Sandbox108: Difference between revisions

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Taewang Lee

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 ==Glutamine synthetase assignment by UMBC undergraduate students==
-{{STRUCTURE_2qc8 |  PDB=2qc8  |  SCENE=  }}
+{{STRUCTURE_2gls |  PDB=2gls  |  SCENE=  }}
-<scene name='User:Taewang_Lee/Exercise_2/1'>Exercise 2</scene>
-<scene name='User:Taewang_Lee/Exercise_3/5'>Exercise 3</scene>
-<scene name='Sandbox108/Exercise_4/1'>Exercise 4</scene>
-<scene name='User:Taewang_Lee/Exercise_4/5'>Exercise 4(Practiced)</scene>
-== OUTLINE ==
-''Tertiary Structure''
+''Glutamine synthetase of Salmonella typhimurium''
-Tertiary structure of protein is characterized by the “global” folding of a polypeptide chain [http://www.stanford.edu/group/pandegroup/folding/education/prstruc.html] and has two domains in refined atomic model of glutamine synthetase from Salmonella typhimurium. Hydrophobic interaction is a major driving force determining the most tertiary structure of the proteins. [http://www.stanford.edu/group/pandegroup/folding/education/prstruc.html] Hydrogen bonding <insert wiki showing the H.B> is crucial in stabilizing the tertiary structure as well. [http://webhost.bridgew.edu/fgorga/proteins/proteins.htm] Also, 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]
-Glutamine synthetase from Salmonella has twenty three helix-helix interactions. [http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=2gls&template=protein.html&o=HELIX_INTERACTIONS&l=1&s=1&c=7&chain=A] Hydrophobic/polar <hydrophobic/polar wiki> (put color) and hydrophilic <hydrophilic wiki>(put color) region of glutamine are combined together to fold proteins.
+Tertiary structure of protein is characterized by the “global” folding of a polypeptide chain [http://www.stanford.edu/group/pandegroup/folding/education/prstruc.html] and mostly affected by <scene name='Sandbox108/Hydrophobic/1'>Hydrophobic(purple)</scene>(<scene name='Sandbox108/Polar/1'>polar(blue)</scene>) interaction and hydrogen bonding. In general, hydrophobic interaction is a major driving force determining the most tertiary structure of the proteins. Hydrogen bonding is crucial in stabilizing the tertiary structure as well.[http://webhost.bridgew.edu/fgorga/proteins/proteins.htm] Also, disulfide bonds stabilize the tertiary structure in residues such as cysteine residues.[http://webhost.bridgew.edu/fgorga/proteins/proteins.htm] However, for Salmonella typhimurium it is mostly influenced by the helix-helix interactions between 12-subunits enzymes within two layers.[http://www.stanford.edu/group/pandegroup/folding/education/prstruc.html]
-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]
+Glutamine synthetase from Salmonella typhimurium is the 12-subunits enzyme, and has 23 helix-helix interactions involving helices of chain A with four different types of interactions. [http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=2gls&template=protein.html&o=HELIX_INTERACTIONS&l=1&s=1&c=7&chain=A] The 12-subunits enzyme are arranged in two layers of six, such as <scene name='Sandbox108/Glu_131/1'>Glu-131</scene> which is the one of the protein residues of Salmonella typhimurium; at the interface of pairs of subunits within each layer, six anti-parallel beta strands formed cylindrical active sites.[http://www.ncbi.nlm.nih.gov/pubmed/2572586?dopt=Abstract] Each active site holds two <scene name='Sandbox108/Mn/3'>Mn2+</scene> ions surrounded by some <scene name='Sandbox108/Histidyl_side_chain/1'>histidyl side chains.</scene> [http://www.ncbi.nlm.nih.gov/pubmed/2572586?dopt=Abstract] Also, the protein ligands to Mn2+ 469 are <scene name='Sandbox108/Glu_131/3'>Glu-131</scene>, <scene name='Sandbox108/Glu_212/3'>Glu-212</scene>, and <scene name='Sandbox108/Glu_220/2'>Glu-220</scene>; those to Mn2+ 470 are <scene name='Sandbox108/Glu_129/2'>Glu-129</scene>, <scene name='Sandbox108/His_269/1'>His-269</scene>, and <scene name='Sandbox108/Glu_357/2'>Glu-357</scene>.[http://www.ncbi.nlm.nih.gov/pubmed/2572586?dopt=Abstract] Glutamine from Salmonella typhimurium has 12-subunits of each of them in pairs within two layers. C-terminus end of the polypetide and a helical thong, which inserts into a <scene name='Sandbox108/Hydrophobic/1'>Hydrophobic(purple)</scene> pocket formed by two neighboring subunits on the opposite ring, hold the two layers of subunits tightly.[http://www.ncbi.nlm.nih.gov/pubmed/2572586?dopt=Abstract] Also, <scene name='Sandbox108/Hydrogen_bonded_beta-sheet/1'>hydrogen-bonded beta sheet interactions(black)</scene> can affect the form of tertiary structure, but <scene name='Sandbox108/Hydrophobic/1'>Hydrophobic(purple)</scene> interactions will contribute to the stability of the intersubunit between two layers more efficiently.[http://www.ncbi.nlm.nih.gov/pubmed/2572586?dopt=Abstract] In the other hand, the most effective interaction in glutamine synthetase from Salmonella typhimurium is the helix-helix interactions. The folding of the proteins can be affected by the 12-subunits in the residues. In the case of Salmonella typhimurium the helices of chain A has <scene name='Sandbox108/Charged_region/1'>the charged regions(blue and red)</scene>, while most glutamine has uncharged side chain which formed by replacing the hydroxyl of glutamic acid with an amine functional group. Moreover, glutamine from Salmonella typhimurium has two domains; "beta-grasp domain" and "catalytic domain."[http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=pfam03951][http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=pfam00120] In short, this is N-terminal and C-terminal domain.[http://www.rcsb.org/pdb/explore/explore.do?structureId=2GLS] The N-terminal domain refers to the end of a polypeptide which has a free amine group,[http://en.wikipedia.org/wiki/N-terminal_domain] and the C-terminal end of the polypeptide has a free carboxyl group.[http://en.wikipedia.org/wiki/C-terminus] As a result, glutamine synthetase for Salmonella typhimurium depends mostly on the helix-helix interactions involving helices with four different types of interactions. 12-subunits enzymes are arranged in two layers of six, where the hydrogen-bonded beta sheet and hydrophobic interactions occur.