Machine learning–driven multiscale modeling reveals lipid-dependent dynamics of RAS signaling proteins

Significance Here we present an unprecedented multiscale simulation platform that enables modeling, hypothesis generation, and discovery across biologically relevant length and time scales to predict mechanisms that can be tested experimentally. We demonstrate that our predictive simulation-experimental validation loop generates accurate insights into RAS-membrane biology. Evaluating over 100,000 correlated simulations, we show that RAS–lipid interactions are dynamic and evolving, resulting in: 1) a reordering and selection of lipid domains in realistic eight-lipid bilayers, 2) clustering of RAS into multimers correlating with specific lipid fingerprints, 3) changes in the orientation of the RAS G-domain impacting its ability to interact with effectors, and 4) demonstration that RAS–RAS G-domain interfaces are nonspecific in these putative signaling domains. RAS is a signaling protein associated with the cell membrane that is mutated in up to 30% of human cancers. RAS signaling has been proposed to be regulated by dynamic heterogeneity of the cell membrane. Investigating such a mechanism requires near-atomistic detail at macroscopic temporal and spatial scales, which is not possible with conventional computational or experimental techniques. We demonstrate here a multiscale simulation infrastructure that uses machine learning to create a scale-bridging ensemble of over 100,000 simulations of active wild-type KRAS on a complex, asymmetric membrane. Initialized and validated with experimental data (including a new structure of active wild-type KRAS), these simulations represent a substantial advance in the ability to characterize RAS-membrane biology. We report distinctive patterns of local lipid composition that correlate with interfacially promiscuous RAS multimerization. These lipid fingerprints are coupled to RAS dynamics, predicted to influence effector binding, and therefore may be a mechanism for regulating cell signaling cascades.

[1]  Qiang Cui Faculty Opinions recommendation of Machine learning-driven multiscale modeling reveals lipid-dependent dynamics of RAS signaling proteins. , 2022, Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature.

[2]  Timothy S. Carpenter,et al.  Dynamic density functional theory of multicomponent cellular membranes , 2021, Physical Review Research.

[3]  M. Ikura,et al.  Oncogenic KRAS G12D mutation promotes dimerization through a second, phosphatidylserine–dependent interface: a model for KRAS oligomerization , 2021, Chemical science.

[4]  A. Gorfe,et al.  RAS Nanoclusters Selectively Sort Distinct Lipid Headgroups and Acyl Chains , 2021, Frontiers in Molecular Biosciences.

[5]  Peer-Timo Bremer,et al.  Machine-learning-based dynamic-importance sampling for adaptive multiscale simulations , 2021, Nature Machine Intelligence.

[6]  Bart M. H. Bruininks,et al.  Martini 3: a general purpose force field for coarse-grained molecular dynamics , 2021, Nature Methods.

[7]  T. E. Balius,et al.  RAS Nanoclusters: Dynamic Signaling Platforms Amenable to Therapeutic Intervention , 2021, Biomolecules.

[8]  Priyanka Prakash,et al.  The KRAS and other prenylated polybasic domain membrane anchors recognize phosphatidylserine acyl chain structure , 2021, Proceedings of the National Academy of Sciences.

[9]  SC20: International Conference for High Performance Computing, Networking, Storage and Analysis , 2020 .

[10]  Rushil Anirudh,et al.  Uncovering interpretable relationships in high-dimensional scientific data through function preserving projections , 2020, Mach. Learn. Sci. Technol..

[11]  A. Gorfe,et al.  Mechanisms of Ras Membrane Organization and Signaling: Ras Rocks Again , 2020, Biomolecules.

[12]  Helgi I. Ingólfsson,et al.  Capturing Biologically Complex Tissue-Specific Membranes at Different Levels of Compositional Complexity , 2020, The journal of physical chemistry. B.

[13]  Felice C Lightstone,et al.  ddcMD: A fully GPU-accelerated molecular dynamics program for the Martini force field. , 2020, The Journal of chemical physics.

[14]  M. Ikura,et al.  Two Distinct Structures of Membrane-associated Homodimers of GTP- and GDP-bound KRAS4B Revealed by Paramagnetic Relaxation Enhancement. , 2020, Angewandte Chemie.

[15]  Peer-Timo Bremer,et al.  A massively parallel infrastructure for adaptive multiscale simulations: modeling RAS initiation pathway for cancer , 2019, SC.

[16]  S. Sligar,et al.  PIP2 Influences the Conformational Dynamics of Membrane bound KRAS4b , 2019, bioRxiv.

[17]  Prabhakar R. Gudla,et al.  Membrane interactions of the globular domain and the hypervariable region of KRAS4b define its unique diffusion behavior , 2020, eLife.

[18]  Paulo C. T. Souza,et al.  Pitfalls of the Martini Model , 2019, Journal of chemical theory and computation.

[19]  E. Tajkhorshid,et al.  Characterization of Lipid-Protein Interactions and Lipid-Mediated Modulation of Membrane Protein Function through Molecular Simulation. , 2019, Chemical reviews.

