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Home / Equine Research Bank / PLoS One / Evidence for a Shared Mechanism in the Formation of Urea-Ind...
PloS one2015; 10(8); e0134238; doi: 10.1371/journal.pone.0134238

Evidence for a Shared Mechanism in the Formation of Urea-Induced Kinetic and Equilibrium Intermediates of Horse Apomyoglobin from Ultrarapid Mixing Experiments.

Abstract: In this study, the equivalence of the kinetic mechanisms of the formation of urea-induced kinetic folding intermediates and non-native equilibrium states was investigated in apomyoglobin. Despite having similar structural properties, equilibrium and kinetic intermediates accumulate under different conditions and via different mechanisms, and it remains unknown whether their formation involves shared or distinct kinetic mechanisms. To investigate the potential mechanisms of formation, the refolding and unfolding kinetics of horse apomyoglobin were measured by continuous- and stopped-flow fluorescence over a time range from approximately 100 μs to 10 s, along with equilibrium unfolding transitions, as a function of urea concentration at pH 6.0 and 8°C. The formation of a kinetic intermediate was observed over a wider range of urea concentrations (0-2.2 M) than the formation of the native state (0-1.6 M). Additionally, the kinetic intermediate remained populated as the predominant equilibrium state under conditions where the native and unfolded states were unstable (at ~0.7-2 M urea). A continuous shift from the kinetic to the equilibrium intermediate was observed as urea concentrations increased from 0 M to ~2 M, which indicates that these states share a common kinetic folding mechanism. This finding supports the conclusion that these intermediates are equivalent. Our results in turn suggest that the regions of the protein that resist denaturant perturbations form during the earlier stages of folding, which further supports the structural equivalence of transient and equilibrium intermediates. An additional folding intermediate accumulated within ~140 μs of refolding and an unfolding intermediate accumulated in <1 ms of unfolding. Finally, by using quantitative modeling, we showed that a five-state sequential scheme appropriately describes the folding mechanism of horse apomyoglobin.
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Publication Date: 2015-08-05 PubMed ID: 26244984PubMed Central: PMC4526358DOI: 10.1371/journal.pone.0134238Google Scholar: Lookup
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Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

The research article primarily explores the shared mechanism in the formation of urea-induced kinetic and equilibrium intermediates in horse apomyoglobin, suggesting that the regions of the protein that resist denaturant perturbations form during the earlier stages of folding.

Exploring kinetic mechanisms

  • The study investigates the equivalence of the mechanisms in the creation of urea-induced kinetic folding intermediates and non-native equilibrium states in apomyoglobin. Despite their similar structural properties, these intermediates build up under different conditions and through different mechanisms.
  • The aim was to determine whether the formation of equilibrium and kinetic intermediates involve shared or distinct kinetic mechanisms. This was investigated by measuring the refolding and unfolding rates of horse apomyoglobin using continuous- and stopped-flow fluorescence over a time range approximately from 100 microseconds to 10 seconds.

Shifting between kinetic and equilibrium intermediates

  • The kinetic intermediate’s formation was observed over a broader range of urea concentrations (0-2.2 M) than the formation of the native state (0-1.6 M). Moreover, under certain conditions where the native and unfolded states were unstable, the kinetic intermediate served as the dominant equilibrium state.
  • An interesting observation is a continuous shift from the kinetic to the equilibrium intermediate as the urea concentration increased. This indicates that these states might share a common kinetic folding pathway, further suggesting that these intermediates are indeed equivalent.

Resistant regions during protein folding

  • Based on the findings, it is proposed that the parts of the protein that resist denouncing perturbations primarily form during the early stages of folding. This idea supports the structural equivalence of transient and equilibrium intermediates.
  • Additionally, another folding intermediate was found to accumulate within approximately 140 microseconds of refolding, and an unfolding intermediate accumulated in less than 1 millisecond of unfolding.

Modeling the folding mechanism

  • Quantitative modeling was used to demonstrate that the folding mechanism of horse apomyoglobin can be accurately described by a five-state sequential scheme.
  • This outcome further supported the hypothesis of a shared mechanism in the formation of urea-induced kinetic and equilibrium intermediates.

Cite This Article

APA
Mizukami T, Abe Y, Maki K. (2015). Evidence for a Shared Mechanism in the Formation of Urea-Induced Kinetic and Equilibrium Intermediates of Horse Apomyoglobin from Ultrarapid Mixing Experiments. PLoS One, 10(8), e0134238. https://doi.org/10.1371/journal.pone.0134238

Publication

PloS one
ISSN: 1932-6203
NlmUniqueID: 101285081
Country: United States
Language: English
Volume: 10
Issue: 8
Pages: e0134238
PII: e0134238

Researcher Affiliations

Mizukami, Takuya
  • Graduate School of Science, Nagoya University, Nagoya, Aichi, Japan.
Abe, Yukiko
  • Graduate School of Science, Nagoya University, Nagoya, Aichi, Japan.
Maki, Kosuke
  • Graduate School of Science, Nagoya University, Nagoya, Aichi, Japan.

MeSH Terms

  • Algorithms
  • Animals
  • Apoproteins / chemistry
  • Circular Dichroism
  • Fluorescence
  • Horses
  • Hydrogen-Ion Concentration
  • Kinetics
  • Models, Chemical
  • Models, Molecular
  • Myoglobin / chemistry
  • Protein Conformation / drug effects
  • Protein Denaturation / drug effects
  • Protein Refolding
  • Protein Unfolding
  • Temperature
  • Thermodynamics
  • Urea / chemistry
  • Urea / pharmacology

Conflict of Interest Statement

The authors have declared that no competing interests exist.

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Citations

This article has been cited 3 times.
  1. Manavalan B, Kuwajima K, Lee J. PFDB: A standardized protein folding database with temperature correction. Sci Rep 2019 Feb 7;9(1):1588.
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  2. Nishimura C. Folding of apomyoglobin: Analysis of transient intermediate structure during refolding using quick hydrogen deuterium exchange and NMR. Proc Jpn Acad Ser B Phys Biol Sci 2017;93(1):10-27.
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  3. Marzi I, Pieraccini G, Bemporad F, Chiti F. Detection of an Intermediate in the Unfolding Process of the N-Terminal Domain of TDP-43. ACS Omega 2025 Feb 18;10(6):5616-5633.
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