Denatured state molecular dynamics simulation

Pan, Y. P. Daggett, V., Direct comparison of experimental and calculated folding free energies for hydrophobic deletion mutants of chymotrypsin inhibitor. 2 Free energy perturbation calculations using transition and denatured states from molecular dynamics simulations of unfolding, Biochemistry 2001,40, 2723-2731. 

N. D. Socci, Z. Luthey Schulten, and P. G. Wolynes, Folding and Design 1,441 (1996).] Bottom Structures of the denatured, intermediate, major transition, and native states for folding of bamase from molecular dynamics simulations that were benchmarked by < > values and NMR experiments. [Data from C. J. Bond, K. B. Wong, J. Clarke,... 

Especially in the case of large molecules like proteins this can lead to severe problems. For instance, the real time for a protein to fold from its denaturated into its globular state lies between a second and several minutes. To simulate this process within a molecular dynamics simulation would take about 108 s, a time interval that exceeds the estimated age of the universe. Still, what can be done is to use cases where the solid-state structure of the protein is known in order to validate the corresponding force field. If the force field is adequate it should reproduce the experimentally observed protein structure as an energetic minimum of the corresponding energy... 

Ferguson et al. have used a combination of NMR and molecular dynamics simulations to characterise the denatured ensemble, and found that it contained very little persistent, residual structure. However, those regions that adopt helical structure in the native state were found by simulation to be poised for helix formation in the denatured state. These regions also showed significant structure in the transition state for folding and suggest that the folding pathway appears to be nucleation-condensation. 

Bamase, like CI2, has been the subject of extensive studies, using the protein engineering method combined with kinetic and equilibrium experiments, to investigate its fold-ing/unfolding pathway." Molecular dynamics simulations of thermal denaturation of the wild-type and two mutant proteins (Tyr 17 —> Gly and He 88 —> Val) have been performed to investigate the effect of mutations on the unfolding pathway and transition state." ... 

To characterize the folding pathway of a protein, one must not focus on a single facet alone but instead identify the native, transition, and denatured states as well as any intermediate states that are present. Although experimental techniques have progressed over the years, with sensitivity improvements and shorter timescale detection, they still lack the ability to provide comprehensive atomistic detail for other than well-folded structures. Molecular dynamics (MD) simulation, developed in 1964, ° remains a more powerful method for providing atomic-level information at the desired temporal resolutions. 

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