[20]  M. Buck,et al.  K-Ras G-domain binding with signaling lipid phosphatidylinositol (4,5)-phosphate (PIP2): membrane association, protein orientation, and function , 2019, The Journal of Biological Chemistry.

[21]  Besian I. Sejdiu,et al.  Emerging Diversity in Lipid–Protein Interactions , 2019, Chemical reviews.

[22]  Helgi I. Ingólfsson,et al.  Computational Modeling of Realistic Cell Membranes , 2019, Chemical reviews.

[23]  D. Fletcher,et al.  Quantitative biophysical analysis defines key components modulating recruitment of the GTPase KRAS to the plasma membrane , 2018, The Journal of Biological Chemistry.

[24]  W. Jahnke,et al.  Inhibition of K-RAS4B by a Unique Mechanism of Action: Stabilizing Membrane-Dependent Occlusion of the Effector-Binding Site. , 2018, Cell chemical biology.

[25]  Angel E García,et al.  Methionine 170 is an Environmentally Sensitive Membrane Anchor in the Disordered HVR of K-Ras4B. , 2018, The journal of physical chemistry. B.

[26]  Timothy Travers,et al.  Molecular recognition of RAS/RAF complex at the membrane: Role of RAF cysteine-rich domain , 2018, Scientific Reports.

[27]  Steven J. M. Jones,et al.  Comprehensive Characterization of Cancer Driver Genes and Mutations , 2018, Cell.

[28]  Haiyun Wang,et al.  KRAS Dimerization Impacts MEK Inhibitor Sensitivity and Oncogenic Activity of Mutant KRAS , 2018, Cell.

[29]  J. Groves,et al.  K-Ras4B Remains Monomeric on Membranes over a Wide Range of Surface Densities and Lipid Compositions. , 2018, Biophysical journal.

[30]  M. Neal Waxham,et al.  Spatiotemporal Analysis of K-Ras Plasma Membrane Interactions Reveals Multiple High Order Homo-oligomeric Complexes. , 2017, Journal of the American Chemical Society.

[31]  Priyanka Prakash,et al.  Membrane orientation dynamics of lipid-modified small GTPases , 2017, Small GTPases.

[32]  Matthias Buck,et al.  Computational Modeling Reveals that Signaling Lipids Modulate the Orientation of K-Ras4A at the Membrane Reflecting Protein Topology. , 2017, Structure.

[33]  Helgi I. Ingólfsson,et al.  Lipid–Protein Interactions Are Unique Fingerprints for Membrane Proteins , 2017, bioRxiv.

[34]  G. Piazza,et al.  The RAS-Effector Interaction as a Drug Target. , 2017, Cancer research.

[35]  Priyanka Prakash,et al.  Lipid-Sorting Specificity Encoded in K-Ras Membrane Anchor Regulates Signal Output , 2017, Cell.

[36]  Wei Chen,et al.  Computational and biochemical characterization of two partially overlapping interfaces and multiple weak-affinity K-Ras dimers , 2017, Scientific Reports.

[37]  Helgi I. Ingólfsson,et al.  Lipid and Peptide Diffusion in Bilayers: The Saffman-Delbrück Model and Periodic Boundary Conditions. , 2017, The journal of physical chemistry. B.

[38]  Ozlem Keskin,et al.  Membrane-associated Ras dimers are isoform-specific: K-Ras dimers differ from H-Ras dimers. , 2016, The Biochemical journal.

[39]  A. Gorfe,et al.  Computational Equilibrium Thermodynamic and Kinetic Analysis of K-Ras Dimerization through an Effector Binding Surface Suggests Limited Functional Role. , 2016, The journal of physical chemistry. B.

[40]  C. Der,et al.  RAS isoforms and mutations in cancer at a glance , 2016, Journal of Cell Science.

[41]  H. Waldmann,et al.  Lipoprotein insertion into membranes of various complexity: lipid sorting, interfacial adsorption and protein clustering. , 2016, Physical chemistry chemical physics : PCCP.

[42]  F. McCormick K-Ras protein as a drug target , 2016, Journal of Molecular Medicine.

[43]  Priyanka Prakash,et al.  Oncogenic K-Ras Binds to an Anionic Membrane in Two Distinct Orientations: A Molecular Dynamics Analysis. , 2016, Biophysical journal.

[44]  Neal Rosen,et al.  Allele-specific inhibitors inactivate mutant KRAS G12C by a trapping mechanism , 2016, Science.

[45]  P. Alexander,et al.  Farnesylated and methylated KRAS4b: high yield production of protein suitable for biophysical studies of prenylated protein-lipid interactions , 2015, Scientific Reports.

[46]  Ozlem Keskin,et al.  GTP-Dependent K-Ras Dimerization. , 2015, Structure.

