α-Helix / β-Sheet Collection (AH)

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Teaching Points View Document as PDF

The linear amino acid sequence defines the primary structure of a protein. Regions of the linear polypeptide chain fold into the stable α-helix and β-sheet structures to form the protein secondary structure. The tertiary protein structure is the overall three-dimensional shape of the protein. With this model collection, students can assemble an α-helix or anti-parallel β-sheet, compare the phi-psi angles of the two secondary structures, and explore the contribution of hydrogen bonding to the stability of the structure. Models of the α-helix and β-sheet, with and without side chains, allow comparison of the features of the two secondary structures. Two protein models display tertiary protein structure. The β-globin protein consists predominantly of α-helices while the green fluorescent protein (GFP) consists predominantly of a β-sheet.

Models in this Collection

• α-helix without sidechains
• α-helix with sidechains
• β-sheet without sidechains
• β-sheet with sidechains
• α-helix β-sheet construction kit
• β-globin protein
• Green fluorescent protein (GFP)

Model Details

• α-helix without side chains
  • 17 amino acids without side chains
  • Ball and stick format
  • Derived from Helix E of β-globin (amino acids 58-74)
  • Pitch is 3.6 amino acids per turn of helix
  • Hydrogen bonds (white) between nitrogen and carbonyl oxygen
  • CPK colors (carbon is gray, nitrogen is blue, oxygen is red)
  • Identical helix to the model α-helix with sidechains
  • Model made of plaster with the ZCorp printer
• α-helix with side chains
  • 17 amino acids with side chains
  • Ball and stick format
  • Derived from Helix E of β-globin (amino acids 58-74)
  • Pitch is 3.6 amino acids per turn of helix
  • Hydrogen bonds (white) between nitrogen and carbonyl oxygen
  • The amino acid side chains are CPK colors (carbon is gray, nitrogen is blue, oxygen is red, sulfur is orange)
  • The amino acid backbone atoms are colored green with the nitrogen colored blue (facilitates counting amino acids in the helix)
  • Amino acid sequence: NH₂ - Pro - Lys - Val - Lys - Ala - His - Gly - Lys - Lys - Val - Leu - Gly - Ala - Phe - Ser - Asp - Gly - CO₂H
  • Model made of plaster with the ZCorp printer
• β-sheet without side chains
  • 30 amino acids without side chains
  • Ball and stick format
  • Made from amino acids 14-32, 120-127 of GFP (the pattern of hydrogen bonds can be used to identify the location in the GFP model)
  • Hydrogen bonds (white) between nitrogen and carbonyl oxygen
  • Two strands are parallel
  • Two strands are anti-parallel
  • CPK colors (carbon is gray, nitrogen is blue, oxygen is red)
  • Identical to β-sheet with sidechains
  • Model made of plaster with the ZCorp printer
• β-sheet with sidechains
  • 30 amino acids with side chains
  • Ball and stick format
  • Amino acid sequence:
  • NH₂ (120) - Val - Gln - Arg - Ile - Glu - Leu - Gly - CO₂H (127),
  • NH₂ (14) - Ile - Leu - Val - Glu - Leu - Asp - Gly - Asp - Val - Gln - Gly - His - Lys - Phe - Ser - Val - Ser - Gly - Glu - CO₂H (32)
  • Hydrogen bonds (white) between nitrogen and carbonyl oxygen
  • Two strands are parallel
  • Two strands are anti-parallel
  • Side chains are CPK colors (carbon is gray, nitrogen is blue, oxygen is red)
  • Backbone atoms of each amino acid are colored alternating yellow and green
  • Made from amino acids 14-32, 120-127 of GFP (the pattern of hydrogen bonds can be used to identify the location in the GFP model)
  • Model made of plaster with the ZCorp printer
• Green fluorescent protein, GFP
  • 1EMB pdb file
  • 236 amino acids
  • α-carbon backbone format
  • Chromophore, Ser 65, Tyr 66, Gly 67 green
  • Amino acid contacts with the chromophore, His 148, Gln 94, Arg 96, Glu 222, Thr 203, Ile 167
  • Model made of plaster with the ZCorp printer
• β-globin
  • 1AN3 pdb file
  • Chain B
  • α-carbon backbone format
  • Protoporphorin IX ring containing iron (Fe)
  • His 63 and His 92 bind the protoporphorin ring
  • Glu 6 is the sidechain that is mutated to valine in sickle cell anemia
  • Model made of plaster with the ZCorp printer
• α-Helix β-Sheet Construction kit
  • a helix
    • Ball and stick format made as individual pieces that attach with magnets
    • Peptide backbone pieces (11)
    • Metal hydrogen bonds (7)
    • Model made of plaster with the ZCorp printer
  • β sheet
    • Ball and stick format made as individual pieces that attach with magnets
    • Anti-parallel β-sheet
    • Peptide backbone pieces (10)
    • Metal hydrogen bonds (4)
    • Model made of plaster with the ZCorp printer
  • 24 sidechains
    • Two each of: alanine, glutamic acid, leucine, serine, valine
    • One each of: arginine, asparagine, aspartic acid, cysteine, glutamine, glycine, histidine, isoleucine, lysine, methioninie, phenylalanine, threonine, tyrosine, tryptophan
    • Note that there is no sidechain for proline

Documentation Included

• Teaching points and inventory
• How do the models fit back in the case?
• Activities for the α-Helix and β-Sheet Construction Kit
• Modeling Helix A of the β-Globin Protein
• Modeling a β-Sheet of Green Fluorescent Protein
• Resources for β-globin and GFP Collection
• Separation of backbone pieces

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