Speaker
Description
This study investigates the mechanisms underlying the interaction between a single-stranded DNA aptamer and vancomycin. Experimental observations indicate that the aptamer exhibits high selectivity in binding to vancomycin, inducing conformational changes that lead to fluorescence quenching. However, the precise mechanisms remain unclear. To clarify these mechanisms, molecular dynamics (MD) simulations were performed in NAMD to examine the interaction dynamics between vancomycin and the aptamer. Two distinct aptamer configurations were prepared for the simulations: (1) the “denature” system, which assumed no initial structural constraints on the aptamer and was initialized from a B-form–derived geometry and relaxed for 10 ns to reduce structural rigidity, and (2) the “hybridize” system, whose secondary structure was predicted by NUPACK, modeling the aptamer with anticipated complementary regions. After these preliminary simulations, vancomycin was positioned to interact with specific regions of each aptamer configuration, followed by an additional 50 ns of simulation. In total, we accumulated 1.8 μs of simulation time across all trajectories. The binding process was visualized using VMD, and contact mapping was used to track vancomycin’s residue interactions and contact probabilities, which have thus far shown no obvious sequence dependence among the tested regions under the sampled timescales. MM-GBSA free energy calculations estimated the binding affinities, revealing minimum energies of approximately −16.8 kcal/mol for the denature system and −5.8 kcal/mol for the hybridize system. In contrast, the hybridize system predominantly exhibited weaker and more transient contacts overall; however, elevated contact probabilities were consistently localized to a loop region, whereas the complementary (paired) segments showed low contact probabilities and often appeared more consistent with surface sliding than stable anchoring. This contact pattern is consistent with a conformation-guided binding tendency in the hybridize configuration, where loop architecture may provide a more defined docking environment. By comparison, the more favorable MM-GBSA energy observed in the denature system may be influenced by broadly distributed, less localized interactions, potentially stabilized by multiple hydrogen bonds between vancomycin and the aptamer’s base regions. To further quantify the binding thermodynamics beyond MM-GBSA, representative loop-associated conformations were selected for umbrella sampling along the ligand–aptamer center-of-mass distance to estimate the standard-state binding free energy (ΔG°), yielding an estimated binding free energy of ~−10.4 kcal/mol. This value is in reasonable agreement with the experimental affinity (Kd ≈ 0.1 μM; ΔG ≈ −9.54 kcal/mol), supporting the plausibility of a loop-associated binding mode under the hybridize configuration.
