https://nesgwiki.chem.buffalo.edu/index.php?action=history&feed=atom&title=Cofactor_optimization 2026-04-13T05:24:18Z Revision history for this page on the wiki MediaWiki 1.38.2 https://nesgwiki.chem.buffalo.edu/index.php?title=Cofactor_optimization&diff=3327&oldid=prev 2009-12-17T15:22:24Z

<p></p> <table style="background-color: #fff; color: #202122;" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 15:22, 17 December 2009</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l18">Line 18:</td> <td colspan="2" class="diff-lineno">Line 18:</td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;br&gt;  </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;br&gt;  </div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>ZincFinder was used to analyze 36,761 full length NESG targets with sequence lengths of less than or equal to 1000 amino ([http://zincfinder.dsi.unifi.it/]). A protein was strongly suspected to bind zinc if three or more Cys, His, Asp or Glu residues were predicted to bind zinc with a probability equal to or greater than 50%; 3,137 targets (8.5% of studied targets) were found that met this criteria. ZincFinder predicts that 24 of the 691 targets structured by the NESG possesses a zinc binding site. Eighteen of the twenty four targets have been deposited with coordinates for their bound zinc atoms. The remaining 6 targets may actually be zinc binding proteins where the zinc was not introduced during fermentation or lost during purification.  </div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>ZincFinder was used to analyze 36,761 full length NESG targets with sequence lengths of less than or equal to 1000 amino ([<ins style="font-weight: bold; text-decoration: none;">http://zincfinder.dsi.unifi.it/ </ins>http://zincfinder.dsi.unifi.it/]). A protein was strongly suspected to bind zinc if three or more Cys, His, Asp or Glu residues were predicted to bind zinc with a probability equal to or greater than 50%; 3,137 targets (8.5% of studied targets) were found that met this criteria. ZincFinder predicts that 24 of the 691 targets structured by the NESG possesses a zinc binding site. Eighteen of the twenty four targets have been deposited with coordinates for their bound zinc atoms. The remaining 6 targets may actually be zinc binding proteins where the zinc was not introduced during fermentation or lost during purification.  </div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;br&gt;  </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;br&gt;  </div></td></tr> </table>

TheresaRamelot https://nesgwiki.chem.buffalo.edu/index.php?title=Cofactor_optimization&diff=3326&oldid=prev 2009-12-17T15:17:49Z

