Bella

• Protein


  Adopts a specific 3D conformation, fulfilling a specific biological function. This structure is called the native fold.

  
• Protein structure


  • Determined by amino acid sequence
  • Function depends on structure
  • One or a few stable structures
  • Most important force is noncovalent bond
  • Structural patterns can be organized
  • Not static

  
• Peptide bond


  Structure partially dictated by peptide bond, a resonance hybrid of two canonical structures. This causes the peptide bonds to be less reactive and quite rigid and nearly planar.

  
• Polypeptide made up of a series of planes linked at α carbons
• The two C-N bond lengths in a peptide bond are different
• Primary structure


  Amino acid sequence

  
• Tertiary structure


  Overall three-dimensional structure of a protein

  
• The three-dimensional structure is determined by the amino-acid sequence

  
• The amino-acid sequence contains all of the information required for the polypeptide chain to fold up into a discrete three-dimensional shape

  
• Covalent bonds (disulfide) and noncovalent bonds (hydrophobic, hydrogen, ionic) stabilize protein structure
• Secondary structure


  Local spatial arrangement of main-chain atoms in a selected segment of polypeptide chain

  
• Common secondary structures


  • α helix
  • β sheet
  • β turn
• α helix


  • Side chains point outward and roughly perpendicular with the axis
  • 3.6 residues per turn
  • Hydrogen bonds between the backbone amides of 1st and 4th peptide bonds

  
• Ala is the strongest helix former, Pro acts as a helix breaker, Gly acts as a helix breaker
• β sheet


  • Held together by hydrogen bonds between the backbone amides in different segments
  • Side chains protrude from the sheet alternating in up and down direction
  • Parallel or antiparallel orientation of two chains within a sheet are possible
• β turn


  • 180° turn accomplished over four amino acids, stabilized by a hydrogen bond
  • Proline in position 2 or glycine in position 3 are common
• Secondary structure describes the relationship and interaction of amino acid residues that are generally near each other in sequence

  
• An α-helix has 3.6 amino acids per turn
• A D-amino acid would interrupt an α-helix made of L-amino acids, and a Pro residue is another naturally occurring hindrance to the formation of an α-helix
• The sequence -Ser-Gly-Pro-Gly- is most probably part of a β turn
• Tertiary structure


  Overall spatial arrangement of atoms in a protein

  
• Quaternary structure


  Arrangement of subunits in a multisubunit protein in three-dimensional complex

  
• Tertiary and quaternary structure are stabilized by numerous weak interactions between amino acid side chains, largely hydrophobic and polar interactions, and can be stabilized by disulfide bonds

  
• Fibrous proteins


  • Long strands or sheets, a single type of secondary structure, provide support, shape, and external protection
• Globular proteins


  • Spherical or globular shape, several types of secondary structure, enzymes and regulatory proteins

  
• Structure of α-keratin in hair

  • Left-handed coiled coil, strength further enhanced by disulfide bonds
• Hair structure consists of right-handed α helix and left-handed coiled coil cross-linked by disulfide bonds
• Structure of collagen


  • Each collagen chain is a long Gly-rich and Pro-rich left-handed helix, three collagen chains intertwine into a right-handed superhelical triple helix, many triple-helices assemble into a collagen fibril
• Fibrous Proteins


  • Long strands or sheets
  • A single type of secondary structure
  • Provide support, shape, and external protection
• Globular Proteins


  • Spherical or globular shape
  • Several types of secondary structure
  • Enzymes and regulatory protein

  
• Fibrous Proteins


  From Structure to Function
• Structure of α-Keratin in Hair

  1. Left-handed coiled coil

  2. Strength further enhanced by disulfide bonds
• Structure of Hair


  1. Right-handed α helix

  2. Left-handed coiled coil

  3. Cross-linked by disulfide bonds
• Structure of Collagen


  1. Each collagen chain is a long Gly-rich and Pro-rich left-handed helix

  2. Three collagen chains intertwine into a right-handed superhelical triple helix

  3. Many triple-helices assemble into a collagen fibril
• Proline & 4-Hydroxyproline in Collagen


  • Repeating unit in collagen: Gly-X-Y (X is often Pro, Y is often 4-Hyp)
  • Three amino acid residues per turn
  • Only Gly can be accommodated at very tight junctions
  • Pro and 4-Hyp permit sharp twisting of collagen helix
  • 4-Hyp forces proline ring into a favorable pucker
  • 4-Hyp offers more hydrogen bonds between three strands of collagen
  • Post-translational processing is catalyzed by prolyl hydroxylase and requires ascorbate (vitamin C)
• Silk Fibroin


  • Antiparallel β sheet structure
  • Small side chains (Ala and Gly) allow the close packing of sheets
  • Structure is stabilized by hydrogen bonding, NOT covalent bonds
• Silk


  Fibroin is the main protein in silk from insects and spiders
• These filaments are NOT individual protein strands. Each collagen monomer consists of three left-handed helical protein strands, wound around each other to form a right-handed triple helix.
• Globular proteins


  • More compact than fibrous proteins
  • A wide array of biological functions (Enzymes, regulatory proteins, transport proteins, etc.)
• Myoglobin


  • A single peptide chain with 153 residues
  • Oxygen binding
  • Contains a single heme group (iron protoporphyrin)