Our latest publications:

Molecular basis for DNA recognition by the maternal pioneer transcription factor FoxH1 – Click to expand

Radoslaw Pluta, Eric Aragón, Nicholas A. Prescott, Lidia Ruiz, Rebeca A. Mees, Blazej Baginski, Julia R. Flood, Pau Martin-Malpartida, Joan Massagué, Yael David, Maria J. Macias Nature Communications volume 13, Article number: 7279 (2022), doi:10.1038/s41467-022-34925-y.

Forkhead box H1 (FoxH1) is an essential maternal pioneer factor during embryonic development that binds to specific GG/GT-containing DNA target sequences. Here we have determined high-resolution structures of three FoxH1 proteins (from human, frog and fish species) and four DNAs to clarify the way in which FoxH1 binds to these sites. We found that the protein-DNA interactions extend to both the minor and major DNA grooves and are thus almost twice as extensive as those of other FOX family members. Moreover, we identified two specific amino acid changes in FoxH1 that allowed the recognition of GG/GT motifs. Consistent with the pioneer factor activity of FoxH1, we found that its affinity for nucleosomal DNA is even higher than for linear DNA fragments. The structures reported herein illustrate how FoxH1 binding to distinct DNA sites provides specificity and avoids cross-regulation by other FOX proteins that also operate during the maternal-zygotic transition and select canonical forkhead sites.

Conformational ensemble of the TNF-derived peptide solnatide in solution – Click to expand

Pau Martin-Malpartida, Silvia Arrastia-Casado, Josep Farrera-Sinfreu, Rudolf Lucas, Hendrik Fischer, Bernhard Fischer, Douglas C.Eaton, Susan Tzotzos, Maria J.Macias Nature Communications volume 13, Article number: 7279 (2022), doi:10.1038/s41467-022-34925-y.

Tumor necrosis factor (TNF) is a homotrimer that has two spatially distinct binding regions, three lectin-like domains (LLD) at the TIP of the protein and three basolaterally located receptor-binding sites, the latter of which are responsible for the inflammatory and cell death-inducing properties of the cytokine. Solnatide (a.k.a. TIP peptide, AP301) is a 17-mer cyclic peptide that mimics the LLD of human TNF which activates the amiloride-sensitive epithelial sodium channel (ENaC) and, as such, recapitulates the capacity of TNF to enhance alveolar fluid clearance, as demonstrated in numerous preclinical studies. TNF and solnatide interact with glycoproteins and these interactions are necessary for their trypanolytic and ENaC-activating activities. In view of the crucial role of ENaC in lung liquid clearance, solnatide is currently being evaluated as a novel therapeutic agent to treat pulmonary edema in patients with moderate-to-severe acute respiratory distress syndrome (ARDS), as well as severe COVID-19 patients with ARDS. To facilitate the description of the functional properties of solnatide in detail, as well as to further target-docking studies, we have analyzed its folding properties by NMR. In solution, solnatide populates a set of conformations characterized by a small hydrophobic core and two electrostatically charged poles. Using the structural information determined here and also that available for the ENaC protein, we propose a model to describe solnatide interaction with the C-terminal domain of the ENaCα subunit. This model may serve to guide future experiments to validate specific interactions with ENaCα and the design of new solnatide analogs with unexplored functionalities.

Our research interests focus on deciphering and illustrating the mechanisms that correlate cell signaling with gene expression, how these processes are regulated and their implications in human diseases.

Our lab combines molecular biology with NMR, X-ray, SAXS techniques and bioinformatic tools to unveil how these complexes look like. We are incorporating the power of cryoEM into our structural biology portfolio, to study large and complex systems.

A large part of our work is devoted to clarifying TGFβ signaling and the role of SMAD transcription factors and bound cofactors. TGFβ signaling acts at the core of early embryogenesis and in development. Many tumors adopt the same native strategies to acquire malignant properties by increasing their invasive properties and to disseminate to distant organs (metastasis). Since 2008, we collaborate with the group of J. Massagué (Memorial Sloan Kettering Cancer Center, NY, USA) in several aspects related to TGFβ signaling and SMAD function.

Together with the gynecologic and oncology medical doctors of the Sant Pau Hospital in Barcelona (R. Rovira and coworkers) and with its research institute (V. Céspedes) we aim to identify diagnosis tools and to predict the probability of relapse and metastasis of Endometrial cancers.

Our collaborators