Understanding Periperal Membrane Protein Interactions | BPS Thematic Meeting

Understanding Peripheral Membrane Protein Interactions: Structure, Dynamics, Function and Therapy

Tuesday Speaker Abstracts

DECODING BIOCHEMICAL COMPLEXITY WITH SIMULATIONS AND AI ENHANCED SAMPLING Marco De Vivo 1 ; 1 Italian Institute of Technology, Genoa, Italy No Abstract

DIVERGENT BREATHINGS MODES OF EHD PARALOGS: INSIGHTS FROM MOLECULAR SIMULATIONS AND IMPLICATIONS IN MEMBRANE REMODELING Vinodhini Selvanarayanan 1 ; Anand Srivastava 1 ; 1 Indian Institute of Science, Molecular Biophysics Unit , Bengaluru, India The endocytic recycling pathway (ERP) maintains cellular homeostasis by recycling membrane components through budding, fission, and fusion of transport vesicles. EPS15 homology domain containing protein (EHD, ~60 kDa ATPase) is vital for membrane remodelling in ERP (Naslavsky and Caplan, TiCB2011). EHDs exist as four paralogs with high sequence identity but exhibit divergent activity inside the cell (Bhattacharya and Pucadyil, Prot. Sci. 2020). Unlike well-characterized dynamins, the interplay between membrane association, oligomerization and ATP-activity leading to membrane remodeling in EHD paralogs remains unclear. This study employs all-atom MD and WT-metadynamics simulations to investigate the structural and conformational dynamics differences among EHDs in solution and on biological membrane.Results from molecular simulations reveal that all EHDs except EHD2 display conformational breathing towards an open-state in solution. Tracking the cause for the EHD2 conformation rigidity, we find that two residues near the hinge region (G284 and L184) as critical for its locked conformation. Interesting, all other EHDs have conserved S284 and R184 (instead of G284 and L184). Using metadynamics simulations, we calculated the free-energy landscape of conformational transition from close to open-state in EHD2/1-WT and EHD2/1 reverse double mutants (G284S and L184R). A thermodynamic barrier separating the open and closed conformations was present in EHD2-WT but absent in the mutant, while the reverse was observed for EHD1. Extending the studies to EHD4 paralog suggests that EHD4 prefers an open conformation in solution but adopts a closed-state upon membrane binding. This conformational dynamics data cleanly reconciles the two structural data from Olivier Daumke and co-workers (PDB IDs: 5MTV and 7SOX) where EHD4 is reported as open structure in solution and as closed structure in membrane-bound oligomers. The membrane adopted closed conformation reveals an intermediate structure that we believe could be facilitating oligomerization and ATP activity may be required to cross the barrier to form the final closed oligomeric filaments on the membrane.

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