<p></p> <table style="background-color: #fff; color: #202122;" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 15:17, 17 December 2009</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l12">Line 12:</td> <td colspan="2" class="diff-lineno">Line 12:</td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=== Addition and removal of Zinc from ''Haemophilus influenzae'' IscU  ===</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=== Addition and removal of Zinc from ''Haemophilus influenzae'' IscU  ===</div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>As many as 30% of proteins are predicted to be metal binding proteins and many of these may require metal for proper folding. In fact, a recent analysis of the PDB revealed that 14% of non-redundant entries contain stoichiometric amounts of six transition metals: Mn, Fe, Co, Ni, Cu or Zn &lt;ref&gt;Shi, W., Zhan, C., Ignatov, A., Manjasetty, B.A., Marinkovic, N., Sullivan, M., Huang, R., and Chance, M.R. (2005). Metalloproteomics: high-throughput structural and functional annotation of proteins in structural genomics. Structure 13, 1473-1486.&lt;/ref&gt;  </div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>As many as 30% of proteins are predicted to be metal binding proteins and many of these may require metal for proper folding. In fact, a recent analysis of the PDB revealed that 14% of non-redundant entries contain stoichiometric amounts of six transition metals: Mn, Fe, Co, Ni, Cu or Zn &lt;ref&gt;Shi, W., Zhan, C., Ignatov, A., Manjasetty, B.A., Marinkovic, N., Sullivan, M., Huang, R., and Chance, M.R. (2005). Metalloproteomics: high-throughput structural and functional annotation of proteins in structural genomics. Structure 13, 1473-1486.&lt;/ref&gt;<ins style="font-weight: bold; text-decoration: none;">&amp;nbsp; Of particular interest is zinc, which is the second most abundant transition metal in living organisms after Fe &lt;ref&gt;Lipscomb, W.N., and Strater, N. (1996). Recent Advances in Zinc Enzymology. Chem Rev 96, 2375-2434.&lt;/ref&gt;. The extent is highlighted in a recent bioinformatics analysis of the human proteome in which it was determined that as much 10% of the proteome is zinc-bound &lt;ref&gt;Andreini, C., Banci, L., Bertini, I., and Rosato, A. (2006). Counting the zinc-proteins encoded in the human genome. J Proteome Res 5, 196-201.&lt;/ref&gt;. In biology zinc is commonly assuming a structural role (structural zinc), and less commonly, a catalytic role &lt;ref&gt;Passerini, A., Andreini, C., Menchetti, S., Rosato, A., and Frasconi, P. (2007). Predicting zinc binding at the proteome level. BMC Bioinformatics 8, 39.&lt;/ref&gt;.&amp;nbsp; Structural zinc is tetrahedrally coordinated by the side-chains of a small subset of amino acids. The coordinating atoms are in-turn are stabilized by a hydrogen bonding network with amino acids in an outer coordinating sphere. </ins></div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">Of particular interest is zinc, which is the second most abundant transition metal in living organisms after Fe &lt;ref&gt;Lipscomb, W.N., and Strater, N. (1996). Recent Advances in Zinc Enzymology. Chem Rev 96, 2375-2434.&lt;/ref&gt;. The extent is highlighted in a recent bioinformatics analysis of the human proteome in which it was determined that as much 10% of the proteome is zinc-bound &lt;ref&gt;Andreini, C., Banci, L., Bertini, I., and Rosato, A. (2006). Counting the zinc-proteins encoded in the human genome. J Proteome Res 5, 196-201.&lt;/ref&gt;. In biology zinc is commonly assuming a structural role (structural zinc), and less commonly, a catalytic role &lt;ref&gt;Passerini, A., Andreini, C., Menchetti, S., Rosato, A., and Frasconi, P. (2007). Predicting zinc binding at the proteome level. BMC Bioinformatics 8, 39.&lt;/ref&gt;. </del></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>&lt;br&gt; In 2006 Passerini et al., developed a de novo predictor of zinc-binding called ZincFinder &lt;ref&gt;Passerini, A., Punta, M., Ceroni, A., Rost, B., and Frasconi, P. (2006). Identifying cysteines and histidines in transition-metal-binding sites using support vector machines and neural networks. Proteins 65, 305-316&lt;/ref&gt;.&amp;nbsp; The algorithm uses sequence specific information and is trained on 230 zinc binding chains to recognize position specific evolutionary profiles. The algorithm also considers global parameters, such as chain length and amino acid composition, as well as local parameters, such as the distance between potential ligands. ZincFinder has a reported precision of 73% and a recall of 61%.  </div></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div> </div></td><td colspan="2" class="diff-side-added"></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">&lt;br&gt; Structural zinc is tetrahedrally coordinated by the side-chains of a small subset of amino acids. The coordinating atoms are in-turn are stabilized by a hydrogen bonding network with amino acids in an outer coordinating sphere. </del></div></td><td colspan="2" class="diff-side-added"></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div> </div></td><td colspan="2" class="diff-side-added"></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>&lt;br&gt; In 2006 Passerini et al., developed a de novo predictor of zinc-binding called ZincFinder &lt;ref&gt;Passerini, A., Punta, M., Ceroni, A., Rost, B., and Frasconi, P. (2006). Identifying cysteines and histidines in transition-metal-binding sites using support vector machines and neural networks. Proteins 65, 305-316<del style="font-weight: bold; text-decoration: none;">&lt;/ref&gt;. Predicting zinc binding at the proteome level. BMC Bioinformatics 8, 39.</del>&lt;/ref&gt;.&amp;nbsp; The algorithm uses sequence specific information and is trained on 230 zinc binding chains to recognize position specific evolutionary profiles. The algorithm also considers global parameters, such as chain length and amino acid composition, as well as local parameters, such as the distance between potential ligands. ZincFinder has a reported precision of 73% and a recall of 61%.  </div></td><td colspan="2" class="diff-side-added"></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;br&gt;  </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;br&gt;  </div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>ZincFinder was used to analyze 36,761 full length NESG targets with sequence lengths of less than or equal to 1000 amino (http://zincfinder.dsi.unifi.it/). A protein was strongly suspected to bind zinc if three or more Cys, His, Asp or Glu residues were predicted to bind zinc with a probability equal to or greater than 50%; 3,137 targets (8.5% of studied targets) were found that met this criteria. ZincFinder predicts that 24 of the 691 targets structured by the NESG possesses a zinc binding site. Eighteen of the twenty four targets have been deposited with coordinates for their bound zinc atoms. The remaining 6 targets may actually be zinc binding proteins where the zinc was not introduced during fermentation or lost during purification.  </div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>ZincFinder was used to analyze 36,761 full length NESG targets with sequence lengths of less than or equal to 1000 amino (<ins style="font-weight: bold; text-decoration: none;">[</ins>http://zincfinder.dsi.unifi.it/<ins style="font-weight: bold; text-decoration: none;">]</ins>). A protein was strongly suspected to bind zinc if three or more Cys, His, Asp or Glu residues were predicted to bind zinc with a probability equal to or greater than 50%; 3,137 targets (8.5% of studied targets) were found that met this criteria. ZincFinder predicts that 24 of the 691 targets structured by the NESG possesses a zinc binding site. Eighteen of the twenty four targets have been deposited with coordinates for their bound zinc atoms. The remaining 6 targets may actually be zinc binding proteins where the zinc was not introduced during fermentation or lost during purification.  </div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;br&gt;  </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;br&gt;  </div></td></tr> </table>

TheresaRamelot https://nesgwiki.chem.buffalo.edu/index.php?title=Cofactor_optimization&diff=3325&oldid=prev 2009-12-17T15:13:22Z

