Effect of ionized protein residues on the nucleation pathway of protein folding

The Journal of Chemical Physics
Yuri Djikaev, Eli Ruckenstein

Abstract

Using a ternary nucleation formalism, we have recently [Y. S. Djikaev and E. Ruckenstein, J. Chem. Phys. 126, 175103 (2007)] proposed a kinetic model for the nucleation mechanism of protein folding. A protein was considered as a heteropolymer consisting of hydrophobic, hydrophilic, and neutral beads with all the bonds having the same constant length and all the bond angles equal and fixed. In this paper, we further develop that model by taking into account of the ionizability of some of the protein residues. As previously, an overall potential around the cluster wherein a protein residue performs a chaotic motion is considered to be a combination of the average dihedral and average pairwise potentials (the latter now including an electrostatic contribution for ionized residues) assigned to the residue and the confining potential due to the polymer connectivity constraint. The overall potential as a function of the distance from the cluster has a double well shape (even for ionized beads) which allows one to determine the rates of emission and absorption of residues by the cluster by using a first passage time analysis. Assuming the equality of the ratios of the numbers of negatively and positively ionized residues in the cluste...Continue Reading

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Citations

Aug 7, 2009·The Journal of Chemical Physics·Y S Djikaev, Eli Ruckenstein
Apr 2, 2009·The Journal of Chemical Physics·Y S Djikaev, Eli Ruckenstein
Nov 14, 2008·Advances in Colloid and Interface Science·Y S Djikaev, Eli Ruckenstein
Dec 17, 2014·Advances in Colloid and Interface Science·Eli RuckensteinGanesan Narsimhan
Sep 4, 2008·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Y S Djikaev, Eli Ruckenstein
Apr 7, 2010·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Y S Djikaev, Eli Ruckenstein
Feb 19, 2010·Advances in Colloid and Interface Science·Y S Djikaev, E Ruckenstein

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Methods Mentioned

BETA
protein folding

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