Early events in the activation of membrane-protein controlled pathways

Membrane proteins and intrinsically disordered regions play fundamental roles in cellular signaling, homeostasis, and stress response, yet remain challenging to characterize structurally and dynamically. In this thesis, molecular dynamics (MD) simulations and computational protein modeling are employed to investigate single-pass transmembrane proteins and disordered regions, complementing experimental structural biology and addressing gaps where high-resolution structures are unavailable. A central focus of this thesis is inositol-requiring enzyme 1 (IRE1), a conserved transmembrane sensor of endoplasmic reticulum (ER) stress and key transducer of the unfolded protein response (UPR). Simulations of the human IRE1α lumenal domain demonstrate that it forms a stable dimer capable of engaging unfolded peptides at its interface, supporting a refined activation model in which both structural integrity and peptide binding drive UPR signaling. Comparative simulations of human and yeast IRE1 transmembrane domains reveal species-specific lipid interactions and asymmetric bilayer deformations, illustrating how IRE1 integrates proteostatic and membrane-derived signals. Building on these findings, generative protein design methods produced de novo peptide binders that interact stably with the IRE1 lumenal domain, establishing a proof of principle for computationally guided modulation of stress signaling. Coarse-grained simulations of IRE1's intrinsically disordered lumenal regions further revealed a propensity for intermolecular association and condensate formation driven by aromatic and charged residues, implicating disordered segments in higher-order oligomerization. Beyond IRE1, the thesis extended its investigation of disordered proteins to the RNA-binding protein IGF2BP1. In contrast with IRE1, simulations of the IGF2BP1 disordered regions showed that its linker regions remain extended and largely non-associating, underscoring the functional diversity of disordered regions across proteins. Finally, simulations of the HIV-1 envelope glycoprotein (Env) transmembrane domain reveal flexible, conical trimers that deform the lipid bilayer and engage lipid headgroups in ways that stabilize antibody-bound conformations, offering mechanistic insight into neutralizing antibody recognition. Together, these studies demonstrate the power of integrative computational approaches to elucidate the structural dynamics of membrane proteins and disordered regions, with implications for our understanding of ER stress signaling, protein phase separation, and viral entry.