Structural insight into enhanced calcium indicator GCaMP3 and GCaMPJ to promote further improvement

doi:10.1007/s13238-013-2103-4

Prot Cell

2013, Vol. 4

Issue (4) : 299-309 https://doi.org/10.1007/s13238-013-2103-4 PMID: 23549615

RESEARCH ARTICLE

Structural insight into enhanced calcium indicator GCaMP3 and GCaMPJ to promote further improvement

Yingxiao Chen, Xianqiang Song, Sheng Ye, Lin Miao, Yun Zhu, Rong-Guang Zhang(

), Guangju Ji(

)

National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China

Download: PDF(961 KB) HTML
Export: BibTeX | EndNote | Reference Manager | ProCite | RefWorks

Abstract

Genetically encoded Ca²⁺ indicators (GECI) are important for the measurement of Ca²⁺in vivo. GCaMP2, a widelyused GECI, has recently been iteratively improved. Among the improved variants, GCaMP3 exhibits significantly better fluorescent intensity. In this study, we developed a new GECI called GCaMPJ and determined the crystal structures of GCaMP3 and GCaMPJ. GCaMPJ has a 1.5- fold increase in fluorescence and 1.3-fold increase in calcium affinity over GCaMP3. Upon Ca²⁺ binding, GCaMP3 exhibits both monomeric and dimeric forms. The structural superposition of these two forms reveals the role of Arg-376 in improving monomer performance. However, GCaMPJ seldom forms dimers under conditions similar to GCaMP3. St ructural and mutagenesis studies on Tyr-380 confirmed its importance in blocking the cpEGFP β-barrel holes. Our study proposes an efficient tool for mapping Ca²⁺ signals in intact organs to facilitate the further improvement of GCaMP sensors.

Keywords genetically encoded calcium indicator mutants crystal structure fluorescentintensity dimerization

Corresponding Author(s): Zhang Rong-Guang,Email:rzhang@sun5.ibp.ac.cn; Ji Guangju,Email:gj28@ibp.ac.cn

Issue Date: 01 April 2013

Cite this article:

Yingxiao Chen,Xianqiang Song,Sheng Ye, et al. Structural insight into enhanced calcium indicator GCaMP3 and GCaMPJ to promote further improvement[J]. Prot Cell, 2013, 4(4): 299-309.

URL:

https://academic.hep.com.cn/pac/EN/10.1007/s13238-013-2103-4
https://academic.hep.com.cn/pac/EN/Y2013/V4/I4/299

