Translocation of a protein-like chain through an interacting channel

• DOI: 10.1007/s10118-011-1067-1
• Publication Date: 2011-06-29T13:17:50Z
• Authors: Ting-ting Sun; Hai-zhu Ma; Shao-ping Deng
• Keywords: 0103 physical sciences; 01 natural sciences

The effect of channel-protein interaction on the translocation of a protein-like chain through a finite channel under certain electric field was studied by using dynamical Monte Carlo simulations. The interior behavior of chain conformation under different interactions was investigated, such as the number of monomers outside of channel nout, monomers inside of channel nm, mean-square radius of gyration 〈 S2 〉 and the average energy 〈 U 〉. It shows that with strong attractive interaction, the translocation is more difficult than moderate interaction. At the same time, the dependence of translocation time with different interactions shows that moderate repulsive interaction (ɛcp = 0.5) accelerates the translocation. Although the waiting time for successful translocation of ɛcp = 1.0 is the longest, the average translocation time is not very large. It is far smaller than that of ɛcp=−1.0. The probability distributions of translocation time p(t′) and the probability distributions of three duration times p(t1′), p(t2′) and p(t3′) were all discussed. Log-normal distributions are found. All these findings will strengthen the understanding of protein translocation.