1.References
1. Raheem A, Prinsen P, Vuppaladadiyam AK, Zhao M, Luque R. A review on sustainable microalgae based biofuel and bioenergy production: Recent development.J. Clean. Prod. 2018;181:42-59.
2. Chia SR, Ong HC, Chew KW, Show PL, Phang SM, Ling TC, Nagarajan D, Lee DJ, Chang JS. Sustainable approaches for algae utilisation in bioenergy production. Renew. Energy 2018;129:838-852.
3. Godfray HCJ, Beddington JR, Crute IR, Haddad L, Lawrence D, Muir JF, Pretty J, Robinson S, Thomas SM, Toulmi C. Food security: the challenge of feeding 9 billion people. Science 2010; 327:812-818.
4. Goli A, Shamiri A, Talaiekhozani A, Eshtiaghi N, Aghamohammadi N, Aroua, MK. An overview of biological processes and their potential for CO2 capture. J. Environ. Manage. 2016;183:41-58.
5. Sipilä K, Johansson A, Saviharju K. Can fuel-based energy production meet the challenge of fighting global warming - a chance for biomass and cogeneration? Bioresour. Technol. 1993;43:7-12.
6. Yuan JS, Tiller KH, Al-Ahmad H, Stewart NR, Stewart CN. Plants to power: bioenergy to fuel the future. Trend Plant Sci. 2008;13:421-429.
7. Eckert C, Xu W, Xiong W, Lynch S, Ungerer J, Tao L, Gill R, Maness PC, Yu J. Ethylene-forming enzyme and bioethylene production. Biotechnol. Biofuels. 2014;7:33.
8. Nobles DR, Brown RM. Transgenic expression of Gluconacetobacter xylinus strain ATCC 53582 cellulose synthase genes in the cyanobacterium Synechococcus leopoliensis strain UTCC 100. Cellulose 2008;15:691-701.
9. Berridge MJ. Rapid accumulation of inositol trisphosphate reveals that agonists hydrolyse polyphosphoinositides instead of phosphatidylinositol. Biochem. J. 1983; 212:849-858.
10. Berridge MJ. Inositol trisphosphate and diacylglycerol as second messengers. Biochem. J. 1984; 220:345-360.
11. Choi KY, Kim HK, Lee SY, Moon KH, Sim SS, Kim JW, Chung HK, Rhee SG. Molecular cloning and expression of a complementary DNA for inositol 1,4,5- trisphosphate 3-kinase. Science 1990;248:64-66.
12. Dewaste V, Roymans D, Moreau C, Erneux C. Cloning and expression of a full- length cDNA encoding human inositol 1,4,5-trisphosphate 3-kinase B. Biochem. Biophys. Res. Commun. 2002;291:400-405.
13. Nalaskowski MM, Bertsch U, Fanick W, Stockebrand MC Schmale H. Mayr GW. Rat inositol 1,4,5-trisphosphate 3-kinase C is enzymatically specialized for basal cellular inositol trisphosphate phosphorylation and shuttles actively between nucleus and cytoplasm. J. Biol. Chem. 2003;278:19765-19776.
14. Windhorst S, Song K, Gazdar AF. Inositol-1,4,5-trisphosphate 3-kinase-A (ITPKA) is frequently over-expressed and functions as an oncogene in several tumor types. Biochem. Pharmacol. 2017;137:1-9.
15. Irvine RF, McNulty TJ, Schell MJ. Inositol 1,3,4,5-tetrakisphosphate as a second messenger–a special role in neurones? Chem. Phys. Lipids 1999;98:49-57.
16. Schurmans S, Pouillon V, Maréchal Y. Regulation of B cell survival, development and function by inositol 1,4,5-trisphosphate 3-kinase B (Itpkb). Adv. Enzyme Regul. 2011;51:66-73.
17. Loscalzo J, Welch G. Nitric Oxide and Its Role in the Cardiovascular System. Prog. Cardiovasc. Dis. 1995;38 87-104.
18. Lei J, Vodovotz Y, Tzeng E, Billiar TR. Nitric oxide, a protective molecule in the cardiovascular system, Nitric Oxide. 2013;35:175-185.
19. Bradley SA, Steinert JR. Nitric Oxide-Mediated Posttranslational Modifications: Impacts at the Synapse. Oxid. Med. Cell. Longevity. 2016;2016:5681036.
20. Steinert JR, Robinson SW, Tong H, Haustein MD, Kopp-Scheinpflug C, Forsythe LD. Nitic Oxide Is an Activity-Dependent Regulator of Target Neuron Intrinsic Excitability. Neuron. 2011;71:291-305.
21. Hirst DG, Robson T. Nitric oxide physiology and pathology. Methods Mol. Biol. 2011;704:1-13.
22. Xu W, Liu LZ, Loizidou M, Ahmed M, Charles IG. The role of nitric oxide in cancer. Cell Res. 2002;12:311-320.
23. Wendehenne D, Durner J, Klessig DF. Nitric Oxide: a new player in plat signaling and defense responses. Curr. Opin. Plant Biol. 2004;7:449-455.
24. Horenberg AL, Houghton AM, Pandey S, Seshadri V, Guilford WH. S-nitrosylation of cytoskeletal proteins. Cytoskeleton. 2019;76:243-252.
25. Wendehenne D, Pugin A, Klessig D, Durner J. Nitric oxide: comparative synthesis and signaling in animal and plant cells. Trends Plant Sci. 2001;6:177-183.