1	Adams, P.D., Afonine, P.V., Bunkoczi, G., Chen, V.B., Davis, I.W., Echols, N., Headd, J.J., Hung, L.W., Kapral, G.J., Grosse-Kunstleve, R.W., . (2010). PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr D Biol Crystallogr 66, 213-221 . doi: 10.1107/S0907444909052925
2	Akerboom, J., Rivera, J.D., Guilbe, M.M., Malave, E.C., Hernandez, H.H., Tian, L., Hires, S.A., Marvin, J.S., Looger, L.L., and Schreiter, E.R. (2009). Crystal structures of the GCaMP calcium sensor reveal the mechanism of fluorescence signal change and aid rational design. J Biol Chem 284, 6455-6464 . doi: 10.1074/jbc.M807657200
3	Borghuis, B.G., Tian, L., Xu, Y., Nikonov, S.S., Vardi, N., Zemelman, B.V., and Looger, L.L. (2011). Imaging light responses of targeted neuron populations in the rodent retina. J Neurosci 31, 2855-2867 . doi: 10.1523/JNEUROSCI.6064-10.2011
4	Brejc, K., Sixma, T.K., Kitts, P.A., Kain, S.R., Tsien, R.Y., Ormo, M., and Remington, S.J. (1997). Structural basis for dual excitation and photoisomerization of the Aequorea victoria green fluorescent protein. Proc Natl Acad Sci U S A 94, 2306-2311 . doi: 10.1073/pnas.94.6.2306
5	Chattoraj, M., King, B.A., Bublitz, G.U., and Boxer, S.G. (1996). Ultra fast excited state dynamics in green fluorescent protein: multiple states and proton transfer. Proc Natl Acad Sci U S A 93, 8362-8367 . doi: 10.1073/pnas.93.16.8362
6	Dombeck, D.A., Harvey, C.D., Tian, L., Looger, L.L., and Tank, D.W. (2010). Functional imaging of hippocampal place cells at cellular resolution during virtual navigation. Nat Neurosci 13, 1433-1440 . doi: 10.1038/nn.2648
7	Elsliger, M.A., Wachter, R.M., Hanson, G.T., Kallio, K., and Remington, S.J. (1999). Structural and spectral response of green fluorescent protein variants to changes in pH. Biochemistry 38, 5296-5301 . doi: 10.1021/bi9902182
8	Emsley, P., and Cowtan, K. (2004). Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 60, 2126-2132 . doi: 10.1107/S0907444904019158
9	Hires, S.A., Tian, L., and Looger, L.L. (2008). Reporting neural activity with genetically encoded calcium indicators. Brain Cell Biol 36, 69-86 . doi: 10.1007/s11068-008-9029-4
10	Ji, G., Feldman, M.E., Deng, K.Y., Greene, K.S., Wilson, J., Lee, J.C., Johnston, R.C., Rishniw, M., Tallini, Y., Zhang, J., . (2004). Ca2+-sensing transgenic mice: postsynaptic signaling in smooth muscle. J Biol Chem 279, 21461-21468 . doi: 10.1074/jbc.M401084200
11	Jung, G., Wiehler, J., and Zumbusch, A. (2005). The photophysics of green fluorescent protein: influence of the key amino acids at positions 65, 203, and 222. Biophys J 88,1932-1947 . doi: 10.1529/biophysj.104.044412
12	Kotlikoff, M.I. (2007). Genetically encoded Ca2+ indicators: using genetics and molecular design to understand complex physiology. J Physiol 578, 55-67 . doi: 10.1113/jphysiol.2006.120212
13	Kummer, A.D., Wiehler, J., Rehaber, H., Kompa, C., Steipe, B., and Michel-Beyerle, M.E. (2000). Effects of threonine 203 replacements on excited-state dynamics and fluorescence properties of the green fluorescent protein (GFP). J Physical Chem B 104, 4791-4798 . doi: 10.1021/jp9942522
