Evidence map›Paper›PMID 25083917›Full record

ArticleJournal of molecular biology2014

Cu,Zn-superoxide dismutase without Zn is folded but catalytically inactive.

Sean Nedd, Rachel L Redler, Elizabeth A Proctor, Nikolay V Dokholyan, Anastassia N Alexandrova

Abstract read
In one paragraph

Article in Journal of molecular biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.

0numbers the graph read from it
0cells of the map it votes in
24citing papers in PubMed
3.0field-weighted citation impact, top 9% of its field
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

24 citing papers in PubMed, 50 citations in OpenAlex.

  1. Article
  2. Review
  3. Article
  4. Review
  5. Article
  6. Mechanism of the Early Catalytic Events in the Collagenolysis by Matrix Metalloproteinase-1.Chemphyschem : a European journal of chemical physics and physical chemistry · 2023
    Article
  7. Review
  8. Development ofIranian journal of biotechnology · 2022
    Article
  9. Evaluation of ZnMolecules (Basel, Switzerland) · 2022
    Article
  10. Article
  11. Review
  12. Article
  13. Article
  14. Article
  15. Article
  16. Article
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  19. Article
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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

5 authors at 3 institutions in 1 country.

Sean NeddDepartment of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA.
Rachel L RedlerDepartment of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA.
Elizabeth A ProctorDepartment of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA; Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, NC 27599, USA.
Nikolay V DokholyanDepartment of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA; Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, NC 27599, USA; Program in Molecular and Cellular Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA; Center for Computational and Systems Biology, University of North Carolina, Chapel Hill, NC 27599, USA. Electronic address: dokh@med.unc.edu.
Anastassia N AlexandrovaDepartment of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA; California NanoSystems Institute, 570 Westwood Plaza, Building 114, Los Angeles, CA 90095, USA. Electronic address: ana@chem.ucla.edu.
University of North Carolina at Chapel Hill · USCalifornia NanoSystems Institute · USUniversity of California, Los Angeles · US

Funding

Protein Misfolding and AggregationR01GM080742 · NIGMS · UNIV OF NORTH CAROLINA CHAPEL HILL · PI DOKHOLYAN, NIKOLAY · 2007 to 2015
$2.8M
The impact of post-translational modification on SOD1 aggregation in ALSF31NS073435 · NINDS · UNIV OF NORTH CAROLINA CHAPEL HILL · PI REDLER, RACHEL · 2011 to 2013
$91k
Identification of drug leads targeting SOD1 dissociation for the treatment of ALSF31AG039266 · NIA · UNIV OF NORTH CAROLINA CHAPEL HILL · PI PROCTOR, ELIZABETH A · 2010 to 2013
$91k
NIA NIH HHS F31 AG039266NIA NIH HHS F31AG039266NIGMS NIH HHS R01 GM080742NIGMS NIH HHS R01GM080742NINDS NIH HHS F31 NS073435NINDS NIH HHS F31NS073435
6 · The paper itself

Abstract

Amyotrophic lateral sclerosis has been linked to the gain of aberrant function of superoxide dismutase, Cu,Zn-SOD1 upon protein misfolding. The mechanism of SOD1 misfolding is thought to involve mutations leading to the loss of Zn, followed by protein unfolding and aggregation. We show that the removal of Zn from SOD1 may not lead to an immediate unfolding but immediately deactivates the enzyme through a combination of subtle structural and electronic effects. Using quantum mechanics/discrete molecular dynamics, we showed that both Zn-less wild-type (WT)-SOD1 and its D124N mutant that does not bind Zn have at least metastable folded states. In those states, the reduction potential of Cu increases, leading to the presence of detectable amounts of Cu(I) instead of Cu(II) in the active site, as confirmed experimentally. The Cu(I) protein cannot participate in the catalytic Cu(I)-Cu(II) cycle. However, even without the full reduction to Cu(I), the Cu site in the Zn-less variants of SOD1 is shown to be catalytically incompetent: unable to bind superoxide in a way comparable to the WT-SOD1. The changes are more radical and different in the D124N Zn-less mutant than in the Zn-less WT-SOD1, suggesting D124N being perhaps not the most adequate model for Zn-less SOD1. Overall, Zn in SOD1 appears to be influencing the Cu site directly by adjusting its reduction potential and geometry. Thus, the role of Zn in SOD1 is not just structural, as was previously thought; it is a vital part of the catalytic machinery.

Indexed as

Protein FoldingBiocatalysisElectrophoresis, Polyacrylamide GelMolecular Dynamics SimulationMutation, MissenseProtein BindingProtein Structure, TertiaryQuantum TheorySaccharomyces cerevisiae ProteinsSuperoxide DismutaseZincSaccharomyces cerevisiae ProteinsSuperoxide DismutaseZincamyotrophic lateral sclerosisCu,Zn-SOD1loss of Zn in SOD1QM/DMDsuperoxide dismutase

Identifiers

PMID25083917
PMCPMC4258539
OpenAlexW2140880971

What OpenQuestion holds

Textmetadata
LicenceTDM
Read underepoch 390

Registered trials

None linked

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.