Water stabilizes an alternate turn conformation in horse heart myoglobin.
Abstract: Comparison of myoglobin structures reveals that protein isolated from horse heart consistently adopts an alternate turn conformation in comparison to its homologues. Analysis of hundreds of high-resolution structures discounts crystallization conditions or the surrounding amino acid protein environment as explaining this difference, that is also not captured by the AlphaFold prediction. Rather, a water molecule is identified as stabilizing the conformation in the horse heart structure, which immediately reverts to the whale conformation in molecular dynamics simulations excluding that structural water.
© 2023. The Author(s).
Publication Date: 2023-04-13 PubMed ID: 37055458PubMed Central: PMC10102282DOI: 10.1038/s41598-023-32821-zGoogle Scholar: Lookup
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- Journal Article
Summary
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The researchers in the journal article are studying why myoglobin, a protein, from horse hearts has a different turn conformation than its homologues (similar structures from different species). They found that the difference isn’t due to crystallization conditions or the surrounding amino acid environment, but is instead stabilized by a water molecule. In simulations where this water molecule is excluded, the horse heart myoglobin’s structure changes to resemble the whale conformation.
Comparison of Myoglobin Structures
- The researchers started by comparing myoglobin structures across different species. Myoglobin is a protein that helps transport oxygen in muscle cells.
- They found that myoglobin from horse hearts consistently assumes an alternate turn conformation (or different 3D shape), when compared to its homologues from other species.
Investigation of Crystallization Conditions and Amino Acid Environment
- The researchers then explored whether crystallization conditions or the surrounding amino acid protein environment explained the differing conformation.
- Through reviewing hundreds of high-resolution structures, they determined neither of these factors explained the difference in the horse heart myoglobin’s conformation.
AlphaFold Prediction Analysis
- AlphaFold is a sophisticated prediction model that uses machine learning to predict protein structures.
- Despite its predictive power, the horse heart myoglobin’s alternate conformation was not captured by the AlphaFold prediction. This suggests that there is a strong influence from some other factor that is causing the alternate conformation.
Influence of a Water Molecule
- After discounting other factors, the researchers identified a water molecule as the factor stabilizing the alternate conformation in horse heart myoglobin.
- Molecular dynamics simulations were performed excluding this structural water molecule, and the alternate conformation immediately reverted to the whale conformation. This shows that the structure of horse heart myoglobin is strongly dependent on the presence of this water molecule.
Cite This Article
APA
Bronstein A, Marx A.
(2023).
Water stabilizes an alternate turn conformation in horse heart myoglobin.
Sci Rep, 13(1), 6094.
https://doi.org/10.1038/s41598-023-32821-z Publication
Researcher Affiliations
- Department of Computer Science, Technion-Israel Institute of Technology, Haifa, Israel.
- Department of Computer Science, Technion-Israel Institute of Technology, Haifa, Israel. ailie@technion.ac.il.
MeSH Terms
- Horses
- Animals
- Myoglobin / chemistry
- Water
- Protein Conformation
- Whales / metabolism
- Heart
Conflict of Interest Statement
The authors declare no competing interests.
References
This article includes 17 references
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Citations
This article has been cited 2 times.- Seffernick JT, Fischer M. An experimental proxy of water displaceability for ligand discovery. Nat Methods 2025 Jul;22(7):1476-1485.
- Haque N, Wagenknecht JB, Ratnasinghe BD, Zimmermann MT. Systematic analysis of the relationship between fold-dependent flexibility and artificial intelligence protein structure prediction. PLoS One 2024;19(11):e0313308.
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