Reconciling Intermediates in Mechanical Unfolding Experiments with Two-State Protein Folding in Bulk.
Most experimentally well-characterized single domain proteins of less than 100 residues have been found to be two-state folders. That is, only two distinct populations can explain both equilibrium and kinetic measurements. Results from single molecule force spectroscopy, where a protein is unfolded by applying a mechanical pulling force to its ends, have largely confirmed this description for proteins found to be two-state in ensemble experiments. Recently, however, stable intermediates have been reported in mechanical unfolding experiments on a cold-shock protein previously found to be a prototypical two-state folder. Here, we tackle this discrepancy using free energy landscapes and Markov state models derived from coarse-grained molecular simulations. We show that protein folding intermediates can be selectively stabilized by the pulling force and that the populations of these intermediates vary in a force-dependent manner. Our model qualitatively captures the experimental results and suggests a possible origin of the apparent discrepancy.
CIC nanoGUNE , 20018 Donostia-San Sebastián, Spain.
David
D
de Sancho
Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892-0520, United States.
Robert B
RB
Best
D001426:Bacterial Proteins / Q000737:chemistry / Q000378:metabolism; D057773:Cold Shock Proteins and Peptides / Q000737:chemistry / Q000378:metabolism; D007700:Kinetics; D008390:Markov Chains; D018625:Microscopy, Atomic Force; D017510:Protein Folding; D058767:Protein Unfolding; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D013816:Thermodynamics; D020124:Thermotoga maritima / Q000378:metabolism
D001426:Bacterial Proteins; D057773:Cold Shock Proteins and Peptides; D011506:Proteins