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| | ==Bicyclic antimibrocial peptides== | | ==Bicyclic antimibrocial peptides== |
| - | <StructureSection load='5i8x' size='340' side='right' caption='[[5i8x]], [[Resolution|resolution]] 1.89Å' scene=''> | + | <StructureSection load='5i8x' size='340' side='right'caption='[[5i8x]], [[Resolution|resolution]] 1.89Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5i8x]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_aeruginosus"_(schroeter_1872)_trevisan_1885 "bacillus aeruginosus" (schroeter 1872) trevisan 1885]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I8X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5I8X FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5i8x]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I8X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5I8X FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=ZDC:3,7-ANHYDRO-2,8-DIDEOXY-L-GLYCERO-D-GLUCO-OCTONIC+ACID'>ZDC</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.89Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DLS:DI-ACETYL-LYSINE'>DLS</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DLS:DI-ACETYL-LYSINE'>DLS</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene>, <scene name='pdbligand=ZDC:3,7-ANHYDRO-2,8-DIDEOXY-L-GLYCERO-D-GLUCO-OCTONIC+ACID'>ZDC</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">lecB, AN280_27645, AN399_05715, AN400_17270, AN446_25935, AN447_15925, AN451_21855, AN453_22575, AN455_18155, AN456_19070, AN457_11175, AN458_15745, AN460_27980, AN462_17515, AOD73_08535, AOX61_23230, AOX62_26425, APG03_22020, APG04_23970, APG05_03535, APG06_28020, APG07_27985, ATC05_02360, ERS445055_01627, PA8380_17510, PAERUG_E15_London_28_01_14_00983, PAERUG_P32_London_17_VIM_2_10_11_00423, PAMH19_1713, PAO1OR1608 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=287 "Bacillus aeruginosus" (Schroeter 1872) Trevisan 1885])</td></tr>
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5i8x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i8x OCA], [https://pdbe.org/5i8x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5i8x RCSB], [https://www.ebi.ac.uk/pdbsum/5i8x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5i8x ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5i8x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i8x OCA], [http://pdbe.org/5i8x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5i8x RCSB], [http://www.ebi.ac.uk/pdbsum/5i8x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5i8x ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/Q9HYN5_PSEAE Q9HYN5_PSEAE] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bonaventura, I Di]] | + | [[Category: Large Structures]] |
| - | [[Category: Darbre, T]]
| + | |
| - | [[Category: Delden, C van]]
| + | |
| - | [[Category: Jin, X]]
| + | |
| - | [[Category: Koehler, T]]
| + | |
| - | [[Category: Michaud, G]]
| + | |
| - | [[Category: Reymond, J L]]
| + | |
| - | [[Category: Robadey, M]]
| + | |
| - | [[Category: Stocker, A]]
| + | |
| - | [[Category: Visini, R]]
| + | |
| - | [[Category: Antimicrobial peptide]]
| + | |
| - | [[Category: Bicycle]]
| + | |
| - | [[Category: Biofilm]]
| + | |
| | [[Category: Pseudomonas aeruginosa]] | | [[Category: Pseudomonas aeruginosa]] |
| - | [[Category: Sugar binding protein]] | + | [[Category: Synthetic construct]] |
| | + | [[Category: Darbre T]] |
| | + | [[Category: Di Bonaventura I]] |
| | + | [[Category: Jin X]] |
| | + | [[Category: Koehler T]] |
| | + | [[Category: Michaud G]] |
| | + | [[Category: Reymond J-L]] |
| | + | [[Category: Robadey M]] |
| | + | [[Category: Stocker A]] |
| | + | [[Category: Visini R]] |
| | + | [[Category: Van Delden C]] |
| Structural highlights
Function
Q9HYN5_PSEAE
Publication Abstract from PubMed
Herein we report the discovery of antimicrobial bridged bicyclic peptides (AMBPs) active against Pseudomonas aeruginosa, a highly problematic Gram negative bacterium in the hospital environment. Two of these AMBPs show strong biofilm inhibition and dispersal activity and enhance the activity of polymyxin, currently a last resort antibiotic against which resistance is emerging. To discover our AMBPs we used the concept of chemical space, which is well known in the area of small molecule drug discovery, to define a small number of test compounds for synthesis and experimental evaluation. Our chemical space was calculated using 2DP, a new topological shape and pharmacophore fingerprint for peptides. This method provides a general strategy to search for bioactive peptides with unusual topologies and expand the structural diversity of peptide-based drugs.
Chemical space guided discovery of antimicrobial bridged bicyclic peptides against Pseudomonas aeruginosa and its biofilms.,Di Bonaventura I, Jin X, Visini R, Probst D, Javor S, Gan BH, Michaud G, Natalello A, Doglia SM, Kohler T, van Delden C, Stocker A, Darbre T, Reymond JL Chem Sci. 2017 Oct 1;8(10):6784-6798. doi: 10.1039/c7sc01314k. Epub 2017 Jul 13. PMID:29147502[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Di Bonaventura I, Jin X, Visini R, Probst D, Javor S, Gan BH, Michaud G, Natalello A, Doglia SM, Kohler T, van Delden C, Stocker A, Darbre T, Reymond JL. Chemical space guided discovery of antimicrobial bridged bicyclic peptides against Pseudomonas aeruginosa and its biofilms. Chem Sci. 2017 Oct 1;8(10):6784-6798. doi: 10.1039/c7sc01314k. Epub 2017 Jul 13. PMID:29147502 doi:http://dx.doi.org/10.1039/c7sc01314k
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