Computer simulations of protein folding by targeted molecular dynamics

TitleComputer simulations of protein folding by targeted molecular dynamics
Publication TypeJournal Article
Year of Publication2000
AuthorsFerrara P., Apostolakis J., Caflisch A.
JournalProteins: Structure, Function, and Bioinformatics
Date Published2000 May 15
Type of ArticleResearch Article
KeywordsComputer Simulation, Models, Molecular, Oncogene Protein p21(ras), Peptides, Plant Proteins, Protein Conformation, Protein Folding, Protein Structure, Secondary, Solutions, Thermodynamics

We have performed 128 folding and 45 unfolding molecular dynamics runs of chymotrypsin inhibitor 2 (CI2) with an implicit solvation model for a total simulation time of 0.4 μs. Folding requires that the three-dimensional structure of the native state is known. It was simulated at 300 K by supplementing the force field with a harmonic restraint which acts on the root-mean-square deviation and allows to decrease the distance to the target conformation. High temperature and/or the harmonic restraint were used to induce unfolding. Of the 62 folding simulations started from random conformations, 31 reached the native structure, while the success rate was 83% for the 66 trajectories which began from conformations unfolded by high-temperature dynamics. A funnel-like energy landscape is observed for unfolding at 475 K, while the unfolding runs at 300 K and 375 K as well as most of the folding trajectories have an almost flat energy landscape for conformations with less than about 50% of native contacts formed. The sequence of events, i.e., secondary and tertiary structure formation, is similar in all folding and unfolding simulations, despite the diversity of the pathways. Previous unfolding simulations of CI2 performed with different force fields showed a similar sequence of events. These results suggest that the topology of the native state plays an important role in the folding process.



Alternate JournalProteins
PubMed ID10737947
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