repeating sequence
• Right-handed
• R-groups are on outside of helix
• Each twist ? 5.4 Å 3.6 residues
• Stabilized by H-bonds between N-H and CO 3
  residues away
• a-helix are polar (positive at amino end
  negative at carboxyl
• Some amino acids are a-helix breakers
• Repeating like-charges
• Repeating bulky groups

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Alpha Helix, continued

• Effects on helical stability
• Electrostatic interactions between adjacent
  residues
• Steric interference between adjacent residues
• Interactions between residues 3-4 amino acids
  away
• Pro and Gly (helix breakers)
• Polarity of residues at both ends of helix

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Beta Conformation

• Extended, zigzag conformation
• Interactions between adjacent amino acids
• Adjacent strands, H-bonded to one another, lead
  to beta sheet
• R-groups protrude opposite of parallel structure

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Beta Sheet

• Parallel ?-sheet
• Same Amino-carboxyl direction
• (6.5 Å repeat)
• Anti-parallel ?-sheet
• Opposite orientation
• (7 Å repeat)

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?-turns

• Interacting strands can be many amino acids apart
• Turns are 180 connect strands in folded
  (globular) proteins
• Interaction is between carbonyl oxygen of aa 1
  and amino hydrogen of aa 4
• Interior amino acids are not involved thus, Pro
  and Gly are often present (Type II turns)
• Gly small and flexible
• Pro Cis conformation makes inclusion in tight
  turn favorable

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Proline isomerization
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?-turns, continued

• Type I (most common) Type II ALWAYS contain Gly
  as amino acid 3.

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Bond angles (?, ?) describe secondary structure
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Tertiary Structure

• Long range protein structure
• Interactions between various secondary structural
  components of protein
• 2 major classifications
• Fibrous (structural proteins) vs. globular

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Fibrous Proteins

• Strong and flexible
• Hydrophobic
• Comprise hair, quills, wool, nails, etc.
• Left-handed helix of intertwined a-helices (of
  smaller repeat period) confer strength this
  forms super-structure called protofilaments,
  which combine to form fibrils

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Alpha-keratin
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Collagen
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Collagen

• Tightly wound left-handed helix
• Gly-X-Y
• X Pro Y 4-Hyp

Hydroxyproline requires Vitamin C for proline
hydroxylationScurvy?