NDLI: Φ-Value analysis by molecular dynamics simulations of reversible folding

Content Provider	PubMed Central
Author	Settanni, Giovanni Rao, Francesco Caflisch, Amedeo
Copyright Year	2005
Abstract	In Φ-value analysis, the effects of mutations on the folding kinetics are compared with the corresponding effects on thermodynamic stability to investigate the structure of the protein-folding transition state (TS). Here, molecular dynamics (MD) simulations (totaling 0.65 ms) have been performed for a large set of single-point mutants of a 20-residue three-stranded antiparallel β-sheet peptide. Between 57 and 120 folding events were sampled at near equilibrium for each mutant, allowing for accurate estimates of folding/unfolding rates and stability changes. The Φ values calculated from folding and unfolding rates extracted from the MD trajectories are reliable if the stability loss upon mutation is larger than ≈0.6 kcal/mol, which is observed for 8 of the 32 single-point mutants. The same heterogeneity of the TS of the wild type was found in the mutated peptides, showing two possible pathways for folding. Single-point mutations can induce significant TS shifts not always detected by Φ-value analysis. Specific nonnative interactions at the TS were observed in most of the peptides studied here. The interpretation of Φ values based on the ratio of atomic contacts at the TS over the native state, which has been used in the past in MD and Monte Carlo simulations, is in agreement with the TS structures of wild-type peptide. However, Φ values tend to overestimate the nativeness of the TS ensemble, when interpreted neglecting the nonnative interactions.
Related Links	http://dx.doi.org/10.1073/pnas.0406754102
Ending Page	633
Page Count	6
Starting Page	628
File Format	PDF
ISSN	00278424
e-ISSN	10916490
Journal	Proceedings of the National Academy of Sciences of the United States of America
Issue Number	3
Volume Number	102
Language	English
Publisher	National Academy of Sciences
Publisher Date	2005-01-18
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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