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Introduction to Protein Structure (IP)

The Introduction to Protein Structure (IP) collection is designed to introduce students to concepts of protein structure and biochemistry. Different activities guide students from the basic building blocks of proteins, amino acids, through the different levels of protein structure.


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This collection is designed to introduce students to concepts of protein structure and biochemistry. Different activities guide students from the basic building blocks of proteins, amino acids, through the different levels of protein structure. Using the MolyMod models, students learn the different atomic components of an amino acid and how a peptide bond is formed through the loss of a water molecule. The Water Cup provides an overview of how water is essential for influencing protein folding. 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 secondary structure. Sidechains allow students to explore the different chemical properties of each group and how these properties help determine protein folding. 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-sheets. The Amino Acid Starter Kit© incorporates plastic amino acid residues on a mini-toober, providing a more advanced protein folding activity. This collection also includes a protein modeling kit that enables students to fold a mini-toober to create a model of a zinc finger.

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1x - Water Cup©

  • 12x - molecules of water with magnets to simulate hydrogen bonds
  • 1x - sodium atom (blue) with magnets for interaction with water molecules
  • 1x - chloride atom (green) with magnets for interaction with water molecules
  • 1x - hydroxyl group with magnets for interaction with water molecules; combines with ethane core to form ethanol
  • 1x - ethane core (2 grey carbon atoms, 5 white hydrogen atoms without magnets to simulate non-polar interactions with water molecules); used to make ethane or ethanol
  • 1x - grey plug and white hydrogen cap without magnet; binds to ethane core to form ethane

1x - MolyMod© models

  • Individual atoms are represented by colored spheres
    • Red: oxygen
    • Black: carbon
    • Blue: nitrogen
    • White: hydrogen
    • Green: represents a generic sidechain
  • Covalent bonds are represented by thick gray bonds
  • Bonding of hydrogens represented by short white bonds
  • Kit contains 4 black spheres, 4 red spheres, 2 blue spheres, 2 green spheres, 8 white spheres, 8 white bonds, 6 long grey bonds, 6 short grey bonds, 1 tan gripping tool

1x - Amino Acid Starter Kit©

  • 1 chemical properties circle
  • 1 laminated amino acid chart
  • 22 plastic amino acid sidechains (1 of each amino acid, plus 1 additional cysteine and histidine); clips are color coded to signify chemical properties
  • 1 four-foot Mini-Toober©
  • 2 Mini-Toober© endcaps (1 each red and blue)
  • 6 Hydrogen Bond Connectors

1x - α-helix/ β-sheet construction kit

  • α-helix
    • Ball and stick format made as individual pieces that attach with magnets
    • Peptide backbone pieces (11)
      • May have green dot on alpha carbon
    • Metal hydrogen bonds with white hydrogen atoms (7)
    • Model made of plaster with the 3D Systems Project printer
  • β-sheet
    • Ball and stick format made as individual pieces that attach with magnets
    • Anti-parallel β-sheet
    • Peptide backbone pieces (10)
      • May have green A (for antiparallel) or yellow dot on alpha carbon
    • Metal hydrogen bonds with white hydrogen atoms (4)
    • Model made of plaster with the 3D Systems Project printer
  • Sidechains
    • Ball and stick format made as individual pieces that attach with magnets
    • 30 sidechains:
      • Four of glutamic acid
      • Three each of: leucine, serine, valine
      • Two each of: alanine, glycine
      • One each of: arginine, asparagine, aspartic acid, cysteine, glutamine, histidine, isoleucine, lysine, methioninie, phenylalanine, threonine, tyrosine, tryptophan
      • Note that there is no sidechain for proline

1x - α-helix backbone without sidechains

  • 17 amino acids without sidechains
  • 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 3D Systems Project printer
  • Based on .pdb file 1a3n.pdb

1x - α-helix backbone with sidechains

  • 17 amino acids with sidechains
  • 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
  • Sidechains are CPK colors (carbon is gray, nitrogen is blue, oxygen is red, sulfur is orange)
  • 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 3D Systems Project printer
  • Based on PDB file 1a3n.pdb

1x - β-sheet backbone without sidechains

  • 30 amino acids without sidechains
  • 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 backbone to β-sheet model with sidechains
  • Model made of plaster with 3D Systems Project printer
  • Based on .pdb file 1emb.pdb

1x - β-sheet backbone with sidechains

  • 30 amino acids with sidechains
  • 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
  • Sidechains are CPK colors (carbon is gray, nitrogen is blue, oxygen is red)
  • Amino acid backbone atoms are colored green with the nitrogen colored blue (facilitates counting amino acids in the sheet)
  • 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 3D Systems Project printer
  • Based on .pdb file 1emb.pdb

1x - β-globin protein

  • 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 3D Systems Project printer
  • α-helices are colored red
  • Based on PDB file 1a3n.pdb

1x - Green fluorescent protein (GFP)

  • 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
  • β-sheets are colored yellow
  • α-helices are colored red
  • Model made of plaster with 3D Systems Project printer
  • Based on .pdb file 1emb.pdb

1x - Zinc finger folding activity

  • 72 cm Mini-Toober©
  • Zinc finger folding map
  • 7 amino acid sidechains: 2 histidine, 2 cysteine, 1 phenylalanine, 1 arginine, 1 leucine
  • 7 magnetic Mini-Toober© clips
  • 1 orange zinc atom with magnets
  • CPK Coloring Dots
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This unique Model Lending Library is jointly supported by MSOE Center for BioMolecular Modeling, the MSOE Walter Schroeder Library and 3D Molecular Designs. Some of the models in the Lending Library were developed with funds from NIH-SEPA and NSF-CCLI awards.

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