Slow protein conformational dynamics from multiple experimental structures: the helix/sheet transition of arc repressor.
Conformational transitions underlie the function of many biomolecular systems. Resolving intermediate structural changes, however, is challenging for both experiments and all-atom simulations because the duration of transitions is short relative to the lifetime of the stable species. Simplified descriptions based on a single experimental structure, such as elastic network models or Gō models, are not immediately applicable. Here, we develop a general method that combines multiple coarse-grained models to capture slow conformational transitions. Individually, each model describes one of the experimental structures; together, they approximate the complete energy surface. We demonstrate the method for the helix-to-sheet transition in Arc repressor N11L. We find that the transition involves the partial unfolding of the switch region, and rapid refolding into the alternate structure. Transient local unfolding is consistent with the low hydrogen exchange protection factors of the switch region. Also in agreement with experiment, the isomerization occurs independently of the global folding/dimerization transition.
Best
Robert B
RB
Laboratory of Chemical Physics, Building 5, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.
Chen
Yng-Gwei
YG
Hummer
Gerhard
G
D019281:Dimerization; D008958:Models, Molecular; D017510:Protein Folding; D017433:Protein Structure, Secondary; D012097:Repressor Proteins / Q000737:chemistry*; D014764:Viral Proteins / Q000737:chemistry*; D054334:Viral Regulatory and Accessory Proteins
D012097:Repressor Proteins; D014764:Viral Proteins; D054334:Viral Regulatory and Accessory Proteins; C016649:phage repressor proteins