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NIH Research Festival

September 23 – 25, 2024

Evaluating an Alphafold-based platform for the discovery and validation of dominant-negative protein fragments

Authors

  • AC Castroverde
  • JH Williams
  • AJ Hu
  • JL Meier

Abstract

Peptide tiling is a method in which small segments of a protein interactor are screened to identify fragments capable of exerting a regulatory function, for instance, inhibition. One challenge of this approach is that – due to the vast size of protein sequence space – screening large libraries of fragments from potential interactors is often prohibitively costly in terms of time and resources. New protein structure prediction technologies, such as Google DeepMind’s AlphaFold, have the potential to decrease experimental hurdles by allowing researchers to focus on high confidence interactors. However, few studies have defined the correlation between the confidence of predicted interaction of peptide fragments and their corresponding functional effects. In this project, we are developing a high-throughput approach to predict dominant negative protein fragments using AlphaFold and then correlating those predictions with growth detects caused by essential fragments in cell culture. Our initial studies have focused on compiling a catalog of enzymes implicated in cancer pathogenesis, their interactors, and protein fragments. Focusing on the Ras-Raf1 interaction, AlphaPulldown identified specific sequences predicted to interact that lie at known protein-protein interfaces and highlighted the importance of mpDock/pDock scoring model in predicting experimentally validated interfaces. These studies set the stage for the large-scale discovery of dominant negative protein fragments and their use as biological probes and in proof-of-concept proximity medicine platforms.

Scientific Focus Area: Computational Biology

This page was last updated on Tuesday, August 6, 2024

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Current Research Festival

  • 2025
    • Posters Session
    • General Schedule of Events
  • 2024
    • General Schedule of Events
    • 2024 NIH Distinguished Scholars Program
    • Poster Sessions
    • Concurrent Workshops
    • NIH Resource Information Fair
    • National Academy of Science Mini-Symposium
    • Special Wednesday Events
    • Vendor Exhibit Information
    • Green Labs Fair
    • Research Festival Committee
  • 2023
    • General Schedule of Events
    • NIH Early–Career Investigator Lectures
    • Poster Sessions
    • Concurrent Workshops
    • NIH Resource Information Fair
    • Vendor Exhibit Information
    • Research Festival Committee
  • 2021
  • 2019
    • General Schedule of Events
    • Plenary Sessions
    • Poster Session
    • Data Blitz
    • FARE Award Ceremony
    • Special Exhibits on Resources for Intramural Research
    • Technical Sales Association (TSA) Research Festival Exhibit Tent Show
    • Research Festival Committee
  • 2018
    • General Schedule of Events
    • Plenary Sessions
    • Concurrent Symposia Sessions
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    • Special Exhibits on Resources for Intramural Research
    • Technical Sales Association (TSA) Research Festival Exhibit Tent Show
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  • 2017
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    • Plenary Sessions
    • Concurrent Symposia Sessions
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  • 2016
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    • Browse by Presenter Name
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    • Research Festival Committees
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