3nog

From Proteopedia

(Difference between revisions)

Revision as of 00:09, 5 August 2016

Designed ankyrin repeat protein (DARPin) Binders to AcrB: Plasticity of the Interface

Structural highlights

3nog is a 5 chain structure with sequence from Ecoli and Synthetic construct sequences. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
NonStd Res:
Related:	2j8s, 3noc
Gene:	acrB, acrE, b0462, JW0451 (ECOLI)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[ACRB_ECOLI] AcrAB is a drug efflux protein with a broad substrate specificity.^[1] ^[2] ^[3]

Publication Abstract from PubMed

The formation of well-diffracting crystals is a major bottleneck in structural analysis of membrane proteins by X-ray crystallography. One approach to improve crystal quality is the use of DARPins as crystallization chaperones. Here, we present a detailed analysis of the interaction between DARPins and the integral membrane protein AcrB. We find that binders selected in vitro by ribosome display share a common epitope. The comparative analysis of three crystal structures of AcrB-DARPin complexes allowed us to study the plasticity of the interaction with this dominant binding site. Seemingly redundant AcrB-DARPin crystals show substantially different diffraction quality as a result of subtle differences in the binding geometry. This work exemplifies the importance to screen a number of crystallization chaperones to obtain optimal diffraction data. Crystallographic analysis is complemented by biophysical characterization of nine AcrB binders. We observe that small variations in the interface can lead to differing behavior of the DARPins with regards to affinity, stoichiometry of the complexes and specificity for their target.

Designed ankyrin repeat protein binders for the crystallization of AcrB: Plasticity of the dominant interface.,Monroe N, Sennhauser G, Seeger MA, Briand C, Grutter MG J Struct Biol. 2011 May;174(2):269-81. Epub 2011 Feb 4. PMID:21296164^[4]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Murakami S, Nakashima R, Yamashita E, Matsumoto T, Yamaguchi A. Crystal structures of a multidrug transporter reveal a functionally rotating mechanism. Nature. 2006 Sep 14;443(7108):173-9. Epub 2006 Aug 16. PMID:16915237 doi:10.1038/nature05076
↑ Seeger MA, Schiefner A, Eicher T, Verrey F, Diederichs K, Pos KM. Structural asymmetry of AcrB trimer suggests a peristaltic pump mechanism. Science. 2006 Sep 1;313(5791):1295-8. PMID:16946072 doi:313/5791/1295
↑ Sennhauser G, Amstutz P, Briand C, Storchenegger O, Grutter MG. Drug export pathway of multidrug exporter AcrB revealed by DARPin inhibitors. PLoS Biol. 2007 Jan;5(1):e7. PMID:17194213 doi:10.1371/journal.pbio.0050007
↑ Monroe N, Sennhauser G, Seeger MA, Briand C, Grutter MG. Designed ankyrin repeat protein binders for the crystallization of AcrB: Plasticity of the dominant interface. J Struct Biol. 2011 May;174(2):269-81. Epub 2011 Feb 4. PMID:21296164 doi:10.1016/j.jsb.2011.01.014

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3nog"

@@ Line 1: / Line 1: @@
 ==Designed ankyrin repeat protein (DARPin) Binders to AcrB: Plasticity of the Interface==
 <StructureSection load='3nog' size='340' side='right' caption='[[3nog]], [[Resolution|resolution]] 3.34&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3nog]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [http://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NOG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3NOG FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3nog]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli] and [http://en.wikipedia.org/wiki/Synthetic_construct_sequences Synthetic construct sequences]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NOG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3NOG FirstGlance]. <br>
 </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=FME:N-FORMYLMETHIONINE'>FME</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2j8s|2j8s]], [[3noc|3noc]]</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">acrB, acrE, b0462, JW0451 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">acrB, acrE, b0462, JW0451 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=3nog FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nog OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3nog RCSB], [http://www.ebi.ac.uk/pdbsum/3nog PDBsum]</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=3nog FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nog OCA], [http://pdbe.org/3nog PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3nog RCSB], [http://www.ebi.ac.uk/pdbsum/3nog PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3nog ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 18: / Line 19: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3nog" style="background-color:#fffaf0;"></div>
 ==See Also==
@@ Line 25: / Line 27: @@
 __TOC__
 </StructureSection>
-[[Category: Escherichia coli]]
+[[Category: Ecoli]]
-[[Category: Synthetic construct]]
+[[Category: Synthetic construct sequences]]
 [[Category: Briand, C]]
 [[Category: Gruetter, M G]]

3nog

From Proteopedia

Revision as of 00:09, 5 August 2016

Designed ankyrin repeat protein (DARPin) Binders to AcrB: Plasticity of the Interface

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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