Membrane interactions of the globular domain and the hypervariable region of KRAS4b define its unique diffusion behavior
Abstract
The RAS proteins are GTP-dependent switches that regulate signaling pathways and are frequently mutated in cancer. RAS proteins concentrate in the plasma membrane via lipid-tethers and hypervariable region side-chain interactions in distinct nano-domains. However, little is known about RAS membrane dynamics and the details of RAS activation of downstream signaling. Here, we characterize RAS in live human and mouse cells using single-molecule-tracking methods and estimate RAS mobility parameters. KRAS4b exhibits confined mobility with three diffusive states distinct from the other RAS isoforms (KRAS4a, NRAS, and HRAS); and although most of the amino acid differences between RAS isoforms lie within the hypervariable region, the additional confinement of KRAS4b is largely determined by the protein’s globular domain. To understand the altered mobility of an oncogenic KRAS4b, we used complementary experimental and molecular dynamics simulation approaches to reveal a detailed mechanism.
- Authors:
-
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, United States
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, United States
- UCSF Helen Diller Family Comprehensive Cancer Center, School of Medicine, University of California, San Francisco, San Francisco, United States
- Publication Date:
- Research Org.:
- Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
- Sponsoring Org.:
- USDOE National Nuclear Security Administration (NNSA); National Cancer Institute (NCI); National Institutes of Health (NIH); Joint Design of Advanced Computing Solutions for Cancer (JDACS4C)
- OSTI Identifier:
- 1592514
- Alternate Identifier(s):
- OSTI ID: 1592515; OSTI ID: 1682527
- Report Number(s):
- LLNL-JRNL-771099
Journal ID: ISSN 2050-084X; e47654
- Grant/Contract Number:
- AC52-07NA27344; HHSN261200800001E
- Resource Type:
- Published Article
- Journal Name:
- eLife
- Additional Journal Information:
- Journal Name: eLife Journal Volume: 9; Journal ID: ISSN 2050-084X
- Publisher:
- eLife Sciences Publications, Ltd.
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; Cancer Biology; Physics Of Living Systems; RAS Diffusion; Cancer; Single Molecule Tracking; Atomistic Simulation
Citation Formats
Goswami, Debanjan, Chen, De, Yang, Yue, Gudla, Prabhakar R., Columbus, John, Worthy, Karen, Rigby, Megan, Wheeler, Madeline, Mukhopadhyay, Suman, Powell, Katie, Burgan, William, Wall, Vanessa, Esposito, Dominic, Simanshu, Dhirendra K., Lightstone, Felice C., Nissley, Dwight V., McCormick, Frank, and Turbyville, Thomas. Membrane interactions of the globular domain and the hypervariable region of KRAS4b define its unique diffusion behavior. United States: N. p., 2020.
Web. doi:10.7554/eLife.47654.
Goswami, Debanjan, Chen, De, Yang, Yue, Gudla, Prabhakar R., Columbus, John, Worthy, Karen, Rigby, Megan, Wheeler, Madeline, Mukhopadhyay, Suman, Powell, Katie, Burgan, William, Wall, Vanessa, Esposito, Dominic, Simanshu, Dhirendra K., Lightstone, Felice C., Nissley, Dwight V., McCormick, Frank, & Turbyville, Thomas. Membrane interactions of the globular domain and the hypervariable region of KRAS4b define its unique diffusion behavior. United States. https://doi.org/10.7554/eLife.47654
Goswami, Debanjan, Chen, De, Yang, Yue, Gudla, Prabhakar R., Columbus, John, Worthy, Karen, Rigby, Megan, Wheeler, Madeline, Mukhopadhyay, Suman, Powell, Katie, Burgan, William, Wall, Vanessa, Esposito, Dominic, Simanshu, Dhirendra K., Lightstone, Felice C., Nissley, Dwight V., McCormick, Frank, and Turbyville, Thomas. Mon .
"Membrane interactions of the globular domain and the hypervariable region of KRAS4b define its unique diffusion behavior". United States. https://doi.org/10.7554/eLife.47654.
