https://proteopedia.org/api.php?action=feedcontributions&feedformat=atom&user=Taewang+LeeProteopedia - User contributions [en]2026-09-25T22:35:46ZUser contributionsMediaWiki 1.43.8https://proteopedia.org/index.php?title=Sandbox108&diff=810760Sandbox1082008-12-20T00:21:25Z<p>Taewang Lee: /* Glutamine synthetase assignment by UMBC undergraduate students */</p>
<hr />
<div>==Glutamine synthetase assignment by UMBC undergraduate students==<br />
{{STRUCTURE_2gls | PDB=2gls | SCENE= }}<br />
<br />
<br />
<br />
''Glutamine synthetase of Salmonella typhimurium''<br />
<br />
<br />
<br />
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] <br />
<br />
<br />
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.</div>Taewang Leehttps://proteopedia.org/index.php?title=Sandbox108&diff=810758Sandbox1082008-12-20T00:19:39Z<p>Taewang Lee: /* Glutamine synthetase assignment by UMBC undergraduate students */</p>
<hr />
<div>==Glutamine synthetase assignment by UMBC undergraduate students==<br />
{{STRUCTURE_2gls | PDB=2gls | SCENE= }}<br />
<br />
<br />
<br />
''Glutamine synthetase of Salmonella typhimurium''<br />
<br />
<br />
<br />
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] <br />
<br />
<br />
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. COOH terminus 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.</div>Taewang Leehttps://proteopedia.org/index.php?title=Sandbox108&diff=810757Sandbox1082008-12-20T00:18:13Z<p>Taewang Lee: /* Glutamine synthetase assignment by UMBC undergraduate students */</p>
<hr />
<div>==Glutamine synthetase assignment by UMBC undergraduate students==<br />
{{STRUCTURE_2gls | PDB=2gls | SCENE= }}<br />
<br />
<br />
<br />
''Glutamine synthetase of Salmonella typhimurium''<br />
<br />
<br />
<br />
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] <br />
<br />
<br />
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. COOH terminus 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] <br />
<br />
<br />
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. The ring type of this glutamine can have more beneficial interactions than others such as glutamine from human.</div>Taewang Leehttps://proteopedia.org/index.php?title=Sandbox108&diff=810749Sandbox1082008-12-19T23:31:45Z<p>Taewang Lee: /* Glutamine synthetase assignment by UMBC undergraduate students */</p>
<hr />
<div>==Glutamine synthetase assignment by UMBC undergraduate students==<br />
{{STRUCTURE_2gls | PDB=2gls | SCENE= }}<br />
<br />
<br />
<br />
''Glutamine synthetase of Salmonella typhimurium''<br />
<br />
<br />
<br />
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] <br />
<br />
<br />
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. COOH terminus 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] <br />
<br />
<br />
As a result, the only helix-helix interactions will be the most powerful sources of being in the glutamine synthetase of Salmonella typhimurium.</div>Taewang Leehttps://proteopedia.org/index.php?title=Sandbox108&diff=810747Sandbox1082008-12-19T23:30:33Z<p>Taewang Lee: /* Glutamine synthetase assignment by UMBC undergraduate students */</p>
<hr />
<div>==Glutamine synthetase assignment by UMBC undergraduate students==<br />
{{STRUCTURE_2gls | PDB=2gls | SCENE= }}<br />
<br />
<br />
<br />
''Glutamine synthetase of Salmonella typhimurium''<br />
<br />
<br />
<br />
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] <br />
<br />
<br />
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. COOH terminus 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"[http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=pfam03951] and "catalytic domain."[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] <br />
<br />
<br />
As a result, the only helix-helix interactions will be the most powerful sources of being in the glutamine synthetase of Salmonella typhimurium.</div>Taewang Leehttps://proteopedia.org/index.php?title=Sandbox108&diff=810744Sandbox1082008-12-19T23:21:54Z<p>Taewang Lee: /* Glutamine synthetase assignment by UMBC undergraduate students */</p>
<hr />
<div>==Glutamine synthetase assignment by UMBC undergraduate students==<br />
{{STRUCTURE_2gls | PDB=2gls | SCENE= }}<br />
<br />
<br />
<br />
''Glutamine synthetase of Salmonella typhimurium''<br />
<br />
<br />
<br />
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] <br />
<br />
<br />
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. COOH terminus 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"[http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=pfam03951] and "catalytic domain."[http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=pfam00120]<br />
<br />
<br />
As a result, the only helix-helix interactions will be the most powerful sources of being in the glutamine synthetase of Salmonella typhimurium.</div>Taewang Leehttps://proteopedia.org/index.php?title=Sandbox108&diff=810742Sandbox1082008-12-19T23:20:28Z<p>Taewang Lee: /* Glutamine synthetase assignment by UMBC undergraduate students */</p>
<hr />
<div>==Glutamine synthetase assignment by UMBC undergraduate students==<br />
{{STRUCTURE_2gls | PDB=2gls | SCENE= }}<br />
<br />
<br />
<br />
''Glutamine synthetase of Salmonella typhimurium''<br />
<br />
<br />
<br />
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] <br />
<br />
<br />
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. COOH terminus 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]<br />
<br />
<br />
As a result, the only helix-helix interactions will be the most powerful sources of being in the glutamine synthetase of Salmonella typhimurium.</div>Taewang Leehttps://proteopedia.org/index.php?title=Sandbox108&diff=810741Sandbox1082008-12-19T23:17:19Z<p>Taewang Lee: /* Glutamine synthetase assignment by UMBC undergraduate students */</p>
<hr />
<div>==Glutamine synthetase assignment by UMBC undergraduate students==<br />
{{STRUCTURE_2gls | PDB=2gls | SCENE= }}<br />
<br />
<br />
<br />
''Glutamine synthetase of Salmonella typhimurium''<br />
<br />
<br />
<br />
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] <br />
<br />
<br />
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. COOH terminus 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. <br />
<br />
<br />
As a result, the only helix-helix interactions will be the most powerful sources of being in the glutamine synthetase of Salmonella typhimurium.</div>Taewang Leehttps://proteopedia.org/index.php?title=Sandbox108&diff=810736Sandbox1082008-12-19T23:00:50Z<p>Taewang Lee: /* Glutamine synthetase assignment by UMBC undergraduate students(Not Complete version) */</p>
<hr />
<div>==Glutamine synthetase assignment by UMBC undergraduate students==<br />
{{STRUCTURE_2gls | PDB=2gls | SCENE= }}<br />
<br />
<br />
<br />
''Glutamine synthetase of Salmonella typhimurium''<br />
<br />
<br />
<br />
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] <br />
<br />
<br />
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. COOH terminus 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. <br />
<br />
<br />
As a result, the only helix-helix interactions will be the most powerful sources of being in the glutamine synthetase of Salmonella typhimurium.</div>Taewang Leehttps://proteopedia.org/index.php?title=Sandbox108&diff=810613Sandbox1082008-12-19T01:11:55Z<p>Taewang Lee: /* Glutamine synthetase assignment by UMBC undergraduate students(Not Complete version) */</p>
<hr />
<div>==Glutamine synthetase assignment by UMBC undergraduate students(Not Complete version)==<br />
{{STRUCTURE_2gls | PDB=2gls | SCENE= }}<br />
<br />
<br />
<br />
''Glutamine synthetase of Salmonella typhimurium''<br />
<br />
<br />
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 between cysteine residues stabilize the tertiary structure. [http://webhost.bridgew.edu/fgorga/proteins/proteins.htm] However, for Salmonella typhimurium it is mainly influenced by the helix-helix interaction between two layers, as well as 12-subunits enzymes.[http://www.stanford.edu/group/pandegroup/folding/education/prstruc.html] <br />
<br />
<br />
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> in 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] In glutamine from Salmonella typhimurium, there are 12-subunits of each of them in pairs within two layers. COOH terminus, 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, even though there is a <scene name='Sandbox108/Hydrogen_bonded_beta-sheet/1'>hydrogen-bonded beta sheet interactions(black)</scene> between layers, <scene name='Sandbox108/Hydrophobic/1'>Hydrophobic(purple)</scene> interactions will contribute to the stability of the intersubunit.[http://www.ncbi.nlm.nih.gov/pubmed/2572586?dopt=Abstract] However, 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, as well as the helix-helix interactions. However, for 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. Also, the only helix-helix interactions will be the most powerful sources of being in the glutamine synthetase of Salmonella typhimurium.</div>Taewang Leehttps://proteopedia.org/index.php?title=Sandbox108&diff=810612Sandbox1082008-12-19T01:10:56Z<p>Taewang Lee: /* Glutamine synthetase assignment by UMBC undergraduate students(Not Complete version) */</p>
<hr />
<div>==Glutamine synthetase assignment by UMBC undergraduate students(Not Complete version)==<br />
{{STRUCTURE_2gls | PDB=2gls | SCENE= }}<br />
<br />
<br />
<br />
''Glutamine synthetase of Salmonella typhimurium''<br />
<br />
<br />
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 between cysteine residues stabilize the tertiary structure. [http://webhost.bridgew.edu/fgorga/proteins/proteins.htm] However, for Salmonella typhimurium it is mainly influenced by the helix-helix interaction between two layers, as well as 12-subunits enzymes.[http://www.stanford.edu/group/pandegroup/folding/education/prstruc.html] <br />
<br />
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> in 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] In glutamine from Salmonella typhimurium, there are 12-subunits of each of them in pairs within two layers. COOH terminus, 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, even though there is a <scene name='Sandbox108/Hydrogen_bonded_beta-sheet/1'>hydrogen-bonded beta sheet interactions(black)</scene> between layers, <scene name='Sandbox108/Hydrophobic/1'>Hydrophobic(purple)</scene> interactions will contribute to the stability of the intersubunit.[http://www.ncbi.nlm.nih.gov/pubmed/2572586?dopt=Abstract] However, 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, as well as the helix-helix interactions. However, for 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. Also, the only helix-helix interactions will be the most powerful sources of being in the glutamine synthetase of Salmonella typhimurium.</div>Taewang Leehttps://proteopedia.org/index.php?title=Sandbox108&diff=810610Sandbox1082008-12-19T00:43:10Z<p>Taewang Lee: /* Glutamine synthetase assignment by UMBC undergraduate students(Not Complete version) */</p>
<hr />
<div>==Glutamine synthetase assignment by UMBC undergraduate students(Not Complete version)==<br />
{{STRUCTURE_2gls | PDB=2gls | SCENE= }}<br />
<br />
<br />
<br />
''Glutamine synthetase of Salmonella typhimurium''<br />
<br />
<br />
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. In general, 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 is crucial in stabilizing the tertiary structure as well. [http://webhost.bridgew.edu/fgorga/proteins/proteins.htm] Also, disulfide bonds between cysteine residues stabilize the tertiary structure. [http://webhost.bridgew.edu/fgorga/proteins/proteins.htm] However, for glutamine synthetase for Salmonella typhimurim, the most important interaction will be the helix-helix interactions. <br />
<br />
<br />
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> in 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] In glutamine from Salmonella typhimurium, there are 12-subunits of each of them in pairs within two layers. COOH terminus, 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, even though there is a <scene name='Sandbox108/Hydrogen_bonded_beta-sheet/1'>hydrogen-bonded beta sheet interactions(black)</scene> between layers, <scene name='Sandbox108/Hydrophobic/1'>Hydrophobic(purple)</scene> interactions will contribute to the stability of the intersubunit.[http://www.ncbi.nlm.nih.gov/pubmed/2572586?dopt=Abstract] However, 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, as well as the helix-helix interactions. In the helix-helix interactions, there are two domains; one has 12 helices, the other has 2 helices. <br />
<br />
