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Characterization of de novo four-helix bundles by molecular dynamics simulations

TitleCharacterization of de novo four-helix bundles by molecular dynamics simulations
Publication TypeJournal Article
Year of Publication2006
AuthorsScott, WRP, Seo, E, Huttunen, H, Wallhorn, D, Sherman, JC, Straus, SK
JournalProteins-Structure Function and Bioinformatics
Volume64
Pagination719-729
Date PublishedAug
Type of ArticleArticle
ISBN Number0887-3585
Keywordscaviteins, de novo four-helix bundle, DESIGN, DOMAIN, HELICAL BUNDLES, molecular dynamics simulations, PEPTIDE, PROTEIN DESIGN, PROTEINS, STATE, SYSTEM, TASP, template-assembled synthetic protein
Abstract

We have investigated the structure and dynamics of three cavitand-based four-helix bundles (caviteins) by computer simulation. In these systems, designed de novo, each of the four helices contain the identical basis sequence EELLKKLEELLKKG (N1). Each cavitein consists of a rigid macrocycle (cavitand) with four aryl linkages, to each of which is connected an NI peptide by means of a linker peptide. The three caviteins studied here differ only in the linker peptide, which consist of one, two, or three glycine residues. Previous experimental work has shown that these systems exhibit very different behavior in terms of stability and oligomerization states despite the small differences in the linker peptide. Given that to date no three-dimensional structure is available for these caviteins, we have undertaken a series of molecular dynamics (MD) simulations in explicit water to try to rationalize the large differences in the experimentally observed behavior of these systems. Our results provide insight, for the first time, into why and how the cavitein with a single glycine linker forms dimers. In addition, our results indicate why although the two- and three-glycine-linked caviteins have similar stabilities, they have different native-like characteristics: the cavitein with three glycines can form a supercoiled helix, whereas the one with two glycines cannot. These findings may provide a useful guide in the rational de novo design of novel proteins with finely tunable structures and functions in the future.

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