How does a simplified-sequence protein fold?

TitleHow does a simplified-sequence protein fold?
Publication TypeJournal Article
Year of Publication2009
AuthorsGuarnera E., Pellarin R., Caflisch A.
JournalBiophys J
Volume97
Issue6
Pagination1737-1746
Date Published2009 Sep 16
Type of ArticleResearch Article
ISSN1542-0086
KeywordsAmino Acid Sequence, Hydrophobic and Hydrophilic Interactions, Kinetics, Models, Molecular, Molecular Sequence Data, Nerve Tissue Proteins, Protein Denaturation, Protein Folding, Protein Structure, Secondary, Protein Structure, Tertiary
Abstract

To investigate a putatively primordial protein we have simplified the sequence of a 56-residue α/β fold (the immunoglobulin-binding domain of protein G) by replacing it with polyalanine, polythreonine, and diglycine segments at regions of the sequence that in the folded structure are α-helical, β-strand, and turns, respectively. Remarkably, multiple folding and unfolding events are observed in a 15-μs molecular dynamics simulation at 330 K. The most stable state (populated at approximately 20%) of the simplified-sequence variant of protein G has the same α/β topology as the wild-type but shows the characteristics of a molten globule, i.e., loose contacts among side chains and lack of a specific hydrophobic core. The unfolded state is heterogeneous and includes a variety of α/β topologies but also fully α-helical and fully β-sheet structures. Transitions within the denatured state are very fast, and the molten-globule state is reached in < 1μs by a framework mechanism of folding with multiple pathways. The native structure of the wild-type is more rigid than the molten-globule conformation of the simplified-sequence variant. The difference in structural stability and the very fast folding of the simplified protein suggest that evolution has enriched the primordial alphabet of amino acids mainly to optimize protein function by stabilization of a unique structure with specific tertiary interactions.

DOI10.1016/j.bpj.2009.06.047
pubindex

0119

Alternate JournalBiophys. J.
PubMed ID19751679
PubMed Central IDPMC2749778
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