<scene name='Sandbox108/Hydrophobic/1'>Hydrophobic(purple)</scene> and <scene name='Sandbox108/Polar/1'>polar(blue)</scene> regions of the protein residues are on the helices of chain A. Also, uncharged polar groups are usually classified as hydrophilic that is found on the outside of proteins, but for glutamine in Salmonella typhimurium 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] Moreover, on the helices of chain A has <scene name='Sandbox108/Charged_region/1'>the charged regions(blue and red)</scene>.</div>Taewang Leehttps://proteopedia.org/index.php?title=Sandbox108&diff=810609Sandbox1082008-12-19T00:34:32Z<p>Taewang Lee: /* Glutamine synthetase assignment by UMBC undergraduate students(Not Complete version) */</p>
<hr />
<div>==Glutamine synthetase assignment by UMBC undergraduate students(Not Complete version)==<br />
{{STRUCTURE_2gls | PDB=2gls | SCENE= }}<br />
<br />
<br />
<br />
''Glutamine synthetase of Salmonella typhimurium''<br />
<br />
<br />
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. In general, 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 is crucial in stabilizing the tertiary structure as well. [http://webhost.bridgew.edu/fgorga/proteins/proteins.htm] Also, disulfide bonds between cysteine residues stabilize the tertiary structure. [http://webhost.bridgew.edu/fgorga/proteins/proteins.htm] However, for glutamine synthetase for Salmonella typhimurim, the most important interaction will be the helix-helix interactions. <br />
<br />
<br />
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> in 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] In glutamine from Salmonella typhimurium, there are 12-subunits of each of them in pairs within two layers. COOH terminus, 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, between layers <br />
<br />
<br />
<br />
Also between layers, there is a <scene name='Sandbox108/Hydrogen_bonded_beta-sheet/1'>hydrogen-bonded beta sheet interaction</scene>, as there is between subunits within a ring, but hydrophobic interactions account for most of the intersubunit stability. The central loop, which extends into the central aqueous channel, is subject to attack by at least five enzymes and is discussed as an enzyme "passive site."}[http://www.ncbi.nlm.nih.gov/pubmed/2572586?dopt=Abstract]<br />
<br />
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, as well as the helix-helix interactions. In the helix-helix interactions, there are two domains; one has 12 helices, the other has 4 helices. <br />
<br />
<scene name='Sandbox108/Hydrophobic/1'>Hydrophobic(purple)</scene> and <scene name='Sandbox108/Polar/1'>polar(blue)</scene> regions of the protein residues are on the helices of chain A. Also, uncharged polar groups are usually classified as hydrophilic that is found on the outside of proteins, but for glutamine in Salmonella typhimurium 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] Moreover, on the helices of chain A has <scene name='Sandbox108/Charged_region/1'>the charged regions(blue and red)</scene>.</div>Taewang Leehttps://proteopedia.org/index.php?title=Sandbox108&diff=810361Sandbox1082008-12-17T23:14:49Z<p>Taewang Lee: /* Glutamine synthetase assignment by UMBC undergraduate students(Not Complete version) */</p>
<hr />
<div>==Glutamine synthetase assignment by UMBC undergraduate students(Not Complete version)==<br />
{{STRUCTURE_2gls | PDB=2gls | SCENE= }}<br />
<br />
<br />
<br />
''Glutamine synthetase of Salmonella typhimurium''<br />
<br />
<br />
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. In general, 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 is crucial in stabilizing the tertiary structure as well. [http://webhost.bridgew.edu/fgorga/proteins/proteins.htm] Also, disulfide bonds between cysteine residues stabilize the tertiary structure. [http://webhost.bridgew.edu/fgorga/proteins/proteins.htm] However, for glutamine synthetase for Salmonella typhimurim, the most important interaction will be the helix-helix interactions. <br />
<br />
<br />
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> in 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] In glutamine from Salmonella typhimurium, there are 12-subunits of each of them in pairs within two layers. COOH terminus, 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, between layers <br />
<br />
<br />
<br />
Also between layers, there is a hydrogen-bonded beta sheet interaction, as there is between subunits within a ring, but hydrophobic interactions account for most of the intersubunit stability. The central loop, which extends into the central aqueous channel, is subject to attack by at least five enzymes and is discussed as an enzyme "passive site."}[http://www.ncbi.nlm.nih.gov/pubmed/2572586?dopt=Abstract]<br />
<br />
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, as well as the helix-helix interactions. In the helix-helix interactions, there are two domains; one has 12 helices, the other has 4 helices. <br />
<br />
<scene name='Sandbox108/Hydrophobic/1'>Hydrophobic(purple)</scene> and <scene name='Sandbox108/Polar/1'>polar(blue)</scene> regions of the protein residues are on the helices of chain A. Also, uncharged polar groups are usually classified as hydrophilic that is found on the outside of proteins, but for glutamine in Salmonella typhimurium 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] Moreover, on the helices of chain A has <scene name='Sandbox108/Charged_region/1'>the charged regions(blue and red)</scene>.</div>Taewang Leehttps://proteopedia.org/index.php?title=Sandbox108&diff=809389Sandbox1082008-12-17T06:10:37Z<p>Taewang Lee: /* Glutamine synthetase assignment by UMBC undergraduate students(Not Complete version) */</p>
<hr />
<div>==Glutamine synthetase assignment by UMBC undergraduate students(Not Complete version)==<br />
{{STRUCTURE_2gls | PDB=2gls | SCENE= }}<br />
<br />
<br />
<br />
''Glutamine synthetase of Salmonella typhimurium''<br />
<br />
<br />
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. In general, 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 is crucial in stabilizing the tertiary structure as well. [http://webhost.bridgew.edu/fgorga/proteins/proteins.htm] Also, disulfide bonds between cysteine residues stabilize the tertiary structure. [http://webhost.bridgew.edu/fgorga/proteins/proteins.htm] However, for glutamine synthetase for Salmonella typhimurim, the most important interaction will be the helix-helix interactions. <br />
<br />
<br />
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> in 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] In glutamine from Salmonella typhimurium, there are 12-subunits of each of them in pairs within two layers. <br />
<br />
The two layers of subunits are held together largely by the apolar COOH terminus, a helical thong, which inserts into a hydrophobic pocket formed by two neighboring subunits on the opposite ring. Also between layers, there is a hydrogen-bonded beta sheet interaction, as there is between subunits within a ring, but hydrophobic interactions account for most of the intersubunit stability. The central loop, which extends into the central aqueous channel, is subject to attack by at least five enzymes and is discussed as an enzyme "passive site."}[http://www.ncbi.nlm.nih.gov/pubmed/2572586?dopt=Abstract]<br />
<br />
Helix-helix interactions are the only interaction that can affect the folding of the proteins in Salmonella typhimurium. <scene name='Sandbox108/Hydrophobic/1'>Hydrophobic(purple)</scene> and <scene name='Sandbox108/Polar/1'>polar(blue)</scene> regions of the protein residues are on the helices of chain A. Also, uncharged polar groups are usually classified as hydrophilic that is found on the outside of proteins, but for glutamine in Salmonella typhimurium 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] Moreover, on the helices of chain A has <scene name='Sandbox108/Charged_region/1'>the charged regions(blue and red)</scene>.</div>Taewang Leehttps://proteopedia.org/index.php?title=Sandbox108&diff=809388Sandbox1082008-12-17T06:04:14Z<p>Taewang Lee: /* Glutamine synthetase assignment by UMBC undergraduate students(Not Complete version) */</p>
<hr />
<div>==Glutamine synthetase assignment by UMBC undergraduate students(Not Complete version)==<br />
{{STRUCTURE_2gls | PDB=2gls | SCENE= }}<br />
<br />
<br />
<br />
''Glutamine synthetase of Salmonella typhimurium''<br />
<br />
<br />
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. In general, 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 is crucial in stabilizing the tertiary structure as well. [http://webhost.bridgew.edu/fgorga/proteins/proteins.htm] Also, disulfide bonds between cysteine residues stabilize the tertiary structure. [http://webhost.bridgew.edu/fgorga/proteins/proteins.htm] However, for glutamine synthetase for Salmonella typhimurim, the most important interaction will be the helix-helix interactions. <br />
<br />
<br />
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> in 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] Each of these residues is the examples of the 12-subunits enzyme facing each other.<br />
<br />
The two layers of subunits are held together largely by the apolar COOH terminus, a helical thong, which inserts into a hydrophobic pocket formed by two neighboring subunits on the opposite ring. Also between layers, there is a hydrogen-bonded beta sheet interaction, as there is between subunits within a ring, but hydrophobic interactions account for most of the intersubunit stability. The central loop, which extends into the central aqueous channel, is subject to attack by at least five enzymes and is discussed as an enzyme "passive site."}[http://www.ncbi.nlm.nih.gov/pubmed/2572586?dopt=Abstract]<br />
<br />
Helix-helix interactions are the only interaction that can affect the folding of the proteins in Salmonella typhimurium. <scene name='Sandbox108/Hydrophobic/1'>Hydrophobic(purple)</scene> and <scene name='Sandbox108/Polar/1'>polar(blue)</scene> regions of the protein residues are on the helices of chain A. Also, uncharged polar groups are usually classified as hydrophilic that is found on the outside of proteins, but for glutamine in Salmonella typhimurium 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] Moreover, on the helices of chain A has <scene name='Sandbox108/Charged_region/1'>the charged regions(blue and red)</scene>.</div>Taewang Leehttps://proteopedia.org/index.php?title=Sandbox108&diff=809387Sandbox1082008-12-17T05:57:54Z<p>Taewang Lee: /* Glutamine synthetase assignment by UMBC undergraduate students(Not Complete version) */</p>
<hr />
<div>==Glutamine synthetase assignment by UMBC undergraduate students(Not Complete version)==<br />
{{STRUCTURE_2gls | PDB=2gls | SCENE= }}<br />
<br />
<br />
<br />
''Glutamine synthetase of Salmonella typhimurium''<br />
<br />
<br />
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. In general, 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 is crucial in stabilizing the tertiary structure as well. [http://webhost.bridgew.edu/fgorga/proteins/proteins.htm] Also, disulfide bonds between cysteine residues stabilize the tertiary structure. [http://webhost.bridgew.edu/fgorga/proteins/proteins.htm] However, for glutamine synthetase for Salmonella typhimurim, the most important interaction will be the helix-helix interactions. <br />
<br />
<br />
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> in 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] <br />
<br />
The two layers of subunits are held together largely by the apolar COOH terminus, a helical thong, which inserts into a hydrophobic pocket formed by two neighboring subunits on the opposite ring. Also between layers, there is a hydrogen-bonded beta sheet interaction, as there is between subunits within a ring, but hydrophobic interactions account for most of the intersubunit stability. The central loop, which extends into the central aqueous channel, is subject to attack by at least five enzymes and is discussed as an enzyme "passive site."}[http://www.ncbi.nlm.nih.gov/pubmed/2572586?dopt=Abstract]<br />
<br />
Helix-helix interactions are the only interaction that can affect the folding of the proteins in Salmonella typhimurium. <scene name='Sandbox108/Hydrophobic/1'>Hydrophobic(purple)</scene> and <scene name='Sandbox108/Polar/1'>polar(blue)</scene> regions of the protein residues are on the helices of chain A. Also, uncharged polar groups are usually classified as hydrophilic that is found on the outside of proteins, but for glutamine in Salmonella typhimurium 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] Moreover, on the helices of chain A has <scene name='Sandbox108/Charged_region/1'>the charged regions(blue and red)</scene>.</div>Taewang Leehttps://proteopedia.org/index.php?title=Sandbox108&diff=809386Sandbox1082008-12-17T05:40:11Z<p>Taewang Lee: /* Glutamine synthetase assignment by UMBC undergraduate students(Not Complete version) */</p>
