KUKU

KU ScholarWorks

  • myKU
  • Email
  • Enroll & Pay
  • KU Directory
    • Login
    View Item 
    •   KU ScholarWorks
    • Molecular Biosciences
    • Molecular Biosciences Scholarly Works
    • View Item
    •   KU ScholarWorks
    • Molecular Biosciences
    • Molecular Biosciences Scholarly Works
    • View Item
    JavaScript is disabled for your browser. Some features of this site may not work without it.

    Chasing Funnels on Protein-Protein Energy Landscapes at Different Resolutions

    Thumbnail
    View/Open
    VakserI_BJ_95(5)2150.pdf (829.8Kb)
    Issue Date
    2008-09-01
    Author
    Ruvinsky, Anatoly M.
    Vakser, Ilya A.
    Publisher
    Biophysical Society
    Type
    Article
    Article Version
    Scholarly/refereed, publisher version
    Metadata
    Show full item record
    Abstract
    Studies of intermolecular energy landscapes are important for understanding protein association and adequate modeling of protein interactions. Landscape representation at different resolutions can be used for the refinement of docking predictions and detection of macro characteristics, like the binding funnel. A representative set of protein-protein complexes was used to systematically map the intermolecular landscape by grid-based docking. The change of the resolution was achieved by varying the range of the potential, according to the variable resolution GRAMM methodology. A formalism was developed to consistently parameterize the potential and describe essential characteristics of the landscape. The results of gradual landscape smoothing, from high to low resolution, indicate that i), the number of energy basins, the landscape ruggedness, and the slope decrease accordingly; ii), the number of near-native matches, defined as those inside the funnel, increases until the trend breaks down at critical resolution; the rate of the increase and the critical resolution are specific to the type of a complex (enzyme inhibitor, antigen-antibody, and other), reflect known underlying recognition factors, and correlate with earlier determined estimates of the funnel size; iii), the native/nonnative energy gap, a major characteristic of the energy minima hierarchy, remains constant; and iv), the putative funnel (defined as the deepest basin) has the largest average depth-related ruggedness and slope, at all resolutions. The results facilitate better understanding of the binding landscapes and suggest directions for implementation in practical docking protocols.
    Description
    This is the published version, also available here: http://dx.doi.org/10.1529/biophysj.108.132977.
    URI
    http://hdl.handle.net/1808/17369
    DOI
    https://doi.org/10.1529/biophysj.108.132977
    Collections
    • Molecular Biosciences Scholarly Works [606]
    Citation
    Ruvinsky, Anatoly M. & Vakser, Ilya A. "Chasing funnels on protein-protein energy landscapes at different resolutions." Biophysical Journal. Volume 95, Issue 5, 1 September 2008, Pages 2150–2159. http://dx.doi.org/10.1529/biophysj.108.132977.

    Items in KU ScholarWorks are protected by copyright, with all rights reserved, unless otherwise indicated.


    We want to hear from you! Please share your stories about how Open Access to this item benefits YOU.


    Contact KU ScholarWorks
    785-864-8983
    KU Libraries
    1425 Jayhawk Blvd
    Lawrence, KS 66045
    785-864-8983

    KU Libraries
    1425 Jayhawk Blvd
    Lawrence, KS 66045
    Image Credits
     

     

    Browse

    All of KU ScholarWorksCommunities & CollectionsThis Collection

    My Account

    Login

    Statistics

    View Usage Statistics

    Contact KU ScholarWorks
    785-864-8983
    KU Libraries
    1425 Jayhawk Blvd
    Lawrence, KS 66045
    785-864-8983

    KU Libraries
    1425 Jayhawk Blvd
    Lawrence, KS 66045
    Image Credits
     

     

    The University of Kansas
      Contact KU ScholarWorks
    Lawrence, KS | Maps
     
    • Academics
    • Admission
    • Alumni
    • Athletics
    • Campuses
    • Giving
    • Jobs

    The University of Kansas prohibits discrimination on the basis of race, color, ethnicity, religion, sex, national origin, age, ancestry, disability, status as a veteran, sexual orientation, marital status, parental status, gender identity, gender expression and genetic information in the University’s programs and activities. The following person has been designated to handle inquiries regarding the non-discrimination policies: Director of the Office of Institutional Opportunity and Access, IOA@ku.edu, 1246 W. Campus Road, Room 153A, Lawrence, KS, 66045, (785)864-6414, 711 TTY.

     Contact KU
    Lawrence, KS | Maps