Exploring ssDNA translocation through alpha-hemolysin using Coarse-Grained Steered Molecular Dynamics

Protein nanopores have proven to be effective for single-molecule studies, particularly for single-stranded DNA (ssDNA) translocation. Previous experiments demonstrated their ability to distinguish differences in purine and pyrimidine bases and in the orientation of the ssDNA molecule inside the nanopore. Unfortunately, the microscopic details of ssDNA translocation over experimental time scales, which are not accessible through all-atom molecular dynamics (MD), have yet to be examined. However, coarse-grained (CG) MD simulations enable systems to be simulated over longer characteristic times closer to experiments than all-atom MD. This paper studies the ssDNA translocation through alpha-hemolysin nanopore exploiting steered MD using MARTINI CG force field. The impact of sequence length, orientation inside the nanopore and DNA charges on translocation dynamics as well as the conformational dynamics of ssDNA during the translocation are explored. Our results highlight the efficacy of CG molecular dynamics in capturing experimental properties of ssDNA translocation, including a wide distribution in translocation time per base. In particular, the phosphate charges of the DNA molecule are crucial in the translocation dynamics and impact the translocation rate. Additionally, the influence of the ssDNA molecule orientation on the translocation rate is explained by conformational differences of ssDNA inside the nanopore during its translocation. Our study emphasizes the significance of sufficient statistics via CG MD, which can elucidate the great variety of translocation processes.