Understanding Periperal Membrane Protein Interactions | BPS Thematic Meeting

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

Tuesday Speaker Abstracts

FROM SEQUENCE TO MECHANISM: INSIGHTS INTO PROTON COUPLING IN CYSTINOSIN FROM MULTISCALE MOLECULAR SIMULATIONS

Jonathan D Colburn 1 ; Simon Newstead 1 ; Philip C. Biggin ; 1 University of Oxford, Biochemistry, Oxford, United Kingdom

Cystinosin is a proton-coupled lysosomal symporter in the SLC family. Dysfunction in this transporter leads to cystine accumulation in lysosomes, which is associated with severe metabolic disorders. Leveraging recent advances in AI-based protein structure prediction models, we explore the mechanism of Cystinosin using enhanced-sampling molecular dynamics. Our results show that AlphaFold with MSA-subsampling can generate diverse structural ensembles that include realistic occluded states and end-states. By applying simple heuristics and dimensionality reduction techniques to these synthetic ensembles, we extract valuable information such as seed-structures and collective variables for umbrella sampling. This enables the calculation of robust, hysteresis-free energetics for the full conformational cycle of the transporter. Thus, our pipeline allows us to distil out essential dynamic and functional insights from sequence alone in a computationally efficient manner, without sacrificing the accuracy of physical models. Finally, QM/MM metadynamics simulations reveal the nature and mechanism of the proton transfer process that drives substrate export in Cystinosin. We show how proton exchange between gating residues is coupled to the dynamic transition between outward- and inward-facing conformations in the alternating access cycle.

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