Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Review Article
  • Published:

Signalling scaffolds and local organization of cellular behaviour

Nature Reviews Molecular Cell Biology volume 16, pages 232–244 (2015)Cite this article

Subjects

Key Points

  • Scaffold proteins are non-catalytic organizational elements that focus enzyme activity by holding members of a signal transduction cascade in place. They confer bidirectional control on cellular processes through the simultaneous recruitment of signal transduction and signal termination enzymes.

  • Rather than functioning enzymatically, scaffolds formed by pseudokinases and pseudophosphatases can function as allosteric modulators of other signalling enzymes.

  • A-kinase anchor proteins (AKAPs) constrain second-messenger-responsive enzymes, such as protein kinase A, in customized macromolecular units. AKAPs are dynamic participants in local signalling, in part owing to their flexibility in structure, transient interactions and combinatorial assembly of binding partners.

  • Protein scaffolds can also be organized around signal termination enzymes that attenuate signalling or promote the degradation of key enzymes. Three examples of this are the scaffolds that target phosphatases, those that control protein ubiquitylation and those that control acetylation and deacetylation.

  • Covalent modification of a scaffold protein can determine which binding partners are included in the complex and thus provide alternative functionality. As a result, several scaffold proteins have been identified as ultra-sensitive switches that toggle between opposing cellular processes.

Abstract

Cellular responses to environmental cues involve the mobilization of GTPases, protein kinases and phosphoprotein phosphatases. The spatial organization of these signalling enzymes by scaffold proteins helps to guide the flow of molecular information. Allosteric modulation of scaffolded enzymes can alter their catalytic activity or sensitivity to second messengers in a manner that augments, insulates or terminates local cellular events. This Review examines the features of scaffold proteins and highlights examples of locally organized groups of signalling enzymes that drive essential physiological processes, including hormone action, heart rate, cell division, organelle movement and synaptic transmission.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Properties of adaptor, docking and scaffold proteins.
Figure 2: Scaffold functions of pseudokinases and pseudophosphatases.
Figure 3: Local coordination of second-messenger signalling by A-kinase anchor proteins.
Figure 4: Signal termination scaffolds.
Figure 5: Scaffold proteins that function as molecular switches.
Figure 6: Emergent technologies for the analysis of signalling scaffolds.

Similar content being viewed by others

Accession codes

Accessions

Protein Data Bank

References

  1. Sadowski, I., Stone, J. C. & Pawson, T. A non-catalytic domain conserved among cytoplasmic protein-tyrosine kinases modifies the kinase function and transforming activity of Fujinami sarcoma virus P130gag-fps. Mol. Cell. Biol. 6, 4396–4408 (1986).

    CAS  PubMed  PubMed Central  Google Scholar 

  2. Pawson, T. Protein modules and signalling networks. Nature 373, 573–580 (1995).

    CAS  PubMed  Google Scholar 

  3. Lemmon, M. A. & Schlessinger, J. Cell signaling by receptor tyrosine kinases. Cell 141, 1117–1134 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  4. Songyang, Z. & Cantley, L. C. Recognition and specificity in protein tyrosine kinase-mediated signalling. Trends Biochem. Sci. 20, 470–475 (1995).

    CAS  PubMed  Google Scholar 

  5. Good, M. C., Zalatan, J. G. & Lim, W. A. Scaffold proteins: hubs for controlling the flow of cellular information. Science 332, 680–686 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  6. Shaw, A. S., Kornev, A. P., Hu, J., Ahuja, L. G. & Taylor, S. S. Kinases and pseudokinases: lessons from RAF. Mol. Cell. Biol. 34, 1538–1546 (2014).

    PubMed  PubMed Central  Google Scholar 

  7. Fields, S. & Song, O. A novel genetic system to detect protein–protein interactions. Nature 340, 245–246 (1989).

    CAS  PubMed  Google Scholar 

  8. Aebersold, R. & Mann, M. Mass spectrometry-based proteomics. Nature 422, 198–207 (2003).

    Article  CAS  PubMed  Google Scholar 

  9. Bowtell, D. D., Simon, M. A. & Rubin, G. M. Ommatidia in the developing Drosophila eye require and can respond to sevenless for only a restricted period. Cell 56, 931–936 (1989).

    CAS  PubMed  Google Scholar 

  10. Simon, M. A., Bowtell, D. D., Dodson, G. S., Laverty, T. R. & Rubin, G. M. Ras1 and a putative guanine nucleotide exchange factor perform crucial steps in signaling by the sevenless protein tyrosine kinase. Cell 67, 701–716 (1991).

    CAS  PubMed  Google Scholar 

  11. Friedman, A. & Perrimon, N. Genetic screening for signal transduction in the era of network biology. Cell 128, 225–231 (2007).

