Sandbox 51: Difference between revisions

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=== ~~Charged~~ Residues ===

===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 structural changes as well as the tertiary structural changes which can be influence 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 can have a very dominant effect on protein folding. In lysozyme, these <scene name='Sandbox_38/Sc/1'>side chains</scene> are displayed for each amino acid residue.

====Polarity====

The nature of the amino acid sidechains in the lysozyme polypeptide sequence leads to regions of varying hydrophobic natures and polarities of the enzyme structure. The presence of certain regions of hydrophilicity and hydrophobicity is a driving force in determining protein structure when folding. The varying polarities of the side chains influence the locations of residues in the enzyme structure. Nonpolar residues appear blue, and Polar residues appear red in the following <scene name='Sandbox_38/Non_polar_blue/1'>polarity</scene> display of lysozyme. Nonpolar residues will display hydrophobic tendencies occurring mostly on the interior of the enzyme while polar residues will increase in abundance on the surface of the protein in order to increase contact with the aqueous solvent satisfying their hydrophilic nature. By observing a spacefilled structural depiction of <scene name='Sandbox_38/Non_polar_blu/1'>lysozyme polarity</scene> with polar molecules colored red and nonpolar molecules colored blue the influence of polarity on nucleotide arrangement and protein folding is evident, with the blue (nonpolar) regions inside the red (polar) regions. The presence of <scene name='Sandbox_38/Water/1'>water molecules</scene> interacting with thee various hydrophilic residues is depicted to further display how polarity affects structure. Water is depicted as yellow, and the polar and nonpolar regions remain their respective color.

====Charge====

Charges of the various regions of the lysozyme structure display a hydrophilic nature and thus also affect the location of that region of polypeptides and overall folding of the protein. Charged regions of the protein will display hydrophilic tendencies and therefore will most often be located on the surface of the lysozyme molecule where they can interact with the aqueous solvent. Non-charged portions will display hydrophobic tendencies and be located on the interior of the molecule. The effect of various <scene name='Sandbox_38/Rb/1'>charges</scene> on protein structure can be visualized with charged molecules represented by red anionic and blue cationic regions, and uncharged regions colored in grey. This depiction of lysozyme uses a spacefill representation of lysozyme to depict <scene name='Sandbox_38/Chargeddd/1'>charges</scene>.

The charged residues, or the most polar portions of the molecule, are seen highlighted to the right in the space-filling model. The blue <scene name='Sandbox_39/Charges/1'>charges</scene> represent cations, and the red charges represent anions. The <scene name='Sandbox_39/Charged_and_polar_residues/1'>charged and polar residues</scene> can also be seen, with the charged residues the same as above and the polar residues in purple. It is important to note that these residues are found almost exclusively on the outside of the protein to increase its interaction of water.

Sandbox 51: Difference between revisions

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@@ Line 55: / Line 55: @@
-=== Charged Residues ===
+===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 structural changes as well as the tertiary structural changes which can be influence 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 can have a very dominant effect on protein folding.  In lysozyme, these <scene name='Sandbox_38/Sc/1'>side chains</scene> are displayed for each amino acid residue.
+====Polarity====
+The nature of the amino acid sidechains in the lysozyme polypeptide sequence leads to regions of varying hydrophobic natures and polarities of the enzyme structure.  The presence of certain regions of hydrophilicity and hydrophobicity is a driving force in determining protein structure when folding.  The varying polarities of the side chains influence the locations of residues in the enzyme structure.  Nonpolar residues appear blue, and Polar residues appear red in the following <scene name='Sandbox_38/Non_polar_blue/1'>polarity</scene> display of lysozyme.  Nonpolar residues will display hydrophobic tendencies occurring mostly on the interior of the enzyme while polar residues will increase in abundance on the surface of the protein in order to increase contact with the aqueous solvent satisfying their hydrophilic nature. By observing a spacefilled structural depiction of <scene name='Sandbox_38/Non_polar_blu/1'>lysozyme polarity</scene> with polar molecules colored red and nonpolar molecules colored blue the influence of polarity on nucleotide arrangement and protein folding is evident, with the blue (nonpolar) regions inside the red (polar) regions.  The presence of <scene name='Sandbox_38/Water/1'>water molecules</scene> interacting with thee various hydrophilic residues is depicted to further display how polarity affects structure.  Water is depicted as yellow, and the polar and nonpolar regions remain their respective color.
+====Charge====
+Charges of the various regions of the lysozyme structure display a hydrophilic nature and thus also affect the location of that region of polypeptides and overall folding of the protein.  Charged regions of the protein will display hydrophilic tendencies and therefore will most often be located on the surface of the lysozyme molecule where they can interact with the aqueous solvent.  Non-charged portions will display hydrophobic tendencies and be located on the interior of the molecule.  The effect of various <scene name='Sandbox_38/Rb/1'>charges</scene> on protein structure can be visualized with charged molecules represented by red anionic and blue cationic regions, and uncharged regions colored in grey. This depiction of lysozyme uses a spacefill representation of lysozyme to depict <scene name='Sandbox_38/Chargeddd/1'>charges</scene>.
-The charged residues, or the most polar portions of the molecule, are seen highlighted to the right in the space-filling model. The blue <scene name='Sandbox_39/Charges/1'>charges</scene> represent cations, and the red charges represent anions. The <scene name='Sandbox_39/Charged_and_polar_residues/1'>charged and polar residues</scene> can also be seen, with the charged residues the same as above and the polar residues in purple. It is important to note that these residues are found almost exclusively on the outside of the protein to increase its interaction of water.