<hr />
<div>==Glutamine synthetase assignment by UMBC undergraduate students(Not Complete version)==<br />
{{STRUCTURE_2gls | PDB=2gls | SCENE= }}<br />
<br />
<br />
<br />
''Glutamine synthetase of Salmonella typhimurium''<br />
<br />
<br />
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. In general, 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 is crucial in stabilizing the tertiary structure as well. [http://webhost.bridgew.edu/fgorga/proteins/proteins.htm] Also, disulfide bonds between cysteine residues stabilize the tertiary structure. [http://webhost.bridgew.edu/fgorga/proteins/proteins.htm] However, for glutamine synthetase for Salmonella typhimurim, the most important interaction will be the helix-helix interactions. <br />
<br />
<br />
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>; 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, <br />
<br />
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_129/1'>Glu-129</scene>, <scene name='Sandbox108/His269/1'>His-269</scene>, and <scene name='Sandbox108/Glu_357/1'>Glu-357</scene>. The two layers of subunits are held together largely by the apolar COOH terminus, a helical thong, which inserts into a hydrophobic pocket formed by two neighboring subunits on the opposite ring. Also between layers, there is a hydrogen-bonded beta sheet interaction, as there is between subunits within a ring, but hydrophobic interactions account for most of the intersubunit stability. The central loop, which extends into the central aqueous channel, is subject to attack by at least five enzymes and is discussed as an enzyme "passive site."}[http://www.ncbi.nlm.nih.gov/pubmed/2572586?dopt=Abstract]<br />
<br />
Helix-helix interactions are the only interaction that can affect the folding of the proteins in Salmonella typhimurium. <scene name='Sandbox108/Hydrophobic/1'>Hydrophobic(purple)</scene> and <scene name='Sandbox108/Polar/1'>polar(blue)</scene> regions of the protein residues are on the helices of chain A. Also, uncharged polar groups are usually classified as hydrophilic that is found on the outside of proteins, but for glutamine in Salmonella typhimurium 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] Moreover, on the helices of chain A has <scene name='Sandbox108/Charged_region/1'>the charged regions(blue and red)</scene>.</div>Taewang Leehttps://proteopedia.org/index.php?title=Sandbox108&diff=809385Sandbox1082008-12-17T05:13:49Z<p>Taewang Lee: /* Glutamine synthetase assignment by UMBC undergraduate students(Not Complete version) */</p>
<hr />
<div>==Glutamine synthetase assignment by UMBC undergraduate students(Not Complete version)==<br />
{{STRUCTURE_2gls | PDB=2gls | SCENE= }}<br />
<br />
<br />
<br />
''Glutamine synthetase of Salmonella typhimurium''<br />
<br />
<br />
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. In general, 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 is crucial in stabilizing the tertiary structure as well. [http://webhost.bridgew.edu/fgorga/proteins/proteins.htm] Also, disulfide bonds between cysteine residues stabilize the tertiary structure. [http://webhost.bridgew.edu/fgorga/proteins/proteins.htm] However, for glutamine synthetase for Salmonella typhimurim, the most important interaction will be the helix-helix interactions. <br />
<br />
<br />
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>; 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, <br />
<br />
The protein ligands to Mn2+ 469 are <scene name='Sandbox108/Glu_131/1'>Glu-131</scene>, <scene name='Sandbox108/Glu_212/1'>Glu-212</scene>, and <scene name='Sandbox108/Glu_220/1'>Glu-220</scene>; those to Mn2+ 470 are <scene name='Sandbox108/Glu_129/1'>Glu-129</scene>, <scene name='Sandbox108/His269/1'>His-269</scene>, and <scene name='Sandbox108/Glu_357/1'>Glu-357</scene>. The two layers of subunits are held together largely by the apolar COOH terminus, a helical thong, which inserts into a hydrophobic pocket formed by two neighboring subunits on the opposite ring. Also between layers, there is a hydrogen-bonded beta sheet interaction, as there is between subunits within a ring, but hydrophobic interactions account for most of the intersubunit stability. The central loop, which extends into the central aqueous channel, is subject to attack by at least five enzymes and is discussed as an enzyme "passive site."}[http://www.ncbi.nlm.nih.gov/pubmed/2572586?dopt=Abstract]<br />
<br />
Helix-helix interactions are the only interaction that can affect the folding of the proteins in Salmonella typhimurium. <scene name='Sandbox108/Hydrophobic/1'>Hydrophobic(purple)</scene> and <scene name='Sandbox108/Polar/1'>polar(blue)</scene> regions of the protein residues are on the helices of chain A. Also, uncharged polar groups are usually classified as hydrophilic that is found on the outside of proteins, but for glutamine in Salmonella typhimurium 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] Moreover, on the helices of chain A has <scene name='Sandbox108/Charged_region/1'>the charged regions(blue and red)</scene>.</div>Taewang Leehttps://proteopedia.org/index.php?title=Sandbox108&diff=809384Sandbox1082008-12-17T05:08:48Z<p>Taewang Lee: /* Glutamine synthetase assignment by UMBC undergraduate students(Not Complete version) */</p>
<hr />
<div>==Glutamine synthetase assignment by UMBC undergraduate students(Not Complete version)==<br />
{{STRUCTURE_2gls | PDB=2gls | SCENE= }}<br />
<br />
<br />
<br />
''Glutamine synthetase of Salmonella typhimurium''<br />
<br />
<br />
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. In general, 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 is crucial in stabilizing the tertiary structure as well. [http://webhost.bridgew.edu/fgorga/proteins/proteins.htm] Also, disulfide bonds between cysteine residues stabilize the tertiary structure. [http://webhost.bridgew.edu/fgorga/proteins/proteins.htm] However, for glutamine synthetase for Salmonella typhimurim, the most important interaction will be the helix-helix interactions. <br />
<br />
<br />
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>; 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> <br />
<br />
with each ion having as ligands three protein side chains and two water molecules (one water shared by both metals), as well as a histidyl side chain just beyond liganding distance. The protein ligands to Mn2+ 469 are <scene name='Sandbox108/Glu_131/1'>Glu-131</scene>, <scene name='Sandbox108/Glu_212/1'>Glu-212</scene>, and <scene name='Sandbox108/Glu_220/1'>Glu-220</scene>; those to Mn2+ 470 are <scene name='Sandbox108/Glu_129/1'>Glu-129</scene>, <scene name='Sandbox108/His269/1'>His-269</scene>, and <scene name='Sandbox108/Glu_357/1'>Glu-357</scene>. The two layers of subunits are held together largely by the apolar COOH terminus, a helical thong, which inserts into a hydrophobic pocket formed by two neighboring subunits on the opposite ring. Also between layers, there is a hydrogen-bonded beta sheet interaction, as there is between subunits within a ring, but hydrophobic interactions account for most of the intersubunit stability. The central loop, which extends into the central aqueous channel, is subject to attack by at least five enzymes and is discussed as an enzyme "passive site."}[http://www.ncbi.nlm.nih.gov/pubmed/2572586?dopt=Abstract]<br />
<br />
Helix-helix interactions are the only interaction that can affect the folding of the proteins in Salmonella typhimurium. <scene name='Sandbox108/Hydrophobic/1'>Hydrophobic(purple)</scene> and <scene name='Sandbox108/Polar/1'>polar(blue)</scene> regions of the protein residues are on the helices of chain A. Also, uncharged polar groups are usually classified as hydrophilic that is found on the outside of proteins, but for glutamine in Salmonella typhimurium 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] Moreover, on the helices of chain A has <scene name='Sandbox108/Charged_region/1'>the charged regions(blue and red)</scene>.</div>Taewang Leehttps://proteopedia.org/index.php?title=Sandbox108&diff=809383Sandbox1082008-12-17T05:03:37Z<p>Taewang Lee: /* Glutamine synthetase assignment by UMBC undergraduate students(Not Complete version) */</p>
<hr />
<div>==Glutamine synthetase assignment by UMBC undergraduate students(Not Complete version)==<br />
{{STRUCTURE_2gls | PDB=2gls | SCENE= }}<br />
<br />
<br />
<br />
''Glutamine synthetase of Salmonella typhimurium''<br />
<br />
<br />
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. In general, 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 is crucial in stabilizing the tertiary structure as well. [http://webhost.bridgew.edu/fgorga/proteins/proteins.htm] Also, disulfide bonds between cysteine residues stabilize the tertiary structure. [http://webhost.bridgew.edu/fgorga/proteins/proteins.htm] However, for glutamine synthetase for Salmonella typhimurim, the most important interaction will be the helix-helix interactions. <br />
<br />
<br />
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>; 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 histidyl side chains. <br />
<br />
with each ion having as ligands three protein side chains and two water molecules (one water shared by both metals), as well as a histidyl side chain just beyond liganding distance. The protein ligands to Mn2+ 469 are <scene name='Sandbox108/Glu_131/1'>Glu-131</scene>, <scene name='Sandbox108/Glu_212/1'>Glu-212</scene>, and <scene name='Sandbox108/Glu_220/1'>Glu-220</scene>; those to Mn2+ 470 are <scene name='Sandbox108/Glu_129/1'>Glu-129</scene>, <scene name='Sandbox108/His269/1'>His-269</scene>, and <scene name='Sandbox108/Glu_357/1'>Glu-357</scene>. The two layers of subunits are held together largely by the apolar COOH terminus, a helical thong, which inserts into a hydrophobic pocket formed by two neighboring subunits on the opposite ring. Also between layers, there is a hydrogen-bonded beta sheet interaction, as there is between subunits within a ring, but hydrophobic interactions account for most of the intersubunit stability. The central loop, which extends into the central aqueous channel, is subject to attack by at least five enzymes and is discussed as an enzyme "passive site."}[http://www.ncbi.nlm.nih.gov/pubmed/2572586?dopt=Abstract]<br />
<br />
Helix-helix interactions are the only interaction that can affect the folding of the proteins in Salmonella typhimurium. <scene name='Sandbox108/Hydrophobic/1'>Hydrophobic(purple)</scene> and <scene name='Sandbox108/Polar/1'>polar(blue)</scene> regions of the protein residues are on the helices of chain A. Also, uncharged polar groups are usually classified as hydrophilic that is found on the outside of proteins, but for glutamine in Salmonella typhimurium 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] Moreover, on the helices of chain A has <scene name='Sandbox108/Charged_region/1'>the charged regions(blue and red)</scene>.</div>Taewang Leehttps://proteopedia.org/index.php?title=Sandbox108&diff=809382Sandbox1082008-12-17T04:52:20Z<p>Taewang Lee: /* Glutamine synthetase assignment by UMBC undergraduate students(Not Complete version) */</p>
<hr />
<div>==Glutamine synthetase assignment by UMBC undergraduate students(Not Complete version)==<br />
{{STRUCTURE_2gls | PDB=2gls | SCENE= }}<br />
<br />
<br />
<br />
''Glutamine synthetase of Salmonella typhimurium''<br />
<br />
<br />
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. In general, 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 is crucial in stabilizing the tertiary structure as well. [http://webhost.bridgew.edu/fgorga/proteins/proteins.htm] Also, disulfide bonds between cysteine residues stabilize the tertiary structure. [http://webhost.bridgew.edu/fgorga/proteins/proteins.htm] However, for glutamine synthetase for Salmonella typhimurim, the most important interaction will be the helix-helix interactions. <br />
<br />
<br />
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>; 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 two <scene name='Sandbox108/Mn/3'>Mn2+</scene> ions, <br />
<br />
with each ion having as ligands three protein side chains and two water molecules (one water shared by both metals), as well as a histidyl side chain just beyond liganding distance. The protein ligands to Mn2+ 469 are <scene name='Sandbox108/Glu_131/1'>Glu-131</scene>, <scene name='Sandbox108/Glu_212/1'>Glu-212</scene>, and <scene name='Sandbox108/Glu_220/1'>Glu-220</scene>; those to Mn2+ 470 are <scene name='Sandbox108/Glu_129/1'>Glu-129</scene>, <scene name='Sandbox108/His269/1'>His-269</scene>, and <scene name='Sandbox108/Glu_357/1'>Glu-357</scene>. The two layers of subunits are held together largely by the apolar COOH terminus, a helical thong, which inserts into a hydrophobic pocket formed by two neighboring subunits on the opposite ring. Also between layers, there is a hydrogen-bonded beta sheet interaction, as there is between subunits within a ring, but hydrophobic interactions account for most of the intersubunit stability. The central loop, which extends into the central aqueous channel, is subject to attack by at least five enzymes and is discussed as an enzyme "passive site."}[http://www.ncbi.nlm.nih.gov/pubmed/2572586?dopt=Abstract]<br />
