Abad MF, Di Benedetto G, Magalhaes PJ, Filippin L, Pozzan T (2004) Mitochondrial pH monitored by a new engineered green fluorescent protein mutant. J Biol Chem 279(12): 11521−11529 doi: 10.1074/jbc.M306766200
|
Akerboom J, Chen T-W, Wardill TJ, Tian L, Marvin JS, Mutlu S, Calderón NC, Esposti F, Borghuis BG, Sun XR, Gordus A, Orger MB, Portugues R, Engert F, Macklin JJ, Filosa A, Aggarwal A, Kerr RA, Takagi R, Kracun S, Shigetomi E, Khakh BS, Baier H, Lagnado L, Wang SSH, Bargmann CI, Kimmel BE, Jayaraman V, Svoboda K, Kim DS, Schreiter ER, Looger LL (2012) Optimization of a GCaMP calcium indicator for neural activity imaging. J Neurosci 32(40): 13819−13840 doi: 10.1523/JNEUROSCI.2601-12.2012
|
Akerboom J, Rivera JDV, Guilbe MMR, Malavé ECA, Hernandez HH, Tian L, Hires SA, Marvin JS, Looger LL, Schreiter ER (2009) Crystal structures of the GCaMP calcium sensor reveal the mechanism of fluorescence signal change and aid rational design. J Biol Chem 284(10): 6455−6464 doi: 10.1074/jbc.M807657200
|
Baird GS, Zacharias DA, Tsien RY (1999) Circular permutation and receptor insertion within green fluorescent proteins. Proc Natl Acad Sci USA 96(20): 11241−11246 doi: 10.1073/pnas.96.20.11241
|
Becke AD (1993) Density‐functional thermochemistry. III. The role of exact exchange. J Chem Phys 98(7): 5648−5652
|
Berna-Erro A, Woodard GE, Rosado JA (2012) Orais and STIMs: physiological mechanisms and disease. J Cell Mol Med 16(3): 407−424 doi: 10.1111/j.1582-4934.2011.01395.x
|
Berridge MJ, Bootman MD, Roderick HL (2003) Calcium signalling: dynamics, homeostasis and remodelling. Nat Rev Mol Cell Biol 4(7): 517−529
|
Best RB, Zhu X, Shim J, Lopes PE, Mittal J, Feig M, Mackerell AD, Jr. (2012) Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone phi, psi and side-chain chi(1) and chi(2) dihedral angles. J Chem Theory Comput 8(9): 3257−3273 doi: 10.1021/ct300400x
|
Bollimuntha S, Pani B, Singh BB (2017) Neurological and motor disorders: neuronal store-operated Ca2+ Signaling: an overview and its function. Adv Exp Med Biol 993: 535−556
|
Chen T-W, Wardill TJ, Sun Y, Pulver SR, Renninger SL, Baohan A, Schreiter ER, Kerr RA, Orger MB, Jayaraman V, Looger LL, Svoboda K, Kim DS (2013) Ultrasensitive fluorescent proteins for imaging neuronal activity. Nature 499(7458): 295−300 doi: 10.1038/nature12354
|
Dana H, Sun Y, Mohar B, Hulse BK, Kerlin AM, Hasseman JP, Tsegaye G, Tsang A, Wong A, Patel R, Macklin JJ, Chen Y, Konnerth A, Jayaraman V, Looger LL, Schreiter ER, Svoboda K, Kim DS (2019) High-performance calcium sensors for imaging activity in neuronal populations and microcompartments. Nat Methods 16(7): 649−657 doi: 10.1038/s41592-019-0435-6
|
Darden T, York D, Pedersen L (1993) Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems. J Chem Phys 98(12): 10089−10092 doi: 10.1063/1.464397
|
Deng X, Yao XQ, Berglund K, Dong B, Ouedraogo D, Ghane MA, Zhuo Y, McBean C, Wei ZZ, Gozem S, Yu SP, Wei L, Fang N, Mabb AM, Gadda G, Hamelberg D, Yang JJ (2021) Tuning protein dynamics to sense rapid endoplasmic‐reticulum calcium dynamics. Angew Chem Int Ed Engl 60(43): 23289−23298 doi: 10.1002/anie.202108443
|
Ding J, Luo AF, Hu L, Wang D, Shao F (2014) Structural basis of the ultrasensitive calcium indicator GCaMP6. Sci China Life Sci 57(3): 269−274 doi: 10.1007/s11427-013-4599-5