26. Alderton WK, Cooper CE, Knowles RG. Nitric oxide synthases: structure, function and inhibition. Biochem. J. 2001;357:593-615.
27. Hess DT, Matsumoto A, Kim SO, Marshall HE, Stamler JS. Protein S-nitrosylation: purview and parameters. Nat. Rev. Mol. Cell Biol. 2005;6:150-166.
28. Johnson DC, Dean DR, Smith AD, Johnson MK. STRUCTURE, FUNCTION, AND FORMATION OF BIOLOGICAL IRON-SULFUR CLUSTERS. Annu. Rev. Biochem. 2005;74:247-281.
29. Radi R. Reaction of Nitric Oxide with Metalloproteins. Chem. Res. Toxicol. 1996;9:828-835.
30. Serrano PN, Wang H, Crack JC, Prior C, Hutchings MI, Thomson AJ, Kamali S, Yoda Y, Zhao J, Hu MY, Alp EE, Oganesyan VS, Le Brun NE. Nitrosylation of Nitiric-Oxide-Sensing Regulatory Proteins Containing [4Fe-4S] Clusters Gives Rise to Multiple Iron-Nitrosyl Complexes. Angew. Chem. Int. Ed. 2016;55:14575-14579.
31. Gonzalez-Cobos JC, Trebak M. TRPC channels in smooth muscle cells. Front Biosci., Landmark Ed. 2010;15:1023-1039.
32. Zhang E, Liao P. Brain Transient Receptor Channels and Stroke. J. Neurosci. Res. 2015;93:1165-1183.
33. Gees M, Colsoul B, Nilius B. The Role of Transient Receptor Potential Cation Channels in Ca2+ Signaling. Cold Spring Harbor Perspect. Biol. 2010;2:a003962.
34. Vazquez G, Wedel B. J, Aziz O, Trebak M, Putney JW. The mammalian TRPC cation channels. Biochim. Biophys. Acta. 2004;1742:21-36.
35. Montell C. Drosophia TRP channels. Pflueg. Arch. Eur. J. Physiol. 2005;451:19-28.
36. Duan J, Li J, Chen GL, Ge Y, Liu J, Xie K, Peng X, Zhou W, Zhong J, Zhang Y, Xu J, Xue C, Liang B, Zhu L, Liu W, Zhang C, Tian XL, Wang J, Clapham DE, Zeng B, Li Z, Zhang J. Cryo-EM structure of TRPC5 at 2.8-Å resolution reveals unique and conserved structural elements essential for channel function. Sci. Adv. 2019;5:eaaw7935.
37. Yoshida T, Inoue R, Morii T, Takahashi N, Yamamoto S, Hara Y, Tominaga M, Shimizu S, Sato Y, Mori Y. Nitric oxide activates TRP channels by cysteine S- nitrosylation. Nat. Chem. Biol. 2006;2:596-607.
38. Nakata E, Liew FF, Nakano S, Morii T. Recent progress in the constructin methodology of fluorescent biosensors based on biomolecules. Biosensors-Emerging materials and Applications. Serra, P. A. Ed. pp. 123-140 (2011).
39. Thevenot DR, Toth K, Durst RA, Wilson GS. Electrochemical biosensors: recommended definitions and classification. J. Biosci. Bioeng. 2001;16:121-131.
40. Jelinek R, Kolusheva S. Carbohydrate biosensors. Chem. Rev. 2004;104:5987-6015.
41. Borisov SM, Wolfbeis OS. Optical Biosensors. Chem. Rev. 2008;108:423-461.
42. Wang H, Nakata E, Hamachi I. Recent Progress in Strategies for the Creation of Protein-Based Fluorescent Biosensors. Chembiochem 2009;10:2560-2577.
43. Giepmans BN, Adams SR, Ellisman MH, Tsien RY. The Fluorescent Toolbox for Assessing Protein Location and Function. Science 2006;312:217-224.
44. Johnsson N, Johnsson K. Chemical Tools for Biomolecular Imaging. ACS Chem. Biol. 2007;2:31-38.
45. Rao J, Dragulescu-Andrasi A, Yao H. Fluorescence Imaging in vivo: Recent Advances. Curr. Opin. Biotechnol. 2007;18:17-25.
46. Johnsson K. Visualizing Biochemical Activities in Living Cells. Nat. Chem. Biol. 2009;5:63-65.
47. Wang H, Nakata E, Hamachi I. Recent Progress in Strategies for the Creation of Protein-Based Fluorescent Biosensors. ChemBioChem 2009;10:2560-2577
48. de Silva AP, Gunaratne HQ, Gunnlaugsson T, Huxley AJ, McCoy CP, Rademacher JT, Rice TE. Signaling Recognition Events with Fluorescent Sensors and Switches. Chem. Rev. 1997;97:1515-1566.
49. Johnson I. Fluorescent Probes for Living Cells. Histochem. J. 1998;30:123-140.
50. Terai T, Nagano T. Fluorescent Probes for Bioimaging Applications. Curr. Opin. Chem. Biol. 2008;12:515-521.
51. Domaille DW, Que EL, Chang CJ. Synthetic Fluorescent Sensors for Studying the Cell Biology of Metals. Nat. Chem. Biol. 2008;4:168-175.
52. Cao H, Heagy MD. Fluorescent Chemosensors for Carbohydrates: a Decade's Worth of Bright Spies for Saccharides in Review. J. Fluoresc. 2004;14:569-584.
53. Gomes A, Fernandes E, Lima JL. Use of Fluorescence Probes for Detection of Reactive Nitrogen Species: a Review. J. Fluoresc. 2006;16:119-139.
