Translocation of a proteinlike chain through a finite channel.
We use the pruned-enriched-Rosenbluth method and the modified orientation-dependent monomer-monomer interaction model to study the translocation of a proteinlike chain through a finite channel. The mean-square radius of gyration per bond <S2>/N and shape factor <delta*> of proteinlike chains with different secondary structures transporting through a finite channel with different channel radii R=1, 2, 3, 4, and 20 are investigated in the translocation. The average Helmholtz free energy per bond A/N and the mechanical force f are also presented. A/N remains unchanged when X(0)<0 and X(0)>1, and decreases monotonously when 0.5<X(0)<0.1. Here X(0)=X/N identical with 2X/L,X is the position of the first monomer, N is chain length, and L is channel length. No free energy barrier is found in our calculation. f is negative and has a plateaulike behavior. The plateau becomes narrow and the value of f increases as R increases. The total energy per bond <U>/N is also calculated in the process of translocation. An energy barrier is shown. The proteinlike chains must cross this energy barrier when they escape from the channel. The position of the maximum of <U>/N depends on the secondary structures and the channel radius. We also discuss the average contact energy per bond <U>c/N, the average alpha-helical energy per bond <U>h/N, and the average beta-sheet energy per bond <U>b/N.
Sun
Tingting
T
Department of Physics, Zhejiang University, Hangzhou 310027, People's Republic of China.
Zhang
Linxi
L
Su
Jiaye
J
D008962:Models, Theoretical; D017434:Protein Structure, Tertiary; D021381:Protein Transport; D013329:Structure-Activity Relationship