Mechanical unfolding of segment-swapped protein G dimer: results from replica exchange molecular dynamics simulations.
The protein G dimer (pdb code 1Q10) is a mutated dimeric form of the immunoglobulin-binding domain B1 of streptococcal protein G, in which the two monomeric units have swapped elements of their secondary structure. We have used replica exchange molecular dynamics simulations to study how this dimer responds to a mechanical force that pulls the N-terminus of one unit and the C-terminus of the other apart. We have further compared the mechanical response of the dimer to that of the protein G monomer. When the pulling force is low enough, the mechanical unfolding can be viewed as a thermally activated barrier crossing process. For each protein, we have computed the corresponding free energy barrier and its dependence on the pulling force. While the dimer is found to be less resistant to mechanical unfolding than its monomeric counterpart, the two proteins exhibit essentially the same mechanical unfolding mechanism involving separation of the terminal parallel strands. On the basis of our results, we speculate that the mechanical properties of natural adhesives, composites, fibers, and other materials may be optimized not only at a single molecule level but also at the mesoscopic level through the interactions among individual chains.
Li
Pai-Chi
PC
Department of Chemistry and Biochemistry and Institute for Theoretical Chemistry, University of Texas at Austin, Austin, TX 78712, USA.
Huang
Lei
L
Makarov
Dmitrii E
DE
D001426:Bacterial Proteins / Q000737:chemistry*; D003198:Computer Simulation; D019281:Dimerization; D007136:Immunoglobulins / Q000737:chemistry; D008956:Models, Chemical; D011487:Protein Conformation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D021122:Protein Subunits / Q000737:chemistry
D001426:Bacterial Proteins; C034284:IgG Fc-binding protein, Streptococcus; D007136:Immunoglobulins; D021122:Protein Subunits