54. Soh N. Recent Advances in Fluorescent Probes for the Detection of Reactive Oxygen Species. Anal. Bioanal. Chem. 2006;386:532-543.
55. Nolan EM, Lippard SJ. Small-Molecule Fluorescent Sensors for Investigating Zinc Metalloneurochemistry. Acc. Chem. Res. 2009;42:193-203.
56. Liu J, Cao Z, Lu Y. Functional Nucleic Acid Sensors. Chem. Rev. 2009;109:1948- 1998.
57. Tainaka K, Sakaguchi R, Hayashi H, Nakano S, Liew FF, Morii T. Design Strategies of Fluorescent Biosensors Based on Biological macromolecular Receptors. Sensors 2010;10:1355-1376.
58. Marvin JS, Corcoran EE, Hattangadi NA, Zhang JV, Gere SA, Hellinga HW. The Rational Design of Allosteric Interactions in a Monomeric Protein and Its Applications to the Construction of Biosensors. Proc. Natl. Acad. Sci. USA 1997; 94:4366-4371.
59. Marvin JS, Hellinga HW. Engineering Biosensors by Introducing Fluorescent Allosteric Signal Transducers: Construction of a Novel Glucose Sensor. J. Am. Chem. Soc. 1998;120:7-11.
60. de Lorimier RM, Smith JJ, Dwyer MA, Looger LL, Sali KM, Paavola C., Rizk SS, Sadigov S, Conrad DW, Loew L, Hellinga HW. Construction of a Fluorescent Biosensor Family. Protein Sci. 2002;11:2655-2675
61. Morii T, Sugimoto K, Makino K, Otsuka M, Imoto K, Mori Y. A New Fluorescent Biosensor for Inositol Trisphosphate. J. Am. Chem. Soc. 2002;124:1138-1139.
62. Sakaguchi R, Tainaka K, Shimada N, Nakano S, Inoue M, Kiyonaka S, Mori Y, Morii T. An in vivo Fluorescent Sensor Reveals Intracellular Ins(1,3,4,5)P4 Dynamics in Single Cells. Angew. Chem. Int. Ed. 2009;49:2150-2153.
63. Marrero MB, Schieffer B, Paxton WG, Schieffer E, Bernstein KE. Electroporation of pp60c-src Antibodies Inhibits the Angiotensin II Activation of Phospholipase C-1 in Rat Aortic Smooth Muscle Cells. J. Biol. Chem. 1995;270:15734-15738.
64. Fenton M, Bone N, Sinclair AJ. The Efficient and Rapid Import of a Peptide into Primary B and T Lymphocytes and a Lymphoblastoid Cell Line. J. Immunol. Methods 1998;212:41-48.
65. Sakaguchi R, Tainaka K, Shimada N, Nakano S, Inoue M, Kiyonaka S, Mori Y, Morii T. An in Vivo Fluorescent Sensor Reveals Intracellular Ins(1,3,4,5)P4 Dynamics in Single Cells. Angew. Chem., Int. Ed. 2010;49:2150-2153.
66. Zelphati O, Wang Y, Kitada S, Reed JC, Felgner PL, Corbeil J. Intracellular Delivery of Proteins with a New Lipid-Mediated Delivery System. J. Biol. Chem. 2001;276:35103-35110.
67. Zheng X, Lundberg M, Karlsson A, Johansson M. Lipid-Mediated Protein Delivery of Suicide Nucleoside Kinases. Cancer Res. 2003;63:6909-6913.
68. Abarzua P, LoSardo JE, Gubler ML, Neri A. Microinjection of MonoclonalAntibody PAb421 into Human SW480 Colorectal Carcinoma Cells Restores the Transcription Activation Function to Mutant p53. Cancer Res. 1995;55:3490-3494.
69. Wadia JS, Dowdy SF. Transmembrane Delivery of Protein and Peptide Drugs by TAT-Mediated Transduction in the Treatment of Cancer. Adv. Drug. Deliv. Rev. 2005;57:579-596.
70. Sugimoto K, Nishida M, Otsuka M, Makino K, Ohkubo K, Mori Y, Morii T. Novel Real-Time Sensors to Quantitatively Assess in Vivo Inositol 1,4,5-Trisphosphate Production in Intact. Cells. Chem. Biol. 2004;11:475-485.
71. Shimomura O, Johnson FH, Saiga Y. Extraction, Purification and Properties of Aequorin, a Bioluminescent Protein from the Luminous Hydromedusan, Aequorea.J. Cell Comp. Physiol. 1962;59:223-239.
72. Sapsford KE, Berti L, Medintz IL. Materials for Fluorescence Resonance Energy Transfer Analysis: Beyond Traditional Donor-Acceptor Combinations. Angew. Chem. Int. Ed. 2006;45:4562-4589.
73. Piston DW, Kremers GJ. Fluorescent Protein FRET: The Good, the Bad and the Ugly. Trends Biochem. Sci. 2007;32:407-414.
74. Mahajan NP, Harrison-Shostak DC, Michaux J, Herman B. Novel mutant green fluorescent protein protease substrates reveal the activation of specific caspases during apoptosis. Chem. Biol. 1999;6:401-409.
75. Luo KQ, Yu VC, Pu Y, Chang DC. Application of the fluorescence resonance energy transfer method for studying the dynamics of caspase-3 activation during UV- induced apoptosis in living HeLa cells. Biochem. Biophys. Res. Commun. 2001; 283:1054-1060.
