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| | + | '''Unreleased structure''' |
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| - | ==Kelch domain of KEAP1 in complex with ortho-dimethylbenzene linked cyclic peptide CP3 (ortho-WRCDEETGEC)==
| + | The entry 8pku is ON HOLD until Paper Publication |
| - | <StructureSection load='8pku' size='340' side='right'caption='[[8pku]], [[Resolution|resolution]] 1.73Å' scene=''>
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| - | == Structural highlights ==
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| - | <table><tr><td colspan='2'>[[8pku]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8PKU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8PKU FirstGlance]. <br>
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| - | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.73Å</td></tr>
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| - | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZK2:(2-methylphenyl)methanol'>ZK2</scene></td></tr>
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| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=8pku FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8pku OCA], [https://pdbe.org/8pku PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8pku RCSB], [https://www.ebi.ac.uk/pdbsum/8pku PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8pku ProSAT]</span></td></tr>
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| - | </table>
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| - | == Function ==
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| - | [https://www.uniprot.org/uniprot/KEAP1_HUMAN KEAP1_HUMAN]
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| - | <div style="background-color:#fffaf0;">
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| - | == Publication Abstract from PubMed ==
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| - | The Nrf2 transcription factor is a master regulator of the cellular response to oxidative stress, and Keap1 is its primary negative regulator. Activating Nrf2 by inhibiting the Nrf2-Keap1 protein-protein interaction has shown promise for treating cancer and inflammatory diseases. A loop derived from Nrf2 has been shown to inhibit Keap1 selectively, especially when cyclized, but there are no reliable design methods for predicting an optimal macrocyclization strategy. In this work, we employed all-atom, explicit-solvent molecular dynamics simulations with enhanced sampling methods to predict the relative degree of preorganization for a series of peptides cyclized with a set of bis-thioether "staples". We then correlated these predictions to experimentally measured binding affinities for Keap1 and crystal structures of the cyclic peptides bound to Keap1. This work showcases a computational method for designing cyclic peptides by simulating and comparing their entire solution-phase ensembles, providing key insights into designing cyclic peptides as selective inhibitors of protein-protein interactions.
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| - | Computational Prediction of Cyclic Peptide Structural Ensembles and Application to the Design of Keap1 Binders.,Fonseca Lopez F, Miao J, Damjanovic J, Bischof L, Braun MB, Ling Y, Hartmann MD, Lin YS, Kritzer JA J Chem Inf Model. 2023 Nov 13;63(21):6925-6937. doi: 10.1021/acs.jcim.3c01337. , Epub 2023 Nov 2. PMID:37917529<ref>PMID:37917529</ref>
| + | Authors: |
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| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
| + | Description: |
| - | </div>
| + | [[Category: Unreleased Structures]] |
| - | <div class="pdbe-citations 8pku" style="background-color:#fffaf0;"></div>
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| - | == References ==
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| - | <references/>
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| - | __TOC__
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| - | </StructureSection>
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| - | [[Category: Homo sapiens]] | + | |
| - | [[Category: Large Structures]]
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| - | [[Category: Bischof L]]
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| - | [[Category: Braun MB]]
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| - | [[Category: Hartmann MD]]
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