Jul 10, 2024
Protein interaction modeling
- 1Duke University
Protocol Citation: Shiyi Wang 2024. Protein interaction modeling. protocols.io https://dx.doi.org/10.17504/protocols.io.5jyl8215rl2w/v1
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: July 10, 2024
Last Modified: July 10, 2024
Protocol Integer ID: 103176
Keywords: ASAPCRN
Funders Acknowledgement:
Aligning Science Across Parkinson’s (ASAP) initiative
Grant ID: ASAP-020607
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Abstract
Protein interaction modeling using Alphafold 2.0 Multimer
**Structure Prediction in AlphaFold 2.0 Multimer** - Use full-length mouse Ezrin (UniProt ID: Q4KML7) and Atg7 (UniProt ID: Q9D906) for structure prediction. - Predict the structure of Ezrin in the open conformation: - Independently predict Ezrin N- and C-termini. - Thread them onto an open ERM hinge structure using PyMOL2 molecular visualization software.
**Modeling Ezrin:Atg7 Interaction** - Predict the structures of Ezrin and the Atg7 homodimer using AlphaFold 2.0 Multimer. - Dock the predicted structures to model the Ezrin:Atg7 interaction and associated conformational changes.
**Assess Conformational Changes** - Use CABS-flex 2.0 (REF: https://doi.org/10.1093/nar/gky356) and PyMOL2 to assess conformational changes in the Ezrin:Atg7 protein complex.
**Select High-Confidence Structures** - For all predicted structure models, select the highest-confidence structures based on the predicted local distance difference test (pLDDT).
**Energy Minimization** - Subject the highest-confidence structures to energy minimization via AMBER relaxation.
**Import and Visualize Minimized Structures** - Import the minimized structures into PyMOL2. - Use PyMOL2 to produce representative models of the structures.