3ned: Difference between revisions
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==mRouge== | ==mRouge== | ||
<StructureSection load='3ned' size='340' side='right' caption='[[3ned]], [[Resolution|resolution]] 0.95Å' scene=''> | <StructureSection load='3ned' size='340' side='right'caption='[[3ned]], [[Resolution|resolution]] 0.95Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3ned]] is a 1 chain structure with sequence from [ | <table><tr><td colspan='2'>[[3ned]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Dissp Dissp]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NED OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3NED FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr> | ||
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CH6:{(4Z)-2-[(1S)-1-AMINO-3-(METHYLSULFANYL)PROPYL]-4-[(4-HYDROXYPHENYL)METHYLIDENE]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC+ACID'>CH6</scene>, <scene name='pdbligand=EYG:{(2R,4Z)-2-[(1R)-1-AMINO-3-(METHYLSULFANYL)PROPYL]-2-HYDROXY-4-[(4-HYDROXYPHENYL)METHYLIDENE]-5-OXOIMIDAZOLIDIN-1-YL}ACETIC+ACID'>EYG</scene>, <scene name='pdbligand=NRQ:{(4Z)-4-(4-HYDROXYBENZYLIDENE)-2-[3-(METHYLTHIO)PROPANIMIDOYL]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC+ACID'>NRQ</scene></td></tr> | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CH6:{(4Z)-2-[(1S)-1-AMINO-3-(METHYLSULFANYL)PROPYL]-4-[(4-HYDROXYPHENYL)METHYLIDENE]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC+ACID'>CH6</scene>, <scene name='pdbligand=EYG:{(2R,4Z)-2-[(1R)-1-AMINO-3-(METHYLSULFANYL)PROPYL]-2-HYDROXY-4-[(4-HYDROXYPHENYL)METHYLIDENE]-5-OXOIMIDAZOLIDIN-1-YL}ACETIC+ACID'>EYG</scene>, <scene name='pdbligand=NRQ:{(4Z)-4-(4-HYDROXYBENZYLIDENE)-2-[3-(METHYLTHIO)PROPANIMIDOYL]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC+ACID'>NRQ</scene></td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PAmCherry, PAmCherry1 ([ | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PAmCherry, PAmCherry1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=86600 DISSP])</td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3ned FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ned OCA], [https://pdbe.org/3ned PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ned RCSB], [https://www.ebi.ac.uk/pdbsum/3ned PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ned ProSAT]</span></td></tr> | ||
</table> | </table> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
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</div> | </div> | ||
<div class="pdbe-citations 3ned" style="background-color:#fffaf0;"></div> | <div class="pdbe-citations 3ned" style="background-color:#fffaf0;"></div> | ||
==See Also== | |||
*[[Green Fluorescent Protein 3D structures|Green Fluorescent Protein 3D structures]] | |||
== References == | == References == | ||
<references/> | <references/> | ||
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</StructureSection> | </StructureSection> | ||
[[Category: Dissp]] | [[Category: Dissp]] | ||
[[Category: Large Structures]] | |||
[[Category: Chica, R A]] | [[Category: Chica, R A]] | ||
[[Category: Mayo, S L]] | [[Category: Mayo, S L]] | ||
Revision as of 10:00, 12 May 2022
mRougemRouge
Structural highlights
Publication Abstract from PubMedThe longer emission wavelengths of red fluorescent proteins (RFPs) make them attractive for whole-animal imaging because cells are more transparent to red light. Although several useful RFPs have been developed using directed evolution, the quest for further red-shifted and improved RFPs continues. Herein, we report a structure-based rational design approach to red-shift the fluorescence emission of RFPs. We applied a combined computational and experimental approach that uses computational protein design as an in silico prescreen to generate focused combinatorial libraries of mCherry mutants. The computational procedure helped us identify residues that could fulfill interactions hypothesized to cause red-shifts without destabilizing the protein fold. These interactions include stabilization of the excited state through H-bonding to the acylimine oxygen atom, destabilization of the ground state by hydrophobic packing around the charged phenolate, and stabilization of the excited state by a pi-stacking interaction. Our methodology allowed us to identify three mCherry mutants (mRojoA, mRojoB, and mRouge) that display emission wavelengths > 630 nm, representing red-shifts of 20-26 nm. Moreover, our approach required the experimental screening of a total of approximately 5,000 clones, a number several orders of magnitude smaller than those previously used to achieve comparable red-shifts. Additionally, crystal structures of mRojoA and mRouge allowed us to verify fulfillment of the interactions hypothesized to cause red-shifts, supporting their contribution to the observed red-shifts. Generation of longer emission wavelength red fluorescent proteins using computationally designed libraries.,Chica RA, Moore MM, Allen BD, Mayo SL Proc Natl Acad Sci U S A. 2010 Nov 23;107(47):20257-62. doi:, 10.1073/pnas.1013910107. Epub 2010 Nov 8. PMID:21059931[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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