Complexity in protein folding: Simulation meets experiment

TitleComplexity in protein folding: Simulation meets experiment
Publication TypeJournal Article
Year of Publication2012
AuthorsCaflisch A., Hamm P.
JournalCurrent Physical Chemistry
Start Page4
Date PublishedJan 2012
Type of ArticleReview Article
KeywordsBackbone, Cross-linked alpha-helix, Free energy surface of folding, Kinetic Partitioning, Misfolded traps, molecular dynamics simulations, peptide, Protein Folding, Steric Encumbrance, Time-resolved infrared spectroscopy

We review our joint experimental-theoretical effort on the folding of photo-switchable α-helices. The folding kinetics of these peptides is profoundly non-exponential, which is attributed to a partitioning of the unfolded state into several misfolded traps. These traps are connected to the folded state in a hub-like fashion with folding barriers of different heights. Molecular dynamics simulations reveal a semi-quantitative agreement with the complex response observed in the experiment, allowing one to discuss the process in unprecedented detail. It is found that the nonexponential response is to a large extent introduced by the photo-linker used to initiate folding. Hence, folding of these cross-linked peptides emulates formation of a helical segment in the context of a globular protein rather than folding of an isolated peptide.



Alternate JournalCurr. Phys. Chem.
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