<p></p> <table style="background-color: #fff; color: #202122;" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 15:13, 17 December 2009</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l18">Line 18:</td> <td colspan="2" class="diff-lineno">Line 18:</td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;br&gt; Structural zinc is tetrahedrally coordinated by the side-chains of a small subset of amino acids. The coordinating atoms are in-turn are stabilized by a hydrogen bonding network with amino acids in an outer coordinating sphere.  </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;br&gt; Structural zinc is tetrahedrally coordinated by the side-chains of a small subset of amino acids. The coordinating atoms are in-turn are stabilized by a hydrogen bonding network with amino acids in an outer coordinating sphere.  </div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>&lt;br&gt; In 2006 Passerini et al., developed a de novo predictor of zinc-binding called ZincFinder &lt;ref&gt;Passerini, A., Punta, M., Ceroni, A., Rost, B., and Frasconi, P. (2006). Identifying cysteines and histidines in transition-metal-binding sites using support vector machines and neural networks. Proteins 65, 305-316&lt;/ref&gt;<del style="font-weight: bold; text-decoration: none;">,&lt;ref&gt;Passerini, A., Andreini, C., Menchetti, S., Rosato, A., and Frasconi, P. (2007)</del>. Predicting zinc binding at the proteome level. BMC Bioinformatics 8, 39.&lt;/ref&gt;.&amp;nbsp; The algorithm uses sequence specific information and is trained on 230 zinc binding chains to recognize position specific evolutionary profiles. The algorithm also considers global parameters, such as chain length and amino acid composition, as well as local parameters, such as the distance between potential ligands. ZincFinder has a reported precision of 73% and a recall of 61%.  </div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>&lt;br&gt; In 2006 Passerini et al., developed a de novo predictor of zinc-binding called ZincFinder &lt;ref&gt;Passerini, A., Punta, M., Ceroni, A., Rost, B., and Frasconi, P. (2006). Identifying cysteines and histidines in transition-metal-binding sites using support vector machines and neural networks. Proteins 65, 305-316&lt;/ref&gt;. Predicting zinc binding at the proteome level. BMC Bioinformatics 8, 39.&lt;/ref&gt;.&amp;nbsp; The algorithm uses sequence specific information and is trained on 230 zinc binding chains to recognize position specific evolutionary profiles. The algorithm also considers global parameters, such as chain length and amino acid composition, as well as local parameters, such as the distance between potential ligands. ZincFinder has a reported precision of 73% and a recall of 61%.  </div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;br&gt;  </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;br&gt;  </div></td></tr> </table>

TheresaRamelot https://nesgwiki.chem.buffalo.edu/index.php?title=Cofactor_optimization&diff=3324&oldid=prev 2009-12-17T15:03:25Z