@article{osti_1592514,
title = {Membrane interactions of the globular domain and the hypervariable region of KRAS4b define its unique diffusion behavior},
author = {Goswami, Debanjan and Chen, De and Yang, Yue and Gudla, Prabhakar R. and Columbus, John and Worthy, Karen and Rigby, Megan and Wheeler, Madeline and Mukhopadhyay, Suman and Powell, Katie and Burgan, William and Wall, Vanessa and Esposito, Dominic and Simanshu, Dhirendra K. and Lightstone, Felice C. and Nissley, Dwight V. and McCormick, Frank and Turbyville, Thomas},
abstractNote = {The RAS proteins are GTP-dependent switches that regulate signaling pathways and are frequently mutated in cancer. RAS proteins concentrate in the plasma membrane via lipid-tethers and hypervariable region side-chain interactions in distinct nano-domains. However, little is known about RAS membrane dynamics and the details of RAS activation of downstream signaling. Here, we characterize RAS in live human and mouse cells using single-molecule-tracking methods and estimate RAS mobility parameters. KRAS4b exhibits confined mobility with three diffusive states distinct from the other RAS isoforms (KRAS4a, NRAS, and HRAS); and although most of the amino acid differences between RAS isoforms lie within the hypervariable region, the additional confinement of KRAS4b is largely determined by the protein’s globular domain. To understand the altered mobility of an oncogenic KRAS4b, we used complementary experimental and molecular dynamics simulation approaches to reveal a detailed mechanism.},
doi = {10.7554/eLife.47654},
journal = {eLife},
number = ,
volume = 9,
place = {United States},
year = {2020},
month = {1}
}
https://doi.org/10.7554/eLife.47654
Figures / Tables:

Works referenced in this record:
Regulating the regulator: post-translational modification of RAS
journal, December 2011
- Ahearn, Ian M.; Haigis, Kevin; Bar-Sagi, Dafna
- Nature Reviews Molecular Cell Biology, Vol. 13, Issue 1
Genetic analysis of Ras signalling pathways in cell proliferation, migration and survival
journal, February 2010
- Drosten, Matthias; Dhawahir, Alma; Sum, Eleanor Y. M.
- The EMBO Journal, Vol. 29, Issue 6
Quantitative Measurement of Intrinsic GTP Hydrolysis for Carcinogenic Glutamine 61 Mutants in H-Ras
journal, October 2018
- Novelli, Elisa T.; First, Jeremy T.; Webb, Lauren J.
- Biochemistry, Vol. 57, Issue 44
Impact of 2′-hydroxyl sampling on the conformational properties of RNA: Update of the CHARMM all-atom additive force field for RNA
journal, April 2011
- Denning, Elizabeth J.; Priyakumar, U. Deva; Nilsson, Lennart
- Journal of Computational Chemistry, Vol. 32, Issue 9
Stimulation of Membrane Ruffling and MAP Kinase Activation by Distinct Effectors of RAS
journal, February 1996
- Joneson, T.; White, M. A.; Wigler, M. H.
- Science, Vol. 271, Issue 5250
Distinct Binding Preferences between Ras and Raf Family Members and the Impact on Oncogenic Ras Signaling
journal, December 2019
- Terrell, Elizabeth M.; Durrant, David E.; Ritt, Daniel A.
- Molecular Cell, Vol. 76, Issue 6
TrackMate: An open and extensible platform for single-particle tracking
journal, February 2017
- Tinevez, Jean-Yves; Perry, Nick; Schindelin, Johannes
- Methods, Vol. 115
Structural basis of recognition of farnesylated and methylated KRAS4b by PDEδ
journal, October 2016
- Dharmaiah, Srisathiyanarayanan; Bindu, Lakshman; Tran, Timothy H.
- Proceedings of the National Academy of Sciences, Vol. 113, Issue 44
Lipid-Sorting Specificity Encoded in K-Ras Membrane Anchor Regulates Signal Output
journal, January 2017
- Zhou, Yong; Prakash, Priyanka; Liang, Hong
- Cell, Vol. 168, Issue 1-2
Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ 1 and χ 2 Dihedral Angles
journal, August 2012
- Best, Robert B.; Zhu, Xiao; Shim, Jihyun
- Journal of Chemical Theory and Computation, Vol. 8, Issue 9
Bright photoactivatable fluorophores for single-molecule imaging
journal, October 2016
- Grimm, Jonathan B.; English, Brian P.; Choi, Heejun
- Nature Methods, Vol. 13, Issue 12
Methionine 170 is an Environmentally Sensitive Membrane Anchor in the Disordered HVR of K-Ras4B
journal, October 2018
- Neale, Chris; García, Angel E.