14	McCoy, A.J., Grosse-Kunstleve, R.W., Adams, P.D., Winn, M.D., Storoni, L.C., and Read, R.J. (2007). Phaser crystallographic software. J Appl Crystallogr 40, 658-674 . doi: 10.1107/S0021889807021206
15	Murshudov, G.N., Vagin, A.A., and Dodson, E.J. (1997). Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr D Biol Crystallogr 53, 240-255 . doi: 10.1107/S0907444996012255
16	Nagai, T., Sawano, A., Park, E.S., and Miyawaki, A. (2001). Circularly permuted green fluorescent proteins engineered to sense Ca2+. Proc Natl Acad Sci U S A 98, 3197-3202 . doi: 10.1073/pnas.051636098
17	Ohkura, M., Matsuzaki, M., Kasai, H., Imoto, K., and Nakai, J. (2005). Genetically encoded bright Ca2+ probe applicable for dynamic Ca2+ imaging of dendritic spines. Anal Chem 77, 5861-5869 . doi: 10.1021/ac0506837
18	Ormo, M., Cubitt, A.B., Kallio, K., Gross, L.A., Tsien, R.Y., and Remington, S.J. (1996). Crystal structure of the Aequorea victoria green fluorescent protein. Science 273, 1392-1395 . doi: 10.1126/science.273.5280.1392
19	Seelig, J.D., Chiappe, M.E., Lott, G.K., Dutta, A., Osborne, J.E., Reiser, M.B., and Jayaraman, V. (2010). Two-photon calcium imaging from head-fixed Drosophila during optomotor walking behavior. Nat Methods 7, 535-540 . doi: 10.1038/nmeth.1468
20	Shiba, Y., Fernandes, S., Zhu, W.Z., Filice, D., Muskheli, V., Kim, J., Palpant, N.J., Gantz, J., Moyes, K.W., Reinecke, H., . (2012). Human ES-cell-derived cardiomyocytes electrically couple and suppress arrhythmias in injured hearts. Nature 489, 322-325 doi: 10.1038/nature11317
21	Stoner-Ma, D., Jaye, A.A., Matousek, P., Towrie, M., Meech, S.R., and Tonge, P.J. (2005). Observation of excited-state proton transfer in green fluorescent protein using ultrafast vibrational spectroscopy. J Am Chem Soc 127, 2864-2865 . doi: 10.1021/ja042466d
22	Tallini, Y.N., Ohkura, M., Choi, B.R., Ji, G., Imoto, K., Doran, R., Lee, J., Plan, P., Wilson, J., Xin, H.B., . (2006). Imaging cellular signals in the heart in vivo: Cardiac expression of the high-signal Ca2+ in- dicator GCaMP2. Proc Natl Acad Sci U S A 103, 4753-4758 . doi: 10.1073/pnas.0509378103
23	Tian, L., Hires, S.A., Mao, T., Huber, D., Chiappe, M.E., Chalasani, S.H., Petreanu, L., Akerboom, J., McKinney, S.A., Schreiter, E.R., . (2009). Imaging neural activity in worms, flies and mice with improved GCaMP calcium indicators. Nat Methods 6, 875-881 . doi: 10.1038/nmeth.1398
24	Tsien, R.Y. (1998). The green fluorescent protein. Annu Rev Biochem 67, 509-544 . doi: 10.1146/annurev.biochem.67.1.509
25	Wang, Q., Shui, B., Kotlikoff, M.I., and Sondermann, H. (2008). Struc tural basis for calcium sensing by GCaMP2. Structure 16, 1817-1827 . doi: 10.1016/j.str.2008.10.008
26	Yang, F., Moss, L.G., and Phillips, G.N., Jr. (1996). The molecular structure of green fluorescent protein. Nat Biotechnol 14, 1246-1251 . doi: 10.1038/nbt1096-1246
27	Zhao, Y., Araki, S., Wu, J., Teramoto, T., Chang, Y.F., Nakano, M., Abdelfattah, A.S., Fujiwara, M., Ishihara, T., Nagai, T., . (2011). An expanded palette of genetically encoded Ca(2)(+) indicators. Science 333, 1888-1891 . doi: 10.1126/science.1208592

