Kinetics and reaction coordinates of the reassembly of protein fragments via forward flux sampling

Biophysical Journal

Volumn 98, Issue 9, 2010, Pages 1911-1920

  Borrero, Ernesto E ^a   Contreras Martínez, Lydia M ^a   Delisa, Matthew P ^a   Escobedo, Fernando A ^a  

^a Cornell University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 77952247545     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2009.12.4329     Document Type: Article

References (35)

1. Hu, C. D., and T. K. Kerppola. 2003. Simultaneous visualization of multiple protein interactions in living cells using multicolor fluorescence complementation analysis. Nat. Biotechnol. 21:539-545.
2. Magliery, T. J., C. G. M. Wilson,L. Regan. 2005. Detecting proteinprotein interactions with a green fluorescent protein fragment reassembly trap: scope and mechanism. J. Am. Chem. Soc. 127:146-157.
3. Ozawa, T., Y. Sako, Y. Umezawa. 2003. A genetic approach to identifying mitochondrial proteins. Nat. Biotechnol. 21:287-293. (Pubitemid 36314813)
4. Remy, I., and S. W. Michnick. 2004. A cDNA library functional screening strategy based on fluorescent protein complementation assays to identify novel components of signaling pathways. Methods. 32:381-388. (Pubitemid 38299329)
5. Stains, C. I., J. R. Porter, . I. Ghosh. 2005. DNA sequence-enabled reassembly of the green fluorescent protein. J. Am. Chem. Soc: 127: 10782-10783. (Pubitemid 41129825)
6. Ghosh, I., A. D. Hamilton, and L. Regan. 2000. Antiparallel leucine zipper-directed protein reassembly: application to the green fluorescent protein. J. Am. Chem. Soc. 122:5658-5659. (Pubitemid 30431094)
7. Johnsson, N., and A. Varshavsky. 1994. Split ubiquitin as a sensor of protein interactions in vivo. Proc. Natl. Acad. Sci. USA. 91:10340-10344. (Pubitemid 24328992)
8. Pelletier, J. N., F. X. Campbell-Valois, and S. W. Michnick. 1998. Oligomerization domain-directed reassembly of active dihydrofolate reductase from rationally designed fragments. Proc. Natl. Acad. Sci. USA. 95:12141-12146.
9. Galarneau, A., M. Primeau, S. W. Michnick. 2002. Beta-lactamase protein fragment complementation assays as in vivo and in vitro sensors of protein protein interactions. Nat. Biotechnol. 20:619-622. (Pubitemid 34595158)
10. Wehrman, T., B. Kleaveland, . H. M. Blau. 2002. Protein-protein interactions monitored in mammalian cells via complementation of beta -lactamase enzyme fragments. Proc. Natl. Acad. Sci. USA. 99: 3469-3474. (Pubitemid 34252132)
11. Paulmurugan, R., and S. S. Gambhir. 2003. Monitoring protein-protein interactions using split synthetic Renilla luciferase protein-fragment-assisted complementation. Anal. Chem. 75:1584-1589.
12. Deo, S. K. 2004. Exploring bioanalytical applications of assisted protein reassembly. Anal. Bioanal. Chem. 379:383-390.
13. Wilson, C. G., T. J. Magliery, and L. Regan. 2004. Detecting proteinprotein interactions with GFP-fragment reassembly. Nat. Methods. 1:255-262.
14. Hennecke, J., P. Sebbel, and R. Glockshuber. 1999. Random circular permutation of DsbA reveals segments that are essential for protein folding and stability. J. Mol. Biol. 286:1197-1215. (Pubitemid 29116685)
15. Iwakura, M., T. Nakamura, . K. Maki. 2000. Systematic circular permutation of an entire protein reveals essential folding elements. Nat. Struct. Biol. 7:580-585. (Pubitemid 30445916)
16. Betton, J. M., and M. Hofnung. 1994. In vivo assembly of active maltose binding protein from independently exported protein fragments. EMBO J. 13:1226-1234.