76. Rehm M, Dussmann H, Janicke RU, Tavare JM, Kogel D, Prehn JH. Single-cell fluorescence resonance energy transfer analysis demonstrates that caspase activation during apoptosis is a rapid process. Role of caspase-3. J Biol. Chem. 2002; 277:24506-24514.
77. Ai HW, Hazelwood KL, Davidson MW, Campbell RE. Fluorescent protein FRET pairs for ratiometric imaging of dual biosensors. Nat. Methods 2008;5:401-403.
78. Sato M, Ozawa T, Inukai K, Asano T. Umezawa Y. Fluorescent Indicators for Imaging Protein Phosphorylation in Single Living Cells. Nature Biotechnol. 2002;20:287-294.
79. Nagai Y, Miyazaki M, Aoki R, Zama T, Inoue S, Hirose K, Iino M, Hagiwara M. A fluorescent indicator for visualizing cAMP-induced phosphorylation in vivo. Nat. Biotechnol. 2000;18:313-316.
80. Newman RH, Zhang J. Visualization of phosphatase activity in living cells with a FRET-based calcineurin activity sensor. Mol. BioSyst. 2008;4:496-501.
81. Miyawaki A, Llopis J, Heim R, McCaffery JM, Adams JA, Ikura M, Tsien RY. Fluorescent Indicators for Ca2+ Based on Green Fluorescent Proteins and Calmodulin. Nature 1997;388:882-887.
82. Romoser VA, Hinkle PM, Persechini A. Detection in Living Cells of Ca2+- Dependent Changes in the Fluorescence Emission of an Indicator Composed of Two Green Fluorescent Protein Variants Linked by a Calmodulin-Binding Sequence. A New Class of Fluorescent Indicators. J. Biol. Chem. 1997;272:13270-13274.
83. Nikolaev V, Bunemann OM, Hein L, Hannawacker A, Lohse MJ. Novel Single Chain cAMP Sensors for Receptor-induced Signal Propagation. J. Biol. Chem. 2004;279:37215-37218.
84. Sato M, Hida N, Ozawa T, Umezawa Y. Fluorescent Indicators for Cyclic GMP Based on Cyclic GMP-Dependent Protein Kinase I and Green Fluorescent Proteins. Anal. Chem. 2000;72:5918-5924.
85. Sato M, Ueada Y, Shibuya M, Umezawa Y. Locating Inositol 1,4,5-trisphosphate in the Nucleus and Neuronal Dendrites with Genetically Encoded Fluorescent Indicators. Anal. Chem. 2005;77:4751-4758.
86. Ohashi T, Galiacy SD, Briscoe G, Erickson HP. Experimental Study of GFP Based FRET, with Application to Intrinsically Unstructured Proteins. Protein Sci. 2007;16:1429-1438.
87. Crivici A, Ikura M. Molecular and structural basis of target recognition by calmodulin. Annu. Rev. Biophys. Biomol. Struct. 1995;24:85-116.
88. Ikura M, Clore GM, Gronenborn AM, Zhu G, Klee CB, Bax A. Solution structure of a calmodulin-target peptide complex by multidimensional NMR. Science. 1992;256:632-638.
89. Nakai J, Ohkura M, Imoto K. A High Signal-to-Noise Ca2+ Probe Composed of a Single Green Fluorescent Protein. Nat. Biotechnol. 2001;19:137-141.
90. Souslova EA, Belousov VV, Lock JG, Stromblad S, Kasparov S, Bolshakov AP, Pinelis VG, Labas YA, Lukyanov S, Mayr LM, Chudakov DM. Single Fluorescent Protein-Based Ca2+ Sensors with Increased Dynamic Range. BMC Biotechnol. 2007;7:37.
91. Baird GS, Zacharias DA, Tsien RY. Circular Permutation and Receptor Insertion within Green Fluorescent Proteins. Proc. Natl. Acad. Sci. USA 1999;96:11241- 11246.
92. Nagai T, Sawano A, Park ES, Miyawaki A. Circularly Permuted Green Fluorescent Proteins Engineered to Sense Ca2+. Proc Natl. Acad. Sci. USA 2001;98:3197-3202.
93. Nausch LW, Ledoux J, Bonev AD, Nelson MT, Dostmann WR. Differential Patterning of cGMP in Vascular Smooth Muscle Cells Revealed by Single GFP- Linked Biosensors. Proc. Natl. Acad. Sci. USA 2008;105:365-370.
94. Belousov VV, Fradkov AF, Lukyanov KA, Staroverov DB, Shakhbazov KS, Terskikh AV, Lukyanov S. Genetically Encoded Fluorescent Indicator for Intracellular Hydrogen Peroxide. Nat. Methods 2006;3:281-286.
95. Dooley CT, Dore TM, Hanson GT, Jackson WC, Remington SJ, Tsien RY. Imaging Dynamic Redox Changes in Mammalian Cells with Green Fluorescent Protein Indicators. J. Biol. Chem. 2004;279:22284-22293.
96. Mizuno T, Murao K, Tanabe Y, Oda M, Tanaka T. Metal-Ion-Dependent GFP Emission in vivo by Combining a Circularly Permutated Green Fluorescent Protein with an Engineered Metal-Ion-Binding Coiled-Coil. J. Am. Chem. Soc. 2007;129:11378-11383.
97. Sakaguchi R, Endoh T, Yamamoto S, Tainaka K, Sugimoto K, Fujieda N, Kiyonaka S, Mori Y, Morii T. A Single Circularly Permuted GFP Sensor for Inositol-1,3,4,5- Tetrakisphosphate Based on a Split PH Domain. Bioorg. Med. Chem. 2009;17:7381- 7386.
