User:Tommie Hata/Protein Structure Tutorial: Difference between revisions
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<applet load='2LYZ' size=' | <applet load='2LYZ' size='550' frame='true' align='right' caption='Insert caption here' scene='User:Tommie_Hata/Protein_Structure_Tutorial/Default/5'/> | ||
Lysozyme, PDB ID [[ | '''Lysozyme, PDB ID [[2lyz]]''' | ||
'''Amino acids and primary structure''' | |||
<scene name='User:Tommie_Hata/Protein_Structure_Tutorial/Amino_acids_and_sidechains/ | 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"]. | ||
'''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''' | |||
<scene name='User:Tommie_Hata/Protein_Structure_Tutorial/ | 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> | |||
Latest revision as of 16:00, 15 July 2009
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Lysozyme, PDB ID 2lyz
Amino acids and primary structure
Proteins are polymers of amino acids. The "backbone" of the protein is made up of carbons and nitrogens. The amino acid sidechain extends out of the backbone. The linear sequence of amino acids in a polypeptide is referred to as its "primary structure".
Interactions between the protein backbone: secondary structure
Hydrogen bonds between backbone amide and carboxyl groups maintain some local structural characteristics referred to as secondary structure. Two common types of secondary structure are the alpha helices and the beta pleated sheet. .
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 tertiary structure.
Types of tertiary interactions
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