NDLI: Simulation of the folding equilibrium of α-helical peptides: A comparison of the generalized Born approximation with explicit solvent

Content Provider	PubMed Central
Author	Nymeyer, Hugh García, Angel E.
Copyright Year	2003
Abstract	We compare simulations using the generalized Born/surface area (GB/SA) implicit solvent model with simulations using explicit solvent (transferable intermolecular potential 3 point, TIP3P) to test the GB/SA algorithm. We use the replica exchange molecular dynamics method to sample the conformational phase space of two α-helical peptides, A21 and the Fs, by using two different classical potentials and both water models. We find that when using GB/SA: (i) A21 is predicted to be more helical than the Fs peptide at all temperatures; (ii) the native structure of the Fs peptide is predicted to be a helical bundle instead of a single helix; and (iii) the persistence length and most probable end-to-end distance are too large in the unfolded state when compared against the explicit solvent simulations. We find that the potential of mean force in the ϕψ plane is markedly different in the two solvents, making the two simulated peptides respond differently when the backbone torsions are perturbed. A fit of the temperature melting curves obtained in these simulations to a Lifson–Roig model finds that the GB/SA model has an unphysically large nucleation parameter, whereas the explicit solvent model produces values similar to experiment.
Related Links	http://dx.doi.org/10.1073/pnas.2232868100
Ending Page	13939
Page Count	6
Starting Page	13934
File Format	PDF
ISSN	00278424
e-ISSN	10916490
Journal	Proceedings of the National Academy of Sciences of the United States of America
Issue Number	24
Volume Number	100
Language	English
Publisher	National Academy of Sciences
Publisher Date	2003-11-25
Access Restriction	Open
Rights Holder	National Academy of Sciences
Subject Keyword	General Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Multidisciplinary

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