<p></p> <table style="background-color: #fff; color: #202122;" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 15:03, 17 December 2009</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l14">Line 14:</td> <td colspan="2" class="diff-lineno">Line 14:</td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>As many as 30% of proteins are predicted to be metal binding proteins and many of these may require metal for proper folding. In fact, a recent analysis of the PDB revealed that 14% of non-redundant entries contain stoichiometric amounts of six transition metals: Mn, Fe, Co, Ni, Cu or Zn &lt;ref&gt;Shi, W., Zhan, C., Ignatov, A., Manjasetty, B.A., Marinkovic, N., Sullivan, M., Huang, R., and Chance, M.R. (2005). Metalloproteomics: high-throughput structural and functional annotation of proteins in structural genomics. Structure 13, 1473-1486.&lt;/ref&gt;  </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>As many as 30% of proteins are predicted to be metal binding proteins and many of these may require metal for proper folding. In fact, a recent analysis of the PDB revealed that 14% of non-redundant entries contain stoichiometric amounts of six transition metals: Mn, Fe, Co, Ni, Cu or Zn &lt;ref&gt;Shi, W., Zhan, C., Ignatov, A., Manjasetty, B.A., Marinkovic, N., Sullivan, M., Huang, R., and Chance, M.R. (2005). Metalloproteomics: high-throughput structural and functional annotation of proteins in structural genomics. Structure 13, 1473-1486.&lt;/ref&gt;  </div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Of particular interest is zinc, which is the second most abundant transition metal in living organisms after Fe &lt;ref&gt;Lipscomb, W.N., and Strater, N. (1996). Recent Advances in Zinc Enzymology. Chem Rev 96, 2375-2434.&lt;/ref&gt;. The extent is highlighted in a recent bioinformatics analysis of the human proteome in which it was determined that as much 10% of the proteome is zinc-bound &lt;ref&gt;Andreini, C., Banci, L., Bertini, I., and Rosato, A. (2006). Counting the zinc-proteins encoded in the human genome. J Proteome Res 5, 196-201.&lt;/ref&gt;. In biology zinc is commonly assuming a structural role (structural zinc), and less commonly, a catalytic role</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Of particular interest is zinc, which is the second most abundant transition metal in living organisms after Fe &lt;ref&gt;Lipscomb, W.N., and Strater, N. (1996). Recent Advances in Zinc Enzymology. Chem Rev 96, 2375-2434.&lt;/ref&gt;. The extent is highlighted in a recent bioinformatics analysis of the human proteome in which it was determined that as much 10% of the proteome is zinc-bound &lt;ref&gt;Andreini, C., Banci, L., Bertini, I., and Rosato, A. (2006). Counting the zinc-proteins encoded in the human genome. J Proteome Res 5, 196-201.&lt;/ref&gt;. In biology zinc is commonly assuming a structural role (structural zinc), and less commonly, a catalytic role &lt;ref&gt;Passerini, A., Andreini, C., Menchetti, S., Rosato, A., and Frasconi, P. (2007). Predicting zinc binding at the proteome level. BMC Bioinformatics 8, 39.&lt;/ref&gt;.  </div></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>&lt;ref&gt;Passerini, A., Andreini, C., Menchetti, S., Rosato, A., and Frasconi, P. (2007). Predicting zinc binding at the proteome level. BMC Bioinformatics 8, 39.&lt;/ref&gt;.</div></td><td colspan="2" class="diff-side-added"></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr> <tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">&lt;br> Structural zinc is tetrahedrally coordinated by the side-chains of a small subset of amino acids. The coordinating atoms are in-turn are stabilized by a hydrogen bonding network with amino acids in an outer coordinating sphere. </ins></div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">Structural zinc is tetrahedrally coordinated by the side-chains of a small subset of amino acids. The coordinating atoms are in-turn are stabilized by a hydrogen bonding network with amino acids in an outer coordinating sphere. </del></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>&lt;br&gt; In 2006 Passerini et al., developed a de novo predictor of zinc-binding called ZincFinder &lt;ref&gt;Passerini, A., Punta, M., Ceroni, A., Rost, B., and Frasconi, P. (2006). Identifying cysteines and histidines in transition-metal-binding sites using support vector machines and neural networks. Proteins 65, 305-316&lt;/ref&gt;<ins style="font-weight: bold; text-decoration: none;">,</ins>&lt;ref&gt;Passerini, A., Andreini, C., Menchetti, S., Rosato, A., and Frasconi, P. (2007). Predicting zinc binding at the proteome level. BMC Bioinformatics 8, 39.&lt;/ref&gt;<ins style="font-weight: bold; text-decoration: none;">.&amp;nbsp; </ins>The algorithm uses sequence specific information and is trained on 230 zinc binding chains to recognize position specific evolutionary profiles. The algorithm also considers global parameters, such as chain length and amino acid composition, as well as local parameters, such as the distance between potential ligands. ZincFinder has a reported precision of 73% and a recall of 61%.  </div></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div> </div></td><td colspan="2" class="diff-side-added"></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>&lt;br&gt; In 2006 Passerini et al., developed a de novo predictor of zinc-binding called ZincFinder  </div></td><td colspan="2" class="diff-side-added"></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>&lt;ref&gt;Passerini, A., Punta, M., Ceroni, A., Rost, B., and Frasconi, P. (2006). Identifying cysteines and histidines in transition-metal-binding sites using support vector machines and neural networks. Proteins 65, 305-316&lt;/ref&gt;<del style="font-weight: bold; text-decoration: none;">. </del></div></td><td colspan="2" class="diff-side-added"></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>&lt;ref&gt;Passerini, A., Andreini, C., Menchetti, S., Rosato, A., and Frasconi, P. (2007). Predicting zinc binding at the proteome level. BMC Bioinformatics 8, 39.&lt;/ref&gt;</div></td><td colspan="2" class="diff-side-added"></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>The algorithm uses sequence specific information and is trained on 230 zinc binding chains to recognize position specific evolutionary profiles. The algorithm also considers global parameters, such as chain length and amino acid composition, as well as local parameters, such as the distance between potential ligands. ZincFinder has a reported precision of 73% and a recall of 61%.  </div></td><td colspan="2" class="diff-side-added"></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;br&gt;  </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;br&gt;  </div></td></tr> </table>

TheresaRamelot https://nesgwiki.chem.buffalo.edu/index.php?title=Cofactor_optimization&diff=3323&oldid=prev 2009-12-17T15:01:11Z

