Characterization of the folding landscape of monomeric lactose repressor: quantitative comparison of theory and experiment.
Recent theoretical/computational studies based on simplified protein models and experimental investigation have suggested that the native structure of a protein plays a primary role in determining the folding rate and mechanism of relatively small single-domain proteins. Here, we extend the study of the relationship between protein topology and folding mechanism to a larger protein with complex topology, by analyzing the folding process of monomeric lactose repressor (MLAc) computationally by using a Gō-like C(alpha) model. Next, we combine simulation and experimental results (see companion article in this issue) to achieve a comprehensive assessment of the folding landscape of this protein. Remarkably, simulated kinetic and equilibrium analyses show an excellent quantitative agreement with the experimental folding data of this study. The results of this comparison show that a simplified, completely unfrustrated C(alpha) model correctly reproduces the complex folding features of a large multidomain protein with complex topology. The success of this effort underlines the importance of synergistic experimental/theoretical approaches to achieve a broader understanding of the folding landscape.
Das
Payel
P
Department of Chemistry, Rice University, Houston, TX 77005, USA.
Wilson
Corey J
CJ
Fossati
Giovanni
G
Wittung-Stafshede
Pernilla
P
Matthews
Kathleen S
KS
Clementi
Cecilia
C
D001426:Bacterial Proteins / Q000737:chemistry*; D055592:Biophysical Phenomena; D001703:Biophysics; D003198:Computer Simulation; D007700:Kinetics; D056968:Lac Repressors; D008958:Models, Molecular; D017510:Protein Folding; D012097:Repressor Proteins / Q000737:chemistry*
D001426:Bacterial Proteins; D056968:Lac Repressors; D012097:Repressor Proteins