pH-Dependent Membrane Binding Specificity of Synaptogyrins 1-3 with Distinct Isoelectric Points (pI) Identified by Structural Bioinformatics and Molecular Dynamics

Synaptogyrins are integral membrane proteins involved in an essential process for neuronal communication: neurotransmitter release from synaptic vesicles. The synaptic vesicles maintain an acidic environment due to the action of proton pumps (V-ATPases), which actively transport HL into the vesicles. This creates a gradient of protons, which enables the transport of neurotransmitters into the vesicles. In contrast, the pH of synaptic vesicles increases upon neuronal activation. To evaluate the effect of varying pH environments on synaptic vesicle proteins, synaptogyrin-1 and synaptogyrin-3 were selected for this study because of their distinct isoelectric points (pI), but highly similar structures (RMSD=1.273Å). We conducted molecular dynamics simulations to examine the membrane binding dynamics of AlphaFold3 predicted structures at the active pH of 7.25 and the resting pH of 5.5. Our results reveal that the electrostatic properties of synaptogyrins affect their membrane binding properties, such as gyration radii and root mean square fluctuations. Their conformational characteristics were analyzed in correlation with variant analysis and evolutionary profiling, which uncovered several key residues contributing to their diversification. The study identifies the potential roles of synaptic vesicle pH in modulating synaptogyrin conformational and variational space, offering new perspectives on their contributions to synaptic function.