1rm9: Difference between revisions
No edit summary |
No edit summary |
||
| (11 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
< | ==Probing the Role of Tryptophans in Aequorea Victoria Green Fluorescent Proteins with an Expanded Genetic Code== | ||
<StructureSection load='1rm9' size='340' side='right'caption='[[1rm9]], [[Resolution|resolution]] 2.90Å' scene=''> | |||
You may | == Structural highlights == | ||
<table><tr><td colspan='2'>[[1rm9]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aequorea_victoria Aequorea victoria]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RM9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RM9 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]] 2.9Å</td></tr> | |||
-- | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=4F3:[2-(1-AMINO-2-HYDROXY-PROPYL)-4-(4-FLUORO-1H-INDOL-3-YLMETHYL)-5-HYDROXY-IMIDAZOL-1-YL]-ACETIC+ACID'>4F3</scene>, <scene name='pdbligand=4FW:4-FLUOROTRYPTOPHANE'>4FW</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=1rm9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rm9 OCA], [https://pdbe.org/1rm9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rm9 RCSB], [https://www.ebi.ac.uk/pdbsum/1rm9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rm9 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/GFP_AEQVI GFP_AEQVI] Energy-transfer acceptor. Its role is to transduce the blue chemiluminescence of the protein aequorin into green fluorescent light by energy transfer. Fluoresces in vivo upon receiving energy from the Ca(2+)-activated photoprotein aequorin. | |||
== Evolutionary Conservation == | |||
[[Image:Consurf_key_small.gif|200px|right]] | |||
Check<jmol> | |||
<jmolCheckbox> | |||
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rm/1rm9_consurf.spt"</scriptWhenChecked> | |||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | |||
<text>to colour the structure by Evolutionary Conservation</text> | |||
</jmolCheckbox> | |||
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1rm9 ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The expanded genetic code in combination with site-directed mutagenesis was used to probe spectroscopic and structural roles of tryptophan (Trp) residues in Aequorea victoria green fluorescent proteins (avGFPs). Nine different halogen-, chalcogen-, and methyl-containing Trp isosteric analogues and surrogates were incorporated into avGFPs containing indole moieties in, and outside of, the chromophore, by the use of the selective pressure incorporation method. Such isosteric replacements introduced minimal local geometry changes in indole moieties, often to the level of single atomic exchange ('atomic mutation') and do not affect three-dimensional structures of avGFPs but induce changes in spectral properties. Our approach offers a new platform to re-evaluate issues like resonance transfer, mechanisms of chromophore formation and maturation, as well as the importance of local geometry and weak sulphur-aromatic interactions for avGFP spectral properties and structural stability. The library of novel tailor-made avGFP mutants and variants generated in this work has demonstrated not only the potentials of the expanded genetic code to study spectroscopic functions, but also a new approach to generate tailor-made proteins with interesting and useful spectral properties. | |||
Probing the role of tryptophans in Aequorea victoria green fluorescent proteins with an expanded genetic code.,Budisa N, Pal PP, Alefelder S, Birle P, Krywcun T, Rubini M, Wenger W, Bae JH, Steiner T Biol Chem. 2004 Feb;385(2):191-202. PMID:15101562<ref>PMID:15101562</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 1rm9" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Green Fluorescent Protein 3D structures|Green Fluorescent Protein 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
== | |||
== | |||
< | |||
[[Category: Aequorea victoria]] | [[Category: Aequorea victoria]] | ||
[[Category: Alefelder | [[Category: Large Structures]] | ||
[[Category: Bae | [[Category: Alefelder S]] | ||
[[Category: Birle | [[Category: Bae JH]] | ||
[[Category: Budisa | [[Category: Birle P]] | ||
[[Category: Krywcun | [[Category: Budisa N]] | ||
[[Category: Pal | [[Category: Krywcun T]] | ||
[[Category: Rubini | [[Category: Pal PP]] | ||
[[Category: Steiner | [[Category: Rubini M]] | ||
[[Category: Wenger | [[Category: Steiner T]] | ||
[[Category: Wenger W]] | |||
Latest revision as of 09:06, 23 August 2023
Probing the Role of Tryptophans in Aequorea Victoria Green Fluorescent Proteins with an Expanded Genetic CodeProbing the Role of Tryptophans in Aequorea Victoria Green Fluorescent Proteins with an Expanded Genetic Code
Structural highlights
FunctionGFP_AEQVI Energy-transfer acceptor. Its role is to transduce the blue chemiluminescence of the protein aequorin into green fluorescent light by energy transfer. Fluoresces in vivo upon receiving energy from the Ca(2+)-activated photoprotein aequorin. Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedThe expanded genetic code in combination with site-directed mutagenesis was used to probe spectroscopic and structural roles of tryptophan (Trp) residues in Aequorea victoria green fluorescent proteins (avGFPs). Nine different halogen-, chalcogen-, and methyl-containing Trp isosteric analogues and surrogates were incorporated into avGFPs containing indole moieties in, and outside of, the chromophore, by the use of the selective pressure incorporation method. Such isosteric replacements introduced minimal local geometry changes in indole moieties, often to the level of single atomic exchange ('atomic mutation') and do not affect three-dimensional structures of avGFPs but induce changes in spectral properties. Our approach offers a new platform to re-evaluate issues like resonance transfer, mechanisms of chromophore formation and maturation, as well as the importance of local geometry and weak sulphur-aromatic interactions for avGFP spectral properties and structural stability. The library of novel tailor-made avGFP mutants and variants generated in this work has demonstrated not only the potentials of the expanded genetic code to study spectroscopic functions, but also a new approach to generate tailor-made proteins with interesting and useful spectral properties. Probing the role of tryptophans in Aequorea victoria green fluorescent proteins with an expanded genetic code.,Budisa N, Pal PP, Alefelder S, Birle P, Krywcun T, Rubini M, Wenger W, Bae JH, Steiner T Biol Chem. 2004 Feb;385(2):191-202. PMID:15101562[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences |
| ||||||||||||||||||