Abstract
Raf kinases play key roles in signal transduction in cells for regulating proliferation, differentiation, and survival. Despite decades of research into functions and dynamics of Raf kinases with respect to other cytosolic proteins, understanding Raf kinases is limited by the lack of their full-length structures at the atomic resolution. Here, we present the first model of the full-length CRaf kinase obtained from artificial intelligence/machine learning algorithms with a converging ensemble of structures simulated by large-scale temperature replica exchange simulations. Our model is validated by comparing simulated structures with the latest cryo-EM structure detailing close contacts among three key domains and regions of the CRaf. Our simulations identify potentially new epitopes of intramolecule interactions within the CRaf and reveal a dynamical nature of CRaf kinases, in which the three domains can move back and forth relative to each other for regulatory dynamics. The dynamic conformations are then used in a docking algorithm to shed insight into the paradoxical effect caused by vemurafenib in comparison with a paradox breaker PLX7904. We propose a model of Raf-heterodimer/KRas-dimer as a signalosome based on the dynamics of the full-length CRaf.
| Original language | English |
|---|---|
| Pages (from-to) | 2623-2637 |
| Number of pages | 15 |
| Journal | Biophysical Journal |
| Volume | 123 |
| Issue number | 16 |
| DOIs | |
| State | Published - Aug 20 2024 |
Funding
This research used resources at the Oak Ridge Leadership Computing Facility (OLCF) at Oak Ridge National Laboratory, which is managed by UT-Battelle, LLC, under contract no. DE-AC05-00OR22725 with the US Department of Energy. I thank Dr. Dilip Asthagiri for useful discussions and comments. This manuscript has been authored by UT-Battelle, LLC, under contract no. DE-AC05-00OR22725 with the US Department of Energy (DOE). The US government retains and the publisher, by accepting the article for publication, acknowledges that the US government retains a nonexclusive, paid-up, irrevocable, worldwide license to publish or reproduce the published form of this manuscript, or allow others to do so, for US government purposes. DOE will provide public access to these results of federally sponsored research in accordance with the DOE Public Access Plan (https://www.energy.gov/doe-public-access-plan). The AF structure was downloaded from AlphaFold Protein Structure Database, https://alphafold.ebi.ac.uk. The RF structures were obtained from Bakerlab's server, https://robetta.bakerlab.org. The authors declare no competing interests. This research used resources at the Oak Ridge Leadership Computing Facility (OLCF) at Oak Ridge National Laboratory , which is managed by UT-Battelle, LLC , under contract no. DE-AC05-00OR22725 with the US Department of Energy. I thank Dr. Dilip Asthagiri for useful discussions and comments. This manuscript has been authored by UT-Battelle, LLC , under contract no. DE-AC05-00OR22725 with the US Department of Energy (DOE). The US government retains and the publisher, by accepting the article for publication, acknowledges that the US government retains a nonexclusive, paid-up, irrevocable, worldwide license to publish or reproduce the published form of this manuscript, or allow others to do so, for US government purposes. DOE will provide public access to these results of federally sponsored research in accordance with the DOE Public Access Plan ( https://www.energy.gov/doe-public-access-plan ). The AlphaFold structure was downloaded from AlphaFold Protein Structure Database, https://alphafold.ebi.ac.uk . The RosettaFold structures were obtained from Bakerlab\u2019s server, https://robetta.bakerlab.org .
| Funders | Funder number |
|---|---|
| DOE Public Access Plan | |
| DOE | |
| U.S. Department of Energy | |
| Oak Ridge National Laboratory | DE-AC05-00OR22725 |
| Oak Ridge National Laboratory |