Binding of Urinary Human Serum Albumin Fragments to Albumin-Selective Aptamer-Bound Graphene Quantum Dots: Simulation Studies

Microalbuminuria is a key indicator of chronic kidney disease (CKD), resulting from the leakage of albumin into urine. The accuracy of microalbuminuria measurement depends on urine freshness as improper storage and slow processing can lead to protease digestion of albumin. Recently, graphene-based aptasensors have been shown to detect albumin in aged urine samples, suggesting that albumin fragments can still be recognized by these sensors. To date, nine urinary albumin fragments (F1–F9) have been reported. Meanwhile, the graphene quantum dot (GQD) has emerged as a promising material due to its noncytotoxicity, high biocompatibility, and intrinsic fluorescence properties. Its comparable size to aptamers makes it particularly attractive for albumin detection. In this study, molecular dynamics (MD) simulations were performed to reveal the binding modes of urinary albumin fragments (F1–F9) to the aptamer-bound GQD (GQDA) complex. The study compares the binding behavior of nonaggregated (N_AG) and preaggregated (AG) albumin fragments with GQDA. The results demonstrate that the spontaneous clustering of GQDA and albumin fragments occurs in all cases. However, aggregated fragments exhibit reduced aptamer accessibility due to geometric confinement and structural rigidity. Lysine-rich regions were found to play a crucial role in fragment–aptamer interactions, with F1 and F8 displaying the highest number of aptamer contacts. Notably, F8, the most stable fragment, showed the strongest interactions with aptamers, highlighting its potential as a urinary biomarker for CKD detection. The findings from this study provide valuable molecular insights into the interactions between urinary albumin fragments and GQDA, paving the way for the development of highly selective and sensitive CKD diagnostic platforms.