98. Akerboom J, Rivera JDV, Guilbe MMR, Malavé ECA, Hernandez HH, Tian L, Hires SA, Marvin JS, Looger LL, Schreiter E.R. Crystal Structures of the GCaMPCalcium Sensor Reveal the Mechanism of Fluorescence Signal Change and Aid Rational Design. J. Biol. Chem. 2009;284:6455-6464.
99. Berg J, Hung YP, Yellen G. A genetically encoded fluorescent reporter of ATP:ADP ratio. Nat. Methods. 2009;6:161-166.
100. Kitaguchi T, Oya M, Wada Y, Tsuboi T, Miyawaki A. Extracellular calcium influx activates adenylate cyclase 1 and potentiates insulin secretion in MIN6 cells. Biochem. J. 2013;450:365-373.
101. Qin Y, Sammond DW, Braselmann E, Carpenter MC, Palmer AM. Development of an Optical Zn2+ Probe Based on a Single Fluorescent protein. ACS Chem. Biol. 2016;11:2744-275.
102. Matsuda S, Harada K, Ito M, Takizawa M, Wongso D, Tsuboi T, Kitaguchi T. Generation of cGMP indicator with an Expanded Dynamic Range by Optimization of Amino Acid Linkers between a Fluorescent Protein and PDE5. ACS Sens. 2017;2:46-51.
2.References
1. Yoshida T, Inoue R, Morii T, Takahashi N, Yamamoto S, Hara Y, Tominaga M, Shimizu S, Sato Y, Mori Y. Nitric oxide activates TRP channels by cysteine S- nitrosylation. Nat. Chem. Biol. 2006;2:596-607.
2. Sakaguchi R, Mori Y. Transient receptor potential (TRP) channels: Biosensors for redox environmental stimuli and cellular status. Free Radical Biol. Med. 2020;146:36-44.
3. Gees M, Colsoul B, Nilius B. The Role of Transient Receptor Potential Cation Channels in Ca2+ Signaling. Cold Spring Harbor Perspect. Biol. 2010;2:a003962.
4. Hess DT, Matsumoto A, Kim SO, Marshall HE, Stamler JS. Protein S-nitrosylation: purview and parameters. Nat. Rev. Mol. Cell Biol. 2005;6:150-166.
5. Duan J, Li J, Chen GL, Ge Y, Liu J, Xie K, Peng X,Zhou W, Zhong J, Zhang Y, Xu J, Xue C, Liang B, Zhu L, Liu W, Zhang C, Tian XL, Wang J, Clapham DE, Zeng B, Li Z, Zhang J. Cryo-EM structure of TRPC5 at 2.8-Å resolution reveals unique and conserved structural elements essential for channel function. Sci. Adv. 2019;5:eaaw7935.
6. Tallini YN, Ohkura M, Choi BR, Ji G, Imoto K, Doran R, Lee J, Plan P, Wilson J, Xin HB, Sanbe A, Gulick J, Mathai J, Robbins J, Salama G, Nakai J, Kotlikoff MI. Imaging cellular signals in the heart in vivo: Cardiac expression of the high-signal Ca2+ indicator GCaMP2. Proc. Natl. Acad. Sci. U. S. A. 2006;103:4753-4758.
7. Zhang J, Campbell, Ting AY, Tsien RY. Creating new fluorescent probes for cell biology. Nat. Rev. Mol. Cell Biol. 2002;3:906-918.
8. Berg J, Hung YP, Yellen G. A genetically encoded fluorescent reporter of ATP:ADP ratio. Nat. aMethods. 2009;6:161-166.
9. Nakai J, Ohkura M, Imoto K. A high signal-to-noise Ca2+ probe composed of a single green fluorescent protein. Nat. Biotechnol. 2001;19:137-141.
10. Morise H, Shimomura O, Johnson FH, Winant J. Intermolecular Energy Transfer in the Bioluminescent System of Aequorea. Biochemistry. 1974;13:2656-2662.
11. Bejec K, Sixma TK, Kitts PA, Kain SR, Tsien RY, Ormö M, Remington SJ. Structural basis for dual excitation and photoisomerization of the Aequorea victoria green fluorescent protein. Proc. Natl. Acad. Sci. U. S. A. 1997;94:2306-2311.
12. Cormack BP, Valdivia RH, Falkow S. FACS-optimized mutants of the green fluorescent protein (GFP). Gene. 1996;173:33-38.
13. Ormo M, Cubitt AB, Kallio K, Gross LA, Tsien RY, Remington SJ, Crystal Structure of the Aquorea victoria Green Fluorsescent Protein. Science. 1996;273:1392-1395.
14. Wong PSY, Hyun J, Fukuto JM, Shirota FN, DeMaster EG, Shoeman DW, Nagasawa HT. Reaction between S-Nitrosothiols and Thiols: Generation of Nitroxyl (HNO) and Subsequent Chemistry. Biochemistry. 1998;37:5362-5371.
15. Percival MD, Ouellet M, Campagnolo C, Claveau D, Li C. Inhibition of Cathepsin K by Nitric Oxide Donors: Evidence for the Formation of Mixed Disulfides and a Sulfenic Acid. Biochemistry. 1999;38:13574-13583.
16. Pédelacq JD, Cabantous S, Tran T, Terwilliger TC, Waldo GS. Engineering and characterization of a superflolder green fluorescent protein. Nat. Biotechnol. 2006;24:79-88.