<p></p> <table style="background-color: #fff; color: #202122;" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 15:01, 17 December 2009</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l14">Line 14:</td> <td colspan="2" class="diff-lineno">Line 14:</td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>As many as 30% of proteins are predicted to be metal binding proteins and many of these may require metal for proper folding. In fact, a recent analysis of the PDB revealed that 14% of non-redundant entries contain stoichiometric amounts of six transition metals: Mn, Fe, Co, Ni, Cu or Zn &lt;ref&gt;Shi, W., Zhan, C., Ignatov, A., Manjasetty, B.A., Marinkovic, N., Sullivan, M., Huang, R., and Chance, M.R. (2005). Metalloproteomics: high-throughput structural and functional annotation of proteins in structural genomics. Structure 13, 1473-1486.&lt;/ref&gt;  </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>As many as 30% of proteins are predicted to be metal binding proteins and many of these may require metal for proper folding. In fact, a recent analysis of the PDB revealed that 14% of non-redundant entries contain stoichiometric amounts of six transition metals: Mn, Fe, Co, Ni, Cu or Zn &lt;ref&gt;Shi, W., Zhan, C., Ignatov, A., Manjasetty, B.A., Marinkovic, N., Sullivan, M., Huang, R., and Chance, M.R. (2005). Metalloproteomics: high-throughput structural and functional annotation of proteins in structural genomics. Structure 13, 1473-1486.&lt;/ref&gt;  </div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Of particular interest is zinc, which is the second most abundant transition metal in living organisms after Fe &lt;ref&gt;Lipscomb, W.N., and Strater, N. (1996). Recent Advances in Zinc Enzymology. Chem Rev 96, 2375-2434.&lt;/ref&gt;. The extent is highlighted in a recent bioinformatics analysis of the human proteome in which it was determined that as much 10% of the proteome is zinc-bound &lt;ref&gt;Andreini, C., Banci, L., Bertini, I., and Rosato, A. (2006). Counting the zinc-proteins encoded in the human genome. J Proteome Res 5, 196-201.&lt;/ref&gt;. In biology zinc is commonly assuming a structural role (structural zinc), and less commonly, a catalytic role&lt;ref <del style="font-weight: bold; text-decoration: none;">name=&quot;Passerini01&quot;</del>&gt;Passerini, A., <del style="font-weight: bold; text-decoration: none;">Punta</del>, <del style="font-weight: bold; text-decoration: none;">M</del>., <del style="font-weight: bold; text-decoration: none;">Ceroni</del>, <del style="font-weight: bold; text-decoration: none;">A</del>., <del style="font-weight: bold; text-decoration: none;">Rost</del>, <del style="font-weight: bold; text-decoration: none;">B</del>., and Frasconi, P. (<del style="font-weight: bold; text-decoration: none;">2006</del>). <del style="font-weight: bold; text-decoration: none;">Identifying cysteines and histidines in transition-metal-</del>binding <del style="font-weight: bold; text-decoration: none;">sites using support vector machines and neural networks</del>. <del style="font-weight: bold; text-decoration: none;">Proteins 65</del>, <del style="font-weight: bold; text-decoration: none;">305-316</del>&lt;/ref&gt;<del style="font-weight: bold; text-decoration: none;">. Structural zinc is tetrahedrally coordinated by the side-chains of a small subset of amino acids. The coordinating atoms are in-turn are stabilized by a hydrogen bonding network with amino acids in an outer coordinating sphere (Konrat et al., 1998)</del>.  </div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Of particular interest is zinc, which is the second most abundant transition metal in living organisms after Fe &lt;ref&gt;Lipscomb, W.N., and Strater, N. (1996). Recent Advances in Zinc Enzymology. Chem Rev 96, 2375-2434.&lt;/ref&gt;. The extent is highlighted in a recent bioinformatics analysis of the human proteome in which it was determined that as much 10% of the proteome is zinc-bound &lt;ref&gt;Andreini, C., Banci, L., Bertini, I., and Rosato, A. (2006). Counting the zinc-proteins encoded in the human genome. J Proteome Res 5, 196-201.&lt;/ref&gt;. In biology zinc is commonly assuming a structural role (structural zinc), and less commonly, a catalytic role</div></td></tr> <tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>&lt;ref&gt;Passerini, A., <ins style="font-weight: bold; text-decoration: none;">Andreini</ins>, <ins style="font-weight: bold; text-decoration: none;">C</ins>., <ins style="font-weight: bold; text-decoration: none;">Menchetti</ins>, <ins style="font-weight: bold; text-decoration: none;">S</ins>., <ins style="font-weight: bold; text-decoration: none;">Rosato</ins>, <ins style="font-weight: bold; text-decoration: none;">A</ins>., and Frasconi, P. (<ins style="font-weight: bold; text-decoration: none;">2007</ins>). <ins style="font-weight: bold; text-decoration: none;">Predicting zinc </ins>binding <ins style="font-weight: bold; text-decoration: none;">at the proteome level</ins>. <ins style="font-weight: bold; text-decoration: none;">BMC Bioinformatics 8</ins>, <ins style="font-weight: bold; text-decoration: none;">39.</ins>&lt;/ref&gt;.</div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>&lt;br&gt; In 2006 Passerini et al.<del style="font-weight: bold; text-decoration: none;">&lt;ref name=&quot;Passerini01&quot;/&gt;</del>, developed a de novo predictor of zinc-binding called ZincFinder &lt;ref&gt;Passerini, A., Andreini, C., Menchetti, S., Rosato, A., and Frasconi, P. (2007). Predicting zinc binding at the proteome level. BMC Bioinformatics 8, 39.&lt;/ref&gt;<del style="font-weight: bold; text-decoration: none;">&lt;ref name=&quot;Passerini01&quot;/&gt; </del>The algorithm uses sequence specific information and is trained on 230 zinc binding chains to recognize position specific evolutionary profiles. The algorithm also considers global parameters, such as chain length and amino acid composition, as well as local parameters, such as the distance between potential ligands. ZincFinder has a reported precision of 73% and a recall of 61%.  </div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr> <tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">Structural zinc is tetrahedrally coordinated by the side-chains of a small subset of amino acids. The coordinating atoms are in-turn are stabilized by a hydrogen bonding network with amino acids in an outer coordinating sphere. </ins></div></td></tr> <tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr> <tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>&lt;br&gt; In 2006 Passerini et al., developed a de novo predictor of zinc-binding called ZincFinder  </div></td></tr> <tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">&lt;ref&gt;Passerini, A., Punta, M., Ceroni, A., Rost, B., and Frasconi, P. (2006). Identifying cysteines and histidines in transition-metal-binding sites using support vector machines and neural networks. Proteins 65, 305-316&lt;/ref&gt;. </ins></div></td></tr> <tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>&lt;ref&gt;Passerini, A., Andreini, C., Menchetti, S., Rosato, A., and Frasconi, P. (2007). Predicting zinc binding at the proteome level. BMC Bioinformatics 8, 39.&lt;/ref&gt;</div></td></tr> <tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>The algorithm uses sequence specific information and is trained on 230 zinc binding chains to recognize position specific evolutionary profiles. The algorithm also considers global parameters, such as chain length and amino acid composition, as well as local parameters, such as the distance between potential ligands. ZincFinder has a reported precision of 73% and a recall of 61%.  </div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;br&gt;  </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;br&gt;  </div></td></tr> </table>

