Allostery can convert binding free energies into concerted domain motions in enzymes
Abstract Enzymatic mechanisms are typically inferred from structural data. However, understanding enzymes require unravelling the intricate dynamic interplay between dynamics, conformational substates, and multiple protein structures. Here, we use single-molecule nanopore analysis to investigate the...
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| Format: | Article |
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Nature Portfolio
2024-11-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-024-54421-9 |
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| author | Nicole Stéphanie Galenkamp Sarah Zernia Yulan B. Van Oppen Marco van den Noort Andreas Milias-Argeitis Giovanni Maglia |
| author_facet | Nicole Stéphanie Galenkamp Sarah Zernia Yulan B. Van Oppen Marco van den Noort Andreas Milias-Argeitis Giovanni Maglia |
| author_sort | Nicole Stéphanie Galenkamp |
| collection | DOAJ |
| description | Abstract Enzymatic mechanisms are typically inferred from structural data. However, understanding enzymes require unravelling the intricate dynamic interplay between dynamics, conformational substates, and multiple protein structures. Here, we use single-molecule nanopore analysis to investigate the catalytic conformational changes of adenylate kinase (AK), an enzyme that catalyzes the interconversion of various adenosine phosphates (ATP, ADP, and AMP). Kinetic analysis validated by hidden Markov models unravels the details of domain motions during catalysis. Our findings reveal that allosteric interactions between ligands and cofactor enable converting binding energies into directional conformational changes of the two catalytic domains of AK. These coordinated motions emerged to control the exact sequence of ligand binding and the affinity for the three different substrates, thereby guiding the reactants along the reaction coordinates. Interestingly, we find that about 10% of enzymes show altered allosteric regulation and ligand affinities, indicating that a subset of enzymes folds in alternative catalytically active forms. Since molecules or proteins might be able to selectively stabilize one of the folds, this observation suggests an evolutionary path for allostery in enzymes. In AK, this complex catalytic framework has likely emerged to prevent futile ATP/ADP hydrolysis and to regulate the enzyme for different energy needs of the cell. |
| format | Article |
| id | doaj-art-2ca5a11c0f8d47b9b521e22c2c6c2630 |
| institution | Kabale University |
| issn | 2041-1723 |
| language | English |
| publishDate | 2024-11-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj-art-2ca5a11c0f8d47b9b521e22c2c6c26302025-01-19T12:29:32ZengNature PortfolioNature Communications2041-17232024-11-0115111310.1038/s41467-024-54421-9Allostery can convert binding free energies into concerted domain motions in enzymesNicole Stéphanie Galenkamp0Sarah Zernia1Yulan B. Van Oppen2Marco van den Noort3Andreas Milias-Argeitis4Giovanni Maglia5Chemical Biology I, Groningen Biomolecular Sciences & Biotechnology Institute, University of GroningenChemical Biology I, Groningen Biomolecular Sciences & Biotechnology Institute, University of GroningenMolecular Systems Biology, Groningen Biomolecular Sciences & Biotechnology Institute, University of GroningenChemical Biology I, Groningen Biomolecular Sciences & Biotechnology Institute, University of GroningenMolecular Systems Biology, Groningen Biomolecular Sciences & Biotechnology Institute, University of GroningenChemical Biology I, Groningen Biomolecular Sciences & Biotechnology Institute, University of GroningenAbstract Enzymatic mechanisms are typically inferred from structural data. However, understanding enzymes require unravelling the intricate dynamic interplay between dynamics, conformational substates, and multiple protein structures. Here, we use single-molecule nanopore analysis to investigate the catalytic conformational changes of adenylate kinase (AK), an enzyme that catalyzes the interconversion of various adenosine phosphates (ATP, ADP, and AMP). Kinetic analysis validated by hidden Markov models unravels the details of domain motions during catalysis. Our findings reveal that allosteric interactions between ligands and cofactor enable converting binding energies into directional conformational changes of the two catalytic domains of AK. These coordinated motions emerged to control the exact sequence of ligand binding and the affinity for the three different substrates, thereby guiding the reactants along the reaction coordinates. Interestingly, we find that about 10% of enzymes show altered allosteric regulation and ligand affinities, indicating that a subset of enzymes folds in alternative catalytically active forms. Since molecules or proteins might be able to selectively stabilize one of the folds, this observation suggests an evolutionary path for allostery in enzymes. In AK, this complex catalytic framework has likely emerged to prevent futile ATP/ADP hydrolysis and to regulate the enzyme for different energy needs of the cell.https://doi.org/10.1038/s41467-024-54421-9 |
| spellingShingle | Nicole Stéphanie Galenkamp Sarah Zernia Yulan B. Van Oppen Marco van den Noort Andreas Milias-Argeitis Giovanni Maglia Allostery can convert binding free energies into concerted domain motions in enzymes Nature Communications |
| title | Allostery can convert binding free energies into concerted domain motions in enzymes |
| title_full | Allostery can convert binding free energies into concerted domain motions in enzymes |
| title_fullStr | Allostery can convert binding free energies into concerted domain motions in enzymes |
| title_full_unstemmed | Allostery can convert binding free energies into concerted domain motions in enzymes |
| title_short | Allostery can convert binding free energies into concerted domain motions in enzymes |
| title_sort | allostery can convert binding free energies into concerted domain motions in enzymes |
| url | https://doi.org/10.1038/s41467-024-54421-9 |
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