Conformational sampling with implicit solvent models: application to the PHF6 peptide in tau protein.
Implicit solvent models approximate the effects of solvent through a potential of mean force and therefore make solvated simulations computationally efficient. Yet despite their computational efficiency, the inherent approximations made by implicit solvent models can sometimes lead to inaccurate results. To test the accuracy of a number of popular implicit solvent models, we determined whether implicit solvent simulations can reproduce the set of potential energy minima obtained from explicit solvent simulations. For these studies, we focus on a six-residue amino-acid sequence, referred to as the paired helical filament 6 (PHF6), which may play an important role in the formation of intracellular aggregates in patients with Alzheimer's disease. Several implicit solvent models form the basis of this work--two based on the generalized Born formalism, and one based on a Gaussian solvent-exclusion model. All three implicit solvent models generate minima that are in good agreement with minima obtained from simulations with explicit solvent. Moreover, free-energy profiles generated with each implicit solvent model agree with free-energy profiles obtained with explicit solvent. For the Gaussian solvent-exclusion model, we demonstrate that a straightforward ranking of the relative stability of each minimum suggests that the most stable structure is extended, a result in excellent agreement with the free-energy profiles. Overall, our data demonstrate that for some peptides like PHF6, implicit solvent can accurately reproduce the set of local energy minimum arising from quenched dynamics simulations with explicit solvent. More importantly, all solvent models predict that PHF6 forms extended beta-structures in solution, a finding consistent with the notion that PHF6 initiates neurofibrillary tangle formation in patients with Alzheimer's disease.
Huang
Austin
A
Harvard-MIT Division of Health Science and Technology, MIT Department of Electrical Engineering and Computer Science, Cambridge, Massachusetts, USA.
Stultz
Collin M
CM
D000544:Alzheimer Disease / Q000378:metabolism; D002352:Carrier Proteins / Q000737:chemistry*; D003198:Computer Simulation; D019277:Entropy; D006801:Humans; D008954:Models, Biological; D008958:Models, Molecular; D015233:Models, Statistical; D016011:Normal Distribution; D009842:Oligopeptides / Q000737:chemistry*; D010455:Peptides / Q000737:chemistry; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D015203:Reproducibility of Results; D012997:Solvents / Q000737:chemistry*; D016875:tau Proteins / Q000737:chemistry*
D002352:Carrier Proteins; D009842:Oligopeptides; D010455:Peptides; D012997:Solvents; D016875:tau Proteins; C000710267:tau hexapeptide PHF6