Mechanical unfolding of segment-swapped protein G dimer: Results from replica exchange molecular dynamics simulations

Article Abstract:

Replica exchange molecular dynamics simulations are used to study the mechanical unfolding of segment-swapped protein G dimer, which is a mutated dimeric form of the immunoglobulin-binding domain B1 of streptococcal protein G. The dimer is found to be less resistant to mechanical unfolding than its monomeric counterpart and the two proteins have displayed the same mechanical unfolding mechanism involving separation of the terminal parallel strands.

Protein binding

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Ubiquitin-like protein domains show high resistance to mechanical unfolding similar to that of the 127 domain in titin: evidence from simulations

Article Abstract:

The mechanical unfolding of the two mixed alpha + beta domains, streptococcal protein G IgG-binding domain III and ubiquitin, both having a beta-grasp fold is examined and it is presented that they display high resistance to unfolding similar to that of 127. It further predicts the outcome of a hypothetical single-molecule AFM pulling experiment, in which one of the 127 domains in titin is replaced by one of the above proteins.

Proteins, Chemistry, Physical and theoretical, Physical chemistry, Ubiquitin, Mechanical properties, Structure, Atomic properties

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Single-molecule electrophoresis of [beta]-hairpin peptides by electrical recordings and Langevin dynamics simulations

Article Abstract:

Single-channel electrical recordings and Langevin molecular dynamics simulations are used to explore the electrophoretic translocation of various [beta]-hairpin peptides across the staphylococcal alpha-hemolysin ([alpha]HL) protein pore at single-molecule resolution. The study has shown that the interaction between a polypeptide and a beta-barrel protein pore is dependent on the folding features of the polypeptide.

Usage, Electrophoresis, Polypeptides

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