Mechanistic Insights into Adaptive Binding of Vitamins and Hormones at Hotspot-Enriched Interfaces of the Synaptotagmin 1 C2AB Domain

Abstract

The present in silico study provided the adaptive binding of seven physiologically active molecules, including four non-peptide hormones (cortisol, estradiol, triiodothyronine, melatonin) and three vitamins (methyltetrahydrofolate, pyridoxal phosphate, thiamine), alongside argireline as a benchmark, at hotspot-enriched interfaces of full C2AB-domain of Synaptotagmin 1 (Syt1), using molecular docking study and molecular dynamics (MD) simulations. Linear correlations of MD-features and nonlinear KPCA-IG-based ranking of features and ligands yielded deeper mechanistic insights. All ligands exhibited spontaneous binding with strong negative {Delta}Gbinding values. Fifteen hotspots, clustered across the C2A, C2B, and C2AB-interlink regions, were dominated by hydrophobic and van der Waals interactions. Several hotspots and non-hotspots corresponded to Syt1 residues that are reported to link with Ca2+-dependent phenomena and membrane vesicular fusion. Solvent-excluded volume (VSE) analyses showed that local hotspot burial and global desolvation together influenced protein adaptability, distinguishing ligands with similar hotspots but divergent thermodynamics. Linear correlations established {Delta}Gbinding as an indicator of hydrophobic hotspot burial. KPCA-IG identified {Delta}VSE and RMSD as dominant mechanistic features capturing cooperative induced-fit responses. Pyridoxal phosphate, melatonin and triiodothyronine emerged as mechanistically top adaptive binders, involving adjustable desolvation, hotspot expansion, optimal flexibility and pose retention. Methyltetrahydrofolate and cortisol showed intermediate burial-dominated cooperativity. Argireline, thiamine and estradiol exhibited ligand-specific burial-dominated, pose-locked and adaptability-limited bindings. Overall, our study demonstrates that desolvation control, induced-fit adaptability and structural flexibility, not {Delta}Gbinding alone, govern Syt1-ligand binding, revealing Syt1 as a versatile presynaptic target for modulation by these bioactive molecules.