TheresaRamelot https://nesgwiki.chem.buffalo.edu/index.php?title=Cofactor_optimization&diff=3305&oldid=prev 2009-12-16T03:04:05Z

<p></p> <table style="background-color: #fff; color: #202122;" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 03:04, 16 December 2009</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l14">Line 14:</td> <td colspan="2" class="diff-lineno">Line 14:</td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>As many as 30% of proteins are predicted to be metal binding proteins and many of these may require metal for proper folding. In fact, a recent analysis of the PDB revealed that 14% of non-redundant entries contain stoichiometric amounts of six transition metals: Mn, Fe, Co, Ni, Cu or Zn &lt;ref&gt;Shi, W., Zhan, C., Ignatov, A., Manjasetty, B.A., Marinkovic, N., Sullivan, M., Huang, R., and Chance, M.R. (2005). Metalloproteomics: high-throughput structural and functional annotation of proteins in structural genomics. Structure 13, 1473-1486.&lt;/ref&gt;  </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>As many as 30% of proteins are predicted to be metal binding proteins and many of these may require metal for proper folding. In fact, a recent analysis of the PDB revealed that 14% of non-redundant entries contain stoichiometric amounts of six transition metals: Mn, Fe, Co, Ni, Cu or Zn &lt;ref&gt;Shi, W., Zhan, C., Ignatov, A., Manjasetty, B.A., Marinkovic, N., Sullivan, M., Huang, R., and Chance, M.R. (2005). Metalloproteomics: high-throughput structural and functional annotation of proteins in structural genomics. Structure 13, 1473-1486.&lt;/ref&gt;  </div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Of particular interest is zinc, which is the second most abundant transition metal in living organisms after Fe &lt;ref&gt;Lipscomb, W.N., and Strater, N. (1996). Recent Advances in Zinc Enzymology. Chem Rev 96, 2375-2434.&lt;/ref&gt;. The extent is highlighted in a recent bioinformatics analysis of the human proteome in which it was determined that as much 10% of the proteome is zinc-bound &lt;ref&gt;Andreini, C., Banci, L., Bertini, I., and Rosato, A. (2006). Counting the zinc-proteins encoded in the human genome. J Proteome Res 5, 196-201.&lt;/ref&gt;. In biology zinc is commonly assuming a structural role (structural zinc), and less commonly, a catalytic role&lt;ref&gt;Passerini, A., Punta, M., Ceroni, A., Rost, B., and Frasconi, P. (2006). Identifying cysteines and histidines in transition-metal-binding sites using support vector machines and neural networks. Proteins 65, 305-316&lt;/ref&gt;. Structural zinc is tetrahedrally coordinated by the side-chains of a small subset of amino acids. The coordinating atoms are in-turn are stabilized by a hydrogen bonding network with amino acids in an outer coordinating sphere (Konrat et al., 1998).  </div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Of particular interest is zinc, which is the second most abundant transition metal in living organisms after Fe &lt;ref&gt;Lipscomb, W.N., and Strater, N. (1996). Recent Advances in Zinc Enzymology. Chem Rev 96, 2375-2434.&lt;/ref&gt;. The extent is highlighted in a recent bioinformatics analysis of the human proteome in which it was determined that as much 10% of the proteome is zinc-bound &lt;ref&gt;Andreini, C., Banci, L., Bertini, I., and Rosato, A. (2006). Counting the zinc-proteins encoded in the human genome. J Proteome Res 5, 196-201.&lt;/ref&gt;. In biology zinc is commonly assuming a structural role (structural zinc), and less commonly, a catalytic role&lt;ref <ins style="font-weight: bold; text-decoration: none;">name=&quot;Passerini01&quot;</ins>&gt;Passerini, A., Punta, M., Ceroni, A., Rost, B., and Frasconi, P. (2006). Identifying cysteines and histidines in transition-metal-binding sites using support vector machines and neural networks. Proteins 65, 305-316&lt;/ref&gt;. Structural zinc is tetrahedrally coordinated by the side-chains of a small subset of amino acids. The coordinating atoms are in-turn are stabilized by a hydrogen bonding network with amino acids in an outer coordinating sphere (Konrat et al., 1998).  </div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>&lt;br&gt; In 2006 Passerini et al.&lt;ref<del style="font-weight: bold; text-decoration: none;">&gt;Passerini, A., Punta, M., Ceroni, A., Rost, B., and Frasconi, P. (2006). Identifying cysteines and histidines in transition-metal-binding sites using support vector machines and neural networks. Proteins 65, 305-316&lt;</del>/<del style="font-weight: bold; text-decoration: none;">ref</del>&gt;, developed a de novo predictor of zinc-binding called ZincFinder &lt;ref&gt;Passerini, A., Andreini, C., Menchetti, S., Rosato, A., and Frasconi, P. (2007). Predicting zinc binding at the proteome level. BMC Bioinformatics 8, 39.&lt;/ref&gt;&lt;ref<del style="font-weight: bold; text-decoration: none;">&gt;Passerini, A., Punta, M., Ceroni, A., Rost, B., and Frasconi, P. (2006). Identifying cysteines and histidines in transition-metal-binding sites using support vector machines and neural networks. Proteins 65, 305-316&lt;</del>/<del style="font-weight: bold; text-decoration: none;">ref</del>&gt; The algorithm uses sequence specific information and is trained on 230 zinc binding chains to recognize position specific evolutionary profiles. The algorithm also considers global parameters, such as chain length and amino acid composition, as well as local parameters, such as the distance between potential ligands. ZincFinder has a reported precision of 73% and a recall of 61%.  </div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>&lt;br&gt; In 2006 Passerini et al.&lt;ref <ins style="font-weight: bold; text-decoration: none;">name=&quot;Passerini01&quot;</ins>/&gt;, developed a de novo predictor of zinc-binding called ZincFinder &lt;ref&gt;Passerini, A., Andreini, C., Menchetti, S., Rosato, A., and Frasconi, P. (2007). Predicting zinc binding at the proteome level. BMC Bioinformatics 8, 39.&lt;/ref&gt;&lt;ref <ins style="font-weight: bold; text-decoration: none;">name=&quot;Passerini01&quot;</ins>/&gt; The algorithm uses sequence specific information and is trained on 230 zinc binding chains to recognize position specific evolutionary profiles. The algorithm also considers global parameters, such as chain length and amino acid composition, as well as local parameters, such as the distance between potential ligands. ZincFinder has a reported precision of 73% and a recall of 61%.  </div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;br&gt;  </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;br&gt;  </div></td></tr> </table>

