Document Detail

Motion of disordered polypeptide chain as studied by PREs, 15N relaxation, and MD simulations: how fast is segmental diffusion in denatured ubiquitin?
MedLine Citation:
PMID:  21819149     Owner:  NLM     Status:  Publisher    
Molecular Dynamics simulations have been widely used to analyze dynamic conformational equilibria of folded proteins, especially in relation to the NMR observables. However, this approach found little use in the studies of disordered proteins, where the sampling of vast conformational space presents a serious problem. In this paper we demonstrate that the latest advances in computation technology make it possible to overcome this limitation. The experimentally validated (calibrated) MD models allow for new insights into structure / dynamics of disordered proteins. As a test system, we have chosen denatured ubiquitin in solution with 8 M urea, pH 2. High-temperature MD simulations in implicit solvent have been carried out for the wild-type ubiquitin as well as MTSL-tagged Q2C, D32C, and R74C mutants. To recalibrate the MD data (500 K) in relation to the experimental conditions (278 K, 8 M urea), the time axes of the MD trajectories were rescaled. The scaling factor was adjusted such as to maximize the agreement between the simulated and experimental 15N relaxation rates. The resulting effective length of the trajectories, 311 μs, ensures good convergence properties of the MD model. The constructed MD model was validated against the array of experimental data, including additional 15N relaxation parameters, multiple sets of PREs, and the radius of gyration. In each case, a near-quantitative agreement has been obtained, suggesting that the model is successful. Of note, the MD-based approach rigorously predicts the quantities that are inherently dynamic, i.e. dependent on the motional correlation times. This cannot be accomplished, other than in empirical fashion, on the basis of static structural models (conformational ensembles). The MD model was further used to investigate the relative translational motion of the MTSL label and the individual HN atoms. The derived segmental diffusion coefficients proved to be sufficiently uniform, averaging to D = 0.49 - 0.55×10-6 cm2/s. This result was verified by direct analysis of the experimental PRE data using the recently proposed Ullman-Podkorytov model. In this model, MTSL and HN moieties are treated as two tethered spheres undergoing mutual diffusion in a harmonic potential. The fitting of the experimental data involving D as a single adjustable parameter leads to D = 0.52×10-6 cm2/s, in agreement with the MD based analyses. This result can be compared with the range of estimates obtained from the resonance energy transfer experiments, D = 0.2 - 6.0×10-6 cm2/s.
Yi Xue; Nikolai R Skrynnikov
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Publication Detail:
Type:  JOURNAL ARTICLE     Date:  2011-8-8
Journal Detail:
Title:  Journal of the American Chemical Society     Volume:  -     ISSN:  1520-5126     ISO Abbreviation:  -     Publication Date:  2011 Aug 
Date Detail:
Created Date:  2011-8-8     Completed Date:  -     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  7503056     Medline TA:  J Am Chem Soc     Country:  -    
Other Details:
Languages:  ENG     Pagination:  -     Citation Subset:  -    
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