    CAS  PubMed  Google Scholar 

  12. Pawson, T. & Scott, J. D. Signaling through scaffold, anchoring, and adaptor proteins. Science 278, 2075–2080 (1997).

    CAS  PubMed  Google Scholar 

  13. Dodge-Kafka, K. L., Langeberg, L. & Scott, J. D. Compartmentation of cyclic nucleotide signaling in the heart: the role of A-kinase anchoring proteins. Circ. Res. 98, 993–1001 (2006).

    CAS  PubMed  Google Scholar 

  14. Scott, J. D. & Pawson, T. Cell communication: the inside story. Sci. Am. 282, 72–79 (2000).

    CAS  PubMed  Google Scholar 

  15. Lowenstein, E. J. et al. The SH2 and SH3 domain-containing protein GRB2 links receptor tyrosine kinases to ras signaling. Cell 70, 431–442 (1992).

    CAS  PubMed  Google Scholar 

  16. Pelicci, G. et al. A novel transforming protein (SHC) with an SH2 domain is implicated in mitogenic signal transduction. Cell 70, 93–104 (1992).

    CAS  PubMed  Google Scholar 

  17. Sun, X. J., Crimmins, D. L., Myers, M. G. J., Miralpeix, M. & White, M. F. Pleiotropic insulin signals are engaged by multisite phosphorylation of IRS-1. Mol. Cell. Biol. 13, 7418–7428 (1993).

    CAS  PubMed  PubMed Central  Google Scholar 

  18. Wolf, G. et al. PTB domains of IRS-1 and Shc have distinct but overlapping binding specificities. J. Biol. Chem. 270, 27407–27410 (1995).

    CAS  PubMed  Google Scholar 

  19. Kouhara, H. et al. A lipid-anchored Grb2-binding protein that links FGF-receptor activation to the Ras/MAPK signaling pathway. Cell 89, 693–702 (1997).

    CAS  PubMed  Google Scholar 

  20. Bhattacharyya, R. P., Remenyi, A., Yeh, B. J. & Lim, W. A. Domains, motifs, and scaffolds: the role of modular interactions in the evolution and wiring of cell signaling circuits. Annu. Rev. Biochem. 75, 655–680 (2006).

    CAS  PubMed  Google Scholar 

  21. Scott, J. D. & Pawson, T. Cell signaling in space and time: where proteins come together and when they're apart. Science 326, 1220–1224 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  22. Boudeau, J., Miranda-Saavedra, D., Barton, G. J. & Alessi, D. R. Emerging roles of pseudokinases. Trends Cell Biol. 16, 443–452 (2006).

    CAS  PubMed  Google Scholar 

  23. Manning, G., Whyte, D. B., Martinez, R., Hunter, T. & Sudarsanam, S. The protein kinase complement of the human genome. Science 298, 1912–1934 (2002).

    CAS  PubMed  Google Scholar 

  24. Manning, G., Plowman, G. D., Hunter, T. & Sudarsanam, S. Evolution of protein kinase signaling from yeast to man. Trends Biochem. Sci. 27, 514–520 (2002).

    CAS  PubMed  Google Scholar 

  25. Egloff, M. P. et al. Structural basis for the recognition of regulatory subunits by the catalytic subunit of protein phosphatase 1. EMBO J. 16, 1876–1887 (1997).

    CAS  PubMed  PubMed Central  Google Scholar 

  26. Canagarajah, B. J., Khokhlatchev, A., Cobb, M. H. & Goldsmith, E. J. Activation mechanism of the MAP kinase ERK2 by dual phosphorylation. Cell 90, 859–869 (1997).

    CAS  PubMed  Google Scholar 

  27. Schulze, W. X., Deng, L. & Mann, M. Phosphotyrosine interactome of the ErbB-receptor kinase family. Mol. Syst. Biol. 1, 2005.0008 (2005).

    PubMed  PubMed Central  Google Scholar 

  28. Zhang, X., Gureasko, J., Shen, K., Cole, P. A. & Kuriyan, J. An allosteric mechanism for activation of the kinase domain of epidermal growth factor receptor. Cell 125, 1137–1149 (2006).

    CAS  PubMed  Google Scholar 

  29. Hemminki, A. et al. A serine/threonine kinase gene defective in Peutz–Jeghers syndrome. Nature 391, 184–187 (1998).

    CAS  PubMed  Google Scholar 

  30. Shaw, R. J. LKB1 and AMP-activated protein kinase control of mTOR signalling and growth. Acta Physiol. 196, 65–80 (2009).

