Distant residues mediate picomolar binding affinity of a protein cofactor
| Autor: | Adrie H. Westphal, Simon Lindhoud, Yves J. M. Bollen, Willem J. H. van Berkel, Carlo P. M. van Mierlo |
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| Přispěvatelé: | Structural Biology, AIMMS, LaserLaB - Analytical Chemistry and Spectroscopy |
| Jazyk: | angličtina |
| Rok vydání: | 2012 |
| Předmět: |
Models
Molecular topology Flavodoxin Stereochemistry Flavin Mononucleotide Amino Acid Motifs nmr relaxation General Physics and Astronomy Flavin mononucleotide Biochemie Flavin group Biochemistry General Biochemistry Genetics and Molecular Biology Cofactor Article Protein Structure Secondary chemistry.chemical_compound thermodynamics hydrogen-exchange oxidized flavodoxin Desulfovibrio vulgaris Binding site VLAG chemistry.chemical_classification Cofactor binding Multidisciplinary Binding Sites biology ligand-binding Chemistry energy landscape Transporter General Chemistry dynamics Amino acid kinetics biology.protein Mutagenesis Site-Directed azotobacter-vinelandii apoflavodoxin |
| Zdroj: | Bollen, Y J M, Westphal, A H, Lindhoud, S, van Berkel, W J & van Mierlo, C P 2012, ' Distant residues mediate picomolar binding affinity of a protein cofactor ', Nature Communications, vol. 3, pp. 1010 . https://doi.org/10.1038/ncomms2010 Nature Communications, 3. Nature Publishing Group Nature Communications, 3 Nature Communications Nature Communications 3 (2012) |
| ISSN: | 2041-1723 |
| DOI: | 10.1038/ncomms2010 |
| Popis: | Numerous proteins require cofactors to be active. Computer simulations suggest that cooperative interaction networks achieve optimal cofactor binding. There is a need for the experimental identification of the residues crucial for stabilizing these networks and thus for cofactor binding. Here we investigate the electron transporter flavodoxin, which contains flavin mononucleotide as non-covalently bound cofactor. We show that after binding flavin mononucleotide with nanomolar affinity, the protein relaxes extremely slowly (time constant ~5 days) to an energetically more favourable state with picomolar-binding affinity. Rare small-scale openings of this state are revealed through H/D exchange of N(3)H of flavin. We find that H/D exchange can pinpoint amino acids that cause tight cofactor binding. These hitherto unknown residues are dispersed throughout the structure, and many are located distantly from the flavin and seem irrelevant to flavodoxin's function. Quantification of the thermodynamics of ligand binding is important for understanding, engineering, designing and evolving ligand-binding proteins. Flavodoxin requires tight binding of its FMN cofactor to be active, but the residues involved are unknown. In this biophysical study, FMN binding is shown to change from nanomolar to picomolar affinity on extremely slow protein relaxation and the residues responsible for cofactor binding are identified. |
| Databáze: | OpenAIRE |
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