|
Dupont G, Combettes L, Bird GS, Putney JW (2011) Calcium oscillations. Cold Spring Harb Perspect Biol 3(3): a004226. https://doi.org/10.1101/cshperspect.a004226 doi: 10.1101/cshperspect.a004226
|
Emrich SM, Yoast RE, Xin P, Arige V, Wagner LE, Hempel N, Gill DL, Sneyd J, Yule DI, Trebak M (2021) Omnitemporal choreographies of all five STIM/Orai and IP(3)Rs underlie the complexity of mammalian Ca(2+) signaling. Cell Rep 34(9): 108760. https://doi.org/10.1016/j.celrep.2021.108760 doi: 10.1016/j.celrep.2021.108760
|
Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Scalmani G, Barone V, Petersson GA, Nakatsuji H, Li X, Caricato M, Marenich AV, Bloino J, Janesko BG, Gomperts R, Mennucci B, Hratchian HP, Ortiz JV, Izmaylov AF, Sonnenberg JL, Williams, Ding F, Lipparini F, Egidi F, Goings J, Peng B, Petrone A, Henderson T, Ranasinghe D, Zakrzewski VG, Gao J, Rega N, Zheng G, Liang W, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Vreven T, Throssell K, Montgomery Jr. JA, Peralta JE, Ogliaro F, Bearpark MJ, Heyd JJ, Brothers EN, Kudin KN, Staroverov VN, Keith TA, Kobayashi R, Normand J, Raghavachari K, Rendell AP, Burant JC, Iyengar SS, Tomasi J, Cossi M, Millam JM, Klene M, Adamo C, Cammi R, Ochterski JW, Martin RL, Morokuma K, Farkas O, Foresman JB, & Fox DJ. (2016). Gaussian 16 Rev. A.03. Wallingford, CT.
|
Goddard TD, Huang CC, Meng EC, Pettersen EF, Couch GS, Morris JH, Ferrin TE (2018) UCSF ChimeraX: Meeting modern challenges in visualization and analysis. Protein Sci 27(1): 14−25 doi: 10.1002/pro.3235
|
Goedhart J, von Stetten D, Noirclerc-Savoye M, Lelimousin M, Joosen L, Hink MA, van Weeren L, Gadella TWJ, Royant A (2012) Structure-guided evolution of cyan fluorescent proteins towards a quantum yield of 93%. Nat Commun 3(1): 751. https://doi.org/10.1038/ncomms1738 doi: 10.1038/ncomms1738
|
Gross LA, Baird GS, Hoffman RC, Baldridge KK, Tsien RY (2000) The structure of the chromophore within DsRed, a red fluorescent protein from coral. Proc Natl Acad Sci USA 97(22): 11990−11995 doi: 10.1073/pnas.97.22.11990
|
Gu W, Li J, Ke Y, Zhou Y, Wang Y (2023) Finding NEMO: The quest for next-generation genetically encoded calcium indicators. Clin Transl Med 13(10): e1428−e1428 doi: 10.1002/ctm2.1428
|
Hehre WJ, Stewart RF, Pople JA (1969) Self‐consistent molecular‐orbital methods. I. Use of Gaussian expansions of slater‐type atomic orbitals. J Chem Phys 51(6): 2657−2664
|
Hou Y, Kitaguchi T, Kriszt R, Tseng YH, Raghunath M, Suzuki M (2017) Ca(2+)-associated triphasic pH changes in mitochondria during brown adipocyte activation. Mol Metab 6(8): 797−808 doi: 10.1016/j.molmet.2017.05.013
|
Humphrey W, Dalke A, Schulten K (1996) VMD: visual molecular dynamics. J Mol Graph 14(1): 33−38,27-38 doi: 10.1016/0263-7855(96)00018-5
|
Icha J, Weber M, Waters JC, Norden C (2017) Phototoxicity in live fluorescence microscopy, and how to avoid it. Bioessays 39(8). doi: 10.1002/bies.201700003
|
Inoue M, Takeuchi A, Manita S, Horigane SI, Sakamoto M, Kawakami R, Yamaguchi K, Otomo K, Yokoyama H, Kim R, Yokoyama T, Takemoto-Kimura S, Abe M, Okamura M, Kondo Y, Quirin S, Ramakrishnan C, Imamura T, Sakimura K, Nemoto T, Kano M, Fujii H, Deisseroth K, Kitamura K, Bito H (2019) Rational engineering of XCaMPs, a multicolor GECI suite for in vivo imaging of complex brain circuit dynamics. Cell 177(5): 1346−1360 doi: 10.1016/j.cell.2019.04.007
