Fluorescence depolarization studies of filamentous actin analyzed with a genetic algorithm

Biophysical Journal

Volumn 93, Issue 9, 2007, Pages 3291-3299

  Marushchak, Denys ^a   Grenklo, Staffan ^b,c   Johansson, Thomas ^b   Karlsson, Roger ^b   Johansson, Lennart B Å ^a  

^a UMEÅ UNIVERSITY   (Sweden)

^b STOCKHOLM UNIVERSITY   (Sweden)

^c KAROLINSKA INSTITUTE   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

F ACTIN;

ARTICLE; DEPOLARIZATION; ENERGY; FLUORESCENCE; GENETIC ALGORITHM; MONTE CARLO METHOD; POLYMERIZATION; PROTEIN ANALYSIS;

EID: 36148947932     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.107.107920     Document Type: Article

References (38)

1. Dickerson, R. E. 1964. X-Ray Analysis and Protein Structure. Academic Press, New York.
2. Blundell, T. L., and L. N. Johnson. 1976. Protein Crystallography. Academic Press, London.
3. Clore, G. M., and A. M. Gronenborn. 1993. Topics in Molecular and Structural Biology. The Macmillan Press, London.
4. Wütrich, K. 1986. NMR of Proteins and Nucleic Acids. Wiley, New York.
5. Van der Meer, B. W., G. Coker III, and S.-Y. S. Chen. 1994. Resonance Energy Transfer: Theory and Data. VCH Publishers, New York.
6. Valeur, B. 2002. Molecular Fluorescence. Principles and Applications. Wiley-VCH, Berlin.
7. Lakowicz, J. R. 1999. Principles of Fluorescence Spectroscopy. Kluwer Academic/Plenum, New York.
8. Vekshin, N. L. 1997. Energy Transfer in Macromolecules. SPIE Press, Bellingham, WA.
9. Kalinin, S., and L. B.-Å. Johansson. 2004. Utility and considerations of donor-donor energy migration as a fluorescence method for exploring protein structure-function. J. Fluor. 14:681-691.
10. Johansson, L. B.-Å., P. Edman, and P.-O. Westlund. 1996. Energy migration and rotational motion within bichromophoric molecules. II. A derivation of the fluorescence anisotropy. J. Chem. Phys. 105:10896-10904.
11. 2-dynamics and fluorophore reorientation. J. Phys. Chem. B. 108:17243-17250.
12. Marushchak, D., and L. B.-Å. Johansson. 2005. On the quantitative treatment of donor-donor energy migration in regularly aggregated proteins. J. Fluoresc. 15:797-804.
13. Egelman, E. 1985. The structure of F-actin. J. Muscle Res. Cell Motil. 6:129-151.
14. 374. Biochemistry. 36:7353-7360.
15. Johansson, T., S. Grenklo, and R. Karlsson. 2004. Detection of binding partners to the profilin:actin complex by far Western and mass spectrometry analyses. Anal. Biochem. 335:228-234.
16. Reference deleted in proof.
17. Charbonneau, P. 1995. Genetic algorithms in astronomy and astrophysics. Astrophys. J. Suppl. Ser. 101:309-334.
18. Darwin, C. 1995. Origin of Species. Gramercy, New York.
19. Fisz, J. J., M. Buczkowski, M. P. Budzinski, and P. Kolenderski. 2005. Genetic algorithms optimization approach supported by the first-order derivative and Newton-Raphson methods: application to fluorescence spectroscopy. Chem. Phys. Lett. 407:8-12.
20. Karolin, J., L. B.-Å. Johansson, L. Strandberg, and T. Ny. 1994. Fluorescence and absorption spectroscopic properties of dipyrrometheneboron difluoride (BODIPY) derivatives in liquids, lipid membranes, and proteins. J. Am. Chem. Soc. 116:7801-7806.