    CAS  Google Scholar 

  31. Zheng, B. & Cantley, L. C. Regulation of epithelial tight junction assembly and disassembly by AMP-activated protein kinase. Proc. Natl Acad. Sci. USA 104, 819–822 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  32. Boudeau, J. et al. MO25α/β interact with STRADα/β enhancing their ability to bind, activate and localize LKB1 in the cytoplasm. EMBO J. 22, 5102–5114 (2003).

    CAS  PubMed  PubMed Central  Google Scholar 

  33. Zeqiraj, E., Filippi, B. M., Deak, M., Alessi, D. R. & van Aalten, D. M. Structure of the LKB1–STRAD–MO25 complex reveals an allosteric mechanism of kinase activation. Science 326, 1707–1711 (2009). This elegant structural study shows how conformational changes induced by protein–protein interactions within the LKB1–STRAD–MO25 scaffold lead to activation of the kinase LKB1.

    CAS  PubMed  PubMed Central  Google Scholar 

  34. Rajakulendran, T. & Sicheri, F. Allosteric protein kinase regulation by pseudokinases: insights from STRAD. Sci. Signal. 3, pe8 (2010).

    PubMed  Google Scholar 

  35. Zeqiraj, E. et al. ATP and MO25α regulate the conformational state of the STRADα pseudokinase and activation of the LKB1 tumour suppressor. PLoS Biol. 7, e1000126 (2009).

    PubMed  PubMed Central  Google Scholar 

  36. Morrison, D. K. KSR: a MAPK scaffold of the Ras pathway? J. Cell Sci. 114, 1609–1612 (2001).

    CAS  PubMed  Google Scholar 

  37. McKay, M. M., Ritt, D. A. & Morrison, D. K. RAF inhibitor-induced KSR1/B-RAF binding and its effects on ERK cascade signaling. Curr. Biol. 21, 563–568 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  38. Brennan, D. F. et al. A Raf-induced allosteric transition of KSR stimulates phosphorylation of MEK. Nature 472, 366–369 (2011). References 37 and 38 are representative of several papers that reveal different mechanistic aspects of KSR action.

    CAS  PubMed  Google Scholar 

  39. Smith, F. D. et al. AKAP-Lbc enhances cyclic AMP control of the ERK1/2 cascade. Nature Cell Biol. 12, 1242–1249 (2010).

    CAS  PubMed  Google Scholar 

  40. Hu, J. et al. Mutation that blocks ATP binding creates a pseudokinase stabilizing the scaffolding function of kinase suppressor of Ras, CRAF and BRAF. Proc. Natl Acad. Sci. USA 108, 6067–6072 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  41. Poulikakos, P. I., Zhang, C., Bollag, G., Shokat, K. M. & Rosen, N. RAF inhibitors transactivate RAF dimers and ERK signalling in cells with wild-type BRAF. Nature 464, 427–430 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  42. Hu, J. et al. Allosteric activation of functionally asymmetric RAF kinase dimers. Cell 154, 1036–1046 (2013).

    CAS  PubMed  Google Scholar 

  43. Wishart, M. J., Denu, J. M., Williams, J. A. & Dixon, J. E. A single mutation converts a novel phosphotyrosine binding domain into a dual-specificity phosphatase. J. Biol. Chem. 270, 26782–26785 (1995).

    CAS  PubMed  Google Scholar 

  44. Tonks, N. K. Pseudophosphatases: grab and hold on. Cell 139, 464–465 (2009).

    CAS  PubMed  Google Scholar 

  45. Cheng, K. C., Klancer, R., Singson, A. & Seydoux, G. Regulation of MBK-2/DYRK by CDK-1 and the pseudophosphatases EGG-4 and EGG-5 during the oocyte-to-embryo transition. Cell 139, 560–572 (2009). This study describes one of the first examples of a pseudophosphatase functioning as a conformational clamp to recruit substrates.

    CAS  PubMed  PubMed Central  Google Scholar 

  46. Parry, J. M. et al. EGG-4 and EGG-5 link events of the oocyte-to-embryo transition with meiotic progression in C. elegans. Curr. Biol. 19, 1752–1757 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  47. Reiterer, V., Fey, D., Kolch, W., Kholodenko, B. N. & Farhan, H. Pseudophosphatase STYX modulates cell-fate decisions and cell migration by spatiotemporal regulation of ERK1/2. Proc. Natl Acad. Sci. USA 110, E2934–E2943 (2013). This paper shows an example of STYX function in a well-defined cellular context.

    CAS  PubMed  PubMed Central  Google Scholar 

  48. Scott, J. D. et al. Type II regulatory subunit dimerization determines the subcellular localization of the cAMP-dependent protein kinase. J. Biol. Chem. 265, 21561–21566 (1990).