17. Jain RK, Joyce PB, Moliente M., Halban PA, Gorr SU. Oligomerization of green fluorescent protein in the secretory pathway of endocrine cells. Biochem. J. 2001;360:645-649.
18. Suzuki T, Arai S, Takeuchi M, Sakurai C, Ebana H, Higashi T, Hashimoto H, Hatsuzawa K, Wada I. Development of Cystein-Free Fluorescent Proteins for Oxidative Environment. PLoS ONE. 2012;7:e37551.
19. Costantini LM, Baloban M, Markwardt ML, Rizzo M, Guo F, Verkhusha VV, Snapp EL. A palette of fluorescent proteins optimized for diverse cellular environments. Nat. Commun. 2015;7670:6.
20. Hrabie JA, Klose JR, Wink DA, Keefer LK. New nitric oxide-releasing zwitterions derived from polyamines. J. Org. Chem. 1993;58:1472-1476.
21. Jaffrey SR, Erdjument-Bromage H, Ferris CD, Tempst P, Snyder SH. Protein S- nitrosylation: a physiological signal for neuronal nitric oxide. Nat. Cell Biol. 2001;3:193-197.
22. Ignarro LJ, Lippton H, Edwards JC, Baricos WH, Hyman AL, Kadowitz PJ, Gruetter CA. Mechanism of Vascular Smooth Muscle Relaxation by Organic Nitrates, Nitrites, Nitroprusside and Nitiric Oxide: Evidence for the Involvement of S-Nitrosothiols as Active Intermediates. J. Pharmacol. Exp. Ther. 1981;218:739-749.
3.References
1. Palmer AE, Qin Y, Park JG, McCombs JE. Design and application of genetically encoded biosensors. Trends Biotechnol. 2011;29:144-152.
2. Wenfeng L, Deng M, Yang C, Liu F, Guan X, Du Y, Wang L, Chu J. Genetically encoded single circularly permuted fluorescent protein-based intensity sensors. J. Phys. D: Appl. Phys. 2020;53:113001
3. Tallini YN, Ohkura M, Choi BR, Ji G, Imoto K, Doran R, Lee J, Plan P, Wilson J, Xin HB, Sanbe A, Gulick J, Mathai J, Robbins J, Salama G, Nakai J, Kotlikoff MI. Imaging cellular signals in the heart in vivo: Cardiac expression of the high-signal Ca2+ indicator GCaMP2. Proc. Natl. Acad. Sci. U. S. A. 2006;103:4753-4758.
4. Zhang J, Campbell RE, Ting AY, Tsien RY. Creating new fluorescent probes for cell biology. Nat. Rev. Mol. Cell Biol. 2002;3:906-918.
5. Berg J, Hung YP, Yellen G. A genetically encoded fluorescent reporter of ATP:ADP ratio. Nat. Methods. 2009;6:161-166.
6. Nakai J, Ohkura M, Imoto K. A high signal-to-noise Ca2+ probe composed of a single green fluorescent protein. Nat. Biotechnol. 2001;19:137-141.
7. Nagai T, Sawano A, Park ES, Miyawaki A. Circulary permutated green fluorescent proteins engineered to sense Ca2+. Proc. Natl. Acad. Sci. U. S. A. 2001;98:3197-3202.
8. Kitaguchi T, Oya M, Wada Y, Tsuboi T, Miyawaki A. Extracellular calcium influx activates adenylate cyclase 1 and potentiates insulin secretion in MIN6 cells. Biochem. J. 2013;450:365-373.
9. Qin Y, Sammond DW, Braselmann E, Carpenter MC, Palmer AM. Development of an Optical Zn2+ Probe Based on a Single Fluorescent protein. ACS Chem. Biol. 2016;11:2744-2751.
10. Matsuda S, Harada K, Ito M, Takizawa M, Wongso D, Tsuboi T, Kitaguchi T. Generation of cGMP indicator with an Expanded Dynamic Range by Optimization of Amino Acid Linkers between a Fluorescent Protein and PDE5. ACS Sens. 2017;2:46-51.
11. Tainaka K, Sakaguchi R, Hayashi H, Nakano S, Liew FF, Morii T. Design strategies of fluorescent biosensors based on biological macromolecular receptors. Sensors 2010;10:1355-1376.
12. Nakata E, Liew FF, Nakano S, Morii T. Recent Progress in the construction methodology of fluorescent biosensors based on biomolecules. Biosensors-Emerging materials and Applications. Serra, P. A. Ed. pp. 123-140 (2011)
13. Marvin JS, Borghuis BG, Tian L, Cichon J, Harnett MT, Akerboom J, Gordus A, Renninger SL, Chen TW, Bargmann CI, Orger MB, Schreiter ER, Demb JB, Gan WB, Hires SA, Looger LL. An optimized fluorescent probe for visualizing glutamate neurotransmission. Nat. Methods 2013;10:162-170.
14. Patriarchi T, Cho JR, Merten K, Howe MW, Marley A, Xiong WH, Folk RW, Broussard GJ, Liang R, Jang MJ, Zhong H, Dombeck D, von Zastrow M, Nimmerjahn A, Gradinaru V, Williams JT, Tian L. Ultrafast neuronal imaging of dopamine dynamics with designed genetically encoded sensors. Science 2018;360:eaat4422.
