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| | ==Computational design of an eight-stranded (beta/alpha)-barrel from fragments of different folds== | | ==Computational design of an eight-stranded (beta/alpha)-barrel from fragments of different folds== |
| - | <StructureSection load='2lle' size='340' side='right' caption='[[2lle]], [[NMR_Ensembles_of_Models | 17 NMR models]]' scene=''> | + | <StructureSection load='2lle' size='340' side='right'caption='[[2lle]]' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2lle]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43589 Atcc 43589]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LLE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2LLE FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2lle]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LLE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2LLE FirstGlance]. <br> |
| - | </td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">cheY, TM_0700, hisF, TM_1036 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2336 ATCC 43589])</td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=2lle FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lle OCA], [http://pdbe.org/2lle PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2lle RCSB], [http://www.ebi.ac.uk/pdbsum/2lle PDBsum]</span></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=2lle FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lle OCA], [https://pdbe.org/2lle PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2lle RCSB], [https://www.ebi.ac.uk/pdbsum/2lle PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2lle ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/CHEY_THEMA CHEY_THEMA]] Involved in the transmission of sensory signals from the chemoreceptors to the flagellar motors. CheY seems to regulate the clockwise (CW) rotation (By similarity). | + | [https://www.uniprot.org/uniprot/HIS6_THEMA HIS6_THEMA] IGPS catalyzes the conversion of PRFAR and glutamine to IGP, AICAR and glutamate. The HisF subunit catalyzes the cyclization activity that produces IGP and AICAR from PRFAR using the ammonia provided by the HisH subunit.[HAMAP-Rule:MF_01013][https://www.uniprot.org/uniprot/CHEY_THEMA CHEY_THEMA] Involved in the transmission of sensory signals from the chemoreceptors to the flagellar motors. CheY seems to regulate the clockwise (CW) rotation (By similarity). |
| - | <div style="background-color:#fffaf0;">
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| - | == Publication Abstract from PubMed ==
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| - | It is hypothesized that protein domains evolved from smaller intrinsically stable subunits via combinatorial assembly. Illegitimate recombination of fragments that encode protein subunits could have quickly led to diversification of protein folds and their functionality. This evolutionary concept presents an attractive strategy to protein engineering, e.g., to create new scaffolds for enzyme design. We previously combined structurally similar parts from two ancient protein folds, the (betaalpha)(8)-barrel and the flavodoxin-like fold. The resulting "hopeful monster" differed significantly from the intended (betaalpha)(8)-barrel fold by an extra beta-strand in the core. In this study, we ask what modifications are necessary to form the intended structure and what potential this approach has for the rational design of functional proteins. Guided by computational design, we optimized the interface between the fragments with five targeted mutations yielding a stable, monomeric protein whose predicted structure was verified experimentally. We further tested binding of a phosphorylated compound and detected that some affinity was already present due to an intact phosphate-binding site provided by one fragment. The affinity could be improved quickly to the level of natural proteins by introducing two additional mutations. The study illustrates the potential of recombining protein fragments with unique properties to design new and functional proteins, offering both a possible pathway of protein evolution and a protocol to rapidly engineer proteins for new applications.
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| - | Potential of fragment recombination for rational design of proteins.,Eisenbeis S, Proffitt W, Coles M, Truffault V, Shanmugaratnam S, Meiler J, Hocker B J Am Chem Soc. 2012 Mar 7;134(9):4019-22. Epub 2012 Feb 23. PMID:22329686<ref>PMID:22329686</ref>
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| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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| - | </div>
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| - | <div class="pdbe-citations 2lle" style="background-color:#fffaf0;"></div>
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| - | == References ==
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| - | <references/>
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Atcc 43589]] | + | [[Category: Large Structures]] |
| - | [[Category: Coles, M]] | + | [[Category: Thermotoga maritima]] |
| - | [[Category: Eisenbeis, S]] | + | [[Category: Coles M]] |
| - | [[Category: Hocker, B]] | + | [[Category: Eisenbeis S]] |
| - | [[Category: Meiler, J]] | + | [[Category: Hocker B]] |
| - | [[Category: Proffitt, W]] | + | [[Category: Meiler J]] |
| - | [[Category: Truffault, V]] | + | [[Category: Proffitt W]] |
| - | [[Category: Chimeric protein]]
| + | [[Category: Truffault V]] |
| - | [[Category: Computationally designed protein]]
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| - | [[Category: Lyase]]
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| - | [[Category: Tim-barrel]]
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