Local interactions dominate folding in a simple protein model

Ron Unger, John Moult

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    93 Scopus citations

    Abstract

    Recent computational studies of simple models of protein folding have concluded that a pronounced energy minimum (i.e, large gap in energy between low-energy states of the model) is a necessary and sufficient condition to ensure folding of a sequence to its lowest-energy conformation. Here, we show that this conclusion strongly depends on the particular temperature scheme selected to govern the simulations. On the other hand, we show that there is a dominant factor determining if a sequence is foldable. That is, the strength of possible interactions between residues close in the sequence. We show that sequences with many possible strong local interactions (either favorable or, more surprisingly, a mixture of strong favorable and unfavorable ones) are easy to fold. Progressively increasing the strength of such local interactions makes sequences easier and easier to fold. These results support the idea that initial formation of local substructures is important to the foldability of real proteins.

    Original languageEnglish
    Pages (from-to)988-994
    Number of pages7
    JournalJournal of Molecular Biology
    Volume259
    Issue number5
    DOIs
    StatePublished - 28 Jun 1996

    Bibliographical note

    Funding Information:
    This work was supported by NIH grant GM 31034 to J.M. and by an Alon fellowship to R.U.

    Keywords

    • Lattice models
    • Local interactions
    • Protein folding

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