    CAS  PubMed  Google Scholar 

  49. Luo, Z., Shafit-Zagardo, B. & Erlichman, J. Identification of the MAP2- and P75- binding domain in the regulatory subunit (RIIβ) of type II cAMP-dependent protein kinase. J. Biol. Chem. 265, 21804–21810 (1990).

    CAS  PubMed  Google Scholar 

  50. Carr, D. W. et al. Interaction of the regulatory subunit (RII) of cAMP-dependent protein kinase with RII-anchoring proteins occurs through an amphipathic helix binding motif. J. Biol. Chem. 266, 14188–14192 (1991).

    CAS  PubMed  Google Scholar 

  51. Rubin, C. S. A kinase anchor proteins and the intracellular targeting of signals carried by cAMP. Biochim. Biophys. Acta 1224, 467–479 (1994).

    PubMed  Google Scholar 

  52. Tasken, K. & Aandahl, E. M. Localized effects of cAMP mediated by distinct routes of protein kinase A. Physiol. Rev. 84, 137–167 (2004).

    CAS  PubMed  Google Scholar 

  53. Welch, E. J., Jones, B. W. & Scott, J. D. Networking with AKAPs: context-dependent regulation of anchored enzymes. Mol. Interv. 10, 86–97 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  54. Wong, W. & Scott, J. D. AKAP signalling complexes: focal points in space and time. Nature Rev. Mol. Cell Biol. 5, 959–971 (2004).

    CAS  Google Scholar 

  55. Smith, F. D. et al. Intrinsic disorder within an AKAP-protein kinase A complex guides local substrate phosphorylation. eLife 2, e01319 (2013). This paper contains the first description of the structure of an intact anchored PKA holoenzyme. This study also highlights the utility of intrinsic disorder as a means to manage substrate specificity.

    PubMed  PubMed Central  Google Scholar 

  56. Newlon, M. G. et al. The molecular basis for protein kinase A anchoring revealed by solution NMR. Nature Struct. Biol. 6, 222–227 (1999).

    CAS  PubMed  Google Scholar 

  57. Gold, M. G. et al. Molecular basis of AKAP specificity for PKA regulatory subunits. Mol. Cell 24, 383–395 (2006).

    CAS  PubMed  Google Scholar 

  58. Kinderman, F. S. et al. A dynamic mechanism for AKAP binding to RII isoforms of cAMP-dependent protein kinase. Mol. Cell 24, 397–408 (2006).

    CAS  PubMed  PubMed Central  Google Scholar 

  59. Sarma, G. N. et al. Structure of D-AKAP2:PKA RI complex: insights into AKAP specificity and selectivity. Structure 18, 155–166 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  60. Carr, D. W., Hausken, Z. E., Fraser, I. D., Stofko-Hahn, R. E. & Scott, J. D. Association of the type II cAMP-dependent protein kinase with a human thyroid RII-anchoring protein. Cloning and characterization of the RII-binding domain. J. Biol. Chem. 267, 13376–13382 (1992).

    CAS  PubMed  Google Scholar 

  61. Lester, L. B., Coghlan, V. M., Nauert, B. & Scott, J. D. Cloning and characterization of a novel A-kinase anchoring protein: AKAP220, association with testicular peroxisomes. J. Biol. Chem. 272, 9460–9465 (1996).

    Google Scholar 

  62. Gao, S., Wang, H. Y. & Malbon, C. C. AKAP12 and AKAP5 form higher-order hetero-oligomers. J. Mol. Signal. 6, 8 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  63. Gold, M. G. et al. Engineering A-kinase anchoring protein (AKAP)-selective regulatory subunits of protein kinase A (PKA) through structure-based phage selection. J. Biol. Chem. 288, 17111–17121 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  64. Carr, D. W., Stofko-Hahn, R. E., Fraser, I. D. C., Cone, R. D. & Scott, J. D. Localization of the cAMP-dependent protein kinase to the postsynaptic densities by A-kinase anchoring proteins: characterization of AKAP79. J. Biol. Chem. 24, 16816–16823 (1992).

    Google Scholar 

  65. Coghlan, V. M. et al. Association of protein kinase A and protein phosphatase 2B with a common anchoring protein. Science 267, 108–112 (1995).

    CAS  PubMed  Google Scholar 

  66. Klauck, T. M. et al. Coordination of three signaling enzymes by AKAP79, a mammalian scaffold protein. Science 271, 1589–1592 (1996).

    CAS  PubMed  Google Scholar 

  67. Hoshi, N., Langeberg, L. K. & Scott, J. D. Distinct enzyme combinations in AKAP signalling complexes permit functional diversity. Nature Cell Biol. 7, 1066–1073 (2005).

