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| | ==Selection of specific protein binders for pre-defined targets from an optimized library of artificial helicoidal repeat proteins (alphaRep)== | | ==Selection of specific protein binders for pre-defined targets from an optimized library of artificial helicoidal repeat proteins (alphaRep)== |
| - | <StructureSection load='4jw3' size='340' side='right' caption='[[4jw3]], [[Resolution|resolution]] 2.60Å' scene=''> | + | <StructureSection load='4jw3' size='340' side='right'caption='[[4jw3]], [[Resolution|resolution]] 2.60Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4jw3]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Gekko_coi Gekko coi] and [http://en.wikipedia.org/wiki/Streptomyces_malayensis Streptomyces malayensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JW3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4JW3 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4jw3]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_malayensis Streptomyces malayensis] 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=4JW3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4JW3 FirstGlance]. <br> |
| - | </td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3ltm|3ltm]], [[4jw2|4jw2]]</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]] 2.6Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ncsA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1918 Streptomyces malayensis])</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=4jw3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jw3 OCA], [https://pdbe.org/4jw3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4jw3 RCSB], [https://www.ebi.ac.uk/pdbsum/4jw3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4jw3 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=4jw3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jw3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4jw3 RCSB], [http://www.ebi.ac.uk/pdbsum/4jw3 PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/NCZS_STRML NCZS_STRML]] NCS has antibiotic activity (for Gram-positive bacteria) and antitumor activity (for certain mouse tumors). NCS binds non-covalently to a chromophore which is the cytotoxic and mutagenic component of the antibiotic. The chromophore binds to DNA as a weak intercalator and causes single- and double-strand breaks. | + | [https://www.uniprot.org/uniprot/NCZS_STRML NCZS_STRML] NCS has antibiotic activity (for Gram-positive bacteria) and antitumor activity (for certain mouse tumors). NCS binds non-covalently to a chromophore which is the cytotoxic and mutagenic component of the antibiotic. The chromophore binds to DNA as a weak intercalator and causes single- and double-strand breaks. |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | </div> | | </div> |
| | + | <div class="pdbe-citations 4jw3" style="background-color:#fffaf0;"></div> |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Gekko coi]] | + | [[Category: Large Structures]] |
| | [[Category: Streptomyces malayensis]] | | [[Category: Streptomyces malayensis]] |
| - | [[Category: Chevrel, A]] | + | [[Category: Synthetic construct]] |
| - | [[Category: Desmadril, M]] | + | [[Category: Chevrel A]] |
| - | [[Category: Fourati-Kammoun, Z]] | + | [[Category: Desmadril M]] |
| - | [[Category: Graille, M]] | + | [[Category: Fourati-Kammoun Z]] |
| - | [[Category: Guellouz, A]] | + | [[Category: Graille M]] |
| - | [[Category: Minard, P]] | + | [[Category: Guellouz A]] |
| - | [[Category: Tilbeurgh, H van]]
| + | [[Category: Minard P]] |
| - | [[Category: Urvoas, A]] | + | [[Category: Urvoas A]] |
| - | [[Category: Valerio-Lepiniec, M]] | + | [[Category: Valerio-Lepiniec M]] |
| - | [[Category: Alpha-helical protein]] | + | [[Category: Van Tilbeurgh H]] |
| - | [[Category: Dna binding protein-de novo protein complex]]
| + | |
| - | [[Category: Ncs 3tes24 variant]]
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| - | [[Category: Protein engineered to interact with protein of interest]]
| + | |
| Structural highlights
Function
NCZS_STRML NCS has antibiotic activity (for Gram-positive bacteria) and antitumor activity (for certain mouse tumors). NCS binds non-covalently to a chromophore which is the cytotoxic and mutagenic component of the antibiotic. The chromophore binds to DNA as a weak intercalator and causes single- and double-strand breaks.
Publication Abstract from PubMed
We previously designed a new family of artificial proteins named alphaRep based on a subgroup of thermostable helicoidal HEAT-like repeats. We have now assembled a large optimized alphaRep library. In this library, the side chains at each variable position are not fully randomized but instead encoded by a distribution of codons based on the natural frequency of side chains of the natural repeats family. The library construction is based on a polymerization of micro-genes and therefore results in a distribution of proteins with a variable number of repeats. We improved the library construction process using a "filtration" procedure to retain only fully coding modules that were recombined to recreate sequence diversity. The final library named Lib2.1 contains 1.7x10(9) independent clones. Here, we used phage display to select, from the previously described library or from the new library, new specific alphaRep proteins binding to four different non-related predefined protein targets. Specific binders were selected in each case. The results show that binders with various sizes are selected including relatively long sequences, with up to 7 repeats. ITC-measured affinities vary with Kd values ranging from micromolar to nanomolar ranges. The formation of complexes is associated with a significant thermal stabilization of the bound target protein. The crystal structures of two complexes between alphaRep and their cognate targets were solved and show that the new interfaces are established by the variable surfaces of the repeated modules, as well by the variable N-cap residues. These results suggest that alphaRep library is a new and versatile source of tight and specific binding proteins with favorable biophysical properties.
Selection of Specific Protein Binders for Pre-Defined Targets from an Optimized Library of Artificial Helicoidal Repeat Proteins (alphaRep).,Guellouz A, Valerio-Lepiniec M, Urvoas A, Chevrel A, Graille M, Fourati-Kammoun Z, Desmadril M, van Tilbeurgh H, Minard P PLoS One. 2013 Aug 27;8(8):e71512. doi: 10.1371/journal.pone.0071512. PMID:24014183[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Guellouz A, Valerio-Lepiniec M, Urvoas A, Chevrel A, Graille M, Fourati-Kammoun Z, Desmadril M, van Tilbeurgh H, Minard P. Selection of Specific Protein Binders for Pre-Defined Targets from an Optimized Library of Artificial Helicoidal Repeat Proteins (alphaRep). PLoS One. 2013 Aug 27;8(8):e71512. doi: 10.1371/journal.pone.0071512. PMID:24014183 doi:10.1371/journal.pone.0071512
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