FPMOD: A modeling tool for sampling the conformational space of fusion proteins

Annual International Conference of the IEEE Engineering in Medicine and Biology - Proceedings

Volumn , Issue , 2006, Pages 4111-4114

  Chiang, Jason ^b   Li, Isaac ^b   Pham, Elizabeth ^b   Truong, Kevin ^a,c  

^a IEEE   (Canada)

^b UNIVERSITY OF TORONTO   (Canada)

^c UNIVERSITY OF TORONTO   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

FLEXIBLE LINKERS; FLUORESCENCE RESONANCE ENERGY TRANSFER (FRET); FUSION PROTEIN MODELLER (FPMOD);

BIOSENSORS; BIOTECHNOLOGY; COMPUTER SIMULATION; ENERGY TRANSFER; FLUORESCENCE;

PROTEINS;

HYBRID PROTEIN; PHOTOPROTEIN;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; FLUORESCENCE RESONANCE ENERGY TRANSFER; GENETIC PROCEDURES; PROTEIN CONFORMATION; PROTEIN DATABASE;

BIOSENSING TECHNIQUES; COMPUTER SIMULATION; DATABASES, PROTEIN; FLUORESCENCE RESONANCE ENERGY TRANSFER; LUMINESCENT PROTEINS; MODELS, MOLECULAR; PROTEIN CONFORMATION; RECOMBINANT FUSION PROTEINS;

EID: 34047135646     PISSN: 05891019     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/IEMBS.2006.259224     Document Type: Conference Paper

References (15)

1. G. Milligan, G. J. Feng, R. J. Ward, N. Sartania, D. Ramsay, A. J. McLean, and J. J. Carrillo, "G protein-coupled receptor fusion proteins in drug discovery," Curr Pharm Des, vol. 10, pp. 1989-2001, 2004.
2. J. Wiedenmann, S. Ivanchenko, F. Oswald, F. Schmitt, C. Rocker, A. Salih, K. D. Spindler, and G. U. Nienhaus, "EosFP, a fluorescent marker protein with UV-inducible green-to-red fluorescence conversion," Proc Natl Acad Sci USA, vol. 101, pp. 15905-10, 2004.
3. J. J. Chiang and K. Truong, "Computational modeling of a new fluorescent biosensor for caspase proteolytic activity improves dynamic range," Nanobioscience, IEEE Transactions on, vol. 5, pp. 41-45, 2006.
4. J. J. Chiang and K. Truong, "Using co-cultures expressing fluorescence resonance energy transfer based protein biosensors to simultaneously image caspase-3 and Ca2+ signaling," Biotechnol Lett, vol. 27, pp. 1219-27, 2005.
5. O. Kohlbacher and H. P. Lenhof, "BALL-rapid software prototyping in computational molecular biology. Biochemicals Algorithms Library," Bioinformatics, vol. 16, pp. 815-24, 2000.
6. W. Humphrey, A. Dalke, and K. Schulten, "VMD: visual molecular dynamics," J Mol Graph, vol. 14, pp. 33-8, 27-8, 1996.
7. A. Fiser and A. Sali, "Modeller: generation and refinement of homology-based protein structure models," Methods Enzymol, vol. 374, pp. 461-91, 2003.
8. W. Kaplan and T. G. Littlejohn, "Swiss-PDB Viewer (Deep View)," Brief Bioinform, vol. 2, pp. 195-7, 2001.
9. J. Hyun Bae, M. Rubini, G. Jung, G. Wiegand, M. H. Seifert, M. K. Azim, J. S. Kim, A. Zumbusch, T. A. Holak, L. Moroder, R. Huber, and N. Budisa, "Expansion of the genetic code enables design of a novel "gold" class of green fluorescent proteins," J Mol Biol, vol. 328, pp. 1071-81, 2003.
10. A. Rekas, J. R. Alattia, T. Nagai, A. Miyawaki, and M. Ikura, "Crystal structure of venus, a yellow fluorescent protein with improved maturation and reduced environmental sensitivity," J Biol Chem, vol. 277, pp. 50573-8, 2002.
11. R. M. Clegg, "Fluorescence resonance energy transfer," Curr Opin Biotechnol, vol. 6, pp. 103-10, 1995.
12. B. Nagar, M. Overduin, M. Ikura, and J. M. Rini, "Structural basis of calcium-induced E-cadherin rigidification and dimerization," Nature, vol. 380, pp. 3604, 1996.
13. J. R. Alattia, H. Kurokawa, and M. Ikura, "Structural view of cadherin-mediated cell-cell adhesion," Cell Mol Life Sci, vol. 55, pp. 359-67, 1999.
14. M. Osawa, H. Tokumitsu, M. B. Swindells, H. Kurihara, M. Orita, T. Shibanuma, T. Furuya, and M. Ikura, "A novel target recognition revealed by calmodulin in complex with Ca2+- calmodulin-dependent kinase kinase," Nat Struct Biol, vol. 6, pp. 819-24, 1999.
15. K. Truong, A. Khorchid, and M. Ikura, "A fluorescent cassette-based strategy for engineering multiple domain fusion proteins," BMC Biotechnol, vol. 3, pp. 8, 2003.