2mi7

From Proteopedia

(Difference between revisions)

Current revision

Solution NMR structure of alpha3Y

Structural highlights

2mi7 is a 1 chain structure with sequence from Synthetic construct. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Solution NMR
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Publication Abstract from PubMed

Tyrosine oxidation-reduction involves proton-coupled electron transfer (PCET) and a reactive radical state. These properties are effectively controlled in enzymes that use tyrosine as a high-potential, one-electron redox cofactor. The alpha3Y model protein contains Y32, which can be reversibly oxidized and reduced in voltammetry measurements. Structural and kinetic properties of alpha3Y are presented. A solution NMR structural analysis reveals that Y32 is the most deeply buried residue in alpha3Y. Time-resolved spectroscopy using a soluble flash-quench generated [Ru(2,2'-bipyridine)3]3+ oxidant provides high-quality Y32-O* absorption spectra. The rate constant of Y32 oxidation (kPCET) is pH dependent: 1.4 x 104 M-1 s-1 (pH 5.5), 1.8 x 105 M-1 s-1 (pH 8.5), 5.4 x 103 M-1 s-1 (pD 5.5), and 4.0 x 104 M-1 s-1 (pD 8.5). kH/kD of Y32 oxidation is 2.5 +/- 0.5 and 4.5 +/- 0.9 at pH(D) 5.5 and 8.5, respectively. These pH and isotope characteristics suggest a concerted or stepwise, proton-first Y32 oxidation mechanism. The photochemical yield of Y32-O* is 28-58% versus the concentration of [Ru(2,2'-bipyridine)3]3+. Y32-O* decays slowly, t1/2 in the range of 2-10 s, at both pH 5.5 and 8.5, via radical-radical dimerization as shown by second-order kinetics and fluorescence data. The high stability of Y32-O* is discussed relative to the structural properties of the Y32 site. Finally, the static alpha3Y NMR structure cannot explain (i) how the phenolic proton released upon oxidation is removed or (ii) how two Y32-O* come together to form dityrosine. These observations suggest that the dynamic properties of the protein ensemble may play an essential role in controlling the PCET and radical decay characteristics of alpha3Y.

Photochemical Tyrosine Oxidation in the Structurally Well-Defined alphaY Protein: Proton-Coupled Electron Transfer and a Long-Lived Tyrosine Radical.,Glover SD, Jorge C, Liang L, Valentine KG, Hammarstrom L, Tommos C J Am Chem Soc. 2014 Aug 14. PMID:25121576^[1]

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

References

↑ Glover SD, Jorge C, Liang L, Valentine KG, Hammarstrom L, Tommos C. Photochemical Tyrosine Oxidation in the Structurally Well-Defined alphaY Protein: Proton-Coupled Electron Transfer and a Long-Lived Tyrosine Radical. J Am Chem Soc. 2014 Aug 14. PMID:25121576 doi:http://dx.doi.org/10.1021/ja503348d