21. Bergström, F., I. Mikhalyov, P. Hägglö f, R. Wortmann, T. Ny, and L. B.-Å. Johansson. 2002. Dimers of dipyrrometheneboron difluoride (BODIPY) with light spectroscopic applications in chemistry and biology. J. Am. Chem. Soc. 124:196-204.
22. Moens, P. D. J., and C. G. dos Remedios. 2001. Analysis of models of F-actin using fluorescence resonance energy transfer spectroscopy. Results Probl. Cell Differ. 32:59-77.
23. Kasprzak, A. A., R. Takashi, and M. F. Morales. 1988. Orientation of actin monomer in the F-actin filament: radial coordinate of glutamine-41 and effect of myosin subfragment 1 binding on the monomer orientation. Biochemistry. 27:4512-4522.
24. Taylor, D. L., J. Reidler, J. A. Spudich, and L. Stryer. 1981. Detection of actin assembly by fluorescence energy transfer. J. Cell Biol. 89:362-367.
25. Holmes, K. C., D. Popp, W. Gebhard, and W. Kasch. 1990. Atomic model of the actin filament. Nature. 347:44-49.
26. Popp, D., V. V. Lednev, and W. Jahn. 1987. Methods of preparing well-oriented sols of F-actin containing filaments suitable for x-ray diffraction. J. Mol. Biol. 224:65-76.
27. Miki, M., S. I. O'Donoghue, and C. G. dos Remedios. 1992. Structure of actin observed by fluorescence resonance energy transfer spectroscopy. J. Muscle Res. Cell Motil. 13:132-145.
28. Malisauskas, M., V. Zamotin, J. Jass, W. Noppe, C. M. Dobson, and L. A. Morozova-Roche. 2003. Amyloid protofilaments from the calcium-binding protein equine lysozyme: formation of ring and linear structures depends on pH and metal ion concentration. J. Mol. Biol. 330:879-890.
29. Malisauskas, M., J. Ostman, A. Darinskas, V. Zamotin, E. Liutkevicius, E. Lundgren, and L. A. Morozova-Roche. 2005. Does the cytotoxic effect of transient amyloid oligomers from common equine lysozyme in vitro imply innate amyloid toxicity? J. Biol. Chem. 280:6269-6275.
30. Aguzzi, A., and M. Polymenidou. 2004. Mammalian prion biology: one century of evolving concepts. Cell. 116:313-327.
31. Houston, F., W. Goldmann, A. Chong, M. Jeffrey, L. Gonzalez, J. Foster, D. Parnham, and N. Hunter. 2003. Prion diseases: BSE in sheep bred for resistance to infection. Nature. 423:498.
32. Stanley, P., V. Koronakis, and C. Hughes. 1998. Acylation of Escherichia coli hemolysin: a unique protein lipidation mechanism underlaying toxin function. Microbiol. Mol. Biol. Rev. 62:309-333.
33. Abrami, L., M. Fivaz, and F. G. van der Goot. 2000. Adventures of a pore-forming toxin at the target cell surface. Trends Microbiol. 8:168-172.
34. Wai, S. N., M. Westermark, J. Oscarsson, J. Jass, E. Maier, R. Benz, and B. E. Uhlin. 2003. Characterization of dominantly negative mutant ClyA cytotoxin proteins in Escherichia coli. J. Bacteriol. 185:5491-5499.
35. 157 in the nucleotide-binding site of β-actin. Eur. J. Chem. 265:210-220.
36. Schüler, H. R. Karlsson, and U. Lindberg. 2006. Purification of non-muscle actin. In Cell Biology, 3rd Ed. J. Celis, editor. Elsevier, San Diego, CA.
37. Chik, J. K., U. Lindberg, and C. E. Schutt. 1996. Structure of bovine γ-actin-profilin complex with actin-bound ATP phosphates solvent-accessible. In Protein Data Bank. 1HLU.
38. Chik, J. K., U. Lindberg, and C. E. Schutt. 1996. The structure of an open state of β-actin at 2.65 Å resolution. J. Mol. Biol. 263:607-623.