Alex https://nesgwiki.chem.buffalo.edu/index.php?title=Cofactor_optimization&diff=2026&oldid=prev 2009-11-19T18:33:36Z

<p></p> <table style="background-color: #fff; color: #202122;" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 18:33, 19 November 2009</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l26">Line 26:</td> <td colspan="2" class="diff-lineno">Line 26:</td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>In this example (NESG ID IscU) the effect of metal chelation on protein stability was probed by a 2D &lt;sup&gt;1&lt;/sup&gt;H–&lt;sup&gt;15&lt;/sup&gt;N HSQC NMR experiment. The well dispersed spectra is indicative of global stability (left), collapsed spectra of unstructured protein (right) &lt;ref&gt;Ramelot, T.A., ''et. al.''  (2004) Solution NMR structure of the iron-sulfur cluster assembly protetin U (IscU) with zinc bound the active site.  Journal of Molecular Biology, 344, 567-583 &lt;/ref&gt;. Interestingly, IscU is an Fe-binding protein in vivo, but the metal is replaced by Zn during NMR sample preparation. &lt;br&gt;  </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>In this example (NESG ID IscU) the effect of metal chelation on protein stability was probed by a 2D &lt;sup&gt;1&lt;/sup&gt;H–&lt;sup&gt;15&lt;/sup&gt;N HSQC NMR experiment. The well dispersed spectra is indicative of global stability (left), collapsed spectra of unstructured protein (right) &lt;ref&gt;Ramelot, T.A., ''et. al.''  (2004) Solution NMR structure of the iron-sulfur cluster assembly protetin U (IscU) with zinc bound the active site.  Journal of Molecular Biology, 344, 567-583 &lt;/ref&gt;. Interestingly, IscU is an Fe-binding protein in vivo, but the metal is replaced by Zn during NMR sample preparation. &lt;br&gt;  </div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div> </div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>[[Image:Iscu nhsqcs.png]]&lt;br&gt;  </div></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">&lt;br&gt; </del></div></td><td colspan="2" class="diff-side-added"></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div> </div></td><td colspan="2" class="diff-side-added"></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>[[Image:Iscu nhsqcs.png]]&lt;br&gt;</div></td><td colspan="2" class="diff-side-added"></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Due to the adverse effect of metal chelation on protein structure, and the high prevalence of zinc, it is likely that a subset of NESG targeted proteins with poorly resolved 2D 1H–15N HSQC spectra, may have inadvertently lost structural zinc during the protein sample preparation.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Due to the adverse effect of metal chelation on protein structure, and the high prevalence of zinc, it is likely that a subset of NESG targeted proteins with poorly resolved 2D 1H–15N HSQC spectra, may have inadvertently lost structural zinc during the protein sample preparation.</div></td></tr> </table>

TheresaRamelot https://nesgwiki.chem.buffalo.edu/index.php?title=Cofactor_optimization&diff=2025&oldid=prev 2009-11-19T18:33:05Z

