Circularly permuted monomeric red fluorescent proteins with new termini in the β-sheet

Protein Science

Volumn 19, Issue 8, 2010, Pages 1490-1499

  Carlson, Haley J ^a   Cotton, Darrel W ^a   Campbell, Robert E ^a  

^a UNIVERSITY OF ALBERTA   (Canada)

Author keywords

Biosensing; Circular permutation; Directed evolution; Fluorescence imaging; mCherry; Protein engineering; Red fluorescent protein

Indexed keywords

RED FLUORESCENT PROTEIN;

AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; ARTICLE; BETA SHEET; BIOSENSOR; BRIGHTNESS; CARBOXY TERMINAL SEQUENCE; FLUORESCENCE; FLUORESCENCE RESONANCE ENERGY TRANSFER; PRIORITY JOURNAL; PROTEIN ENGINEERING;

AMINO ACID SEQUENCE; BIOSENSING TECHNIQUES; CALCIUM; DIRECTED MOLECULAR EVOLUTION; FLUORESCENT DYES; LUMINESCENT PROTEINS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN FOLDING; PROTEIN ISOFORMS; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; SEQUENCE ALIGNMENT;

EID: 77955100340     PISSN: 09618368     EISSN: 1469896X     Source Type: Journal    
DOI: 10.1002/pro.428     Document Type: Article

References (35)