<br />
Helix-helix interactions are the only interaction that can affect the folding of the proteins in Salmonella typhimurium. <scene name='Sandbox108/Hydrophobic/1'>Hydrophobic(purple)</scene> and <scene name='Sandbox108/Polar/1'>polar(blue)</scene> regions of the protein residues are on the helices of chain A. Also, uncharged polar groups are usually classified as hydrophilic that is found on the outside of proteins, but for glutamine in Salmonella typhimurium 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] Moreover, on the helices of chain A has <scene name='Sandbox108/Charged_region/1'>the charged regions(blue and red)</scene>.</div>Taewang Leehttps://proteopedia.org/index.php?title=Sandbox108&diff=809381Sandbox1082008-12-17T04:50:41Z<p>Taewang Lee: /* Glutamine synthetase assignment by UMBC undergraduate students(Not Complete version) */</p>
<hr />
<div>==Glutamine synthetase assignment by UMBC undergraduate students(Not Complete version)==<br />
{{STRUCTURE_2gls | PDB=2gls | SCENE= }}<br />
<br />
<br />
<br />
''Glutamine synthetase of Salmonella typhimurium''<br />
<br />
<br />
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. In general, 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 is crucial in stabilizing the tertiary structure as well. [http://webhost.bridgew.edu/fgorga/proteins/proteins.htm] Also, disulfide bonds between cysteine residues stabilize the tertiary structure. [http://webhost.bridgew.edu/fgorga/proteins/proteins.htm] However, for glutamine synthetase for Salmonella typhimurim, the most important interaction will be the helix-helix interactions. <br />
<br />
<br />
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>; at the interface of pairs of subunits within each layer, six anti-parallel beta strands <beta strands> formed cylindrical active sites.[http://www.ncbi.nlm.nih.gov/pubmed/2572586?dopt=Abstract] <br />
<br />
Each active site cylinder holds two <scene name='Sandbox108/Mn/3'>Mn2+</scene> ions, with each ion having as ligands three protein side chains and two water molecules (one water shared by both metals), as well as a histidyl side chain just beyond liganding distance. The protein ligands to Mn2+ 469 are <scene name='Sandbox108/Glu_131/1'>Glu-131</scene>, <scene name='Sandbox108/Glu_212/1'>Glu-212</scene>, and <scene name='Sandbox108/Glu_220/1'>Glu-220</scene>; those to Mn2+ 470 are <scene name='Sandbox108/Glu_129/1'>Glu-129</scene>, <scene name='Sandbox108/His269/1'>His-269</scene>, and <scene name='Sandbox108/Glu_357/1'>Glu-357</scene>. The two layers of subunits are held together largely by the apolar COOH terminus, a helical thong, which inserts into a hydrophobic pocket formed by two neighboring subunits on the opposite ring. Also between layers, there is a hydrogen-bonded beta sheet interaction, as there is between subunits within a ring, but hydrophobic interactions account for most of the intersubunit stability. The central loop, which extends into the central aqueous channel, is subject to attack by at least five enzymes and is discussed as an enzyme "passive site."}[http://www.ncbi.nlm.nih.gov/pubmed/2572586?dopt=Abstract]<br />
<br />
Helix-helix interactions are the only interaction that can affect the folding of the proteins in Salmonella typhimurium. <scene name='Sandbox108/Hydrophobic/1'>Hydrophobic(purple)</scene> and <scene name='Sandbox108/Polar/1'>polar(blue)</scene> regions of the protein residues are on the helices of chain A. Also, uncharged polar groups are usually classified as hydrophilic that is found on the outside of proteins, but for glutamine in Salmonella typhimurium 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] Moreover, on the helices of chain A has <scene name='Sandbox108/Charged_region/1'>the charged regions(blue and red)</scene>.</div>Taewang Leehttps://proteopedia.org/index.php?title=Sandbox108&diff=809380Sandbox1082008-12-17T04:40:17Z<p>Taewang Lee: /* Glutamine synthetase assignment by UMBC undergraduate students(Not Complete version) */</p>
<hr />
<div>==Glutamine synthetase assignment by UMBC undergraduate students(Not Complete version)==<br />
{{STRUCTURE_2gls | PDB=2gls | SCENE= }}<br />
<br />
<br />
<br />
''Glutamine synthetase of Salmonella typhimurium''<br />
<br />
<br />
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. In general, 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 is crucial in stabilizing the tertiary structure as well. [http://webhost.bridgew.edu/fgorga/proteins/proteins.htm] Also, disulfide bonds between cysteine residues stabilize the tertiary structure. [http://webhost.bridgew.edu/fgorga/proteins/proteins.htm] However, for glutamine synthetase for Salmonella typhimurim, the most important interaction will be the helix-helix interactions. <br />
<br />
<br />
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>; at the interface of pairs of subunits within each layer, six anti-parallel beta strands <beta strands> formed cylindrical active sites.[http://www.ncbi.nlm.nih.gov/pubmed/2572586?dopt=Abstract] <br />
<br />
Each active site cylinder holds two <scene name='Sandbox108/Mn/2'>Mn2+</scene> ions, with each ion having as ligands three protein side chains and two water molecules (one water shared by both metals), as well as a histidyl side chain just beyond liganding distance. The protein ligands to Mn2+ 469 are <scene name='Sandbox108/Glu_131/1'>Glu-131</scene>, <scene name='Sandbox108/Glu_212/1'>Glu-212</scene>, and <scene name='Sandbox108/Glu_220/1'>Glu-220</scene>; those to Mn2+ 470 are <scene name='Sandbox108/Glu_129/1'>Glu-129</scene>, <scene name='Sandbox108/His269/1'>His-269</scene>, and <scene name='Sandbox108/Glu_357/1'>Glu-357</scene>. The two layers of subunits are held together largely by the apolar COOH terminus, a helical thong, which inserts into a hydrophobic pocket formed by two neighboring subunits on the opposite ring. Also between layers, there is a hydrogen-bonded beta sheet interaction, as there is between subunits within a ring, but hydrophobic interactions account for most of the intersubunit stability. The central loop, which extends into the central aqueous channel, is subject to attack by at least five enzymes and is discussed as an enzyme "passive site."}[http://www.ncbi.nlm.nih.gov/pubmed/2572586?dopt=Abstract]<br />
<br />
Helix-helix interactions are the only interaction that can affect the folding of the proteins in Salmonella typhimurium. <scene name='Sandbox108/Hydrophobic/1'>Hydrophobic(purple)</scene> and <scene name='Sandbox108/Polar/1'>polar(blue)</scene> regions of the protein residues are on the helices of chain A. Also, uncharged polar groups are usually classified as hydrophilic that is found on the outside of proteins, but for glutamine in Salmonella typhimurium 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] Moreover, on the helices of chain A has <scene name='Sandbox108/Charged_region/1'>the charged regions(blue and red)</scene>.</div>Taewang Leehttps://proteopedia.org/index.php?title=Sandbox108&diff=809379Sandbox1082008-12-17T04:38:35Z<p>Taewang Lee: /* Glutamine synthetase assignment by UMBC undergraduate students(Not Complete version) */</p>
<hr />
<div>==Glutamine synthetase assignment by UMBC undergraduate students(Not Complete version)==<br />
{{STRUCTURE_2gls | PDB=2gls | SCENE= }}<br />
<br />
<br />
<br />
''Glutamine synthetase of Salmonella typhimurium''<br />
<br />
<br />
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. In general, 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 is crucial in stabilizing the tertiary structure as well. [http://webhost.bridgew.edu/fgorga/proteins/proteins.htm] Also, disulfide bonds between cysteine residues stabilize the tertiary structure. [http://webhost.bridgew.edu/fgorga/proteins/proteins.htm] However, for glutamine synthetase for Salmonella typhimurim, the most important interaction will be the helix-helix interactions. <br />
<br />
<br />
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>; at the interface of pairs of subunits within each layer, six anti-parallel beta strands <beta strands> formed cylindrical active sites.[http://www.ncbi.nlm.nih.gov/pubmed/2572586?dopt=Abstract] <br />
<br />
Each active site cylinder holds two Mn2+ ions, with each ion having as ligands three protein side chains and two water molecules (one water shared by both metals), as well as a histidyl side chain just beyond liganding distance. The protein ligands to <scene name='Sandbox108/Mn/2'>Mn2+</scene> 469 are <scene name='Sandbox108/Glu_131/1'>Glu-131</scene>, <scene name='Sandbox108/Glu_212/1'>Glu-212</scene>, and <scene name='Sandbox108/Glu_220/1'>Glu-220</scene>; those to <scene name='Sandbox108/Mn/2'>Mn2+</scene> 470 are <scene name='Sandbox108/Glu_129/1'>Glu-129</scene>, <scene name='Sandbox108/His269/1'>His-269</scene>, and <scene name='Sandbox108/Glu_357/1'>Glu-357</scene>. The two layers of subunits are held together largely by the apolar COOH terminus, a helical thong, which inserts into a hydrophobic pocket formed by two neighboring subunits on the opposite ring. Also between layers, there is a hydrogen-bonded beta sheet interaction, as there is between subunits within a ring, but hydrophobic interactions account for most of the intersubunit stability. The central loop, which extends into the central aqueous channel, is subject to attack by at least five enzymes and is discussed as an enzyme "passive site."}[http://www.ncbi.nlm.nih.gov/pubmed/2572586?dopt=Abstract]<br />
<br />
Helix-helix interactions are the only interaction that can affect the folding of the proteins in Salmonella typhimurium. <scene name='Sandbox108/Hydrophobic/1'>Hydrophobic(purple)</scene> and <scene name='Sandbox108/Polar/1'>polar(blue)</scene> regions of the protein residues are on the helices of chain A. Also, uncharged polar groups are usually classified as hydrophilic that is found on the outside of proteins, but for glutamine in Salmonella typhimurium 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] Moreover, on the helices of chain A has <scene name='Sandbox108/Charged_region/1'>the charged regions(blue and red)</scene>.</div>Taewang Leehttps://proteopedia.org/index.php?title=Sandbox108&diff=809373Sandbox1082008-12-17T04:16:25Z<p>Taewang Lee: /* Glutamine synthetase assignment by UMBC undergraduate students(Not Complete version) */</p>
<hr />
<div>==Glutamine synthetase assignment by UMBC undergraduate students(Not Complete version)==<br />
{{STRUCTURE_2gls | PDB=2gls | SCENE= }}<br />
<br />
<br />
<br />
''Glutamine synthetase of Salmonella typhimurium''<br />
<br />
<br />
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. In general, 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 is crucial in stabilizing the tertiary structure as well. [http://webhost.bridgew.edu/fgorga/proteins/proteins.htm] Also, disulfide bonds between cysteine residues stabilize the tertiary structure. [http://webhost.bridgew.edu/fgorga/proteins/proteins.htm] However, for glutamine synthetase for Salmonella typhimurim, the most important interaction will be the helix-helix interactions. <br />
<br />
<br />
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>; at the interface of pairs of subunits within each layer, six anti-parallel beta strands <beta strands> formed cylindrical active sites.[http://www.ncbi.nlm.nih.gov/pubmed/2572586?dopt=Abstract] <br />
<br />
Each active site cylinder holds two Mn2+ ions, with each ion having as ligands three protein side chains and two water molecules (one water shared by both metals), as well as a histidyl side chain just beyond liganding distance. The protein ligands to Mn2+ 469 are <scene name='Sandbox108/Glu_131/1'>Glu-131</scene>, <scene name='Sandbox108/Glu_212/1'>Glu-212</scene>, and <scene name='Sandbox108/Glu_220/1'>Glu-220</scene>; those to Mn2+ 470 are <scene name='Sandbox108/Glu_129/1'>Glu-129</scene>, <scene name='Sandbox108/His269/1'>His-269</scene>, and <scene name='Sandbox108/Glu_357/1'>Glu-357</scene>. The two layers of subunits are held together largely by the apolar COOH terminus, a helical thong, which inserts into a hydrophobic pocket formed by two neighboring subunits on the opposite ring. Also between layers, there is a hydrogen-bonded beta sheet interaction, as there is between subunits within a ring, but hydrophobic interactions account for most of the intersubunit stability. The central loop, which extends into the central aqueous channel, is subject to attack by at least five enzymes and is discussed as an enzyme "passive site."}[http://www.ncbi.nlm.nih.gov/pubmed/2572586?dopt=Abstract]<br />