    CAS  PubMed  Google Scholar 

  68. Huganir, R. L. & Nicoll, R. A. AMPARs and synaptic plasticity: the last 25 years. Neuron 80, 704–717 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  69. Tavalin, S. J. et al. Regulation of GluR1 by the A-kinase anchoring protein 79 (AKAP79) signaling complex shares properties with long-term depression. J. Neurosci. 22, 3044–3051 (2002).

    CAS  PubMed  PubMed Central  Google Scholar 

  70. Sanderson, J. L. et al. AKAP150-anchored calcineurin regulates synaptic plasticity by limiting synaptic incorporation of Ca2+-permeable AMPA receptors. J. Neurosci. 32, 15036–15052 (2012). This paper provides compelling evidence that AKAP150-anchored PP2B is a dominant effectorin the modulation of synaptic transmission.

    CAS  PubMed  PubMed Central  Google Scholar 

  71. Suh, B. C., Inoue, T., Meyer, T. & Hille, B. Rapid chemically induced changes of PtdIns(4,5)P2 gate KCNQ ion channels. Science 314, 1454–1457 (2006).

    CAS  PubMed  PubMed Central  Google Scholar 

  72. Hoshi, N. et al. AKAP150 signaling complex promotes suppression of the M-current by muscarinic agonists. Nature Neurosci. 6, 564–571 (2003).

    CAS  PubMed  Google Scholar 

  73. Tunquist, B. J. et al. Loss of AKAP150 perturbs distinct neuronal processes in mice. Proc. Natl Acad. Sci. USA 105, 12557–12562 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  74. Hoshi, N., Langeberg, L. K., Gould, C. M., Newton, A. C. & Scott, J. D. Interaction with AKAP79 modifies the cellular pharmacology of PKC. Mol. Cell 37, 541–550 (2010). Using a combination of biochemistry and live-cell imaging, these authors demonstrate that selected ATP-directed kinase inhibitor drugs are refractory to their targets when the enzymes are located in AKAP complexes.

    CAS  PubMed  PubMed Central  Google Scholar 

  75. Dyachok, O., Isakov, Y., Sagetorp, J. & Tengholm, A. Oscillations of cyclic AMP in hormone-stimulated insulin-secreting β-cells. Nature 439, 349–352 (2006).

    CAS  PubMed  Google Scholar 

  76. Lester, L. B., Faux, M. C., Nauert, J. B. & Scott, J. D. Targeted protein kinase A and PP-2B regulate insulin secretion through reversible phosphorylation. Endocrinology 142, 1218–1227 (2001).

    CAS  PubMed  Google Scholar 

  77. Bauman, A. L. et al. Dynamic regulation of cAMP synthesis through anchored PKA-adenylyl cyclase V/VI complexes. Mol. Cell 23, 925–931 (2006).

    CAS  PubMed  PubMed Central  Google Scholar 

  78. Dessauer, C. W. Adenylyl cyclase — A-kinase anchoring protein complexes: the next dimension in cAMP signaling. Mol. Pharmacol. 76, 935–941 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  79. Hinke, S. A. et al. Anchored phosphatases modulate glucose homeostasis. EMBO J. 31, 3991–4004 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  80. Cohen, P. The origins of protein phosphorylation. Nature Cell Biol. 4, E127–E130 (2002).

    CAS  PubMed  Google Scholar 

  81. Cohen, P. T. Protein phosphatase 1 — targeted in many directions. J. Cell Sci. 115, 241–256 (2002).

    CAS  PubMed  Google Scholar 

  82. Vazquez-Martin, C., Rouse, J. & Cohen, P. T. Characterization of the role of a trimeric protein phosphatase complex in recovery from cisplatin-induced versus noncrosslinking DNA damage. FEBS J. 275, 4211–4221 (2008).

    CAS  PubMed  Google Scholar 

  83. Bollen, M. Combinatorial control of protein phosphatase-1. Trends Biochem. Sci. 26, 426–431 (2001).

    CAS  PubMed  Google Scholar 

  84. Hendrickx, A. et al. Docking motif-guided mapping of the interactome of protein phosphatase-1. Chem. Biol. 16, 365–371 (2009).

    CAS  PubMed  Google Scholar 

  85. De Munter, S., Kohn, M. & Bollen, M. Challenges and opportunities in the development of protein phosphatase-directed therapeutics. ACS Chem. Biol. 8, 36–45 (2013).

    CAS  PubMed  Google Scholar 

  86. Hartshorne, D. J. & Hirano, K. Interactions of protein phosphatase type 1, with a focus on myosin phosphatase. Mol. Cell. Biochem. 190, 79–84 (1999).

    CAS  PubMed  Google Scholar 

  87. Surks, H. K. et al. Regulation of myosin phosphatase by a specific interaction with cGMP-dependent protein kinase Iα. Science 286, 1583–1587 (1999).

    CAS  PubMed  Google Scholar 

  88. Lincoln, T. M. Myosin phosphatase regulatory pathways: different functions or redundant functions? Circ. Res. 100, 10–12 (2007).

    CAS  PubMed  Google Scholar 

  89. Matsumura, F. & Hartshorne, D. J. Myosin phosphatase target subunit: many roles in cell function. Biochem. Biophys. Res. Commun. 369, 149–156 (2008).

    CAS  PubMed  Google Scholar 

  90. Lee, M. R., Li, L. & Kitazawa, T. Cyclic GMP causes Ca2+ desensitization in vascular smooth muscle by activating the myosin light chain phosphatase. J. Biol. Chem. 272, 5063–5068 (1997).

    CAS  PubMed  Google Scholar 

  91. Kaneko-Kawano, T. et al. Dynamic regulation of myosin light chain phosphorylation by Rho-kinase. PLoS ONE 7, e39269 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  92. McKay, M. M. & Morrison, D. K. Integrating signals from RTKs to ERK/MAPK. Oncogene 26, 3113–3121 (2007).

    CAS  PubMed  Google Scholar 

  93. Malumbres, M. & Barbacid, M. RAS oncogenes: the first 30 years. Nature Rev. Cancer 3, 459–465 (2003).

    CAS  Google Scholar 

  94. Cordeddu, V. et al. Mutation of SHOC2 promotes aberrant protein N-myristoylation and causes Noonan-like syndrome with loose anagen hair. Nature Genet. 41, 1022–1026 (2009).

    CAS  PubMed  Google Scholar 

  95. Young, L. C. et al. An MRAS, SHOC2, and SCRIB complex coordinates ERK pathway activation with polarity and tumorigenic growth. Mol. Cell 52, 679–692 (2013). This study provides evidence that, in the context of some macromolecular scaffolds, rival targeting subunits compete for PP1 binding.

    CAS  PubMed  Google Scholar 

  96. Rodriguez-Viciana, P., Oses-Prieto, J., Burlingame, A., Fried, M. & McCormick, F. A phosphatase holoenzyme comprised of Shoc2/Sur8 and the catalytic subunit of PP1 functions as an M-Ras effector to modulate Raf activity. Mol. Cell 22, 217–230 (2006).

    CAS  PubMed  Google Scholar 

  97. Wolff, S., Weissman, J. S. & Dillin, A. Differential scales of protein quality control. Cell 157, 52–64 (2014).

    CAS  PubMed  Google Scholar 

  98. Grabbe, C. & Dikic, I. Cell biology. Going global on ubiquitin. Science 322, 872–873 (2008).

    CAS  PubMed  Google Scholar 

  99. Shaid, S., Brandts, C. H., Serve, H. & Dikic, I. Ubiquitination and selective autophagy. Cell. Death Differ. 20, 21–30 (2013).

    CAS  PubMed  Google Scholar 

  100. Gardner, R. G., Nelson, Z. W. & Gottschling, D. E. Degradation-mediated protein quality control in the nucleus. Cell 120, 803–815 (2005). This paper describes the discovery of the nuclear protein San1. Together with reference 101, this study defines a new mechanism whereby this E3 ligase recognizes hydrophobic stretches of amino acids in unfolded protein targets. This represents a new paradigm in protein quality control.

    CAS  PubMed  Google Scholar 

  101. Rosenbaum, J. C. et al. Disorder targets misorder in nuclear quality control degradation: a disordered ubiquitin ligase directly recognizes its misfolded substrates. Mol. Cell 41, 93–106 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  102. Frescas, D. & Pagano, M. Deregulated proteolysis by the F-box proteins SKP2 and β-TrCP: tipping the scales of cancer. Nature Rev. Cancer 8, 438–449 (2008).

    CAS  Google Scholar 

  103. Singh, B. N. et al. Nonhistone protein acetylation as cancer therapy targets. Expert Rev. Anticancer Ther. 10, 935–954 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  104. Suganuma, T. et al. ATAC is a double histone acetyltransferase complex that stimulates nucleosome sliding. Nature Struct. Mol. Biol. 15, 364–372 (2008).

    CAS  Google Scholar 

  105. Suganuma, T. et al. The ATAC acetyltransferase complex coordinates MAP kinases to regulate JNK target genes. Cell 142, 726–736 (2010). This study provides compelling evidence for a signalling scaffold that synchronizes protein acetylation and phosphorylation events.

    CAS  PubMed  Google Scholar 

  106. Jiang, W. et al. Acetylation regulates gluconeogenesis by promoting PEPCK1 degradation via recruiting the UBR5 ubiquitin ligase. Mol. Cell 43, 33–44 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  107. Choudhary, C. et al. Lysine acetylation targets protein complexes and co-regulates major cellular functions. Science 325, 834–840 (2009).

    CAS  PubMed  Google Scholar 

  108. Wang, Q. et al. Acetylation of metabolic enzymes coordinates carbon source utilization and metabolic flux. Science 327, 1004–1007 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  109. Zhao, S. et al. Regulation of cellular metabolism by protein lysine acetylation. Science 327, 1000–1004 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  110. Kranz, J. E., Satterberg, B. & Elion, E. A. The MAP kinase Fus3 associates with and phosphorylates the upstream signaling component Ste5. Genes Dev. 8, 313–327 (1994).

    CAS  PubMed  Google Scholar 

  111. Sette, C., Inouye, C. J., Stroschein, S. L., Iaquinta, P. J. & Thorner, J. Mutational analysis suggests that activation of the yeast pheromone response mitogen-activated protein kinase pathway involves conformational changes in the Ste5 scaffold protein. Mol. Biol. Cell 11, 4033–4049 (2000).

    CAS  PubMed  PubMed Central  Google Scholar 

  112. Elion, E. A. The Ste5p scaffold. J. Cell Sci. 114, 3967–3978 (2001).

    CAS  PubMed  Google Scholar 

  113. Strickfaden, S. C. et al. A mechanism for cell-cycle regulation of MAP kinase signaling in a yeast differentiation pathway. Cell 128, 519–531 (2007). This is an elegant study that describes the role of MAPKs in the modulation of yeast cell division.

    CAS  PubMed  PubMed Central  Google Scholar 

  114. Malleshaiah, M. K., Shahrezaei, V., Swain, P. S. & Michnick, S. W. The scaffold protein Ste5 directly controls a switch-like mating decision in yeast. Nature 465, 101–105 (2010).

    CAS  PubMed  Google Scholar 

  115. Zalatan, J. G., Coyle, S. M., Rajan, S., Sidhu, S. S. & Lim, W. A. Conformational control of the Ste5 scaffold protein insulates against MAP kinase misactivation. Science 337, 1218–1222 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  116. Whitmarsh, A. J., Cavanagh, J., Tournier, C., Yasuda, J. & Davis, R. J. A mammalian scaffold complex that selectively mediates MAP kinase activation. Science 281, 1671–1674 (1998).

    CAS  PubMed  Google Scholar 

  117. Bonny, C., Nicod, P. & Waeber, G. IB1, a JIP-1-related nuclear protein present in insulin-secreting cells. J. Biol. Chem. 273, 1843–1846 (1998).

    CAS  PubMed  Google Scholar 

  118. Fu, M. M. & Holzbaur, E. L. JIP1 regulates the directionality of APP axonal transport by coordinating kinesin and dynein motors. J. Cell Biol. 202, 495–508 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  119. Willoughby, E. A., Perkins, G. R., Collins, M. K. & Whitmarsh, A. J. The JNK-interacting protein-1 scaffold protein targets MAPK phosphatase-7 to dephosphorylate JNK. J. Biol. Chem. 278, 10731–10736 (2003).

    CAS  PubMed  Google Scholar 

  120. Fu, M. M., Nirschl, J. J. & Holzbaur, E. L. LC3 binding to the scaffolding protein JIP1 regulates processive dynein-driven transport of autophagosomes. Dev. Cell 29, 577–590 (2014). This study provides mechanistic evidence for the JIP1 scaffold as a dynamic regulator of organelle movement.

    CAS  PubMed  PubMed Central  Google Scholar 

  121. Robinson, C. V., Sali, A. & Baumeister, W. The molecular sociology of the cell. Nature 450, 973–982 (2007).

    CAS  PubMed  Google Scholar 

  122. Heck, A. J. Native mass spectrometry: a bridge between interactomics and structural biology. Nature Methods 5, 927–933 (2008).

    CAS  PubMed  Google Scholar 

  123. Gold, M. G. et al. Architecture and dynamics of an A-kinase anchoring protein 79 (AKAP79) signaling complex. Proc. Natl Acad. Sci. USA 108, 6426–6431 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  124. Jain, A. et al. Probing cellular protein complexes using single-molecule pull-down. Nature 473, 484–488 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  125. Means, C. K. et al. An entirely specific type I A-kinase anchoring protein that can sequester two molecules of protein kinase A at mitochondria. Proc. Natl Acad. Sci. USA 108, E1227–E1235 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  126. Cao, E., Liao, M., Cheng, Y. & Julius, D. TRPV1 structures in distinct conformations reveal activation mechanisms. Nature 504, 113–118 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  127. Li, X. et al. Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM. Nature Methods 10, 584–590 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  128. Bai, X. C., Fernandez, I. S., McMullan, G. & Scheres, S. H. Ribosome structures to near-atomic resolution from thirty thousand cryo-EM particles. eLife 2, e00461 (2013).

    PubMed  PubMed Central  Google Scholar 

  129. Lu, P. et al. Three-dimensional structure of human γ-secretase. Nature 512, 166–170 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  130. Scheres, S. H. Beam-induced motion correction for sub-megadalton cryo-EM particles. eLife 3, e03665 (2014).

    PubMed  PubMed Central  Google Scholar 

  131. Fernandez-Medarde, A. & Santos, E. Ras in cancer and developmental diseases. Genes Cancer 2, 344–358 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  132. Hatzivassiliou, G. et al. RAF inhibitors prime wild-type RAF to activate the MAPK pathway and enhance growth. Nature 464, 431–435 (2010).

    CAS  PubMed  Google Scholar 

  133. Halaban, R. et al. PLX4032, a selective BRAFV600E kinase inhibitor, activates the ERK pathway and enhances cell migration and proliferation of BRAFWT melanoma cells. Pigment Cell Melanoma Res. 23, 190–200 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  134. Rubinstein, J. C. et al. Incidence of the V600K mutation among melanoma patients with BRAF mutations, and potential therapeutic response to the specific BRAF inhibitor PLX4032. J. Transl. Med. 8, 67 (2010).

    PubMed  PubMed Central  Google Scholar 

  135. Reiterer, V., Eyers, P. A. & Farhan, H. Day of the dead: pseudokinases and pseudophosphatases in physiology and disease. Trends Cell Biol. 24, 489–505 (2014).

    CAS  PubMed  Google Scholar 

  136. Shi, F. & Lemmon, M. A. KSR plays CRAF-ty. Science 332, 1043–1044 (2011).

    CAS  PubMed  Google Scholar 

  137. Carnegie, G. K., Means, C. K. & Scott, J. D. A-kinase anchoring proteins: from protein complexes to physiology and disease. IUBMB Life 61, 394–406 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  138. Li, H. et al. Balanced interactions of calcineurin with AKAP79 regulate Ca2+–calcineurin–NFAT signaling. Nature Struct. Mol. Biol. 19, 337–345 (2012).

    Google Scholar 

  139. Morrison, D. K. & Davis, R. J. Regulation of MAP kinase signaling modules by scaffold proteins in mammals. Annu. Rev. Cell Dev. Biol. 19, 91–118 (2003).

    CAS  PubMed  Google Scholar 

  140. Scholten, A. et al. Analysis of the cGMP/cAMP interactome using a chemical proteomics approach in mammalian heart tissue validates sphingosine kinase type 1-interacting protein as a genuine and highly abundant AKAP. J. Proteome Res. 5, 1435–1447 (2006).

    CAS  PubMed  Google Scholar 

Download references

Acknowledgements

The authors apologize to all colleagues whose work has not been cited owing to space limitations. The authors thank F. D. Smith for providing the negative-stain electron microscopy images presented in Figure 4f, and members of the Scott Lab for discussions. Support for this work was provided by the US National Institutes of Health (NIH) grants DK105542 and DK054441, and the Howard Hughes Medical Institute.

Author information

Authors and Affiliations

  1. Howard Hughes Medical Institute and Department of Pharmacology, University of Washington, 1959 NE Pacific Street, Seattle, 98195, Washington, USA

    Lorene K. Langeberg & John D. Scott

Authors
  1. Lorene K. Langeberg
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. John D. Scott
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to John D. Scott.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

PowerPoint slides

Related links

Related links

DATABASES

RCSB Protein Data Bank

3C9W

3N5U

3J4Q

Glossary

Allosteric modulators

Proteins that bind to a site that is distinct from the orthosteric agonist-binding site. They usually induce a conformational change within the protein structure.

Long-term potentiation

(LTP). A process whereby brief periods of synaptic activity can produce a long-lasting increase in the strength of a neuronal synapse. LTP has an important role in learning and memory.

Long-term depression

(LTD). A long-lasting decrease in the synaptic response of neurons to stimulation of their afferents following a long patterned stimulus.

M channels

Muscarinic receptor-sensitive potassium channels that coordinate the depolarization of neurons and prepare these cells for the next action potential.

L-type Ca2+ channels

Ion channels that control Ca2+ influx into a large number of cell types. They are one of the most studied types of ion channels.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Langeberg, L., Scott, J. Signalling scaffolds and local organization of cellular behaviour. Nat Rev Mol Cell Biol 16, 232–244 (2015). https://doi.org/10.1038/nrm3966

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nrm3966

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing