Browsing by Author "Babul, Jorge"

Now showing 1 - 6 of 6
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    Dissecting the structural and functional consequences of the evolutionary proline-glycine deletion in the wing 1 region of the forkhead domain of human FoxP1
    (2024) Tamarin, Stephanie; Galaz-Davison, Pablo; Ramirez-Sarmiento, Cesar A.; Babul, Jorge; Medina, Exequiel
    The human FoxP transcription factors dimerize via three-dimensional domain swapping, a unique feature among the human Fox family, as result of evolutionary sequence adaptations in the forkhead domain. This is the case for the conserved glycine and proline residues in the wing 1 region, which are absent in FoxP proteins but present in most of the Fox family. In this work, we engineered both glycine (G) and proline-glycine (PG) insertion mutants to evaluate the deletion events in FoxP proteins in their dimerization, stability, flexibility, and DNA-binding ability. We show that the PG insertion only increases protein stability, whereas the single glycine insertion decreases the association rate and protein stability and promotes affinity to the DNA ligand.
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    DNA controls the dimerization of the human FoxP1 forkhead domain
    (2024) Kolimi, Narendar; Ballard, Jake; Peulen, Thomas; Goutam, Rajen; Duffy III, Francis X.; Ramirez-Sarmiento, Cesar A.; Babul, Jorge; Medina, Exequiel; Sanabria, Hugo
    Transcription factors (TFs) regulate gene expression by binding to specific DNA sequences and gating access to genes. Even when the binding of TFs and their cofactors to DNA is reversible, indicating a reversible control of gene expression, there is little knowledge about the molecular effect DNA has on TFs. Using single -molecule multiparameter fluorescence spectroscopy, molecular dynamics simulations, and biochemical assays, we find that the monomeric form of the forkhead (FKH) domain of the human FoxP1 behaves as a disordered protein and increases its folded population when it dimerizes. Notably, DNA binding promotes a disordered FKH dimer bound to DNA, negatively controlling the stability of the dimeric FoxP1:DNA complex. The DNA -mediated reversible regulation on FKH dimers suggests that FoxP1-dependent gene suppression is unstable, and it must require the presence of other dimerization domains or cofactors to revert the negative impact exerted by the DNA.
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    DNA facilitates heterodimerization between human transcription factors FoxP1 and FoxP2 by increasing their conformational flexibility
    (2023) Conuecar, Ricardo; Asela, Isabel; Rivera, Maira; Galaz-Davison, Pablo; Gonzalez-Higueras, Jorge; Hamilton, George L.; Engelberger, Felipe; Ramirez-Sarmiento, Cesar A.; Babul, Jorge; Sanabria, Hugo; Medina, Exequiel
    Transcription factors regulate gene expression by binding to DNA. They have disordered regions and specific DNA-binding domains. Binding to DNA causes structural changes, including folding and interactions with other molecules. The FoxP subfamily of transcription factors in humans is unique because they can form heterotypic interactions without DNA. However, it is unclear how they form heterodimers and how DNA binding affects their function. We used computational and experimental methods to study the structural changes in FoxP1's DNA-binding domain when it forms a heterodimer with FoxP2. We found that FoxP1 has complex and diverse conformational dynamics, transitioning between compact and extended states. Surprisingly, DNA binding increases the flexibility of FoxP1, contrary to the typical folding-upon-binding mechanism. In addition, we observed a 3-fold increase in the rate of heterodimerization after FoxP1 binds to DNA. These findings emphasize the importance of structural flexibility in promoting heterodimerization to form transcriptional complexes.
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    The Folding Unit of Phosphofructokinase-2 as Defined by the Biophysical Properties of a Monomeric Mutant
    (2015) Ramírez Sarmiento, Cesar Antonio; Báez, Mauricio; Zamora, Ricardo A.; Balasubramaniam, Deepa; Babul, Jorge; Komives, Elizabeth A.; Guixé, Victoria
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    Unraveling the folding and dimerization properties of the human FoxP subfamily of transcription factors
    (2023) Villalobos, Pablo; Carvajal, Alonso I. I.; Castro-Fernandez, Victor; Babul, Jorge; Ramirez-Sarmiento, Cesar A.; Medina, Exequiel
    Human FoxP proteins share a highly conserved DNA-binding domain that dimerizes via three-dimensional domain swapping, although showing varying oligomerization propensities among its members. Here, we present an experimental and computational characterization of all human FoxP proteins to unravel how their amino acid substitutions impact their folding and dimerization mechanism. We solved the crystal structure of the forkhead domain of FoxP4 to then perform a comparison across all members, finding that their sequence changes impact not only the structural heterogeneity of their forkhead domains but also the protein-protein association energy barrier. Lastly, we demonstrate that the accumulation of a monomeric intermediate is an oligomerization-dependent feature rather than a common aspect of monomers and dimers in this protein subfamily.
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    Unusual dimerization of a BcCsp mutant leads to reduced conformational dynamics
    (2017) Carvajal, Alonso I.; Vallejos, Gabriel; Komives, Elizabeth A.; Castro Fernández, Víctor; Leonardo, Diego A.; Garratt, Richard C.; Ramírez Sarmiento, Cesar Antonio; Babul, Jorge