Introduction to Protein Structure Collection

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This collection is designed to introduce students to the 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. A flexible foam Toober (made with wire in the center and 48" long) allows students to create their own protein structures while exploring basic protein-folding principles. The Amino Acid Starter Kit^© incorporates foam 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.

Models in this Collection

Water Cup©
Water Cup© CD
MolyMod© models
15 Tacks and a 4 Foot Toober
Amino Acid Starter Kit©
Amino Acid Starter Kit© CD
α-helix/ β-sheet construction kit
α-helix backbone without sidechains
α-helix backbone with sidechains
β-sheet backbone without sidechains
β-sheet backbone with sidechains
β-globin protein
Green fluorescent protein (GFP)
Zinc finger folding activity

Model Details

Water Cup©

12 molecules of water with magnets to simulate hydrogen bonds
1 sodium atom (blue) with magnets for interaction with water molecules
1 chloride atom (green) with magnets for interaction with water molecules
1 hydroxyl group with magnets for interaction with water molecules; combines with ethane core to form ethanol
1 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
1 grey plug and white hydrogen cap without magnet; binds to ethane core to form ethane

Water Kit© CD

Water Kit Basic Lesson Plans
Water Kit Constructivist Lab
Water Kit Flip Card
Ice and Snowflake Instructions
Project Wet and the Water Kit
Other Water Resources

MolyMod© models for 2 amino acids

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, 4 red, 2 blue, 2 green, 8 white, 8 white bonds, 6 long grey bonds, 6 short grey bonds, 1 tan gripping tool

15 Tacks and a 4 Foot Toober©

4 foot flexible foam toober© (wire in the center)
15 colored pushpins (6 yellow, 3 white, 2 blue, 2 red, 2 green)

Amino Acid Starter Kit©

1 magnetic chemical properties circle
1 laminated amino acid chart
22 magnetic amino acid sidechains (1 of each amino acid, plus 1 additional cysteine and histidine)
1 four-foot Mini-Toober©
15 magnetic Mini-Toober© clips
2 Mini-Toober© endcaps (1 each red and blue)
CPK Coloring Dots
6 Hydrogen Bond Connectors

Amino Acid Starter Kit CD

Jmol tutorials
Images
PDF files with documentation

AASK Introduction and contents
AASK Standard Genetic Code
AASK Student Handout 1
AASK Student Handout 1 Key
AASK Student Handout 2
AASK Student Handout 2 Key
AASK Teacher Notes
AASK Toober Variations
AASK Toober Variations Key
Tertiary and Quaternary Protein Structure

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 ZCorp 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 ZCorp 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

α-helix 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 ZCorp printer
Based on PDB file 1AN3

α-helix 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 ZCorp printer
Based on PDB file 1AN3

β-sheet 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 ZCorp printer
Based on PDB file 1EMB

β-sheet 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 ZCorp printer
Based on PDB file 1EMB

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
β-sheets are colored yellow
α-helices are colored red
Model made of plaster with 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 ZCorp printer
α-helices are colored red

Zinc finger folding activity

Zinc finger folding map
7 amino acid sidechains: 2 histidine, 2 cysteine, 1 phenylalanine, 1 arginine, 1 leucine
1 orange zinc atom with magnets
CPK Coloring Dots

Documentation included