Content of review 1, reviewed on April 24, 2019
Jephthah et al. used computer simulation tools combined with experimental measurements to study the temperature induced conformational change of an intrinsically disordered protein (IDP). Their results show disagreement between simulations and experiments in terms of capturing the secondary structure of IDP and its temperature dependence. The disagreement also exists among different combinations of force field they used. This study revealed limitations of the current classical biomolecular fixed-charge force fields. Several open questions can be asked for the community of computational scientists: how does the solvent affect the secondary structures of IDPs? Is it possible to tune the parameters of current force fields (water or/and proteins) to better explain the temperature induced conformational changes of IDPs and meanwhile maintain their performance on regular globular proteins? How will the application of enhanced sampling technique influence the conclusions that the authors drew here?
Source
© 2019 the Reviewer (CC BY 4.0).
References
S., J., L., S., B., K. B., M., S. 2019. Temperature Dependence of Intrinsically Disordered Proteins in Simulations: What are We Missing?. Journal of Chemical Theory and Computation.