[47]  Xiaolin Nan,et al.  Ras-GTP dimers activate the Mitogen-Activated Protein Kinase (MAPK) pathway , 2015, Proceedings of the National Academy of Sciences.

[48]  Mitsuhiko Ikura,et al.  Oncogenic and RASopathy-associated K-RAS mutations relieve membrane-dependent occlusion of the effector-binding site , 2015, Proceedings of the National Academy of Sciences.

[49]  M. Therrien,et al.  Regulation of RAF protein kinases in ERK signalling , 2015, Nature Reviews Molecular Cell Biology.

[50]  Yong Zhou,et al.  Ras nanoclusters: Versatile lipid-based signaling platforms. , 2015, Biochimica et biophysica acta.

[51]  Helgi I Ingólfsson,et al.  Lipid organization of the plasma membrane. , 2014, Journal of the American Chemical Society.

[52]  D. Esposito,et al.  Dragging ras back in the ring. , 2014, Cancer cell.

[53]  Travis L. Rodkey,et al.  Signal Integration by Lipid-Mediated Spatial Cross Talk between Ras Nanoclusters , 2013, Molecular and Cellular Biology.

[54]  Helgi I Ingólfsson,et al.  The power of coarse graining in biomolecular simulations , 2013, Wiley interdisciplinary reviews. Computational molecular science.

[55]  M. Shirts,et al.  Effects of Temperature Control Algorithms on Transport Properties and Kinetics in Molecular Dynamics Simulations. , 2013, Journal of chemical theory and computation.

[56]  Herbert Waldmann,et al.  N-Ras forms dimers at POPC membranes. , 2012, Biophysical journal.

[57]  H. Waldmann,et al.  The role of G-domain orientation and nucleotide state on the Ras isoform-specific membrane interaction , 2012, European Biophysics Journal.

[58]  H. Waldmann,et al.  Dissociation of the K-Ras4B/PDEδ complex upon contact with lipid membranes: membrane delivery instead of extraction. , 2012, Journal of the American Chemical Society.

[59]  A. Valencia,et al.  The Ras protein superfamily: Evolutionary tree and role of conserved amino acids , 2012, The Journal of Cell Biology.

[60]  Akihiro Kusumi,et al.  Hierarchical mesoscale domain organization of the plasma membrane. , 2011, Trends in biochemical sciences.

[61]  Hayder Amin,et al.  Membrane protein sequestering by ionic protein-lipid interactions , 2011, Nature.

[62]  A. Gorfe,et al.  Ras membrane orientation and nanodomain localization generate isoform diversity , 2010, Proceedings of the National Academy of Sciences.

[63]  Marc Therrien,et al.  A dimerization-dependent mechanism drives RAF catalytic activation , 2009, Nature.

[64]  Jodi Gureasko,et al.  Membrane-dependent signal integration by the Ras activator Son of sevenless , 2008, Nature Structural &Molecular Biology.

[65]  Thorsten Wohland,et al.  Molecular diffusion measurement in lipid bilayers over wide concentration ranges: a comparative study. , 2008, Chemphyschem : a European journal of chemical physics and physical chemistry.

[66]  J Andrew McCammon,et al.  A novel switch region regulates H‐ras membrane orientation and signal output , 2008, The EMBO journal.

[67]  G. Meer,et al.  Membrane lipids: where they are and how they behave , 2008, Nature Reviews Molecular Cell Biology.

[68]  D. Tieleman,et al.  The MARTINI force field: coarse grained model for biomolecular simulations. , 2007, The journal of physical chemistry. B.

[69]  J. Mccammon,et al.  Structure and dynamics of the full-length lipid-modified H-Ras protein in a 1,2-dimyristoylglycero-3-phosphocholine bilayer. , 2007, Journal of medicinal chemistry.

[70]  Robert G. Parton,et al.  Direct visualization of Ras proteins in spatially distinct cell surface microdomains , 2003, The Journal of cell biology.

[71]  U. Rapp,et al.  Active Ras induces heterodimerization of cRaf and BRaf. , 2001, Cancer research.

[72]  K. Inouye,et al.  Formation of the Ras Dimer Is Essential for Raf-1 Activation* , 2000, The Journal of Biological Chemistry.

[73]  J. Hancock,et al.  N-terminally myristoylated Ras proteins require palmitoylation or a polybasic domain for plasma membrane localization , 1994, Molecular and cellular biology.

[74]  A Valencia,et al.  The ras protein family: evolutionary tree and role of conserved amino acids. , 1991, Biochemistry.

[75]  Frank McCormick,et al.  The GTPase superfamily: a conserved switch for diverse cell functions , 1990, Nature.

[76]  D. Lowy,et al.  The p21 ras C-terminus is required for transformation and membrane association , 1984, Nature.

[77]  N. Opitz,et al.  Membrane-mediated induction and sorting of K-Ras microdomain signaling platforms. , 2011, Journal of the American Chemical Society.

[78]  Evon M. O. Abu-Taieh,et al.  Comparative Study , 2020, Definitions.