Sandbox 51: Difference between revisions

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Lysozyme, like all proteins, also contains a <scene name='Sandbox_39/C_and_n_terminal_residues/1'> 3'C and 5'N terminal </scene>, and these can be seen by following the colors of the rainbow across the molecule. Starting at the red end, the 3' C terminal end, one can work the entire way through to the 5' N terminal end, showing the folding pattern and chain of the protein.
Lysozyme, like all proteins, also contains a <scene name='Sandbox_39/C_and_n_terminal_residues/1'> 3'C and 5'N terminal </scene>, and these can be seen by following the colors of the rainbow across the molecule. Starting at the red end, the 3' C terminal end, one can work the entire way through to the 5' N terminal end, showing the folding pattern and chain of the protein.
== Secondary Structure ==
Lysozyme contains five <scene name='Sandbox_38/A/2'>alpha helical</scene> regions and five regions containing <scene name='Sandbox_38/B/1'>beta sheets</scene> as displayed in this <scene name='Sandbox_38/Alphab/1'>image</scene>.  Linking these secondary structures, a number of beta turns and a large number of random coils make up the remainder of the polypeptide backbone.  The polypeptide backbone of lysozyme involved in the 3 antiparallel beta sheets display the beta hairpin motif of supersecondary structure. This depiction of lysozyme contains an antiparallel beta-pleated sheet, which contributes greatly to the stability of the molecule by providing the correct alignment of hydrogen bonds. Lysozyme also contains a great deal of random coil, which is seen in the white regions of the molecule.
==Amino Acid Residues==
The amino acids present in the lysozyme polypeptide sequence have a direct influence not only on primary structure, but also on the secondary and tertiary structures, which can be influenced by polarity and charge of the sidechains.  The various amino acid <scene name='Sandbox_38/Aminoi/1'>residues</scene> differ in their properties because of the great variety of side chains present on each amino acid.  Polar and nonpolar (and charged and uncharged) side chains lead to various degrees of hydrophobicity and hydrophilicity, which affects protein folding.  In lysozyme, these <scene name='Sandbox_38/Sc/1'>side chains</scene> are displayed for each amino acid residue.
= Bonding Interactions =


=== Disulfide Bonding in Lysozyme ===
=== Disulfide Bonding in Lysozyme ===
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Lysozyme contains four <scene name='Sandbox_39/Disulfide_bonds/1'>disulfide bonds</scene> involving eight cysteine residues, which are highlighted in yellow on the left. Disulfide bonds are intramolecular forces that stabilize the tertiary structure of many proteins. Disulfide bonds are present in four locations in lysozyme: between Cys 6 and Cys 127, between Cys 30 and Cys 115, between Cys 64 and Cys 80 and between Cys 76 and Cys 94.  
Lysozyme contains four <scene name='Sandbox_39/Disulfide_bonds/1'>disulfide bonds</scene> involving eight cysteine residues, which are highlighted in yellow on the left. Disulfide bonds are intramolecular forces that stabilize the tertiary structure of many proteins. Disulfide bonds are present in four locations in lysozyme: between Cys 6 and Cys 127, between Cys 30 and Cys 115, between Cys 64 and Cys 80 and between Cys 76 and Cys 94.  


=== Secondary Structure ===
=== Hydrogen Bonding ===
 
In all proteins <scene name='Sandbox_39/Hydrogen_bonds/2'>hydrogen bonds</scene> are essential for stability. In this ribbon diagram, the hydrogen bonds can be seen between the secondary structures of lysozyme highlighted in orange. Since the double bonds of the alpha carbons in the main chain of lysozyme cause torsional strain, lysozyme is limited to very specific hydrogen bonding between the amino acid residues. This representation clearly shows how crucial hydrogen bonding is to help maintain the stability of the protein. 
 


Lysozyme contains five <scene name='Sandbox_38/A/2'>alpha helical</scene> regions and five regions containing <scene name='Sandbox_38/B/1'>beta sheets</scene> as displayed in this <scene name='Sandbox_38/Alphab/1'>image</scene>.  Linking these secondary structures, a number of beta turns and a large number of random coils make up the remainder of the polypeptide backbone.  The polypeptide backbone of lysozyme involved in the 3 antiparallel beta sheets display the beta hairpin motif of supersecondary structure. This depiction of lysozyme contains an antiparallel beta-pleated sheet, which contributes greatly to the stability of the molecule by providing the correct alignment of hydrogen bonds. Lysozyme also contains a great deal of random coil, which is seen in the white regions of the molecule.




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===Amino Acid Residues===


The amino acids present in the lysozyme polypeptide sequence have a direct influence not only on primary structure, but also on the secondary and tertiary structures, which can be influenced by polarity and charge of the sidechains.  The various amino acid <scene name='Sandbox_38/Aminoi/1'>residues</scene> differ in their properties because of the great variety of side chains present on each amino acid.  Polar and nonpolar (and charged and uncharged) side chains lead to various degrees of hydrophobicity and hydrophilicity, which affects protein folding.  In lysozyme, these <scene name='Sandbox_38/Sc/1'>side chains</scene> are displayed for each amino acid residue.




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