15. Jing M, Zhang P, Wang G, Feng J, Mesik L, Zeng J, Jiang H, Wang S, Looby JC, Guagliardo NA, Langma LW, Lu J, Zuo Y, Talmage DA, Role LW, Barrett PQ, Zhang LI, Luo M, Song Y, Zhu JJ, Li Y. A genetically encoded fluorescent acetylcholine indicator for in vitro and in vivo studies. Nat. Biotechnol. 2018;36:726- 737.
16. Marvin JS, Shimoda Y, Magloire V, Leite M, Kawashima T, Jensen TP, Kolb I, Knott EL, Novak O, Podgorski K, Leidenheimer NJ, Rusakov DA, Ahrens MB, Kullman DM, Looger L. L. A genetically encoded fluorescent sensor for in vivo imaging of GABA. Nat. Methods 2019;16:763-770.
17. Yoshida T, Inoue R, Morii T, Takahashi N, Yamamoto S, Hara Y, Tominaga M, Shimizu S, Sato Y, Mori Y. Nitric oxide activates TRP channels by cysteine S- nitrosylation. Nat. Chem. Biol. 2006;2:596-607.
18. Tajima S, Nakata E, Sakaguchi R, Saimura M, Mori Y, Morii T. Fluorescence detection of the nitric oxide-induced structural change at the putative nitric oxide sensing segment of TRPC5. Bioorg. Med. Chem. 2020;28:115430.
19. Pédelacq JD, Cabantous S, Tran T, Terwilliger TC, Waldo GS. Engineering and characterization of a superflolder green fluorescent protein. Nat. Biotechnol. 2006;24:79-88.
20. Elsliger MA, Wachter RM, Hanson GT, Kallio K, Remington J. Structural and Spectral Response of Green Fluorescent Protein Variants to Changes in pH. Biochemistry 1999;38:5296-5301.
4.References
1. Loscalzo J, Welch G. Nitric Oxide and Its Role in the Cardiovascular System. Prog. Cardiovasc. Dis. 1995;38:87-104.
2. Lei J, Vodovotz Y, Tzeng E, Billiar TR. Nitric oxide, a protective molecule in the cardiovascular system, Nitric Oxide. 2013;35:175-185.
3. Bradley SA, Steinert JR. Nitric Oxide-Mediated Posttranslational Modifications: Impacts at the Synapse. Oxid. Med. Cell. Longevity. 2016;2016:5681036.
4. Steinert JR, Robinson SW, Tong H, Haustein MD, Kopp-Scheinpflug C, Forsythe LD. Nitic Oxide Is an Activity-Dependent Regulator of Target Neuron Intrinsic Excitability. Neuron. 2011;71:291-305.
5. Hirst DG, Robson T. Nitric oxide physiology and pathology. Methods Mol. Biol. 2011;704:1-13.
6. Xu W, Liu LZ, Loizidou M, Ahmed M, Charles IG. The role of nitric oxide in cancer. Cell Res. 2002;12:311-320.
7. Wendehenne D, Durner J, Klessig DF. Nitric Oxide: a new player in plat signaling and defense responses. Curr. Opin. Plant Biol. 2004;7:449-455.
8. Horenberg AL, Houghton AM, Pandey S, Seshadri V, Guilford WH. S-nitrosylation of cytoskeletal proteins. Cytoskeleton. 2019;76:243-252.
9. Hess DT, Matsumoto A, Kim SO, Marshall HE, Stamler JS. Protein S-nitrosylation: purview and parameters. Nat. Rev. Mol. Cell Biol. 2005;6:150-166.
10. Johnson DC, Dean DR, Smith AD, Johnson MK. STRUCTURE, FUNCTION, AND FORMATION OF BIOLOGICAL IRON-SULFUR CLUSTERS. Annu. Rev. Biochem. 2005;74:247-281.
11. Radi R. Reaction of Nitric Oxide with Metalloproteins. Chem. Res. Toxicol. 1996;9:828-835.
12. Serrano PN, Wang H, Crack JC, Prior C, Hutchings MI, Thomson AJ, Kamali S, Yoda Y, Zhao J, Hu MY, Alp EE, Oganesyan VS, Le Brun NE. Nitrosylation of Nitiric-Oxide-Sensing Regulatory Proteins Containing [4Fe-4S] Clusters Gives Rise to Multiple Iron-Nitrosyl Complexes. Angew. Chem. Int. Ed. 2016;55:14575- 14579.
13. Tallini YN, Ohkura M, Choi BR, Ji G, Imoto K, Doran R, Lee J, Plan P, Wilson J, Xin HB, Sanbe A, Gulick J, Mathai J, Robbins J, Salama G, Nakai J, Kotlikoff MI. Imaging cellular signals in the heart in vivo: Cardiac expression of the high-signal Ca2+ indicator GCaMP2. Proc. Natl. Acad. Sci. U. S. A. 2006;103:4753-4758.
14. Zhang J, Campbell RE, Ting AY, Tsien RY. Creating new fluorescent probes for cell biology. Nat. Rev. Mol. Cell Biol. 2002;3:906-918.
15. Berg J, Hung YP, Yellen G. A genetically encoded fluorescent reporter of ATP:ADP ratio. Nat. Methods. 2009;6:161-166.
16. Eroglu E, Gottschalk B, Charoensin S, Blass S, Bischof H, Rost R, Madreiter- Sokolowski CT, Pelzmann B, Bernhart E, Sattler W, Hallström S, Malinski T, Waldeck-Weiermair M, Graier WF, Malli R. Development of novel FP-based probes for live-cell imaging of nitric oxide dynamics. Nat. Commun. 2016;7:10623.