17. Paszkiewicz, K. H., M. J. E. Sternberg, and M. Lappe. 2006. Prediction of viable circular permutants using a graph theoretic approach. Bioinformatics. 22:1353-1358.
18. Cabantous, S., T. C. Terwilliger, and G. S. Waldo. 2005. Protein tagging and detection with engineered self- assembling fragments of green fluorescent protein. Nat. Biotechnol. 23:102-107. (Pubitemid 41724632)
19. Paulmurugan, R., and S. S. Gambhir. 2007. Combinatorial library screening for developing an improved split-firefly luciferase fragmentassisted complementation system for studying protein-protein interactions. Anal. Chem. 79:2346-2353. (Pubitemid 46449015)
20. Demidov, V. V., N. V. Dokholyan, . N. E. Broude. 2006. Fast complementation of split fluorescent protein triggered by DNA hybridization. Proc. Natl. Acad. Sci. USA. 103:2052-2056.
21. Daggett, V., and A. R. Fersht. 2003. Is there a unifying mechanism for protein folding? Trends Biochem. Sci. 28:18-25. (Pubitemid 36051002)
22. Abkevich, V. I., A. M. Gutin, and E. I. Shakhnovich. 1994. Specific nucleus as the transition state for protein folding: evidence from the lattice model. Biochemistry. 33:10026-10036. (Pubitemid 24286081)
23. Fersht, A. R. 1995. Optimization of rates of protein folding: the nucleation-condensation mechanism and its implications. Prot: Natl. Acad. Sci. USA. 92:10869-10873.
24. Fersht, A. R. 1997. Nucleation mechanisms in protein folding. Curr. Opin. Struct. Biol. 7:3-9.
25. Contreras Martínez, L. M., E. E. Borrero Quintana, M. P. DeLisa. 2008. In silico protein fragmentation reveals the importance of critical nuclei on domain reassembly. Biophys. J. 94:1575-1588.
26. Krantz, B. A., R. S. Dothager, and T. R. Sosnick. 2004. Discerning the structure and energy of multiple transition states in protein folding using psi-analysis. J. Mol. Biol. 337:463-475.
27. Levy, Y., P. G. Wolynes, and J. N. Onuchic. 2004. Protein topology determines binding mechanism. Proc. Natl. Acad. Sci. USA. 101: 511-516. (Pubitemid 38084667)
28. Dellago, C., and P. G. Bolhuis. 2007. Transition path sampling simulations of biological systems. In Atomistic Approaches in Modern Biology: from Quantum Chemistry to Molecular Simulations., Vol.268 Springer-Verlag Berlin, Berlin, pp. 291-317.
29. Dellago, C., P. G. Bolhuis, and P. L. Geissler. 2002. Transition path sampling. Adv. Chem. Phys. 123:1-78.
30. Borrero, E. E., and F. A. Escobedo. 2006. Folding kinetics of a lattice protein via a forward flux sampling approach. J. Chem. Phys. 125:164904-164914.
31. Vendruscolo, M., E. Paci, . M. Karplus. 2001. Three key residues form a critical contact network in a protein folding transition state. Nature. 409:641-645.
32. Borrero, E. E., and F. A. Escobedo. 2007. Reaction coordinates and transition pathways of rare events via forward flux sampling. J. Chem. Phys. 127:164101-164117.
33. Borrero, E. E., and F. A. Escobedo. 2008. Optimizing the sampling and staging for simulations of rare events via forward flux sampling schemes. J. Chem. Phys. 129:024115-024116.
34. Frenkel, D., and B. Smit. 2002. Understanding Molecular Simulation: From Algorithms to Applications,2nd ed . Academic, Boston, MA.
35. Zhu, W. L., Y. M. Song, S. Y. Shin. 2007. Substitution of the leucine zipper sequence in melittin with peptoid residues affects selfassociation, cell selectivity, and mode of action. Biochim. Biophys. Acta. 1768:1506-1517.