Premium
Computer simulations of protein translocation
Author(s) -
Kirmizialtin Serdal,
Huang Lei,
Makarov Dmitrii E.
Publication year - 2006
Publication title -
physica status solidi (b)
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.51
H-Index - 109
eISSN - 1521-3951
pISSN - 0370-1972
DOI - 10.1002/pssb.200666812
Subject(s) - chromosomal translocation , chemistry , molecular dynamics , biophysics , physics , chemical physics , biology , computational chemistry , biochemistry , gene
Many biological processes, e.g. protein degradation by ATP dependent proteases and mitochondrial protein import, involve protein translocation through nanometer‐sized pores. In this paper, we report on computer simulations of two models of protein translocation. In the first model, a protein domain is pulled mechanically through a narrow neutral pore. We compare the free energy cost of squeezing an initially folded protein into the pore with that for a random‐coil‐like homopolymer and show that the former case involves several partially folded intermediates. The second model involves electrophoretically driven translocation of a β‐hairpin forming peptide across the α‐hemolysin protein pore. The distribution of the time the peptide spends inside the pore is exponential at low forces, suggesting a single rate limiting barrier crossing step for the translocation process, while at higher forces this distribution tends to be a bell shaped curve. The dependence of the average translocation time 〈 t 〉 on the applied force f is well described by the exponential relationship: 〈 t 〉 = af + b at low forces, while at high forces the inverse translocation time is a linear function of the force, 〈 t 〉 –1 = Af – B . (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)