17. Tajima S, Nakata E, Sakaguchi R, Saimura M, Mori Y, Morii T. Fluorescence detection of the nitric oxide-induced structural change at the putative nitric oxide sensing segment of TRPC5. Bioorg. Med. Chem. 2020;28:115430.
18. Hrabie JA, Klose JR, Wink DA, Keefer LK. New nitric oxide-releasing zwitterions derived from polyamines. J. Org. Chem. 1993;58:1472-1476.
19. Hess DT, Matsumoto A, Kim SO, Marshall HE, Stamler JS. Protein S-nitrosylation: purview and parameters. Nat. Rev. Mol. Cell Biol. 2005;6:150-166.
20. Yoshida T, Inoue R, Morii T, Takahashi N, Yamamoto S, Hara Y, Tominaga M, Shimizu S, Sato Y, Mori Y. Nitric oxide activates TRP channels by cysteine S- nitrosylation. Nat. Chem. Biol. 2006;2:596-607.
21. Duan J, Li J, Chen GL, Ge Y, Liu J, Xie K, Peng X, Zhou W, Zhong J, Zhang Y, Xu J, Xue C, Liang B, Zhu L, Liu W, Zhang C, Tian XL, Wang J, Clapham DE, Zeng B, Li Z, Zhang J. Cryo-EM structure of TRPC5 at 2.8-Å resolution reveals unique and conserved structural elements essential for channel function. Sci. Adv. 2019;5:eaaw7935.
5.References
1. Jaffrey SR, Erdjument-Bromage H, Ferris CD, Tempst P, Snyder SH. Protein S- nitrosylation: a physiological signal for neuronal nitric oxide. Nature Cell Biol. 2001;3:193-197.
2. Leonard SE, Reddle KG, Carroll KS. Mining the thiol proteome for sulfenic acid modifications reveals new targets for oxidation in cells. ACS Chem. Biol. 2009;4:783-799.
3. Hunter T. Signaling-2000 and Beyond. Cell. 2000;100:113-127.
4. Wilson GS, Gifford R. Biosensors for real-time in vivo measurement. Biosens. Bioelectron. 2005;20:23882403.
5. Liu W, Deng M, Yang C, Liu F, Guan X, Du Y, Wang L, Chu J. Genetically encoded single circularly permuted fluorescent protein-based intensity indicators. J. Phys. D: Appl. Phys. 2020;53:113001.
6. Stephens DJ, Allan VJ. Light Microscopy Techniques for Live Cell Imaging. Science. 2003;300:82-86.
7. Giepmans BN, Adams SR, Ellisman MH, Tsien RY. The Fluorescent Toolbox for Assessing Protein Location and Function. Science 2006;312:217-224.
8. Johnsson N, Johnsson K. Chemical Tools for Biomolecular Imaging. ACS Chem. Biol. 2007;2:31-38.
9. Rao J, Dragulescu-Andrasi A, Yao H. Fluorescence Imaging in vivo: Recent Advances. Curr. Opin. Biotechnol. 2007;18:17-25.
10. Johnsson K. Visualizing Biochemical Activities in Living Cells. Nat. Chem. Biol. 2009;5:63-65.
11. Wang H, Nakata E, Hamachi I. Recent Progress in Strategies for the Creation of Protein-Based Fluorescent Biosensors. ChemBioChem 2009;10:2560-2577.
12. Nakata E, Liew FF, Nakano S, Morii T. Recent progress in the constructin methodology of fluorescent biosensors based on biomolecules. Biosensors-Emerging materials and Applications. Serra, P. A. Ed. pp. 123-140 (2011).
13. Rodriguez EA, Campbell RE, Lin JY, Michael Z, Lin MZ, Miyawaki A, Amy E, Palmer AE, Shu X, Zhang J, Tsien RY. The Growing and Glowing Toolbox of Fluorescent and Photoactive Proteins. Trends Biochem. Sci. 2017;42:111-129.
14. Heim R, Tsien RY. Engineering green fluorescent protein for improved brightness, longer wavelengths and fluorescence resonance energy transfer. Curr. Biol. 1996;6:178-182.
15. Campbell RE, Tour O, Palmer AE, Steinbach PA, Baird GS, Zacharias DA, Tsien RY. A monomeric red fluorescent protein. Proc. Natl. Acad. Sci. U.S.A. 2002;99: 7877-7882.
16. Shaner NC, Campbell RE, Steinbach PA, Giepmans BNG, Palmer AE, Tsien RY. Improved monomeric red, orange and yellow fluorescent proteins derived from Discosoma sp. red fluorescent protein. Nat. Biotechnol. 2004;22:1567-1572.
17. Yoshida T, Inoue R, Morii T, Takahashi N, Yamamoto S, Hara Y, Tominaga M, Shimizu S, Sato Y, Mori Y. Nitric oxide activates TRP channels by cysteine S- nitrosylation. Nat. Chem. Biol. 2006;2:596-607.
18. Tajima S, Nakata E, Sakaguchi R, Saimura M, Mori Y, Morii T. Fluorescence detection of the nitric oxide-induced structural change at the putative nitric oxide sensing segment of TRPC5. Bioorg. Med. Chem. 2020;28:115430.
19. Schaefer PM, Kalinina S, Rueck A, von Arnim CAF, von Einem B. NADH Autofluorescence—A Marker on its Way to Boost Bioenergetic Research. Cytometry A. 2019;95:34-46.
20. Wagnieres GA, Star WM, Wilson BC. ln Vivo Fluorescence Spectroscopy and Imaging for Oncological Applications Photochem Photobiol. 1998;68:603-632.