3ned: Difference between revisions
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< | ==mRouge== | ||
<StructureSection load='3ned' size='340' side='right'caption='[[3ned]], [[Resolution|resolution]] 0.95Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[3ned]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Discosoma_sp. Discosoma sp.]. 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='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 0.95Å</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=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=NA:SODIUM+ION'>NA</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='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> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/D1MPT3_DISSP D1MPT3_DISSP] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The 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<ref>PMID:21059931</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 3ned" style="background-color:#fffaf0;"></div> | |||
== | ==See Also== | ||
*[[Green Fluorescent Protein 3D structures|Green Fluorescent Protein 3D structures]] | |||
[[Category: Discosoma sp | == References == | ||
[[Category: | <references/> | ||
[[Category: | __TOC__ | ||
[[Category: | </StructureSection> | ||
[[Category: | [[Category: Discosoma sp]] | ||
[[Category: Large Structures]] | |||
[[Category: Chica RA]] | |||
[[Category: Mayo SL]] | |||
[[Category: Moore MM]] | |||
Latest revision as of 12:03, 15 November 2023
mRougemRouge
Structural highlights
FunctionPublication 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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