1 Structural highlights
2 Publication Abstract from PubMed
3 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2mi7"

@@ Line 1: / Line 1: @@
 ==Solution NMR structure of alpha3Y==
-<StructureSection load='2mi7' size='340' side='right' caption='[[2mi7]], [[NMR_Ensembles_of_Models | 32 NMR models]]' scene=''>
+<StructureSection load='2mi7' size='340' side='right'caption='[[2mi7]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2mi7]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2MI7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2MI7 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2mi7]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2MI7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2MI7 FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1lq7|1lq7]], [[2lxy|2lxy]]</td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
-<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2mi7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2mi7 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2mi7 RCSB], [http://www.ebi.ac.uk/pdbsum/2mi7 PDBsum]</span></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=2mi7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2mi7 OCA], [https://pdbe.org/2mi7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2mi7 RCSB], [https://www.ebi.ac.uk/pdbsum/2mi7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2mi7 ProSAT]</span></td></tr>
-<table>
+</table>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
-Catalytically essential side-chain radicals have been recognized in a growing number of redox enzymes. Here we present a novel approach to study this class of redox cofactors. Our aim is to construct a de novo protein, a radical maquette, that will provide a protein framework in which to investigate how side-chain radicals are generated, controlled, and directed toward catalysis. A tryptophan and a tyrosine radical maquette, denoted alpha(3)W(1) and alpha(3)Y(1), respectively, have been synthesized. alpha(3)W(1) and alpha(3)Y(1) contain 65 residues each and have molecular masses of 7.4 kDa. The proteins differ only in residue 32, which is the position of their single aromatic side chain. Structural characterization reveals that the proteins fold in water solution into thermodynamically stable, alpha-helical conformations with well-defined tertiary structures. The proteins are resistant to pH changes and remain stable through the physiological pH range. The aromatic residues are shown to be located within the protein interior and shielded from the bulk phase, as designed. Differential pulse voltammetry was used to examine the reduction potentials of the aromatic side chains in alpha(3)W(1) and alpha(3)Y(1) and compare them to the potentials of tryptophan and tyrosine when dissolved in water. The tryptophan and tyrosine potentials were raised considerably when moved from a solution environment to a well-ordered protein milieu. We propose that the increase in reduction potential of the aromatic residues buried within the protein, relative to the solution potentials, is due to a lack of an effective protonic contact between the aromatic residues and the bulk solution.
+Tyrosine oxidation-reduction involves proton-coupled electron transfer (PCET) and a reactive radical state. These properties are effectively controlled in enzymes that use tyrosine as a high-potential, one-electron redox cofactor. The alpha3Y model protein contains Y32, which can be reversibly oxidized and reduced in voltammetry measurements. Structural and kinetic properties of alpha3Y are presented. A solution NMR structural analysis reveals that Y32 is the most deeply buried residue in alpha3Y. Time-resolved spectroscopy using a soluble flash-quench generated [Ru(2,2'-bipyridine)3]3+ oxidant provides high-quality Y32-O* absorption spectra. The rate constant of Y32 oxidation (kPCET) is pH dependent: 1.4 x 104 M-1 s-1 (pH 5.5), 1.8 x 105 M-1 s-1 (pH 8.5), 5.4 x 103 M-1 s-1 (pD 5.5), and 4.0 x 104 M-1 s-1 (pD 8.5). kH/kD of Y32 oxidation is 2.5 +/- 0.5 and 4.5 +/- 0.9 at pH(D) 5.5 and 8.5, respectively. These pH and isotope characteristics suggest a concerted or stepwise, proton-first Y32 oxidation mechanism. The photochemical yield of Y32-O* is 28-58% versus the concentration of [Ru(2,2'-bipyridine)3]3+. Y32-O* decays slowly, t1/2 in the range of 2-10 s, at both pH 5.5 and 8.5, via radical-radical dimerization as shown by second-order kinetics and fluorescence data. The high stability of Y32-O* is discussed relative to the structural properties of the Y32 site. Finally, the static alpha3Y NMR structure cannot explain (i) how the phenolic proton released upon oxidation is removed or (ii) how two Y32-O* come together to form dityrosine. These observations suggest that the dynamic properties of the protein ensemble may play an essential role in controlling the PCET and radical decay characteristics of alpha3Y.
-De novo proteins as models of radical enzymes.,Tommos C, Skalicky JJ, Pilloud DL, Wand AJ, Dutton PL Biochemistry. 1999 Jul 20;38(29):9495-507. PMID:10413527<ref>PMID:10413527</ref>
+Photochemical Tyrosine Oxidation in the Structurally Well-Defined alphaY Protein: Proton-Coupled Electron Transfer and a Long-Lived Tyrosine Radical.,Glover SD, Jorge C, Liang L, Valentine KG, Hammarstrom L, Tommos C J Am Chem Soc. 2014 Aug 14. PMID:25121576<ref>PMID:25121576</ref>
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 2mi7" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Glover, S D.]]
+[[Category: Large Structures]]
-[[Category: Hammarstrom, L.]]
+[[Category: Synthetic construct]]
-[[Category: Jorge, C.]]
+[[Category: Glover SD]]
-[[Category: Liang, L.]]
+[[Category: Hammarstrom L]]
-[[Category: Tommos, C.]]
+[[Category: Jorge C]]
-[[Category: Valentine, K G.]]
+[[Category: Liang L]]
-[[Category: De novo protein]]
+[[Category: Tommos C]]
-[[Category: Proton-coupled electron transfer]]
+[[Category: Valentine KG]]
-[[Category: Redox protein]]
-[[Category: Three-helix bundle]]
-[[Category: Tyrosine radical]]

2mi7

From Proteopedia

Current revision

Solution NMR structure of alpha3Y

Structural highlights

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox