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Crystal structures of the GCaMP calcium sensor reveal the mechanism of fluorescence signal change and aid rational design.

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Akerboom J, Rivera JD, Guilbe MM, Malavé EC, Hernandez HH, Tian L, Hires SA, Marvin JS, Looger LL, Schreiter ER
OpenAccess logo J Biol Chem 284 6455-64 (2009)
Related entries: 3ek4, 3ek7, 3ek8, 3ekj

Cited: 147 times
EuropePMC logo PMID: 19098007

Abstract

The genetically encoded calcium indicator GCaMP2 shows promise for neural network activity imaging, but is currently limited by low signal-to-noise ratio. We describe x-ray crystal structures as well as solution biophysical and spectroscopic characterization of GCaMP2 in the calcium-free dark state, and in two calcium-bound bright states: a monomeric form that dominates at intracellular concentrations observed during imaging experiments and an unexpected domain-swapped dimer with decreased fluorescence. This series of structures provides insight into the mechanism of Ca2+-induced fluorescence change. Upon calcium binding, the calmodulin (CaM) domain wraps around the M13 peptide, creating a new domain interface between CaM and the circularly permuted enhanced green fluorescent protein domain. Residues from CaM alter the chemical environment of the circularly permuted enhanced green fluorescent protein chromophore and, together with flexible inter-domain linkers, block solvent access to the chromophore. Guided by the crystal structures, we engineered a series of GCaMP2 point mutants to probe the mechanism of GCaMP2 function and characterized one mutant with significantly improved signal-to-noise. The mutation is located at a domain interface and its effect on sensor function could not have been predicted in the absence of structural data.

Articles - 3ekh mentioned but not cited (3)

  1. Crystal structures of the GCaMP calcium sensor reveal the mechanism of fluorescence signal change and aid rational design. Akerboom J, Rivera JD, Guilbe MM, Malavé EC, Hernandez HH, Tian L, Hires SA, Marvin JS, Looger LL, Schreiter ER. J Biol Chem 284 6455-6464 (2009)
  2. Impact of mutations on the allosteric conformational equilibrium. Weinkam P, Chen YC, Pons J, Sali A. J Mol Biol 425 647-661 (2013)
  3. Self-association of a highly charged arginine-rich cell-penetrating peptide. Tesei G, Vazdar M, Jensen MR, Cragnell C, Mason PE, Heyda J, Skepö M, Jungwirth P, Lund M. Proc Natl Acad Sci U S A 114 11428-11433 (2017)


Reviews citing this publication (44)

  1. The Growing and Glowing Toolbox of Fluorescent and Photoactive Proteins. Rodriguez EA, Campbell RE, Lin JY, Lin MZ, Miyawaki A, Palmer AE, Shu X, Zhang J, Tsien RY. Trends Biochem Sci 42 111-129 (2017)
  2. Genetically encodable fluorescent biosensors for tracking signaling dynamics in living cells. Newman RH, Fosbrink MD, Zhang J. Chem Rev 111 3614-3666 (2011)
  3. Genetically encoded biosensors based on engineered fluorescent proteins. Frommer WB, Davidson MW, Campbell RE. Chem Soc Rev 38 2833-2841 (2009)
  4. A Critical and Comparative Review of Fluorescent Tools for Live-Cell Imaging. Specht EA, Braselmann E, Palmer AE. Annu Rev Physiol 79 93-117 (2017)
  5. Design and application of genetically encoded biosensors. Palmer AE, Qin Y, Park JG, McCombs JE. Trends Biotechnol 29 144-152 (2011)
  6. Quantitative imaging with fluorescent biosensors. Okumoto S, Jones A, Frommer WB. Annu Rev Plant Biol 63 663-706 (2012)
  7. Genetically encoded neural activity indicators. Looger LL, Griesbeck O. Curr Opin Neurobiol 22 18-23 (2012)
  8. Advanced optoacoustic methods for multiscale imaging of in vivo dynamics. Deán-Ben XL, Gottschalk S, Mc Larney B, Shoham S, Razansky D. Chem Soc Rev 46 2158-2198 (2017)
  9. Genetically encoded Ca(2+) indicators: properties and evaluation. Pérez Koldenkova V, Nagai T. Biochim Biophys Acta 1833 1787-1797 (2013)
  10. Structure- and mechanism-guided design of single fluorescent protein-based biosensors. Nasu Y, Shen Y, Kramer L, Campbell RE. Nat Chem Biol 17 509-518 (2021)
  11. Fluorescent proteins as genetically encoded FRET biosensors in life sciences. Hochreiter B, Garcia AP, Schmid JA. Sensors (Basel) 15 26281-26314 (2015)
  12. Circularly Permuted Fluorescent Protein-Based Indicators: History, Principles, and Classification. Kostyuk AI, Demidovich AD, Kotova DA, Belousov VV, Bilan DS. Int J Mol Sci 20 E4200 (2019)
  13. Molecular tools and approaches for optogenetics. Mei Y, Zhang F. Biol Psychiatry 71 1033-1038 (2012)
  14. Optogenetic reporters: Fluorescent protein-based genetically encoded indicators of signaling and metabolism in the brain. Tantama M, Hung YP, Yellen G. Prog Brain Res 196 235-263 (2012)
  15. Investigation of Pain Mechanisms by Calcium Imaging Approaches. Anderson M, Zheng Q, Dong X. Neurosci Bull 34 194-199 (2018)
  16. Tools for resolving functional activity and connectivity within intact neural circuits. Jennings JH, Stuber GD. Curr Biol 24 R41-R50 (2014)
  17. The biosensor toolbox for plant developmental biology. Uslu VV, Grossmann G. Curr Opin Plant Biol 29 138-147 (2016)
  18. Genetically encoded molecular probes to visualize and perturb signaling dynamics in living biological systems. Sample V, Mehta S, Zhang J. J Cell Sci 127 1151-1160 (2014)
  19. Sensors for the quantification, localization and analysis of the dynamics of plant hormones. Isoda R, Yoshinari A, Ishikawa Y, Sadoine M, Simon R, Frommer WB, Nakamura M. Plant J 105 542-557 (2021)
  20. In vivo biochemistry: quantifying ion and metabolite levels in individual cells or cultures of yeast. Bermejo C, Ewald JC, Lanquar V, Jones AM, Frommer WB. Biochem J 438 1-10 (2011)
  21. Calcium Dynamics Mediated by the Endoplasmic/Sarcoplasmic Reticulum and Related Diseases. Reddish FN, Miller CL, Gorkhali R, Yang JJ. Int J Mol Sci 18 E1024 (2017)
  22. Multiplexed visualization of dynamic signaling networks using genetically encoded fluorescent protein-based biosensors. Depry C, Mehta S, Zhang J. Pflugers Arch 465 373-381 (2013)
  23. Imaging and analysis of genetically encoded calcium indicators linking neural circuits and behaviors. Oh J, Lee C, Kaang BK. Korean J Physiol Pharmacol 23 237-249 (2019)
  24. In Vivo Imaging of Microglial Calcium Signaling in Brain Inflammation and Injury. Tvrdik P, Kalani MYS. Int J Mol Sci 18 E2366 (2017)
  25. Designs, applications, and limitations of genetically encoded fluorescent sensors to explore plant biology. Sadoine M, Ishikawa Y, Kleist TJ, Wudick MM, Nakamura M, Grossmann G, Frommer WB, Ho CH. Plant Physiol 187 485-503 (2021)
  26. Fast kinetics of calcium signaling and sensor design. Tang S, Reddish F, Zhuo Y, Yang JJ. Curr Opin Chem Biol 27 90-97 (2015)
  27. Probing pain pathways with light. Wang F, Bélanger E, Paquet ME, Côté DC, De Koninck Y. Neuroscience 338 248-271 (2016)
  28. Advancements in the Quest to Map, Monitor, and Manipulate Neural Circuitry. Swanson JL, Chin PS, Romero JM, Srivastava S, Ortiz-Guzman J, Hunt PJ, Arenkiel BR. Front Neural Circuits 16 886302 (2022)
  29. How cells process information: quantification of spatiotemporal signaling dynamics. Ganesan A, Zhang J. Protein Sci 21 918-928 (2012)
  30. Dynamic visualization of calcium-dependent signaling in cellular microdomains. Mehta S, Zhang J. Cell Calcium 58 333-341 (2015)
  31. Capturing single L-type Ca(2+) channel function with optics. Nystoriak MA, Nieves-Cintrón M, Navedo MF. Biochim Biophys Acta 1833 1657-1664 (2013)
  32. Calcium imaging for analgesic drug discovery. Iseppon F, Linley JE, Wood JN. Neurobiol Pain 11 100083 (2022)
  33. Mapping brain circuit function in vivo using two-photon fluorescence microscopy. Bovetti S, Moretti C, Fellin T. Microsc Res Tech 77 492-501 (2014)
  34. [Principles and applications of optogenetics in neuroscience]. Dugué GP, Tricoire L. Med Sci (Paris) 31 291-303 (2015)
  35. Genetically encoded fluorescent sensors for imaging neuronal dynamics in vivo. Day-Cooney J, Dalangin R, Zhong H, Mao T. J Neurochem 164 284-308 (2023)
  36. Convergence Circuit Mapping: Genetic Approaches From Structure to Function. Yook JS, Kim J, Kim J. Front Syst Neurosci 15 688673 (2021)
  37. Deep-brain optical recording of neural dynamics during behavior. Zhou ZC, Gordon-Fennell A, Piantadosi SC, Ji N, Smith SL, Bruchas MR, Stuber GD. Neuron 111 3716-3738 (2023)
  38. Monitoring nutrients in plants with genetically encoded sensors: achievements and perspectives. Sadoine M, De Michele R, Župunski M, Grossmann G, Castro-Rodríguez V. Plant Physiol 193 195-216 (2023)
  39. Applications of advances in mRNA-based platforms as therapeutics and diagnostics in reproductive technologies. Bafleh WS, Abdulsamad HMR, Al-Qaraghuli SM, El Khatib RY, Elbahrawi RT, Abdukadir AM, Alsawae SM, Dimassi Z, Hamdan H, Kashir J. Front Cell Dev Biol 11 1198848 (2023)
  40. Fluorescent PSC-Derived Cardiomyocyte Reporter Lines: Generation Approaches and Their Applications in Cardiovascular Medicine. Sontayananon N, Redwood C, Davies B, Gehmlich K. Biology (Basel) 9 E402 (2020)
  41. Rare earth elements in biology: From biochemical curiosity to solutions for extractive industries. Rocha RA, Alexandrov K, Scott C. Microb Biotechnol 17 e14503 (2024)
  42. Epilepsy insights revealed by intravital functional optical imaging. Stern MA, Dingledine R, Gross RE, Berglund K. Front Neurol 15 1465232 (2024)
  43. Optical sensing and control of T cell signaling pathways. Lee HN, Lee SE, Inn KS, Seong J. Front Physiol 14 1321996 (2023)
  44. Perspective of Calcium Imaging Technology Applied to Acupuncture Research. Li S, Liu Y, Zhang N, Li W, Xu WJ, Xu YQ, Chen YY, Cui X, Zhu B, Gao XY. Chin J Integr Med 30 3-9 (2024)

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