Positive feedback can lead to dynamic nanometer-scale clustering on cell membranes.

Clustering of molecules on biological membranes is a widely observed phenomenon. A key example is the clustering of the oncoprotein Ras, which is known to be important for signal transduction in mammalian cells. Yet, the mechanism by which Ras clusters form and are maintained remains unclear. Recently, it has been discovered that activated Ras promotes further Ras activation. Here we show using particle-based simulation that this positive feedback is sufficient to produce persistent clusters of active Ras molecules at the nanometer scale via a dynamic nucleation mechanism. Furthermore, we find that our cluster statistics are consistent with experimental observations of the Ras system. Interestingly, we show that our model does not support a Turing regime of macroscopic reaction-diffusion patterning, and therefore that the clustering we observe is a purely stochastic effect, arising from the coupling of positive feedback with the discrete nature of individual molecules. These results underscore the importance of stochastic and dynamic properties of reaction diffusion systems for biological behavior.

[1]  F. Tostevin,et al.  Spatial partitioning improves the reliability of biochemical signaling , 2013, Proceedings of the National Academy of Sciences.

[2]  J. Sethna,et al.  Minimal model of plasma membrane heterogeneity requires coupling cortical actin to criticality. , 2010, Biophysical journal.

[3]  J. Hancock,et al.  Three Separable Domains Regulate GTP-Dependent Association of H-ras with the Plasma Membrane , 2004, Molecular and Cellular Biology.

[4]  Robert G Parton,et al.  H-ras, K-ras, and inner plasma membrane raft proteins operate in nanoclusters with differential dependence on the actin cytoskeleton , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[5]  Boris N. Kholodenko,et al.  Signalling ballet in space and time , 2010, Nature Reviews Molecular Cell Biology.

[6]  Kerry A Landman,et al.  Generalized index for spatial data sets as a measure of complete spatial randomness. , 2012, Physical review. E, Statistical, nonlinear, and soft matter physics.

[7]  H. Waldmann,et al.  Raft Protein Clustering Alters N-Ras Membrane Interactions and Activation Pattern , 2011, Molecular and Cellular Biology.

[8]  G. Edelman,et al.  Degeneracy and complexity in biological systems , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[9]  Dharini van der Hoeven,et al.  Fendiline Inhibits K-Ras Plasma Membrane Localization and Blocks K-Ras Signal Transmission , 2012, Molecular and Cellular Biology.

[10]  T. R. Sokolowski A computational study of robust formation of spatial protein patterns , 2013 .

[11]  Thorsten Wiegand,et al.  Rings, circles, and null-models for point pattern analysis in ecology , 2004 .

[12]  Akihiro Kusumi,et al.  Single-molecule imaging analysis of Ras activation in living cells. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[13]  Judith P Armitage,et al.  Spatial organization in bacterial chemotaxis , 2010, The EMBO journal.

[14]  Sadri Hassani,et al.  Nonlinear Dynamics and Chaos , 2000 .

[15]  Akihiro Kusumi,et al.  Paradigm shift of the plasma membrane concept from the two-dimensional continuum fluid to the partitioned fluid: high-speed single-molecule tracking of membrane molecules. , 2005, Annual review of biophysics and biomolecular structure.

[16]  Hernán E. Grecco,et al.  Signaling from the Living Plasma Membrane , 2011, Cell.

[17]  Alan J McKane,et al.  Quasicycles in a spatial predator-prey model. , 2008, Physical review. E, Statistical, nonlinear, and soft matter physics.

[18]  Yong Zhou,et al.  Nonsteroidal Anti-inflammatory Drugs Alter the Spatiotemporal Organization of Ras Proteins on the Plasma Membrane* , 2012, The Journal of Biological Chemistry.

[19]  I. Prior,et al.  Compartmentalized signalling: Ras proteins and signalling nanoclusters , 2009, The FEBS journal.

[20]  J. Hancock,et al.  Ras trafficking, localization and compartmentalized signalling. , 2012, Seminars in cell & developmental biology.

[21]  J. Hancock,et al.  Galectin-1 is a novel structural component and a major regulator of h-ras nanoclusters. , 2008, Molecular biology of the cell.

[22]  H. Lodish Molecular Cell Biology , 1986 .

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

[24]  Sarah J. Plowman,et al.  H-Ras Nanocluster Stability Regulates the Magnitude of MAPK Signal Output , 2010, PloS one.

[25]  Alexandra Jilkine,et al.  A Density-Dependent Switch Drives Stochastic Clustering and Polarization of Signaling Molecules , 2011, PLoS Comput. Biol..

[26]  Kai Simons,et al.  Lipid Rafts As a Membrane-Organizing Principle , 2010, Science.

[27]  P. R. ten Wolde,et al.  Membrane clustering and the role of rebinding in biochemical signaling. , 2011, Biophysical journal.

[28]  R. Rosenfeld Nature , 2009, Otolaryngology--head and neck surgery : official journal of American Academy of Otolaryngology-Head and Neck Surgery.

[29]  A. Chakraborty,et al.  Positive feedback regulation results in spatial clustering and fast spreading of active signaling molecules on a cell membrane. , 2009, The Journal of chemical physics.

[30]  P. R. ten Wolde,et al.  Spatio-temporal correlations can drastically change the response of a MAPK pathway , 2009, Proceedings of the National Academy of Sciences.

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

[32]  T. Fujisawa,et al.  The hydration of Ras p21 in solution during GTP hydrolysis based on solution X-ray scattering profile. , 1994, Journal of biochemistry.

[33]  A. Mugler,et al.  The Macroscopic Effects of Microscopic Heterogeneity in Cell Signaling , 2012, 1210.0104.

[34]  S. Marqusee,et al.  A Ras-induced conformational switch in the Ras activator Son of sevenless , 2006, Proceedings of the National Academy of Sciences.

[35]  Thomas Butler,et al.  Fluctuation-driven Turing patterns. , 2010, Physical review. E, Statistical, nonlinear, and soft matter physics.

[36]  J. Hancock,et al.  Individual Palmitoyl Residues Serve Distinct Roles in H-Ras Trafficking, Microlocalization, and Signaling , 2005, Molecular and Cellular Biology.

[37]  John Kuriyan,et al.  Molecular mechanisms in signal transduction at the membrane , 2010, Nature Structural &Molecular Biology.

[38]  J. Hancock,et al.  On the use of Ripley's K-function and its derivatives to analyze domain size. , 2009, Biophysical journal.

[39]  Sigurd B. Angenent,et al.  On the spontaneous emergence of cell polarity , 2008, Nature.

[40]  Thomas Butler,et al.  Robust ecological pattern formation induced by demographic noise. , 2009, Physical review. E, Statistical, nonlinear, and soft matter physics.

[41]  Andre Hoelz,et al.  Structural Evidence for Feedback Activation by Ras·GTP of the Ras-Specific Nucleotide Exchange Factor SOS , 2003, Cell.

[42]  L. Pike The challenge of lipid rafts This work was supported by National Institutes of Health grants RO1 GM064491 and R01 GM082824 to LJP. Published, JLR Papers in Press, October 27, 2008. , 2009, Journal of Lipid Research.

[43]  Jayajit Das,et al.  Digital Signaling and Hysteresis Characterize Ras Activation in Lymphoid Cells , 2009, Cell.

[44]  Holger Sondermann,et al.  Structural Analysis of Autoinhibition in the Ras Activator Son of Sevenless , 2004, Cell.

[45]  Matthias Peter,et al.  Scaffold proteins in MAP kinase signaling: more than simple passive activating platforms , 2006, BioEssays : news and reviews in molecular, cellular and developmental biology.

[46]  A. Kusumi,et al.  Raf Inhibitors Target Ras Spatiotemporal Dynamics , 2012, Current Biology.

[47]  Thomas Schmidt,et al.  Single-molecule diffusion measurements of H-Ras at the plasma membrane of live cells reveal microdomain localization upon activation , 2005, Journal of Cell Science.

[48]  Ras plasma membrane signalling platforms. , 2005 .

[49]  Tianhai Tian,et al.  Plasma membrane nanoswitches generate high-fidelity Ras signal transduction , 2007, Nature Cell Biology.