Homology modeling and molecular dynamics techniques in the study of the functionality of gsdmb and the cohesin complex

• Autores: David Ros Pardo
• Directores de la Tesis: Paulino Gómez Puertas (dir. tes.), Iñigo Marcos Alcalde (codir. tes.)
• Lectura: En la Universidad Autónoma de Madrid ( España ) en 2024
• Idioma: español
• Tribunal Calificador de la Tesis: Pedro Antonio Reche Gallardo (presid.), Cristina Sanz Sanz (secret.), Ugo Bastolla (voc.), Marisela Vélez Tirado (voc.), Jesús Mingorance Cruz (voc.)
• Programa de doctorado: Programa de Doctorado en Biociencias Moleculares por la Universidad Autónoma de Madrid
• Materias:
  • Matemáticas
    • Ciencia de los ordenadores
      • Simulación
  • Ciencias de la vida
    • Biofísica
    • Biología molecular
• Enlaces
  • Tesis en acceso abierto en: Biblos-e Archivo
• Resumen

  • Homology modeling and molecular dynamics provide researchers with tools to investigate the mechanical behavior of both crystallized and non-crystallized proteins under various conditions. In this doctoral thesis, we focused on two systems: GSDMB and the STAG2/RAD21 complex.

    GSDMB is a protein involved in pore formation during pyroptosis, with isoforms defined by the presence or absence of exons 6 and 7. Our investigation of GSDMB encompassed studying the impact of exon 6 on the protein's structure and monomer-monomer interactions, as well as examining the effect of different GSDMB isoforms in regulating pyroptotic activity.

    The STAG2/RAD21 dimer is part of the cohesin complex, crucial for chromatid cohesion during replication, DNA expression regulation, DNA repair, and three-dimensional structure management. Variants in the cohesin complex are associated with various cancers and genetic diseases. In our research, the STAG2/RAD21 complex was addressed in two complementary works: the mechanistic rationalization of disease-causing variants in humans and the proposal of a new mechanism of action of the complex in the loop extrusion process.

    We conducted atomistic simulations to investigate mutations in STAG2, RAD21, and NIPBL, aiming to understand their effects on complex-DNA interactions. Most mutations resulted in local conformational changes that could disrupt complex activity.

    Furthermore, we explored whether the STAG2/RAD21 complex could work as a molecular ratchet, apart from its already known function as anchor of the cohesin complex. Through coarse-grained molecular dynamics simulations with external forces, we observed that the complex could easily shift to the left side but adopted a closed conformation when pushed to the right. Additionally, we found that RAD21 is necessary to regulate STAG2 flexibility and maintain its closed crystal-like structure.