<br />
Helix-helix interactions are the only interaction that can affect the folding of the proteins in Salmonella typhimurium. <scene name='Sandbox108/Hydrophobic/1'>Hydrophobic(purple)</scene> and <scene name='Sandbox108/Polar/1'>polar(blue)</scene> regions of the protein residues are on the helices of chain A. Also, uncharged polar groups are usually classified as hydrophilic that is found on the outside of proteins, but for glutamine in Salmonella typhimurium 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] Moreover, on the helices of chain A has <scene name='Sandbox108/Charged_region/1'>the charged regions(blue and red)</scene>.</div>Taewang Leehttps://proteopedia.org/index.php?title=Sandbox108&diff=809370Sandbox1082008-12-17T01:39:35Z<p>Taewang Lee: /* Glutamine synthetase assignment by UMBC undergraduate students */</p>
<hr />
<div>==Glutamine synthetase assignment by UMBC undergraduate students(Not Complete version)==<br />
{{STRUCTURE_2gls | PDB=2gls | SCENE= }}<br />
<br />
<br />
<br />
''Glutamine synthetase of Salmonella typhimurium''<br />
<br />
<br />
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 is crucial in stabilizing the tertiary structure as well. [http://webhost.bridgew.edu/fgorga/proteins/proteins.htm] Also, disulfide bonds between cysteine residues stabilize the tertiary structure. [http://webhost.bridgew.edu/fgorga/proteins/proteins.htm] However, for glutamine synthetase for Salmonella, the most important interaction will be the helix-helix interactions. <br />
<br />
<br />
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; at the interface of pairs of subunits within each layer, cylindrical active sites are formed by six anti-parallel beta strands contributed by one subunit and two strands by the neighboring subunit. <br />
<br />
This interpretation of the electron density map has now been supported by comparison with glutamine synthetase from Escherichia coli by the Fourier difference method. Each active site cylinder holds two Mn2+ ions, with each ion having as ligands three protein side chains and two water molecules (one water shared by both metals), as well as a histidyl side chain just beyond liganding distance. The protein ligands to Mn2+ 469 are <scene name='Sandbox108/Glu_131/1'>Glu-131</scene>, <scene name='Sandbox108/Glu_212/1'>Glu-212</scene>, and <scene name='Sandbox108/Glu_220/1'>Glu-220</scene>; those to Mn2+ 470 are <scene name='Sandbox108/Glu_129/1'>Glu-129</scene>, <scene name='Sandbox108/His269/1'>His-269</scene>, and <scene name='Sandbox108/Glu_357/1'>Glu-357</scene>. The two layers of subunits are held together largely by the apolar COOH terminus, a helical thong, which inserts into a hydrophobic pocket formed by two neighboring subunits on the opposite ring. Also between layers, there is a hydrogen-bonded beta sheet interaction, as there is between subunits within a ring, but hydrophobic interactions account for most of the intersubunit stability. The central loop, which extends into the central aqueous channel, is subject to attack by at least five enzymes and is discussed as an enzyme "passive site."}[http://www.ncbi.nlm.nih.gov/pubmed/2572586?dopt=Abstract]<br />
<br />
Helix-helix interactions are the only interaction that can affect the folding of the proteins in Salmonella typhimurium. <scene name='Sandbox108/Hydrophobic/1'>Hydrophobic(purple)</scene> and <scene name='Sandbox108/Polar/1'>polar(blue)</scene> regions of the protein residues are on the helices of chain A. Also, uncharged polar groups are usually classified as hydrophilic that is found on the outside of proteins, but for glutamine in Salmonella typhimurium 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] Moreover, on the helices of chain A has <scene name='Sandbox108/Charged_region/1'>the charged regions(blue and red)</scene>.</div>Taewang Leehttps://proteopedia.org/index.php?title=Sandbox108&diff=809369Sandbox1082008-12-17T01:39:05Z<p>Taewang Lee: </p>
<hr />
<div>==Glutamine synthetase assignment by UMBC undergraduate students==<br />
{{STRUCTURE_2gls | PDB=2gls | SCENE= }}<br />
<br />
<br />
<br />
''Glutamine synthetase of Salmonella typhimurium''(not complete)<br />
<br />
<br />
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 is crucial in stabilizing the tertiary structure as well. [http://webhost.bridgew.edu/fgorga/proteins/proteins.htm] Also, disulfide bonds between cysteine residues stabilize the tertiary structure. [http://webhost.bridgew.edu/fgorga/proteins/proteins.htm] However, for glutamine synthetase for Salmonella, the most important interaction will be the helix-helix interactions. <br />
<br />
<br />
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; at the interface of pairs of subunits within each layer, cylindrical active sites are formed by six anti-parallel beta strands contributed by one subunit and two strands by the neighboring subunit. <br />
<br />
This interpretation of the electron density map has now been supported by comparison with glutamine synthetase from Escherichia coli by the Fourier difference method. Each active site cylinder holds two Mn2+ ions, with each ion having as ligands three protein side chains and two water molecules (one water shared by both metals), as well as a histidyl side chain just beyond liganding distance. The protein ligands to Mn2+ 469 are <scene name='Sandbox108/Glu_131/1'>Glu-131</scene>, <scene name='Sandbox108/Glu_212/1'>Glu-212</scene>, and <scene name='Sandbox108/Glu_220/1'>Glu-220</scene>; those to Mn2+ 470 are <scene name='Sandbox108/Glu_129/1'>Glu-129</scene>, <scene name='Sandbox108/His269/1'>His-269</scene>, and <scene name='Sandbox108/Glu_357/1'>Glu-357</scene>. The two layers of subunits are held together largely by the apolar COOH terminus, a helical thong, which inserts into a hydrophobic pocket formed by two neighboring subunits on the opposite ring. Also between layers, there is a hydrogen-bonded beta sheet interaction, as there is between subunits within a ring, but hydrophobic interactions account for most of the intersubunit stability. The central loop, which extends into the central aqueous channel, is subject to attack by at least five enzymes and is discussed as an enzyme "passive site."}[http://www.ncbi.nlm.nih.gov/pubmed/2572586?dopt=Abstract]<br />
<br />
Helix-helix interactions are the only interaction that can affect the folding of the proteins in Salmonella typhimurium. <scene name='Sandbox108/Hydrophobic/1'>Hydrophobic(purple)</scene> and <scene name='Sandbox108/Polar/1'>polar(blue)</scene> regions of the protein residues are on the helices of chain A. Also, uncharged polar groups are usually classified as hydrophilic that is found on the outside of proteins, but for glutamine in Salmonella typhimurium 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] Moreover, on the helices of chain A has <scene name='Sandbox108/Charged_region/1'>the charged regions(blue and red)</scene>.</div>Taewang Leehttps://proteopedia.org/index.php?title=Sandbox108&diff=809368Sandbox1082008-12-17T01:37:31Z<p>Taewang Lee: /* OUTLINE */</p>
<hr />
<div>==Glutamine synthetase assignment by UMBC undergraduate students==<br />
{{STRUCTURE_2gls | PDB=2gls | SCENE= }}<br />
<br />
<br />
<br />
''Glutamine synthetase of Salmonella typhimurium''<br />
<br />
<br />
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 is crucial in stabilizing the tertiary structure as well. [http://webhost.bridgew.edu/fgorga/proteins/proteins.htm] Also, disulfide bonds between cysteine residues stabilize the tertiary structure. [http://webhost.bridgew.edu/fgorga/proteins/proteins.htm] However, for glutamine synthetase for Salmonella, the most important interaction will be the helix-helix interactions. <br />
<br />
<br />
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; at the interface of pairs of subunits within each layer, cylindrical active sites are formed by six anti-parallel beta strands contributed by one subunit and two strands by the neighboring subunit. <br />
<br />
This interpretation of the electron density map has now been supported by comparison with glutamine synthetase from Escherichia coli by the Fourier difference method. Each active site cylinder holds two Mn2+ ions, with each ion having as ligands three protein side chains and two water molecules (one water shared by both metals), as well as a histidyl side chain just beyond liganding distance. The protein ligands to Mn2+ 469 are <scene name='Sandbox108/Glu_131/1'>Glu-131</scene>, <scene name='Sandbox108/Glu_212/1'>Glu-212</scene>, and <scene name='Sandbox108/Glu_220/1'>Glu-220</scene>; those to Mn2+ 470 are <scene name='Sandbox108/Glu_129/1'>Glu-129</scene>, <scene name='Sandbox108/His269/1'>His-269</scene>, and <scene name='Sandbox108/Glu_357/1'>Glu-357</scene>. The two layers of subunits are held together largely by the apolar COOH terminus, a helical thong, which inserts into a hydrophobic pocket formed by two neighboring subunits on the opposite ring. Also between layers, there is a hydrogen-bonded beta sheet interaction, as there is between subunits within a ring, but hydrophobic interactions account for most of the intersubunit stability. The central loop, which extends into the central aqueous channel, is subject to attack by at least five enzymes and is discussed as an enzyme "passive site."}[http://www.ncbi.nlm.nih.gov/pubmed/2572586?dopt=Abstract]<br />
<br />
Helix-helix interactions are the only interaction that can affect the folding of the proteins in Salmonella typhimurium. <scene name='Sandbox108/Hydrophobic/1'>Hydrophobic(purple)</scene> and <scene name='Sandbox108/Polar/1'>polar(blue)</scene> regions of the protein residues are on the helices of chain A. Also, uncharged polar groups are usually classified as hydrophilic that is found on the outside of proteins, but for glutamine in Salmonella typhimurium 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] Moreover, on the helices of chain A has <scene name='Sandbox108/Charged_region/1'>the charged regions(blue and red)</scene>.</div>Taewang Leehttps://proteopedia.org/index.php?title=Sandbox108&diff=809367Sandbox1082008-12-17T01:27:05Z<p>Taewang Lee: /* OUTLINE */</p>
<hr />
<div>==Glutamine synthetase assignment by UMBC undergraduate students==<br />
{{STRUCTURE_2gls | PDB=2gls | SCENE= }}<br />
<br />
== OUTLINE ==<br />
<br />
''Glutamine synthetase of Salmonella typhimurium''<br />
<br />
<br />
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 is crucial in stabilizing the tertiary structure as well. [http://webhost.bridgew.edu/fgorga/proteins/proteins.htm] Also, disulfide bonds between cysteine residues stabilize the tertiary structure. [http://webhost.bridgew.edu/fgorga/proteins/proteins.htm] However, for glutamine synthetase for Salmonella, the most important interaction will be the helix-helix interactions. <br />
<br />
<br />
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; at the interface of pairs of subunits within each layer, cylindrical active sites are formed by six anti-parallel beta strands contributed by one subunit and two strands by the neighboring subunit. <br />
<br />
This interpretation of the electron density map has now been supported by comparison with glutamine synthetase from Escherichia coli by the Fourier difference method. Each active site cylinder holds two Mn2+ ions, with each ion having as ligands three protein side chains and two water molecules (one water shared by both metals), as well as a histidyl side chain just beyond liganding distance. The protein ligands to Mn2+ 469 are <scene name='Sandbox108/Glu_131/1'>Glu-131</scene>, <scene name='Sandbox108/Glu_212/1'>Glu-212</scene>, and <scene name='Sandbox108/Glu_220/1'>Glu-220</scene>; those to Mn2+ 470 are <scene name='Sandbox108/Glu_129/1'>Glu-129</scene>, <scene name='Sandbox108/His269/1'>His-269</scene>, and <scene name='Sandbox108/Glu_357/1'>Glu-357</scene>. The two layers of subunits are held together largely by the apolar COOH terminus, a helical thong, which inserts into a hydrophobic pocket formed by two neighboring subunits on the opposite ring. Also between layers, there is a hydrogen-bonded beta sheet interaction, as there is between subunits within a ring, but hydrophobic interactions account for most of the intersubunit stability. The central loop, which extends into the central aqueous channel, is subject to attack by at least five enzymes and is discussed as an enzyme "passive site."}[http://www.ncbi.nlm.nih.gov/pubmed/2572586?dopt=Abstract]<br />
<br />
