Sandbox108: Difference between revisions
Taewang Lee (talk | contribs) |
Taewang Lee (talk | contribs) |
||
| Line 8: | Line 8: | ||
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] | 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] | ||
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. | 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. | ||
Revision as of 04:11, 19 December 2008
Glutamine synthetase assignment by UMBC undergraduate students(Not Complete version)Glutamine synthetase assignment by UMBC undergraduate students(Not Complete version)
Glutamine synthetase of Salmonella typhimurium
Tertiary structure of protein is characterized by the “global” folding of a polypeptide chain [1] and mostly affected by () 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.[2] Also, disulfide bonds between cysteine residues stabilize the tertiary structure. [3] However, for Salmonella typhimurium it is mainly influenced by the helix-helix interaction between two layers, as well as 12-subunits enzymes.[4]
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. [5] The 12-subunits enzyme are arranged in two layers of six, such as 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.[6] Each active site holds two ions surrounded by some [7] Also, the protein ligands to Mn2+ 469 are , , and ; those to Mn2+ 470 are , , and .[8] 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 pocket formed by two neighboring subunits on the opposite ring, hold the two layers of subunits tightly.[9] Also, even though there is a between layers, interactions will contribute to the stability of the intersubunit.[10] 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 , 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.