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Some thermodynamics properties of compact polymer chains are investigated during the translocation process, such as average Helmholtz free energy 〈A〉, average energy per bond 〈U〉, and average contact energy per bond 〈Uc〉.
We first calculate the chain size and shape of compact chains transporting through an infinite channel, such as mean-square end-to-end distance per bond 〈R2〉/N, mean-square radii of gyration per bond 〈S2〉/N, 〈S2〉xy/N and 〈S2〉z/N, and shape factor 〈δ〉 for the changes in the size and shape of compact chains during the translocation process.
Tracing the variation of the square radius of gyration, R2g, and the polymer configuration during translocation, we observe that the chain is elongated when it is passing through the pore, which manifests that the chain is not in equilibrium during the translocation process.
Based on the excluded volume theory, the conformational change of proteins is estimated during the translocation process, and the unfolding of the protein stretched by intensive electric forces is confirmed at high voltages.
The middle portion of the toxins is considered to mediate membrane insertion during the translocation process and is probably responsible for pore formation in membranes.
However, it has often been suggested that one of the major biological functions of mRNA localization is to restrict the production of the encoded protein to the appropriate region, implying that mRNA is not translated during the translocation process.
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In agreement, Savory et al. suggested the possibility of GR homodimerization occurring during or even before the translocation process [36].
We applied molecular dynamics simulations to investigate the translocation process of ampicillin (Amp) through OmpF.
We extracted the speed of dsDNA translocation from the dwell time distribution and estimated the various forces involved in the translocation process.
We present quantitative kinetic models of the translocation process based on Markov State Model analysis.
We next examined the ATP-dependence of the translocation process.
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