<p></p> <table style="background-color: #fff; color: #202122;" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 18:33, 19 November 2009</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l24">Line 24:</td> <td colspan="2" class="diff-lineno">Line 24:</td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;br&gt;  </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;br&gt;  </div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>In this example (NESG ID IscU) the effect of metal chelation on protein stability was probed by a 2D &lt;sup&gt;1&lt;/sup&gt;H–&lt;sup&gt;15&lt;/sup&gt;N HSQC NMR experiment. <del style="font-weight: bold; text-decoration: none;">A </del>well dispersed spectra is indicative of global stability, collapsed spectra of <del style="font-weight: bold; text-decoration: none;">instability </del>&lt;ref&gt;Ramelot, T.A., ''et. al.''  (2004) Solution NMR structure of the iron-sulfur cluster assembly protetin U (IscU) with zinc bound the active site.  Journal of Molecular Biology, 344, 567-583 &lt;/ref&gt;. <del style="font-weight: bold; text-decoration: none;">Due to the adverse effect of metal chelation on </del>protein <del style="font-weight: bold; text-decoration: none;">stability</del>, <del style="font-weight: bold; text-decoration: none;">and </del>the <del style="font-weight: bold; text-decoration: none;">high prevalence of zinc, it </del>is <del style="font-weight: bold; text-decoration: none;">likely that a subset of NESG targeted proteins with poorly resolved 2D 1H–15N HSQC spectra, may have inadvertently lost structural zinc </del>during <del style="font-weight: bold; text-decoration: none;">the protein </del>sample preparation.  </div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>In this example (NESG ID IscU) the effect of metal chelation on protein stability was probed by a 2D &lt;sup&gt;1&lt;/sup&gt;H–&lt;sup&gt;15&lt;/sup&gt;N HSQC NMR experiment. <ins style="font-weight: bold; text-decoration: none;">The </ins>well dispersed spectra is indicative of global stability <ins style="font-weight: bold; text-decoration: none;">(left)</ins>, collapsed spectra of <ins style="font-weight: bold; text-decoration: none;">unstructured protein (right) </ins>&lt;ref&gt;Ramelot, T.A., ''et. al.''  (2004) Solution NMR structure of the iron-sulfur cluster assembly protetin U (IscU) with zinc bound the active site.  Journal of Molecular Biology, 344, 567-583 &lt;/ref&gt;. <ins style="font-weight: bold; text-decoration: none;">Interestingly, IscU is an Fe-binding </ins>protein <ins style="font-weight: bold; text-decoration: none;">in vivo</ins>, <ins style="font-weight: bold; text-decoration: none;">but </ins>the <ins style="font-weight: bold; text-decoration: none;">metal </ins>is <ins style="font-weight: bold; text-decoration: none;">replaced by Zn </ins>during <ins style="font-weight: bold; text-decoration: none;">NMR </ins>sample preparation. <ins style="font-weight: bold; text-decoration: none;">&lt;br&gt; </ins></div></td></tr> <tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;br&gt;  </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;br&gt;  </div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">Interestingly, IscU is an Fe-binding protein in vivo, but the metal is replaced by Zn during NMR sample preparation</del>. <del style="font-weight: bold; text-decoration: none;">&lt;br&gt; </del></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">[[Image:Iscu nhsqcs</ins>.<ins style="font-weight: bold; text-decoration: none;">png]]</ins>&lt;br&gt;</div></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div> </div></td><td colspan="2" class="diff-side-added"></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>&lt;br&gt;  </div></td><td colspan="2" class="diff-side-added"></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">[[Image:iscu nhsqcs</del>.<del style="font-weight: bold; text-decoration: none;">png]]&lt;br&gt;</del></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">Due to the adverse effect of metal chelation on protein structure, and the high prevalence of zinc, it is likely that a subset of NESG targeted proteins with poorly resolved 2D 1H–15N HSQC spectra, may have inadvertently lost structural zinc during the protein sample preparation</ins>.</div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=== Addition of acetyl CoA to ''E. coli'' YhhK  ===</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=== Addition of acetyl CoA to ''E. coli'' YhhK  ===</div></td></tr> </table>

TheresaRamelot https://nesgwiki.chem.buffalo.edu/index.php?title=Cofactor_optimization&diff=2023&oldid=prev 2009-11-19T18:26:34Z

<p></p> <table style="background-color: #fff; color: #202122;" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 18:26, 19 November 2009</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l32">Line 32:</td> <td colspan="2" class="diff-lineno">Line 32:</td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;br&gt;  </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;br&gt;  </div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>[[Image:<del style="font-weight: bold; text-decoration: none;">iscu_nhsqcs</del>.png]]&lt;br&gt;</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>[[Image:<ins style="font-weight: bold; text-decoration: none;">iscu nhsqcs</ins>.png]]&lt;br&gt;</div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=== Addition of acetyl CoA to ''E. coli'' YhhK  ===</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=== Addition of acetyl CoA to ''E. coli'' YhhK  ===</div></td></tr> </table>

TheresaRamelot https://nesgwiki.chem.buffalo.edu/index.php?title=Cofactor_optimization&diff=2022&oldid=prev 2009-11-19T18:25:42Z

<p></p> <table style="background-color: #fff; color: #202122;" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 18:25, 19 November 2009</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l30">Line 30:</td> <td colspan="2" class="diff-lineno">Line 30:</td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Interestingly, IscU is an Fe-binding protein in vivo, but the metal is replaced by Zn during NMR sample preparation. &lt;br&gt;  </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Interestingly, IscU is an Fe-binding protein in vivo, but the metal is replaced by Zn during NMR sample preparation. &lt;br&gt;  </div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr> <tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">&lt;br> </ins></div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div> </div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">[[Image:iscu_nhsqcs.png]]</ins>&lt;br&gt;</div></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">''Insert IscU NHSQC figures here'' </del>&lt;br&gt;</div></td><td colspan="2" class="diff-side-added"></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=== Addition of acetyl CoA to ''E. coli'' YhhK  ===</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=== Addition of acetyl CoA to ''E. coli'' YhhK  ===</div></td></tr> </table>

TheresaRamelot