|
Ishii K, Hirose K, Iino M (2006) Ca2+ shuttling between endoplasmic reticulum and mitochondria underlying Ca2+ oscillations. EMBO Rep 7(4): 390−396 doi: 10.1038/sj.embor.7400620
|
Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML (1983) Comparison of simple potential functions for simulating liquid water. J Chem Phys 79(2): 926−935 doi: 10.1063/1.445869
|
Kostyuk AI, Demidovich AD, Kotova DA, Belousov VV, Bilan DS (2019) Circularly permuted fluorescent protein-based indicators: history, principles, and classification. Int J Mol Sci 20(17): 4200. https://doi.org/10.3390/ijms20174200 doi: 10.3390/ijms20174200
|
Lelimousin M, Noirclerc-Savoye M, Lazareno-Saez C, Paetzold B, Le Vot S, Chazal R, Macheboeuf P, Field MJ, Bourgeois D, Royant A (2009) Intrinsic dynamics in ECFP and cerulean control fluorescence quantum yield. Biochemistry 48(42): 10038−10046 doi: 10.1021/bi901093w
|
Li J, Shang Z, Chen J-H, Gu W, Yao L, Yang X, Sun X, Wang L, Wang T, Liu S, Li J, Hou T, Xing D, Gill DL, Li J, Wang S-Q, Hou L, Zhou Y, Tang A-H, Zhang X, Wang Y (2023) Engineering of NEMO as calcium indicators with large dynamics and high sensitivity. Nat Methods 20(6): 918−924 doi: 10.1038/s41592-023-01852-9
|
Li J, Wang L, Chen Y, Yang Y, Liu J, Liu K, Lee Y-T, He N, Zhou Y, Wang Y (2020) Visible light excited ratiometric-GECIs for long-term in-cellulo monitoring of calcium signals. Cell Calcium 87: 102165. https://doi.org/10.1016/j.ceca.2020.102165 doi: 10.1016/j.ceca.2020.102165
|
Liu A, Huang X, He W, Xue F, Yang Y, Liu J, Chen L, Yuan L, Xu P (2021) pHmScarlet is a pH-sensitive red fluorescent protein to monitor exocytosis docking and fusion steps. Nat Commun 12(1): 1413. https://doi.org/10.1038/s41467-021-21666-7 doi: 10.1038/s41467-021-21666-7
|
Malli R, Graier WF (2017) The role of mitochondria in the activation/maintenance of SOCE: the contribution of mitochondrial Ca(2+) uptake, mitochondrial motility, and location to store-operated Ca(2+) entry. Adv Exp Med Biol 993: 297−319
|
Nasu Y, Shen Y, Kramer L, Campbell RE (2021) Structure- and mechanism-guided design of single fluorescent protein-based biosensors. Nat Chem Biol 17(5): 509−518 doi: 10.1038/s41589-020-00718-x
|
Pan Z, Brotto M, Ma J (2014) Store-operated Ca2+ entry in muscle physiology and diseases. BMB Reports 47(2): 69−79 doi: 10.5483/BMBRep.2014.47.2.015
|
Pendin D, Greotti E, Filadi R, Pozzan T (2015) Spying on organelle Ca(2)(+) in living cells: the mitochondrial point of view. J Endocrinol Invest 38(1): 39−45 doi: 10.1007/s40618-014-0178-2
|
Phillips JC, Hardy DJ, Maia JDC, Stone JE, Ribeiro JV, Bernardi RC, Buch R, Fiorin G, Henin J, Jiang W, McGreevy R, Melo MCR, Radak BK, Skeel RD, Singharoy A, Wang Y, Roux B, Aksimentiev A, Luthey-Schulten Z, Kale LV, Schulten K, Chipot C, Tajkhorshid E (2020) Scalable molecular dynamics on CPU and GPU architectures with NAMD. J Chem Phys 153(4): 044130. https://doi.org/10.1063/5.0014475 doi: 10.1063/5.0014475
|
Pinto MCX, Kihara AH, Goulart VAM, Tonelli FMP, Gomes KN, Ulrich H, Resende RR (2015) Calcium signaling and cell proliferation. Cell Signal 27(11): 2139−2149 doi: 10.1016/j.cellsig.2015.08.006