- The Journal of Physical Chemistry B, Vol. 122, Issue 44
Brownian motion in biological membranes.
journal, August 1975
- Saffman, P. G.; Delbruck, M.
- Proceedings of the National Academy of Sciences, Vol. 72, Issue 8
Comparison of simple potential functions for simulating liquid water
journal, July 1983
- Jorgensen, William L.; Chandrasekhar, Jayaraman; Madura, Jeffry D.
- The Journal of Chemical Physics, Vol. 79, Issue 2
All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins †
journal, April 1998
- MacKerell, A. D.; Bashford, D.; Bellott, M.
- The Journal of Physical Chemistry B, Vol. 102, Issue 18
Localizer: fast, accurate, open-source, and modular software package for superresolution microscopy
journal, December 2012
- Dedecker, Peter; Duwé, Sam; Neely, Robert K.
- Journal of Biomedical Optics, Vol. 17, Issue 12
Complexes of Ras.GTP with Raf-1 and mitogen-activated protein kinase kinase
journal, June 1993
- Moodie, S.; Willumsen, B.; Weber, M.
- Science, Vol. 260, Issue 5114
Single-molecule diffusion measurements of H-Ras at the plasma membrane of live cells reveal microdomain localization upon activation
journal, May 2005
- Lommerse, P. H. M.
- Journal of Cell Science, Vol. 118, Issue 9
Extracting intracellular diffusive states and transition rates from single-molecule tracking data
journal, February 2013
- Persson, Fredrik; Lindén, Martin; Unoson, Cecilia
- Nature Methods, Vol. 10, Issue 3
Dynamic multiple-target tracing to probe spatiotemporal cartography of cell membranes
journal, July 2008
- Sergé, Arnauld; Bertaux, Nicolas; Rigneault, Hervé
- Nature Methods, Vol. 5, Issue 8
Dragging Ras Back in the Ring
journal, March 2014
- Stephen, Andrew G.; Esposito, Dominic; Bagni, Rachel K.
- Cancer Cell, Vol. 25, Issue 3
Single-molecule imaging analysis of Ras activation in living cells
journal, April 2004
- Murakoshi, H.; Iino, R.; Kobayashi, T.
- Proceedings of the National Academy of Sciences, Vol. 101, Issue 19
Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types
journal, June 2010
- Klauda, Jeffery B.; Venable, Richard M.; Freites, J. Alfredo
- The Journal of Physical Chemistry B, Vol. 114, Issue 23
Dynamic Organizing Principles of the Plasma Membrane that Regulate Signal Transduction: Commemorating the Fortieth Anniversary of Singer and Nicolson's Fluid-Mosaic Model
journal, November 2012
- Kusumi, Akihiro; Fujiwara, Takahiro K.; Chadda, Rahul
- Annual Review of Cell and Developmental Biology, Vol. 28, Issue 1
Ras-GTP dimers activate the Mitogen-Activated Protein Kinase (MAPK) pathway
journal, June 2015
- Nan, Xiaolin; Tamgüney, Tanja M.; Collisson, Eric A.
- Proceedings of the National Academy of Sciences, Vol. 112, Issue 26
Direct interaction of Ras and the amino-terminal region of Raf-1 in vitro
journal, July 1993
- Warne, Patricia H.; Vician, Pablo Rodrigueza; Downward, Julian
- Nature, Vol. 364, Issue 6435
RAS Proteins and Their Regulators in Human Disease
journal, June 2017
- Simanshu, Dhirendra K.; Nissley, Dwight V.; McCormick, Frank
- Cell, Vol. 170, Issue 1
TrackArt: the user friendly interface for single molecule tracking data analysis and simulation applied to complex diffusion in mica supported lipid bilayers
journal, May 2014
- Matysik, Artur; Kraut, Rachel S.
- BMC Research Notes, Vol. 7, Issue 1
Complex formation between RAS and RAF and other protein kinases.
journal, July 1993
- Van Aelst, L.; Barr, M.; Marcus, S.
- Proceedings of the National Academy of Sciences, Vol. 90, Issue 13
Figures / Tables found in this record: