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

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'''Lysozyme, PDB ID [[2lyz]]'''
'''Lysozyme, PDB ID [[2lyz]]'''


Proteins are polymers of amino acids.  Yada yada yada...
'''Amino acids and primary structure'''


The "backbone" of the protein is made up of carbons and nitrogens.  The amino acid sidechain extends out of the backbone.   
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/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 "primary structure".


<scene name='User:Tommie_Hata/Protein_Structure_Tutorial/Secondary_structure/2'>Secondary Structure</scene> is a
'''Interactions between the protein backbone: secondary structure'''


<scene name='User:Tommie_Hata/Protein_Structure_Tutorial/Ionic_interaction/1'>Ionic Interactions</scene>
[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>.
<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>
'''3D structure of a protein maintained by interactions between amino acid sidechains: tertiary structure'''


<scene name='User:Tommie_Hata/Protein_Structure_Tutorial/Hydrophobic_core/1'>Hydrophobic core</scene>
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/Ssbond-sidechain/1'>SS bond, sidechain</scene>
<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/Ssbond-alpha-carbon/1'>SS bond, between alpha carbons</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/Default/5'>Default</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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