Helix-helix interactions are the only interaction that can affect the folding of the proteins in Salmonella typhimurium. <scene name='Sandbox108/Hydrophobic/1'>Hydrophobic(purple)</scene> and <scene name='Sandbox108/Polar/1'>polar(blue)</scene> regions of the protein residues are on the helices of chain A. Also, uncharged polar groups are usually classified as hydrophilic that is found on the outside of proteins, but for glutamine in Salmonella typhimurium 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] Moreover, on the helices of chain A has <scene name='Sandbox108/Charged_region/1'>the charged regions(blue and red)</scene>.</div>Taewang Leehttps://proteopedia.org/index.php?title=Sandbox108&diff=809366Sandbox1082008-12-17T01:22:01Z<p>Taewang Lee: /* OUTLINE */</p>
<hr />
<div>==Glutamine synthetase assignment by UMBC undergraduate students==<br />
{{STRUCTURE_2gls | PDB=2gls | SCENE= }}<br />
<br />
== OUTLINE ==<br />
<br />
''Glutamine synthetase of Salmonella typhimurium''<br />
<br />
<br />
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 is crucial in stabilizing the tertiary structure as well. [http://webhost.bridgew.edu/fgorga/proteins/proteins.htm] Also, disulfide bonds between cysteine residues stabilize the tertiary structure. [http://webhost.bridgew.edu/fgorga/proteins/proteins.htm] However, for glutamine synthetase for Salmonella, the most important interaction will be the helix-helix interactions. <br />
<br />
<br />
Glutamine synthetase from Salmonella typhimurium is the 12-subunit 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] <br />
<br />
{the 12 subunits are arranged in two layers of six; at the interface of pairs of subunits within each layer, cylindrical active sites are formed by six anti-parallel beta strands contributed by one subunit and two strands by the neighboring subunit. This interpretation of the electron density map has now been supported by comparison with glutamine synthetase from Escherichia coli by the Fourier difference method. Each active site cylinder holds two Mn2+ ions, with each ion having as ligands three protein side chains and two water molecules (one water shared by both metals), as well as a histidyl side chain just beyond liganding distance. The protein ligands to Mn2+ 469 are <scene name='Sandbox108/Glu_131/1'>Glu-131</scene>, <scene name='Sandbox108/Glu_212/1'>Glu-212</scene>, and <scene name='Sandbox108/Glu_220/1'>Glu-220</scene>; those to Mn2+ 470 are <scene name='Sandbox108/Glu_129/1'>Glu-129</scene>, <scene name='Sandbox108/His269/1'>His-269</scene>, and <scene name='Sandbox108/Glu_357/1'>Glu-357</scene>. The two layers of subunits are held together largely by the apolar COOH terminus, a helical thong, which inserts into a hydrophobic pocket formed by two neighboring subunits on the opposite ring. Also between layers, there is a hydrogen-bonded beta sheet interaction, as there is between subunits within a ring, but hydrophobic interactions account for most of the intersubunit stability. The central loop, which extends into the central aqueous channel, is subject to attack by at least five enzymes and is discussed as an enzyme "passive site."}[http://www.ncbi.nlm.nih.gov/pubmed/2572586?dopt=Abstract]<br />
<br />
Helix-helix interactions are the only interaction that can affect the folding of the proteins in Salmonella typhimurium. <scene name='Sandbox108/Hydrophobic/1'>Hydrophobic(purple)</scene> and <scene name='Sandbox108/Polar/1'>polar(blue)</scene> regions of the protein residues are on the helices of chain A. Also, uncharged polar groups are usually classified as hydrophilic that is found on the outside of proteins, but for glutamine in Salmonella typhimurium 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] Moreover, on the helices of chain A has <scene name='Sandbox108/Charged_region/1'>the charged regions(blue and red)</scene>.</div>Taewang Leehttps://proteopedia.org/index.php?title=Sandbox108&diff=809365Sandbox1082008-12-17T01:19:17Z<p>Taewang Lee: /* OUTLINE */</p>
<hr />
<div>==Glutamine synthetase assignment by UMBC undergraduate students==<br />
{{STRUCTURE_2gls | PDB=2gls | SCENE= }}<br />
<br />
== OUTLINE ==<br />
<br />
''Glutamine synthetase of Salmonella typhimurium''<br />
<br />
<br />
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 is crucial in stabilizing the tertiary structure as well. [http://webhost.bridgew.edu/fgorga/proteins/proteins.htm] Also, disulfide bonds between cysteine residues stabilize the tertiary structure. [http://webhost.bridgew.edu/fgorga/proteins/proteins.htm] However, for glutamine synthetase for Salmonella, the most important interaction will be the helix-helix interactions. <br />
<br />
<br />
Glutamine synthetase from Salmonella typhimurium is the 12-subunit 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] <br />
<br />
{the 12 subunits are arranged in two layers of six; at the interface of pairs of subunits within each layer, cylindrical active sites are formed by six anti-parallel beta strands contributed by one subunit and two strands by the neighboring subunit. This interpretation of the electron density map has now been supported by comparison with glutamine synthetase from Escherichia coli by the Fourier difference method. Each active site cylinder holds two Mn2+ ions, with each ion having as ligands three protein side chains and two water molecules (one water shared by both metals), as well as a histidyl side chain just beyond liganding distance. The protein ligands to Mn2+ 469 are <scene name='Sandbox108/Glu_131/1'>Glu-131</scene>, <scene name='Sandbox108/Glu_212/1'>Glu-212</scene>, and <scene name='Sandbox108/Glu_220/1'>Glu-220</scene>; those to Mn2+ 470 are <scene name='Sandbox108/Glu_129/1'>Glu-129</scene>, <scene name='Sandbox108/His269/1'>His-269</scene>, and Glu-357. The two layers of subunits are held together largely by the apolar COOH terminus, a helical thong, which inserts into a hydrophobic pocket formed by two neighboring subunits on the opposite ring. Also between layers, there is a hydrogen-bonded beta sheet interaction, as there is between subunits within a ring, but hydrophobic interactions account for most of the intersubunit stability. The central loop, which extends into the central aqueous channel, is subject to attack by at least five enzymes and is discussed as an enzyme "passive site."}[http://www.ncbi.nlm.nih.gov/pubmed/2572586?dopt=Abstract]<br />
<br />
Helix-helix interactions are the only interaction that can affect the folding of the proteins in Salmonella typhimurium. <scene name='Sandbox108/Hydrophobic/1'>Hydrophobic(purple)</scene> and <scene name='Sandbox108/Polar/1'>polar(blue)</scene> regions of the protein residues are on the helices of chain A. Also, uncharged polar groups are usually classified as hydrophilic that is found on the outside of proteins, but for glutamine in Salmonella typhimurium 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] Moreover, on the helices of chain A has <scene name='Sandbox108/Charged_region/1'>the charged regions(blue and red)</scene>.</div>Taewang Leehttps://proteopedia.org/index.php?title=Sandbox108&diff=809364Sandbox1082008-12-17T01:16:27Z<p>Taewang Lee: /* OUTLINE */</p>
<hr />
<div>==Glutamine synthetase assignment by UMBC undergraduate students==<br />
{{STRUCTURE_2gls | PDB=2gls | SCENE= }}<br />
<br />
== OUTLINE ==<br />
<br />
''Glutamine synthetase of Salmonella typhimurium''<br />
<br />
<br />
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 is crucial in stabilizing the tertiary structure as well. [http://webhost.bridgew.edu/fgorga/proteins/proteins.htm] Also, disulfide bonds between cysteine residues stabilize the tertiary structure. [http://webhost.bridgew.edu/fgorga/proteins/proteins.htm] However, for glutamine synthetase for Salmonella, the most important interaction will be the helix-helix interactions. <br />
<br />
<br />
Glutamine synthetase from Salmonella typhimurium is the 12-subunit 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] <br />
<br />
{the 12 subunits are arranged in two layers of six; at the interface of pairs of subunits within each layer, cylindrical active sites are formed by six anti-parallel beta strands contributed by one subunit and two strands by the neighboring subunit. This interpretation of the electron density map has now been supported by comparison with glutamine synthetase from Escherichia coli by the Fourier difference method. Each active site cylinder holds two Mn2+ ions, with each ion having as ligands three protein side chains and two water molecules (one water shared by both metals), as well as a histidyl side chain just beyond liganding distance. The protein ligands to Mn2+ 469 are <scene name='Sandbox108/Glu_131/1'>Glu-131</scene>, <scene name='Sandbox108/Glu_212/1'>Glu-212</scene>, and <scene name='Sandbox108/Glu_220/1'>Glu-220</scene>; those to Mn2+ 470 are <scene name='Sandbox108/Glu_129/1'>Glu-129</scene>, His-269, and Glu-357. The two layers of subunits are held together largely by the apolar COOH terminus, a helical thong, which inserts into a hydrophobic pocket formed by two neighboring subunits on the opposite ring. Also between layers, there is a hydrogen-bonded beta sheet interaction, as there is between subunits within a ring, but hydrophobic interactions account for most of the intersubunit stability. The central loop, which extends into the central aqueous channel, is subject to attack by at least five enzymes and is discussed as an enzyme "passive site."}[http://www.ncbi.nlm.nih.gov/pubmed/2572586?dopt=Abstract]<br />
<br />
Helix-helix interactions are the only interaction that can affect the folding of the proteins in Salmonella typhimurium. <scene name='Sandbox108/Hydrophobic/1'>Hydrophobic(purple)</scene> and <scene name='Sandbox108/Polar/1'>polar(blue)</scene> regions of the protein residues are on the helices of chain A. Also, uncharged polar groups are usually classified as hydrophilic that is found on the outside of proteins, but for glutamine in Salmonella typhimurium 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] Moreover, on the helices of chain A has <scene name='Sandbox108/Charged_region/1'>the charged regions(blue and red)</scene>.</div>Taewang Leehttps://proteopedia.org/index.php?title=Sandbox108&diff=809363Sandbox1082008-12-17T01:12:26Z<p>Taewang Lee: /* OUTLINE */</p>
<hr />
<div>==Glutamine synthetase assignment by UMBC undergraduate students==<br />
{{STRUCTURE_2gls | PDB=2gls | SCENE= }}<br />
<br />
== OUTLINE ==<br />
<br />
''Glutamine synthetase of Salmonella typhimurium''<br />
<br />
<br />
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 is crucial in stabilizing the tertiary structure as well. [http://webhost.bridgew.edu/fgorga/proteins/proteins.htm] Also, disulfide bonds between cysteine residues stabilize the tertiary structure. [http://webhost.bridgew.edu/fgorga/proteins/proteins.htm] However, for glutamine synthetase for Salmonella, the most important interaction will be the helix-helix interactions. <br />
<br />
<br />
Glutamine synthetase from Salmonella typhimurium is the 12-subunit 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] <br />
<br />
{the 12 subunits are arranged in two layers of six; at the interface of pairs of subunits within each layer, cylindrical active sites are formed by six anti-parallel beta strands contributed by one subunit and two strands by the neighboring subunit. This interpretation of the electron density map has now been supported by comparison with glutamine synthetase from Escherichia coli by the Fourier difference method. Each active site cylinder holds two Mn2+ ions, with each ion having as ligands three protein side chains and two water molecules (one water shared by both metals), as well as a histidyl side chain just beyond liganding distance. The protein ligands to Mn2+ 469 are <scene name='Sandbox108/Glu_131/1'>Glu-131</scene>, <scene name='Sandbox108/Glu_212/1'>Glu-212</scene>, and <scene name='Sandbox108/Glu_220/1'>Glu-220</scene>; those to Mn2+ 470 are Glu-129, His-269, and Glu-357. The two layers of subunits are held together largely by the apolar COOH terminus, a helical thong, which inserts into a hydrophobic pocket formed by two neighboring subunits on the opposite ring. Also between layers, there is a hydrogen-bonded beta sheet interaction, as there is between subunits within a ring, but hydrophobic interactions account for most of the intersubunit stability. The central loop, which extends into the central aqueous channel, is subject to attack by at least five enzymes and is discussed as an enzyme "passive site."}[http://www.ncbi.nlm.nih.gov/pubmed/2572586?dopt=Abstract]<br />
<br />
