• FAQ
    • Deposit your work
    • Login
    View Item 
    •   Rice Scholarship Home
    • Faculty & Staff Research
    • Wiess School of Natural Sciences
    • Chemistry
    • Chemistry Publications
    • View Item
    •   Rice Scholarship Home
    • Faculty & Staff Research
    • Wiess School of Natural Sciences
    • Chemistry
    • Chemistry Publications
    • View Item
    JavaScript is disabled for your browser. Some features of this site may not work without it.

    Funneling and frustration in the energy landscapes of some designed and simplified proteins

    Thumbnail
    Name:
    JChemPhys_139_121908.pdf
    Size:
    3.436Mb
    Format:
    PDF
    View/Open
    Author
    Truong, Ha H.
    Kim, Bobby L.
    Schafer, Nicholas P.
    Wolynes, Peter G.
    Date
    2013
    Citation
    Truong, Ha H., Kim, Bobby L., Schafer, Nicholas P., et al.. "Funneling and frustration in the energy landscapes of some designed and simplified proteins." The Journal of Chemical Physics, 139, (2013) http://dx.doi.org/10.1063/1.4813504.
    Published Version
    http://dx.doi.org/10.1063/1.4813504
    Abstract
    We explore the similarities and differences between the energy landscapes of proteins that have been selected by nature and those of some proteins designed by humans. Natural proteins have evolved to function as well as fold, and this is a source of energetic frustration. The sequence of Top7, on the other hand, was designed with architecture alone in mind using only native state stability as the optimization criterion. Its topology had not previously been observed in nature. Experimental studies show that the folding kinetics of Top7 is more complex than the kinetics of folding of otherwise comparable naturally occurring proteins. In this paper, we use structure prediction tools, frustration analysis, and free energy profiles to illustrate the folding landscapes of Top7 and two other proteins designed by Takada. We use both perfectly funneled (structure-based) and predictive (transferable) models to gain insight into the role of topological versus energetic frustration in these systems and show how they differ from those found for natural proteins. We also study how robust the folding of these designs would be to the simplification of the sequences using fewer amino acid types. Simplification using a five amino acid type code results in comparable quality of structure prediction to the full sequence in some cases, while the two-letter simplification scheme dramatically reduces the quality of structure prediction.
    Type
    Journal article
    Citable link to this page
    http://hdl.handle.net/1911/71717
    Metadata
    Show full item record
    Collections
    • Chemistry Publications [403]
    • Faculty Publications [2827]
    • Physics and Astronomy Publications [955]

    Home | FAQ | Contact Us
    Managed by the Digital Scholarship Services at Fondren Library, Rice University
    Physical Address: 6100 Main Street, Houston, Texas 77005
    Mailing Address: MS-44, P.O.BOX 1892, Houston, Texas 77251-1892
     

     

    Browse

    Entire ArchiveCommunities & CollectionsBy Issue DateAuthorsTitlesSubjectsTypeThis CollectionBy Issue DateAuthorsTitlesSubjectsType

    My Account

    Login

    Statistics

    View Usage Statistics

    Home | FAQ | Contact Us
    Managed by the Digital Scholarship Services at Fondren Library, Rice University
    Physical Address: 6100 Main Street, Houston, Texas 77005
    Mailing Address: MS-44, P.O.BOX 1892, Houston, Texas 77251-1892