서강대학교

초록/요약

The translocation of a DNA into a capsid shell via a molecular motor is a critical step in viral infection. Recent experiments suggested that the translocation would occur so fast that the conformation of the packaged DNA inside the capsid hardly relaxed during the translocation. More interestingly, when the packaged DNA was allowed intermittently to relax its conformation in those experiments, the translocation velocity was increased by about 50%. This indicates that the conformational relaxation relates closely to the translocation process. In this paper, we perform extensive Langevin dynamics simulations and observe directly the conformation relaxation of a DNA (modeled by a generic coarse-grained polymer) during the translocation. The conformational relaxation time of a polymer inside a sufficiently small capsid is increased by a factor of up to 500 compared to that of the polymer in a dilute bulk solution. We mimic the previous experiments and allow the polymer to relax its conformation for a designated time (τstall) during the translocation. When τstall is larger than the conformational relaxation time, the translocation velocity is increased by about 20%, which is consistent with experiments. We calculate contact probability distribution functions and find that the conformation of the polymer changes significantly depending on whether the polymer is allowed to relax or not. This indicates that the conformational relaxation affects the translocation rate significantly.