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User:Tommie Hata/Protein Structure Tutorial: Difference between revisions

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<applet load='2LYZ' size='600' frame='true' align='right' caption='Insert caption here' scene='User:Tommie_Hata/Protein_Structure_Tutorial/Default/2'/>
<applet load='2LYZ' size='550' frame='true' align='right' caption='Insert caption here' scene='User:Tommie_Hata/Protein_Structure_Tutorial/Default/5'/>


<scene name='User:Tommie_Hata/Protein_Structure_Tutorial/Amino_acids_and_sidechains/1'>Amino acids</scene>
'''Lysozyme, PDB ID [[2lyz]]'''


<scene name='User:Tommie_Hata/Protein_Structure_Tutorial/Secondary_structure/1'>secondary structure</scene>
'''Amino acids and primary structure'''


Proteins are polymers of [http://en.wikipedia.org/wiki/Amino_acid amino acids].  The "backbone" of the protein is made up of carbons and nitrogens.  The amino acid sidechain extends out of the backbone.  <scene name='User:Tommie_Hata/Protein_Structure_Tutorial/Amino_acids_and_sidechains/2'>Here, the backbone is colored in CPK coloring and the sidechains are colored green.</scene>  The linear sequence of amino acids in a polypeptide is referred to as its [http://en.wikipedia.org/wiki/Primary_structure "primary structure"].


<scene name='User:Tommie_Hata/Protein_Structure_Tutorial/Default/2'>Default</scene>
'''Interactions between the protein backbone: secondary structure'''
 
[http://en.wikipedia.org/wiki/Hydrogen_bond Hydrogen bonds] between backbone amide and carboxyl groups maintain some local structural characteristics referred to as [http://en.wikipedia.org/wiki/Secondary_structure secondary structure].  Two common types of secondary structure are the [http://en.wikipedia.org/wiki/Alpha_helices alpha helices] and the [http://en.wikipedia.org/wiki/Beta_sheet beta pleated sheet].  <scene name='User:Tommie_Hata/Protein_Structure_Tutorial/Secondary_structure/2'>Here, alpha helices are colored red and beta pleated sheets colored blue in a "ribbons" display</scene>.
 
'''3D structure of a protein maintained by interactions between amino acid sidechains: tertiary structure'''
 
The overall shape of a protein is maintained by the interaction between amino acid sidechains.  The distribution of these sidechains across the protein (the primary structure) is largely responsible for determining [http://en.wikipedia.org/wiki/Tertiary_structure tertiary structure].
 
Types of tertiary interactions
 
<scene name='User:Tommie_Hata/Protein_Structure_Tutorial/Hydrophobic_core/1'>Nonpolar sidechains and the hydrophobic core</scene>.
 
<scene name='User:Tommie_Hata/Protein_Structure_Tutorial/Ionic_interaction/1'>Charged sidechains and ionic interactions</scene>.
 
<scene name='User:Tommie_Hata/Protein_Structure_Tutorial/Ionic_interaction_with_surface/1'>Ionic Interactions with surface</scene>.
 
<scene name='User:Tommie_Hata/Protein_Structure_Tutorial/Polar_and_charged/1'>Polar and charged sidechains</scene>.
 
<scene name='User:Tommie_Hata/Protein_Structure_Tutorial/Ssbond-sidechain/1'>Cysteines and disulfide bond formation in oxidizing environments</scene>. 
 
<scene name='User:Tommie_Hata/Protein_Structure_Tutorial/Ssbond-alpha-carbon/1'>SS bond shown between alpha carbons in backbone view</scene>.
 
<scene name='User:Tommie_Hata/Protein_Structure_Tutorial/Default/5'>Return to default view</scene>
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