[1]	Vsevolod V. Gurevich, Eugenia V. Gurevich, Vladimir N. Uversky. Arrestins: structural disorder creates rich functionality[J]. Protein Cell, 2018, 9(12): 986-1003.
[2]	Yusuke Mimura, Toshihiko Katoh, Radka Saldova, Roisin O’Flaherty, Tomonori Izumi, Yuka Mimura-Kimura, Toshiaki Utsunomiya, Yoichi Mizukami, Kenji Yamamoto, Tsuneo Matsumoto, Pauline M. Rudd. Glycosylation engineering of therapeutic IgG antibodies: challenges for the safety, functionality and efficacy[J]. Protein Cell, 2018, 9(1): 47-62.
[3]	Hongliang Tian,Xiaoyun Ji,Xiaoyun Yang,Zhongxin Zhang,Zuokun Lu,Kailin Yang,Cheng Chen,Qi Zhao,Heng Chi,Zhongyu Mu,Wei Xie,Zefang Wang,Huiqiang Lou,Haitao Yang,Zihe Rao. Structural basis of Zika virus helicase in recognizing its substrates[J]. Protein Cell, 2016, 7(8): 562-570.
[4]	Shishang Dong,Peng Yang,Guobang Li,Baocheng Liu,Wenming Wang,Xiang Liu,Boran Xia,Cheng Yang,Zhiyong Lou,Yu Guo,Zihe Rao. Insight into the Ebola virus nucleocapsid assembly mechanism: crystal structure of Ebola virus nucleoprotein core domain at 1.8 ? resolution[J]. Protein Cell, 2015, 6(5): 351-362.
[5]	Ping Wang,Chang Sun,Tingting Zhu,Yanhui Xu. Structural insight into mechanisms for dynamic regulation of PKM2[J]. Protein Cell, 2015, 6(4): 275-287.
[6]	Ning Hao,Yutao Chen,Ming Xia,Ming Tan,Wu Liu,Xiaotao Guan,Xi Jiang,Xuemei Li,Zihe Rao. Crystal structures of GI.8 Boxer virus P dimers in complex with HBGAs, a novel evolutionary path selected by the Lewis epitope[J]. Protein Cell, 2015, 6(2): 101-116.
[7]	Chenjun Jia,Mei Li,Jianjun Li,Jingjing Zhang,Hongmei Zhang,Peng Cao,Xiaowei Pan,Xuefeng Lu,Wenrui Chang. Structural insights into the catalytic mechanism of aldehyde-deformylating oxygenases[J]. Protein Cell, 2015, 6(1): 55-67.
[8]	Kelei Bi,Yueting Zheng,Feng G"ao,Jianshu Dong,Jiangyun Wang,Yi Wang,Weimin Gong. *Crystal structure of E. coli* arginyl-tRNA synthetase and ligand binding studies revealed key residues in arginine recognition**[J]. Protein Cell, 2014, 5(2): 151-159.
[9]	Fengfeng Niu, Heng Ru, Wei Ding, Songying Ouyang, Zhi-Jie Liu. Structural biology study of human TNF receptor associated factor 4 TRAF domain[J]. Prot Cell, 2013, 4(9): 687-694.
[10]	Jun Li, Yu Dong, Xingru Lü, Lu Wang, Wei Peng, Xuejun C. Zhang, Zihe Rao. Crystal structures and biochemical studies of human lysophosphatidic acid phosphatase type 6[J]. Prot Cell, 2013, 4(7): 548-561.
[11]	Honggang Zhou, Yuna Sun, Ying Wang, Min Liu, Chao Liu, Wenming Wang, Xiang Liu, Le Li, Fei Deng, Hualin Wang, Yu Guo, Zhiyong Lou. The nucleoprotein of severe fever with thrombocytopenia syndrome virus processes a stable hexameric ring to facilitate RNA encapsidation[J]. Prot Cell, 2013, 4(6): 445-455.
[12]	Yu-Chung Chang, Hao Zhang, Mark L. Brennan, Jinhua Wu. Crystal structure of Lamellipodin implicates diverse functions in actin polymerization and Ras signaling[J]. Prot Cell, 2013, 4(3): 211-219.
[13]	Neil Shaw, Songying Ouyang, Zhi-Jie Liu. Binding of bacterial secondary messenger molecule c di-GMP is a STING operation[J]. Prot Cell, 2013, 4(2): 117-129.
[14]	Demeng Sun, Qing Liu, Yao He, Chengliang Wang, Fangming Wu, Changlin Tian, Jianye Zang. The putative propeptide of MycP1 in mycobacterial type VII secretion system does not inhibit protease activity but improves protein stability[J]. Prot Cell, 2013, 4(12): 921-931.
[15]	Gol Nam, Yi Shi, Myongchol Ryu, Qihui Wang, Hao Song, Jun Liu, Jinghua Yan, Jianxun Qi, George F Gao. Crystal structures of the two membrane-proximal Ig-like domains (D3D4) of LILRB1/B2: alternative models for their involvement in peptide-HLA binding[J]. Prot Cell, 2013, 4(10): 761-770.

Viewed

Full text

Abstract

Cited

Shared

Discussed