Mechanical unfolding of ubiquitin molecules.
Mechanical stretching of ubiquitin and of its several repeats are studied through molecular-dynamics simulations. A Go-type model [H. Abe and N. Go, Biopolymers 20, 1013 (1981)] with a realistic contact map and with Lennard-Jones contact interactions is used. The model qualitatively reproduces the experimentally observed differences between force-extension patterns obtained on polyubiquitins stretched by various linkages. The terminal-to-terminal stretching of polyubiquitin results in peak forces similar to those measured for titin-based polyproteins and of a magnitude that matches measurements. Consistent with the experimental measurements, the simulated peak forces depend on the pulling speed logarithmically when thermal fluctuations are explicitly introduced. These results validate the application of topology-based models in the study of the mechanical stretching of proteins.
Cieplak
Marek
M
Institute of Physics, Polish Academy of Sciences, Alesa Lotników 32/46, 02-668 Warsaw, Poland. mc@ifpan.edu.pl
Marszalek
Piotr E
PE
D000596:Amino Acids / Q000737:chemistry; D005998:Glycine / Q000737:chemistry; D006801:Humans; D008958:Models, Molecular; D015233:Models, Statistical; D008962:Models, Theoretical; D008968:Molecular Conformation; D025821:Polyubiquitin / Q000737:chemistry*; D011487:Protein Conformation; D011489:Protein Denaturation; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D013314:Stress, Mechanical; D025801:Ubiquitin / Q000737:chemistry*
D000596:Amino Acids; D011506:Proteins; D025801:Ubiquitin; D025821:Polyubiquitin; D005998:Glycine