Evidence map›Paper›PMID 26154739›Full record

ArticleBiochemistry2015

Systematic Perturbations of Binuclear Non-heme Iron Sites: Structure and Dioxygen Reactivity of de Novo Due Ferri Proteins.

Rae Ana Snyder, Justine Betzu, Susan E Butch, Amanda J Reig, William F DeGrado, Edward I Solomon

Abstract read
In one paragraph

Article in Biochemistry, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.

0numbers the graph read from it
0cells of the map it votes in
13citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

13 citing papers in PubMed.

  1. Article
  2. Review
  3. Catalysis and Electron Transfer inChemical reviews · 2022
    Review
  4. Review
  5. Allosteric cooperation in a de novo-designed two-domain protein.Proceedings of the National Academy of Sciences of the United States of America · 2020
    Article
  6. Article
  7. Quarterly reviews of biophysics · 2020
    Review
  8. Article
  9. The ascent of man(made oxidoreductases).Current opinion in structural biology · 2018
    Review
  10. Review
  11. Structure, function and evolution of the hemerythrin-like domain superfamily.Protein science : a publication of the Protein Society · 2018
    Article
  12. Review
  13. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

6 authors.

Rae Ana Snyder†Department of Chemistry, Stanford University, Stanford, California 94305, United States.
Justine Betzu‡Department of Chemistry, Ursinus College, Collegeville, Pennsylvania 19426, United States.
Susan E Butch‡Department of Chemistry, Ursinus College, Collegeville, Pennsylvania 19426, United States.
Amanda J Reig‡Department of Chemistry, Ursinus College, Collegeville, Pennsylvania 19426, United States.
William F DeGrado§Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94143, United States.
Edward I Solomon†Department of Chemistry, Stanford University, Stanford, California 94305, United States.

Funding

De novo design of alpha-helical bundlesR37GM054616 · NIGMS · UNIVERSITY OF PENNSYLVANIA · PI DEGRADO, WILLIAM · 2004 to 2013
$3.6M
DE NOVO DESIGN OF ALPHA HELICAL BUNDLESR01GM054616 · NIGMS · UNIVERSITY OF PENNSYLVANIA · PI DEGRADO, WILLIAM · 1996 to 2016
$2.4M
Charge-Transfer Dynamics Relevant to Protein-Mediated Energy TransductionR01GM071628 · NIGMS · UNIVERSITY OF PENNSYLVANIA · PI THERIEN, MICHAEL J · 2004 to 2014
$2.3M
Using De Novo Protein Models to Understand Functional Tuning in Di-Iron CarboxylaR15GM110657 · NIGMS · URSINUS COLLEGE · PI REIG, AMANDA · 2014 to 2014
$222k
NIGMS NIH HHS F32-GM808852NIGMS NIH HHS GM54616NIGMS NIH HHS GM71628NIGMS NIH HHS R01 GM054616NIGMS NIH HHS R01 GM071628NIGMS NIH HHS R15 GM110657NIGMS NIH HHS R15-GM110657NIGMS NIH HHS R37 GM054616
6 · The paper itself

Abstract

DFsc (single-chain due ferri) proteins allow for modeling binuclear non-heme iron enzymes with a similar fold. Three 4A → 4G variants of DFsc were studied to investigate the effects of (1) increasing the size of the substrate/solvent access channel (G4DFsc), (2) including an additional His residue in the first coordination sphere along with three additional helix-stabilizing mutations [3His-G4DFsc(Mut3)], and (3) the three helix-stabilizing mutations alone [G4DFsc(Mut3)] on the biferrous structures and their O2 reactivities. Near-infrared circular dichroism and magnetic circular dichroism (MCD) spectroscopy show that the 4A → 4G mutations increase coordination of the diiron site from 4-coordinate/5-coordinate to 5-coordinate/5-coordinate, likely reflecting increased solvent accessibility. While the three helix-stabilizing mutations [G4DFsc(Mut3)] do not affect the coordination number, addition of the third active site His residue [3His-G4DFsc(Mut3)] results in a 5-coordinate/6-coordinate site. Although all 4A→ 4G variants have significantly slower pseudo-first-order rates when reacting with excess O2 than DFsc (∼2 s(-1)), G4DFsc and 3His-G4DFsc(Mut3) have rates (∼0.02 and ∼0.04 s(-1)) faster than that of G4DFsc(Mut3) (∼0.002 s(-1)). These trends in the rate of O2 reactivity correlate with exchange coupling between the Fe(II) sites and suggest that the two-electron reduction of O2 occurs through end-on binding at one Fe(II) rather than through a peroxy-bridged intermediate. UV-vis absorption and MCD spectroscopies indicate that an Fe(III)Fe(III)-OH species first forms in all three variants but converts into an Fe(III)-μ-OH-Fe(III) species only in the 2-His forms, a process inhibited by the additional active site His ligand that coordinatively saturates one of the iron centers in 3His-G4DFsc(Mut3).

Indexed as

Binding SitesIronMetalloproteinsOxygenPoint MutationProtein Structure, SecondaryIronMetalloproteinsOxygen

Identifiers

PMID26154739
PMCPMC4857603

What OpenQuestion holds

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.