Helix-helix interactions are the only interaction that can affect the folding of the proteins in Salmonella typhimurium. <scene name='Sandbox108/Hydrophobic/1'>Hydrophobic(purple)</scene> and <scene name='Sandbox108/Polar/1'>polar(blue)</scene> regions of the protein residues are on the helices of chain A. Also, uncharged polar groups are usually classified as hydrophilic that is found on the outside of proteins, but for glutamine in Salmonella typhimurium 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] Moreover, on the helices of chain A has <scene name='Sandbox108/Charged_region/1'>the charged regions(blue and red)</scene>.</div>Taewang Leehttps://proteopedia.org/index.php?title=Sandbox108&diff=809362Sandbox1082008-12-17T01:09:10Z<p>Taewang Lee: /* OUTLINE */</p>
<hr />
<div>==Glutamine synthetase assignment by UMBC undergraduate students==<br />
{{STRUCTURE_2gls | PDB=2gls | SCENE= }}<br />
<br />
== OUTLINE ==<br />
<br />
''Glutamine synthetase of Salmonella typhimurium''<br />
<br />
<br />
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 is crucial in stabilizing the tertiary structure as well. [http://webhost.bridgew.edu/fgorga/proteins/proteins.htm] Also, disulfide bonds between cysteine residues stabilize the tertiary structure. [http://webhost.bridgew.edu/fgorga/proteins/proteins.htm] However, for glutamine synthetase for Salmonella, the most important interaction will be the helix-helix interactions. <br />
<br />
<br />
Glutamine synthetase from Salmonella typhimurium is the 12-subunit 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] <br />
<br />
{the 12 subunits are arranged in two layers of six; at the interface of pairs of subunits within each layer, cylindrical active sites are formed by six anti-parallel beta strands contributed by one subunit and two strands by the neighboring subunit. This interpretation of the electron density map has now been supported by comparison with glutamine synthetase from Escherichia coli by the Fourier difference method. Each active site cylinder holds two Mn2+ ions, with each ion having as ligands three protein side chains and two water molecules (one water shared by both metals), as well as a histidyl side chain just beyond liganding distance. The protein ligands to Mn2+ 469 are <scene name='Sandbox108/Glu_131/1'>Glu-131</scene>, <scene name='Sandbox108/Glu_212/1'>Glu-212</scene>, and Glu-220; those to Mn2+ 470 are Glu-129, His-269, and Glu-357. The two layers of subunits are held together largely by the apolar COOH terminus, a helical thong, which inserts into a hydrophobic pocket formed by two neighboring subunits on the opposite ring. Also between layers, there is a hydrogen-bonded beta sheet interaction, as there is between subunits within a ring, but hydrophobic interactions account for most of the intersubunit stability. The central loop, which extends into the central aqueous channel, is subject to attack by at least five enzymes and is discussed as an enzyme "passive site."}[http://www.ncbi.nlm.nih.gov/pubmed/2572586?dopt=Abstract]<br />
<br />
Helix-helix interactions are the only interaction that can affect the folding of the proteins in Salmonella typhimurium. <scene name='Sandbox108/Hydrophobic/1'>Hydrophobic(purple)</scene> and <scene name='Sandbox108/Polar/1'>polar(blue)</scene> regions of the protein residues are on the helices of chain A. Also, uncharged polar groups are usually classified as hydrophilic that is found on the outside of proteins, but for glutamine in Salmonella typhimurium 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] Moreover, on the helices of chain A has <scene name='Sandbox108/Charged_region/1'>the charged regions(blue and red)</scene>.</div>Taewang Leehttps://proteopedia.org/index.php?title=Sandbox108&diff=809361Sandbox1082008-12-17T01:05:24Z<p>Taewang Lee: /* OUTLINE */</p>
<hr />
<div>==Glutamine synthetase assignment by UMBC undergraduate students==<br />
{{STRUCTURE_2gls | PDB=2gls | SCENE= }}<br />
<br />
== OUTLINE ==<br />
<br />
''Glutamine synthetase of Salmonella typhimurium''<br />
<br />
<br />
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 is crucial in stabilizing the tertiary structure as well. [http://webhost.bridgew.edu/fgorga/proteins/proteins.htm] Also, disulfide bonds between cysteine residues stabilize the tertiary structure. [http://webhost.bridgew.edu/fgorga/proteins/proteins.htm] However, for glutamine synthetase for Salmonella, the most important interaction will be the helix-helix interactions. <br />
<br />
<br />
Glutamine synthetase from Salmonella typhimurium is the 12-subunit 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] <br />
<br />
{the 12 subunits are arranged in two layers of six; at the interface of pairs of subunits within each layer, cylindrical active sites are formed by six anti-parallel beta strands contributed by one subunit and two strands by the neighboring subunit. This interpretation of the electron density map has now been supported by comparison with glutamine synthetase from Escherichia coli by the Fourier difference method. Each active site cylinder holds two Mn2+ ions, with each ion having as ligands three protein side chains and two water molecules (one water shared by both metals), as well as a histidyl side chain just beyond liganding distance. The protein ligands to Mn2+ 469 are <scene name='Sandbox108/Glu_131/1'>Glu-131</scene>, Glu-212, and Glu-220; those to Mn2+ 470 are Glu-129, His-269, and Glu-357. The two layers of subunits are held together largely by the apolar COOH terminus, a helical thong, which inserts into a hydrophobic pocket formed by two neighboring subunits on the opposite ring. Also between layers, there is a hydrogen-bonded beta sheet interaction, as there is between subunits within a ring, but hydrophobic interactions account for most of the intersubunit stability. The central loop, which extends into the central aqueous channel, is subject to attack by at least five enzymes and is discussed as an enzyme "passive site."}[http://www.ncbi.nlm.nih.gov/pubmed/2572586?dopt=Abstract]<br />
<br />
Helix-helix interactions are the only interaction that can affect the folding of the proteins in Salmonella typhimurium. <scene name='Sandbox108/Hydrophobic/1'>Hydrophobic(purple)</scene> and <scene name='Sandbox108/Polar/1'>polar(blue)</scene> regions of the protein residues are on the helices of chain A. Also, uncharged polar groups are usually classified as hydrophilic that is found on the outside of proteins, but for glutamine in Salmonella typhimurium 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] Moreover, on the helices of chain A has <scene name='Sandbox108/Charged_region/1'>the charged regions(blue and red)</scene>.</div>Taewang Leehttps://proteopedia.org/index.php?title=Sandbox108&diff=809360Sandbox1082008-12-17T00:56:42Z<p>Taewang Lee: /* OUTLINE */</p>
<hr />
<div>==Glutamine synthetase assignment by UMBC undergraduate students==<br />
{{STRUCTURE_2gls | PDB=2gls | SCENE= }}<br />
<br />
== OUTLINE ==<br />
<br />
''Glutamine synthetase of Salmonella typhimurium''<br />
<br />
<br />
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 is crucial in stabilizing the tertiary structure as well. [http://webhost.bridgew.edu/fgorga/proteins/proteins.htm] Also, disulfide bonds between cysteine residues stabilize the tertiary structure. [http://webhost.bridgew.edu/fgorga/proteins/proteins.htm] However, for glutamine synthetase for Salmonella, the most important interaction will be the helix-helix interactions. <br />
<br />
<br />
Glutamine synthetase from Salmonella typhimurium is the 12-subunit 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] <br />
<br />
{the 12 subunits are arranged in two layers of six; at the interface of pairs of subunits within each layer, cylindrical active sites are formed by six anti-parallel beta strands contributed by one subunit and two strands by the neighboring subunit. This interpretation of the electron density map has now been supported by comparison with glutamine synthetase from Escherichia coli by the Fourier difference method. Each active site cylinder holds two Mn2+ ions, with each ion having as ligands three protein side chains and two water molecules (one water shared by both metals), as well as a histidyl side chain just beyond liganding distance. The protein ligands to Mn2+ 469 are Glu-131, Glu-212, and Glu-220; those to Mn2+ 470 are Glu-129, His-269, and Glu-357. The two layers of subunits are held together largely by the apolar COOH terminus, a helical thong, which inserts into a hydrophobic pocket formed by two neighboring subunits on the opposite ring. Also between layers, there is a hydrogen-bonded beta sheet interaction, as there is between subunits within a ring, but hydrophobic interactions account for most of the intersubunit stability. The central loop, which extends into the central aqueous channel, is subject to attack by at least five enzymes and is discussed as an enzyme "passive site."}[http://www.ncbi.nlm.nih.gov/pubmed/2572586?dopt=Abstract]<br />
<br />
Helix-helix interactions are the only interaction that can affect the folding of the proteins in Salmonella typhimurium. <scene name='Sandbox108/Hydrophobic/1'>Hydrophobic(purple)</scene> and <scene name='Sandbox108/Polar/1'>polar(blue)</scene> regions of the protein residues are on the helices of chain A. Also, uncharged polar groups are usually classified as hydrophilic that is found on the outside of proteins, but for glutamine in Salmonella typhimurium 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] Moreover, on the helices of chain A has <scene name='Sandbox108/Charged_region/1'>the charged regions(blue and red)</scene>.</div>Taewang Leehttps://proteopedia.org/index.php?title=Sandbox108&diff=809356Sandbox1082008-12-17T00:37:40Z<p>Taewang Lee: /* OUTLINE */</p>
<hr />
<div>==Glutamine synthetase assignment by UMBC undergraduate students==<br />
{{STRUCTURE_2gls | PDB=2gls | SCENE= }}<br />
<br />
== OUTLINE ==<br />
<br />
''Glutamine synthetase of Salmonella typhimurium''<br />
<br />
<br />
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 is crucial in stabilizing the tertiary structure as well. [http://webhost.bridgew.edu/fgorga/proteins/proteins.htm] Also, disulfide bonds between cysteine residues stabilize the tertiary structure. [http://webhost.bridgew.edu/fgorga/proteins/proteins.htm] However, for glutamine synthetase for Salmonella, the most important interaction will be the helix-helix interactions. <br />
<br />
<br />
Glutamine synthetase from Salmonella typhimurium has 23 helix-helix interactions involving helices of chain A and 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] Helix-helix interactions are the only interaction that can affect the folding of the proteins in Salmonella typhimurium. <scene name='Sandbox108/Hydrophobic/1'>Hydrophobic(purple)</scene> and <scene name='Sandbox108/Polar/1'>polar(blue)</scene> regions of the protein residues are on the helices of chain A. Also, uncharged polar groups are usually classified as hydrophilic that is found on the outside of proteins, but for glutamine in Salmonella typhimurium 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] Moreover, on the helices of chain A has <scene name='Sandbox108/Charged_region/1'>the charged regions(blue and red)</scene>.</div>Taewang Leehttps://proteopedia.org/index.php?title=Sandbox108&diff=809355Sandbox1082008-12-17T00:36:46Z<p>Taewang Lee: /* OUTLINE */</p>
<hr />
<div>==Glutamine synthetase assignment by UMBC undergraduate students==<br />
{{STRUCTURE_2gls | PDB=2gls | SCENE= }}<br />
<br />
== OUTLINE ==<br />
<br />
''Glutamine synthetase of Salmonella typhimurium''<br />
<br />
<br />
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 is crucial in stabilizing the tertiary structure as well. [http://webhost.bridgew.edu/fgorga/proteins/proteins.htm] Also, disulfide bonds between cysteine residues stabilize the tertiary structure. [http://webhost.bridgew.edu/fgorga/proteins/proteins.htm] However, for glutamine synthetase for Salmonella, the most important interaction will be the helix-helix interactions. <br />
<br />
<br />
Glutamine synthetase from Salmonella typhimurium has 23 helix-helix interactions involving helices of chain A and 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] Helix-helix interactions are the only interaction that can affect the folding of the proteins in Salmonella typhimurium. <scene name='Sandbox108/Hydrophobic/1'>Hydrophobic(purple)</scene> and <scene name='Sandbox108/Polar/1'>polar (blue)</scene> regions of the protein residues are on the helices of chain A. Also, uncharged polar groups are usually classified as hydrophilic that is found on the outside of proteins, but for glutamine in Salmonella typhimurium 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] Moreover, on the helices of chain A has <scene name='Sandbox108/Charged_region/1'>the charged regions</scene>.</div>Taewang Leehttps://proteopedia.org/index.php?title=Sandbox108&diff=809350Sandbox1082008-12-17T00:21:49Z<p>Taewang Lee: /* OUTLINE */</p>
<hr />
<div>==Glutamine synthetase assignment by UMBC undergraduate students==<br />
{{STRUCTURE_2gls | PDB=2gls | SCENE= }}<br />
<br />
== OUTLINE ==<br />
<br />
''Glutamine synthetase of Salmonella typhimurium''<br />
<br />
<br />
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 is crucial in stabilizing the tertiary structure as well. [http://webhost.bridgew.edu/fgorga/proteins/proteins.htm] Also, disulfide bonds between cysteine residues stabilize the tertiary structure. [http://webhost.bridgew.edu/fgorga/proteins/proteins.htm] However, for glutamine synthetase for Salmonella, the most important interaction will be the helix-helix interactions. <br />
<br />
<br />
Glutamine synthetase from Salmonella typhimurium has 23 helix-helix interactions involving helices of chain A and 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] Helix-helix interactions are the only interaction that can affect the folding of the proteins in Salmonella typhimurium. <scene name='Sandbox108/Hydrophobic/1'>Hydrophobic(purple)</scene> and <scene name='Sandbox108/Polar/1'>polar (blue)</scene> regions of the protein residues are on the helices of chain A. <br />
<br />
<br />
<br />
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]</div>Taewang Leehttps://proteopedia.org/index.php?title=Sandbox108&diff=809349Sandbox1082008-12-16T23:59:57Z<p>Taewang Lee: /* OUTLINE */</p>
<hr />
<div>==Glutamine synthetase assignment by UMBC undergraduate students==<br />
{{STRUCTURE_2gls | PDB=2gls | SCENE= }}<br />
<br />
== OUTLINE ==<br />
<br />
''Glutamine synthetase of Salmonella typhimurium''<br />
<br />
<br />
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 is crucial in stabilizing the tertiary structure as well. [http://webhost.bridgew.edu/fgorga/proteins/proteins.htm] Also, disulfide bonds between cysteine residues stabilize the tertiary structure. [http://webhost.bridgew.edu/fgorga/proteins/proteins.htm] However, for glutamine synthetase for Salmonella, the most important interaction will be the helix-helix interactions. <br />
<br />
<br />
Glutamine synthetase from Salmonella typhimurium has twenty three helix-helix interactions, and is 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] <scene name='Sandbox108/Hydrophobic/1'>Hydrophobic(purple)</scene> and <scene name='Sandbox108/Polar/1'>polar (blue)</scene> regions of the protein residues <br />
<br />
<br />
<br />
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]</div>Taewang Leehttps://proteopedia.org/index.php?title=Sandbox108&diff=809348Sandbox1082008-12-16T23:58:26Z<p>Taewang Lee: /* OUTLINE */</p>
<hr />
<div>==Glutamine synthetase assignment by UMBC undergraduate students==<br />
{{STRUCTURE_2gls | PDB=2gls | SCENE= }}<br />
<br />
== OUTLINE ==<br />
<br />
''Glutamine synthetase of Salmonella''<br />
<br />
<br />
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 is crucial in stabilizing the tertiary structure as well. [http://webhost.bridgew.edu/fgorga/proteins/proteins.htm] Also, disulfide bonds between cysteine residues stabilize the tertiary structure. [http://webhost.bridgew.edu/fgorga/proteins/proteins.htm] However, for glutamine synthetase for Salmonella, the most important interaction will be the helix-helix interactions. <br />
<br />
<br />
Glutamine synthetase from Salmonella has twenty three helix-helix interactions, and is 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] <scene name='Sandbox108/Hydrophobic/1'>Hydrophobic(purple)</scene> and <scene name='Sandbox108/Polar/1'>polar (blue)</scene> regions of the protein residues <br />
<br />
<br />
<br />
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]</div>Taewang Leehttps://proteopedia.org/index.php?title=Sandbox108&diff=809347Sandbox1082008-12-16T23:57:04Z<p>Taewang Lee: /* OUTLINE */</p>
<hr />
<div>==Glutamine synthetase assignment by UMBC undergraduate students==<br />
{{STRUCTURE_2gls | PDB=2gls | SCENE= }}<br />
<br />
== OUTLINE ==<br />
<br />
''Glutamine synthetase of Salmonella''<br />
<br />
<br />
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 is crucial in stabilizing the tertiary structure as well. [http://webhost.bridgew.edu/fgorga/proteins/proteins.htm] Also, disulfide bonds between cysteine residues stabilize the tertiary structure. [http://webhost.bridgew.edu/fgorga/proteins/proteins.htm] However, for glutamine synthetase for Salmonella, the most important interaction will be the helix-helix interactions. <br />
<br />
Glutamine synthetase from Salmonella has twenty three helix-helix interactions, and is 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] <scene name='Sandbox108/Hydrophobic/1'>Hydrophobic(purple)</scene> and <scene name='Sandbox108/Polar/1'>polar (blue)</scene> regions of the protein residues are represented by deep blue color. <br />
<br />
<br />
<br />
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]</div>Taewang Leehttps://proteopedia.org/index.php?title=Sandbox108&diff=809346Sandbox1082008-12-16T23:45:37Z<p>Taewang Lee: </p>
<hr />
<div>==Glutamine synthetase assignment by UMBC undergraduate students==<br />
{{STRUCTURE_2gls | PDB=2gls | SCENE= }}<br />
<br />
== OUTLINE ==<br />
<br />
''Glutamine synthetase of Salmonella''<br />
<br />
<br />
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 is crucial in stabilizing the tertiary structure as well. [http://webhost.bridgew.edu/fgorga/proteins/proteins.htm] Also, disulfide bonds between cysteine residues stabilize the tertiary structure. [http://webhost.bridgew.edu/fgorga/proteins/proteins.htm] However, for glutamine synthetase for Salmonella, the most important interaction will be the helix-helix interactions. <br />
<br />
Glutamine synthetase from Salmonella has twenty three helix-helix interactions and is 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] <scene name='Sandbox108/Hydrophobic/1'>Hydrophobic (purple)</scene> on the protein residues and <scene name='Sandbox108/Polar/1'>polar</scene> regions of the protein residues are represented by deep blue color. <br />
<br />
<br />
<br />
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]</div>Taewang Leehttps://proteopedia.org/index.php?title=Sandbox108&diff=809340Sandbox1082008-12-16T23:29:28Z<p>Taewang Lee: /* Glutamine synthetase assignment by UMBC undergraduate students */</p>
<hr />
<div>==Glutamine synthetase assignment by UMBC undergraduate students==<br />
{{STRUCTURE_2gls | PDB=2gls | SCENE= }}<br />
<scene name='User:Taewang_Lee/Exercise_2/1'>Exercise 2</scene><br />
<scene name='User:Taewang_Lee/Exercise_3/5'>Exercise 3</scene><br />
<scene name='Sandbox108/Exercise_4/1'>Exercise 4</scene><br />
<scene name='User:Taewang_Lee/Exercise_4/5'>Exercise 4(Practiced)</scene><br />
<br />
== OUTLINE ==<br />
<br />
''Tertiary Structure''<br />
<br />
<br />
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]<br />
<br />
Glutamine synthetase from Salmonella has twenty three helix-helix interactions and is 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] <scene name='Sandbox108/Hydrophobic/1'>Hydrophobic (purple)</scene> on the protein residues and polar <polar wiki> (put color) region is represented by gray and light purple, and this characteristic strenthens the folding of proteins. And, it has charged region in the inside of molecules as well. <br />
<br />
<br />
<br />
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]</div>Taewang Leehttps://proteopedia.org/index.php?title=Sandbox108&diff=809338Sandbox1082008-12-16T23:26:48Z<p>Taewang Lee: /* OUTLINE */</p>
<hr />
<div>==Glutamine synthetase assignment by UMBC undergraduate students==<br />
{{STRUCTURE_2qc8 | PDB=2qc8 | SCENE= }}<br />
<scene name='User:Taewang_Lee/Exercise_2/1'>Exercise 2</scene><br />
<scene name='User:Taewang_Lee/Exercise_3/5'>Exercise 3</scene><br />
<scene name='Sandbox108/Exercise_4/1'>Exercise 4</scene><br />
<scene name='User:Taewang_Lee/Exercise_4/5'>Exercise 4(Practiced)</scene><br />
<br />
== OUTLINE ==<br />
<br />
''Tertiary Structure''<br />
<br />
<br />
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]<br />
<br />
Glutamine synthetase from Salmonella has twenty three helix-helix interactions and is 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] <scene name='Sandbox108/Hydrophobic/1'>Hydrophobic (purple)</scene> on the protein residues and polar <polar wiki> (put color) region is represented by gray and light purple, and this characteristic strenthens the folding of proteins. And, it has charged region in the inside of molecules as well. <br />
<br />
<br />
<br />
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]</div>Taewang Leehttps://proteopedia.org/index.php?title=Sandbox108&diff=809337Sandbox1082008-12-16T22:26:39Z<p>Taewang Lee: /* OUTLINE */</p>
<hr />
<div>==Glutamine synthetase assignment by UMBC undergraduate students==<br />
{{STRUCTURE_2qc8 | PDB=2qc8 | SCENE= }}<br />
<scene name='User:Taewang_Lee/Exercise_2/1'>Exercise 2</scene><br />
<scene name='User:Taewang_Lee/Exercise_3/5'>Exercise 3</scene><br />
<scene name='Sandbox108/Exercise_4/1'>Exercise 4</scene><br />
<scene name='User:Taewang_Lee/Exercise_4/5'>Exercise 4(Practiced)</scene><br />
<br />
== OUTLINE ==<br />
<br />
''Tertiary Structure''<br />
<br />
<br />
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]<br />
<br />
Glutamine synthetase from Salmonella has twenty three helix-helix interactions and is 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] Hydrophobic/polar <hydrophobic/polar wiki> (put color) and hydrophilic <hydrophilic wiki>(put color) region of glutamine are combined together to fold proteins. <br />
<br />
<br />
<br />
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]</div>Taewang Leehttps://proteopedia.org/index.php?title=Sandbox108&diff=809336Sandbox1082008-12-16T22:26:07Z<p>Taewang Lee: /* OUTLINE */</p>
<hr />
<div>==Glutamine synthetase assignment by UMBC undergraduate students==<br />
{{STRUCTURE_2qc8 | PDB=2qc8 | SCENE= }}<br />
<scene name='User:Taewang_Lee/Exercise_2/1'>Exercise 2</scene><br />
<scene name='User:Taewang_Lee/Exercise_3/5'>Exercise 3</scene><br />
<scene name='Sandbox108/Exercise_4/1'>Exercise 4</scene><br />
<scene name='User:Taewang_Lee/Exercise_4/5'>Exercise 4(Practiced)</scene><br />
<br />
== OUTLINE ==<br />
<br />
''Tertiary Structure''<br />
<br />
<br />
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]<br />
<br />
Glutamine synthetase from Salmonella has twenty three helix-helix interactions and is 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] Hydrophobic/polar <hydrophobic/polar wiki> (put color) and hydrophilic <hydrophilic wiki>(put color) region of glutamine are combined together to fold proteins. <br />
<br />
<br />
<br />
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]</div>Taewang Leehttps://proteopedia.org/index.php?title=Sandbox108&diff=809335Sandbox1082008-12-16T22:25:41Z<p>Taewang Lee: /* OUTLINE */</p>
<hr />
<div>==Glutamine synthetase assignment by UMBC undergraduate students==<br />
{{STRUCTURE_2qc8 | PDB=2qc8 | SCENE= }}<br />
<scene name='User:Taewang_Lee/Exercise_2/1'>Exercise 2</scene><br />
<scene name='User:Taewang_Lee/Exercise_3/5'>Exercise 3</scene><br />
<scene name='Sandbox108/Exercise_4/1'>Exercise 4</scene><br />
<scene name='User:Taewang_Lee/Exercise_4/5'>Exercise 4(Practiced)</scene><br />
<br />
== OUTLINE ==<br />
<br />
''Tertiary Structure''<br />
<br />
<br />
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]<br />
<br />
Glutamine synthetase from Salmonella has twenty three helix-helix interactions and is 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] Hydrophobic/polar <hydrophobic/polar wiki> (put color) and hydrophilic <hydrophilic wiki>(put color) region of glutamine are combined together to fold proteins. <br />
<br />
<br />
<br />
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]</div>Taewang Leehttps://proteopedia.org/index.php?title=Sandbox108&diff=809334Sandbox1082008-12-16T22:23:52Z<p>Taewang Lee: /* OUTLINE */</p>
<hr />
<div>==Glutamine synthetase assignment by UMBC undergraduate students==<br />
{{STRUCTURE_2qc8 | PDB=2qc8 | SCENE= }}<br />
<scene name='User:Taewang_Lee/Exercise_2/1'>Exercise 2</scene><br />
<scene name='User:Taewang_Lee/Exercise_3/5'>Exercise 3</scene><br />
<scene name='Sandbox108/Exercise_4/1'>Exercise 4</scene><br />
<scene name='User:Taewang_Lee/Exercise_4/5'>Exercise 4(Practiced)</scene><br />
<br />
== OUTLINE ==<br />
<br />
''Tertiary Structure''<br />
<br />
<br />
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]<br />
<br />
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. <br />
<br />
<br />
<br />
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]</div>Taewang Lee