|
Poburko D, Santo-Domingo J, Demaurex N (2011) Dynamic regulation of the mitochondrial proton gradient during cytosolic calcium elevations. J Biol Chem 286(13): 11672−11684 doi: 10.1074/jbc.M110.159962
|
Prakriya M, Lewis RS (2015) Store-Operated Calcium Channels. Physiol Rev 95(4): 1383−1436 doi: 10.1152/physrev.00020.2014
|
Roopa, Kumar N, Kumar M, Bhalla V (2019) Design and applications of small molecular probes for calcium detection. Chem Asian J 14(24): 4493−4505 doi: 10.1002/asia.201901149
|
Shaw PJ, Qu B, Hoth M, Feske S (2012) Molecular regulation of CRAC channels and their role in lymphocyte function. Cell Mol Life Sci 70(15): 2637−2656
|
Striker G, Subramaniam V, Seidel CAM, Volkmer A (1999) Photochromicity and fluorescence lifetimes of green fluorescent protein. J Phys Chem B 103(40): 8612−8617 doi: 10.1021/jp991425e
|
Subach OM, Sotskov VP, Plusnin VV, Gruzdeva AM, Barykina NV, Ivashkina OI, Anokhin KV, Nikolaeva AY, Korzhenevskiy DA, Vlaskina AV, Lazarenko VA, Boyko KM, Rakitina TV, Varizhuk AM, Pozmogova GE, Podgorny OV, Piatkevich KD, Boyden ES, Subach FV (2020) Novel genetically encoded bright positive calcium indicator NCaMP7 based on the mNeonGreen fluorescent protein. Int J Mol Sci 21(5): 1644. https://doi.org/10.3390/ijms21051644 doi: 10.3390/ijms21051644
|
Suzuki J, Kanemaru K, Iino M (2016) Genetically encoded fluorescent indicators for organellar calcium imaging. Biophys J 111(6): 1119−1131 doi: 10.1016/j.bpj.2016.04.054
|
Suzuki J, Kanemaru K, Ishii K, Ohkura M, Okubo Y, Iino M (2014) Imaging intraorganellar Ca2+ at subcellular resolution using CEPIA. Nat Commun 5: 4153. https://doi.org/10.1038/ncomms5153 doi: 10.1038/ncomms5153
|
Tian L, Hires SA, Mao T, Huber D, Chiappe ME, Chalasani SH, Petreanu L, Akerboom J, McKinney SA, Schreiter ER, Bargmann CI, Jayaraman V, Svoboda K, Looger LL (2009) Imaging neural activity in worms, flies and mice with improved GCaMP calcium indicators. Nat Methods 6(12): 875−881 doi: 10.1038/nmeth.1398
|
Tomasi J, Mennucci B, Cammi R (2005) Quantum mechanical continuum solvation models. Chem Rev 105(8): 2999−3094 doi: 10.1021/cr9904009
|
Tsien R, Pozzan T (1989) Measurement of cytosolic free Ca2+ with quin2. Methods Enzymol 172: 230−262
|
van der Linden FH, Mahlandt EK, Arts JJG, Beumer J, Puschhof J, de Man SMA, Chertkova AO, Ponsioen B, Clevers H, van Buul JD, Postma M, Gadella TWJ, Jr., Goedhart J (2021) A turquoise fluorescence lifetime-based biosensor for quantitative imaging of intracellular calcium. Nat Commun 12(1): 7159. https://doi.org/10.1038/s41467-021-27249-w doi: 10.1038/s41467-021-27249-w
|
Wedel B, Boyles RR, Putney JW, Jr. , Bird GS (2007) Role of the store-operated calcium entry proteins Stim1 and Orai1 in muscarinic cholinergic receptor-stimulated calcium oscillations in human embryonic kidney cells. J Physiol 579(Pt 3): 679-689
|
Xie J, Pan H, Yao J, Zhou Y, Han W (2015) SOCE and cancer: recent progress and new perspectives. Int J Cancer 138(9): 2067−2077
|
Zhao Y, Araki S, Wu J, Teramoto T, Chang YF, Nakano M, Abdelfattah AS, Fujiwara M, Ishihara T, Nagai T, Campbell RE (2011) An expanded palette of genetically encoded Ca(2)(+) indicators. Science 333(6051): 1888−1891 doi: 10.1126/science.1208592
|