Sequence and force effects on ssDNA translocation through a protein nanopore: Coarse-grained steered molecular dynamics simulations

Protein nanopores are highly effective for single-molecule studies, especially in the context of single-stranded DNA (ssDNA) translocation. Previous experiments have successfully distinguished between purine and pyrimidine bases and have revealed insights into the effect of applied electric voltage on the ssDNA translocation dynamics. Unfortunately, the microscopic details of ssDNA translocation over experimental timescales, which are not easily accessible through all-atom molecular dynamics (MD), remain to be further explored. Coarse-grained (CG) MD simulations offer a promising avenue to bridge this gap, allowing simulations over longer timescales closer to the experimental ones. This paper investigates ssDNA translocation through the alpha-hemolysin (aHL) nanopore using constant-force steered MD with the MARTINI CG force-field, building on our previous work validating this approach for ionic and ssDNA transport through this nanopore. We simulated the translocation of poly(dA) and poly(dC) molecules with varying lengths through the aHL nanopore, under different pulling forces to mimic the effect of the voltage applied in the experiments. The influence of the sequence and of the magnitude of the pulling force on translocation dynamics is explored. The simulations were run in two replicas for several microseconds for all systems. Our results demonstrate that CG MD simulations efficiently generate statistically significant data and are successful in capturing experimental properties of ssDNA translocation, such as the shorter translocation times of pyrimidine bases over purine and the effect of the applied force. They also provide new insights into the role of the DNA conformation dynamics during translocation. Despite the simplification of the CG model, our findings are in accordance with previous experimental and all-atom MD simulation results, underscoring the potential of the model for studying further nanopore systems.