2lle

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[[Image:2lle.jpg|left|200px]]
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==Computational design of an eight-stranded (beta/alpha)-barrel from fragments of different folds==
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<StructureSection load='2lle' size='340' side='right' caption='[[2lle]], [[NMR_Ensembles_of_Models | 17 NMR models]]' scene=''>
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== Structural highlights ==
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[[2lle]] is a 1 chain structure with sequence from [http://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]. <br>
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<b>Activity:</b> <span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span><br>
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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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The line below this paragraph, containing "STRUCTURE_2lle", creates the "Structure Box" on the page.
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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or leave the SCENE parameter empty for the default display.
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{{STRUCTURE_2lle| PDB=2lle | SCENE= }}
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===Computational design of an eight-stranded (beta/alpha)-barrel from fragments of different folds===
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From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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== References ==
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<references/>
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The line below this paragraph, {{ABSTRACT_PUBMED_22329686}}, adds the Publication Abstract to the page
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</StructureSection>
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(as it appears on PubMed at http://www.pubmed.gov), where 22329686 is the PubMed ID number.
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{{ABSTRACT_PUBMED_22329686}}
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==About this Structure==
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[[2lle]] is a 1 chain structure with sequence from [http://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].
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==Reference==
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<ref group="xtra">PMID:022329686</ref><references group="xtra"/>
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[[Category: Thermotoga maritima]]
[[Category: Thermotoga maritima]]
[[Category: Coles, M.]]
[[Category: Coles, M.]]

Revision as of 08:37, 30 April 2014

Computational design of an eight-stranded (beta/alpha)-barrel from fragments of different folds

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