Computer simulations of protein translocation and stretching

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Title: Computer simulations of protein translocation and stretching
Author: Kirmizialtin, Serdal, 1975-
Abstract: Many biomolecular processes involve mechanical force -induced reactions in the cell , such as translocation , and mechanical stretching of biopolymers . Recent advances in single molecule manipulation techniques make it possible to apply mechanical force to individual biomolecules and study their dynamics . To gain molecular level understanding of these processes and to interpret the single -molecule experiments , we used Langevin dynamics simulations of coarse -grained biopolymer models . Our result show that the mechanism of translocation of proteins through pores depends on the pore diameter , on the magnitude of the pulling force and on whether the force is applied at the N - or the C -terminus of the chain . In addition , the translocation kinetics of peptides varies with their stability . The mechanism of protein translocation is found to be different from that of a structureless polypeptide of the same length . We further showed that unfolding mechanism of translocation process is different from when the same protein is stretched between its C - and N -termini . We also studied the mechanical and chemical /thermal denaturation of proteins . We observed that the free energy profile along the mechanical reaction coordinate and the chemical reaction coordinate are different . In our protein model , the mechanical and chemical /thermal denaturation cannot be simply explained in terms of a simple onedimensional free energy landscape . We further analyzed the spontaneous folding and refolding under a constant force and found that refolding generally occurs via different mechanisms . Similarly , we investigated the protein unfolding /refolding under the applied force that varies with a constant loading rate . This study shows that unfolding /refolding pathways are generally similar for low loading /unloading rates while they become different for high loading /unloading rates . Finally , we studied the dynamics of molecular friction knots formed by a pair of polymer strands . We examined different knot types , and different polymer sequences . Depending on the knot type and the nature of the polymer , we observed two different behaviors when the force F is exerted to separate the polymer strands . The knot between polymer strands can be strong (the time [tau] the knot stays tied increases with the force F applied to separate the strands ) or weak ([tau]decreases with increasing F ) .
URI: http : / /hdl .handle .net /2152 /3385
Date: 2008-08-28


Computer simulations of protein translocation and stretching. Doctoral dissertation, The University of Texas at Austin. Available electronically from http : / /hdl .handle .net /2152 /3385 .

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