1. Campbell RE (2008) Fluorescent proteins. Scholarpedia J 3:5410.
2. Yang F, Moss LG, Phillips GNJ (1996) The molecular structure of green fluorescent protein. Nat Biotechnol 14:1246-1251. (Pubitemid 26332784)
3. VanEngelenburg SB, Palmer AE (2008) Fluorescent biosensors of protein function. Curr Opin Chem Biol 12:60-65.
4. Campbell RE (2009) Fluorescent-protein-based biosensors: modulation of energy transfer as a design principle. Anal Chem 81:5972-5979.
5. Zhang J, Campbell RE, Ting AY, Tsien RY (2002) Creating new fluorescent probes for cell biology. Nat Rev Mol Cell Biol 3:906-918. (Pubitemid 35477369)
6. Johnson DE, Ai HW, Wong P, Young JD, Campbell RE, Casey JR (2009) Red fluorescent protein pH biosensor to detect concentrative nucleoside transport. J Biol Chem 284:20499-20511.
7. Jayaraman S, Haggie P, Wachter RM, Remington SJ, Verkman AS (2000) Mechanism and cellular applications of a green fluorescent protein-based halide sensor. J Biol Chem 275:6047-6050. (Pubitemid 30129883)
8. Baird GS, Zacharias DA, Tsien RY (1999) Circular permutation and receptor insertion within green fluorescent proteins. Proc Natl Acad Sci USA 96:11241-11246.
9. 2+ concentrations. Biochemistry 46:12275-12288.
10. Chen N, Zou J, Wang S, Ye Y, Huang Y, Gadda G, Yang JJ (2009) Designing protease sensors for real-time imaging of trypsin activation in pancreatic cancer cells. Biochemistry 48:3519-3526.
11. Topell S, Hennecke J, Glockshuber R (1999) Circularly permuted variants of the green fluorescent protein. FEBS Lett 457:283-289. (Pubitemid 29401943)
12. 2+. Proc Natl Acad Sci USA 98:3197-3202.
13. Nakai J, Ohkura M, Imoto K (2001) A high signal-to-noise Ca(2+) probe composed of a single green fluorescent protein. Nat Biotechnol 19:137-141. (Pubitemid 32144441)
14. Souslova EA, Belousov VV, Lock JG, Strömblad S, Kasparov S, Bolshakov AP, Pinelis VG, Labas YA, Lukyanov S, Mayr LM, Chudakov DM (2007) Single fluorescent protein-based Ca2+ sensors with increased dynamic range. BMC Biotechnol 7:37.
15. Wang Q, Shui B, Kotlikoff MI, Sondermann H (2008) Structural basis for calcium sensing by GCaMP2. Structure 16:1817-1827.
16. Akerboom J, Rivera JD, Guilbe MM, Malavé EC, 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 284:6455-6464.
17. Shcherbo D, Merzlyak EM, Chepurnykh TV, Fradkov AF, Ermakova GV, Solovieva EA, Lukyanov KA, Bogdanova EA, Zaraisky AG, Lukyanov S, Chudakov DM. (2007) Bright far-red fluorescent protein for whole-body imaging. Nat Methods 4:741-746.
18. Gautam SG, Perron A, Mutoh H, Knöpfel T (2009) Exploration of fluorescent protein voltage probes based on circularly permuted fluorescent proteins. Front Neuroengineering 2:14.
19. Carlson HJ, Campbell RE (2009) Genetically encoded FRET-based biosensors for multiparameter fluorescence imaging. Curr Opin Biotechnol 20:19-27.
20. Ai H, Hazelwood KL, Davidson MW, Campbell RE (2008) Fluorescent protein FRET pairs for ratiometric imaging of dual biosensors. Nat Methods 5:401-403. (Pubitemid 351619097)
21. Li Y, Sierra AM, Ai HW, Campbell RE (2008) Identification of sites within a monomeric red fluorescent protein that tolerate peptide insertion and testing of corresponding circular permutations. Photochem Photobiol 84:111-119. (Pubitemid 350265082)
22. Matz MV, Fradkov AF, Labas YA, Savitsky AP, Zaraisky AG, Markelov ML, Lukyanov SA (1999) Fluorescent proteins from nonbioluminescent Anthozoa species. Nat Biotechnol 17:969-973.
23. Shaner NC, Campbell RE, Steinbach PA, Giepmans BN, Palmer AE, Tsien RY (2004) Improved monomeric red, orange and yellow fluorescent proteins derived from Discosoma sp. red fluorescent protein. Nat Biotechnol 22:1567-1572.
24. Shu X, Shaner NC, Yarbrough CA, Tsien RY, Remington SJ (2006) Novel chromophores and buried charges control color in mFruits. Biochemistry 45:9639-9647. (Pubitemid 44257411)
25. Akemann W, Raj CD, Knopfel T (2001) Functional characterization of permuted enhanced green fluorescent proteins comprising varying linker peptides. Photochem Photobiol 74:356-363.
26. Cormack BP, Valdivia RH, Falkow S (1996) FACS-optimized mutants of the green fluorescent protein (GFP). Gene 173:33-38. (Pubitemid 26239677)
27. Kiss C, Temirov J, Chasteen L, Waldo GS, Bradbury AR (2009) Directed evolution of an extremely stable fluorescent protein. Protein Eng Des Sel 22:313-323.
28. Zapata-Hommer O, Griesbeck O (2003) Efficiently folding and circularly permuted variants of the Sapphire mutant of GFP. BMC Biotechnol 3:5.
29. Pedelacq JD, Cabantous S, Tran T, Terwilliger TC, Waldo GS (2006) Engineering and characterization of a superfolder green fluorescent protein. Nat Biotechnol 24:79-88.
30. Nagai T, Yamada S, Tominaga T, Ichikawa M, Miyawaki A (2004) Expanded dynamic range of fluorescent indicators for Ca(2+) by circularly permuted yellow fluorescent proteins. Proc Natl Acad Sci USA 101:10554-10559.
31. Griesbeck O, Baird GS, Campbell RE, Zacharias DA, Tsien RY (2001) Reducing the environmental sensitivity of yellow fluorescent protein. Mechanism and applications. J Biol Chem 276:29188-29194.
32. Cheng Z, Campbell RE (2006) Assessing the structural stability of designed beta-hairpin peptides in the cytoplasm of live cells. ChemBioChem 7:1147-1150. (Pubitemid 44230833)
33. Fiser A, Sali A (2003) ModLoop: automated modeling of loops in protein structures. Bioinformatics 19: 2500-2501. (Pubitemid 38016660)
34. Rohl CA, Strauss CE, Chivian D, Baker D (2004) Modeling structurally variable regions in homologous proteins with rosetta. Proteins 55:656-677.
35. DeLano WL (2008) The PyMOL Molecular Graphics System. Available at http://www.pymol.org [accessed May 10, 2010].