This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.
Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.
Sandbox108
From Proteopedia
| Line 14: | Line 14: | ||
| - | Glutamine is within uncharged polar < | + | Glutamine is within uncharged polar <insert wiki showing the uncharged polar groups>. Usually, uncharged polar groups are classified as hydrophilic <insert wiki showing the hydrophilic> that is found on the outside of proteins. Also, amino acids with the character of acidic or basic side chains are polar, showing on the outside of molecules <insert wiki showing the polar>. For glutamine, its side chain is uncharged and formed by replacing the hydroxyl of glutamic acid with an amine functional group. [http://en.wikipedia.org/wiki/Glutamine] In the other hand, glutamine has no side chain on non-polar group, however the side chain on non-polar groups of the proteins usually tends to be hydrophobic <insert wiki showing the hydrophobic of cysteine> and to cluster together on the inside.[http://www.bmb.uga.edu/wampler/tutorial/prot3.html] |
| - | Tertiary structure of protein is characterized by the “global” folding of a polypeptide chain. [http://www.stanford.edu/group/pandegroup/folding/education/prstruc.html] Hydrophobic interaction is a major driving force determining the tertiary structure of the proteins. [http://www.stanford.edu/group/pandegroup/folding/education/prstruc.html] The reason why hydrophobic interaction is important is because of relationship with the hydrogen bonding. The peptide backbone is hydrophilic, but in the middle of proteins is mostly in a hydrophobic circumstance. So, in order to reduce the hydrophilicity, to maximize the hydrogen bonding, the α-helix < | + | Tertiary structure of protein is characterized by the “global” folding of a polypeptide chain. [http://www.stanford.edu/group/pandegroup/folding/education/prstruc.html] Hydrophobic interaction is a major driving force determining the tertiary structure of the proteins. [http://www.stanford.edu/group/pandegroup/folding/education/prstruc.html] The reason why hydrophobic interaction is important is because of relationship with the hydrogen bonding. The peptide backbone is hydrophilic, but in the middle of proteins is mostly in a hydrophobic circumstance. So, in order to reduce the hydrophilicity, to maximize the hydrogen bonding, the α-helix <insert wiki showing α-helix> and the β-sheet <insert wiki showing the β-sheet> can break down the C=O and N-H groups in the peptide bonds so that the hydrogen bonds are maximum. [http://www.massey.ac.nz/~wwbioch/Prot/thirds/framset.htm] Also, all polar and hydrophilic side chains interact with H-bonds. Hydrogen bonding <insert wiki showing the H.B> is crucial in stabilizing the tertiary structure. [http://webhost.bridgew.edu/fgorga/proteins/proteins.htm] On the other hand, disulfide bonds <insert wiki showing the disulfide bonds of cysteine> between cysteine residues stabilize the tertiary structure. [http://webhost.bridgew.edu/fgorga/proteins/proteins.htm] |
Revision as of 23:18, 7 December 2008
Glutamine synthetase assignment by UMBC undergraduate students
| |||||||||
| 2qc8, resolution 2.60Å () | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Ligands: | , , , | ||||||||
| Gene: | GLUL, GLNS (Homo sapiens) | ||||||||
| Activity: | Glutamate--ammonia ligase, with EC number 6.3.1.2 | ||||||||
| Related: | 2ojw | ||||||||
| |||||||||
| |||||||||
| Resources: | FirstGlance, OCA, RCSB, PDBsum | ||||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||||
OUTLINE
Tertiary Structure
Different groups of amino acids specify a variety of properties of their side chains. In general, there are five categories; non-polar and aliphatic R groups, aromatic R groups, polar and uncharged R groups, positively charged R groups, and negatively charged R groups.
Glutamine is within uncharged polar <insert wiki showing the uncharged polar groups>. Usually, uncharged polar groups are classified as hydrophilic <insert wiki showing the hydrophilic> that is found on the outside of proteins. Also, amino acids with the character of acidic or basic side chains are polar, showing on the outside of molecules <insert wiki showing the polar>. For glutamine, its side chain is uncharged and formed by replacing the hydroxyl of glutamic acid with an amine functional group. [1] In the other hand, glutamine has no side chain on non-polar group, however the side chain on non-polar groups of the proteins usually tends to be hydrophobic <insert wiki showing the hydrophobic of cysteine> and to cluster together on the inside.[2]
Tertiary structure of protein is characterized by the “global” folding of a polypeptide chain. [3] Hydrophobic interaction is a major driving force determining the tertiary structure of the proteins. [4] The reason why hydrophobic interaction is important is because of relationship with the hydrogen bonding. The peptide backbone is hydrophilic, but in the middle of proteins is mostly in a hydrophobic circumstance. So, in order to reduce the hydrophilicity, to maximize the hydrogen bonding, the α-helix <insert wiki showing α-helix> and the β-sheet <insert wiki showing the β-sheet> can break down the C=O and N-H groups in the peptide bonds so that the hydrogen bonds are maximum. [5] Also, all polar and hydrophilic side chains interact with H-bonds. Hydrogen bonding <insert wiki showing the H.B> is crucial in stabilizing the tertiary structure. [6] On the other hand, disulfide bonds <insert wiki showing the disulfide bonds of cysteine> between cysteine residues stabilize the tertiary structure. [7]
