Molecular simulations of mutually exclusive folding in a two-domain protein switch

Biophysical Journal

Volumn 100, Issue 3, 2011, Pages 756-764

  Mills, Brandon M ^a   Chong, Lillian T ^a  

^a UNIVERSITY OF PITTSBURGH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 79551619424     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2010.12.3710     Document Type: Article

References (46)

1. Bourne, H. R., D. A. Sanders, and F. McCormick. 1990. The GTPase superfamily: a conserved switch for diverse cell functions. Nature. 348:125-132.
2. Huse, M., and J. Kuriyan. 2002. The conformational plasticity of protein kinases. Cell. 109:275-282.
3. Koide, S. 2009. Generation of new protein functions by nonhomologous combinations and rearrangements of domains and modules. Curr. Opin. Biotechnol. 20:398-404.
4. Ostermeier, M. 2009. Designing switchable enzymes. Curr. Opin. Struct. Biol. 19:442-448.
5. Ambroggio, X. I., and B. Kuhlman. 2006. Design of protein conformational switches. Curr. Opin. Struct. Biol. 16:525-530.
6. Radley, T. L., A. I. Markowska, S. N. Loh. 2003. Allosteric switching by mutually exclusive folding of protein domains. J. Mol. Biol. 332:529-536.
7. Cutler, T. A., and S. N. Loh. 2007. Thermodynamic analysis of an antagonistic folding-unfolding equilibrium between two protein domains. J. Mol. Biol. 371:308-316.
8. Cutler, T. A., B. M. Mills, S. N. Loh. 2009. Effect of interdomain linker length on an antagonistic folding-unfolding equilibrium between two protein domains. J. Mol. Biol. 386:854-868.
9. Ha, J. H., J. S. Butler, S. N. Loh. 2006. Modular enzyme design: regulation by mutually exclusive protein folding. J. Mol. Biol. 357:1058-1062.
10. Sallee, N. A., B. J. Yeh, and W. A. Lim. 2007. Engineering modular protein interaction switches by sequence overlap. J. Am. Chem. Soc. 129:4606-4611.
11. 2+-sensing molecular switch based on alternate frame protein folding. ACS Chem. Biol. 3:723-732.
12. Strickland, D., K. Moffat, and T. R. Sosnick. 2008. Light-activated DNA binding in a designed allosteric protein. Proc. Natl. Acad. Sci. USA. 105:10709-10714.
13. Mitrea, D. M., L. S. Parsons, and S. N. Loh. 2010. Engineering an artificial zymogen by alternate frame protein folding. Proc. Natl. Acad. Sci. USA. 107:2824-2829.
14. Stratton, M. M., and S. N. Loh. 2010. On the mechanism of protein fold-switching by a molecular sensor. Proteins. 78:3260-3269.
15. Go, N. 1983. Theoretical studies of protein folding. Annu. Rev. Biophys. Bioeng. 12:183-210.
16. Takada, S. 1999. Go-ing for the prediction of protein folding mechanisms. Proc. Natl. Acad. Sci. USA. 96:11698-11700.
17. Clementi, C. 2008. Coarse-grained models of protein folding: toy models or predictive tools? Curr. Opin. Struct. Biol. 18:10-15.
18. Mauguen, Y., R. W. Hartley, A. Jack. 1982. Molecular structure of a new family of ribonucleases. Nature. 297:162-164.
19. Vijay-Kumar, S., C. E. Bugg, and W. J. Cook. 1987. Structure of ubiquitin refined at 1.8 Å resolution. J. Mol. Biol. 194:531-544.
20. Buckle, A. M., G. Schreiber, and A. R. Fersht. 1994. Protein-protein recognition: crystal structural analysis of a barnase-barstar complex at 2.0-Å resolution. Biochemistry. 33:8878-8889. (Pubitemid 24257995)
21. Jha, A. K., A. Colubri, T. R. Sosnick. 2005. Statistical coil model of the unfolded state: resolving the reconciliation problem. Proc. Natl. Acad. Sci. USA. 102:13099-13104.
22. Elcock, A. H. 2006. Molecular simulations of cotranslational protein folding: fragment stabilities, folding cooperativity, and trapping in the ribosome. PLOS Comput. Biol. 2: e98.
23. Knott, M., H. Kaya, and H. S. Chan. 2004. Energetics of protein thermodynamic cooperativity: contributions of local and nonlocal interactions. Polymer (Guildf.). 45:623-632.
24. Ermak, D. L., and J. A. McCammon. 1978. Brownian dynamics with hydrodynamic interactions. J. Chem. Phys. 69:1352-1360.
25. Frembgen-Kesner, T., and A. H. Elcock. 2009. Striking effects of hydrodynamic interactions on the simulated diffusion and folding of proteins. J. Chem. Theory Comput. 5:242-256.
26. Hess, B., H. Bekker, J. G. E. M. Fraaije. 1997. LINCS: a linear constraint solver for molecular simulations. J. Comput. Chem. 18:1463-1472.
27. Clementi, C., H. Nymeyer, and J. N. Onuchic. 2000. Topological and energetic factors: what determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins. J. Mol. Biol. 298:937-953.
28. Koga, N., and S. Takada. 2001. Roles of native topology and chainlength scaling in protein folding: a simulation study with a Go-like model. J. Mol. Biol. 313:171-180.
29. Yang, S., S. S. Cho, J. N. Onuchic. 2004. Domain swapping is a consequence of minimal frustration. Proc. Natl. Acad. Sci. USA. 101:13786-13791.
30. Ding, F., K. C. Prutzman, N. V. Dokholyan. 2006. Topological determinants of protein domain swapping. Structure. 14:5-14.
31. Ding, F., N. V. Dokholyan, E. I. Shakhnovich. 2002. Molecular dynamics simulation of the SH3 domain aggregation suggests a generic amyloidogenesis mechanism. J. Mol. Biol. 324:851-857.
32. Lazar, G. A., J. R. Desjarlais, and T. M. Handel. 1997. De novo design of the hydrophobic core of ubiquitin. Protein Sci. 6:1167-1178.
33. Daggett, V., and A. R. Fersht. 2003. The present view of the mechanism of protein folding. Nat. Rev. Mol. Cell Biol. 4:497-502.
34. Serrano, L., A. Horovitz, A. R. Fersht. 1990. Estimating the contribution of engineered surface electrostatic interactions to protein stability by using double-mutant cycles. Biochemistry. 29:9343-9352.
35. Zhou, H.-X. 2001. Single-chain versus dimeric protein folding: thermodynamic and kinetic consequences of covalent linkage. J. Am. Chem. Soc. 123:6730-6731.
36. Peng, Q., and H. Li. 2009. Direct observation of tug-of-war during the folding of a mutually exclusive protein. J. Am. Chem. Soc. 131:13347-13354.
37. Ladurner, A. G., and A. R. Fersht. 1997. Glutamine, alanine or glycine repeats inserted into the loop of a protein have minimal effects on stability and folding rates. J. Mol. Biol. 273:330-337.
38. Nagi, A. D., K. S. Anderson, and L. Regan. 1999. Using loop length variants to dissect the folding pathway of a four-helix-bundle protein. J. Mol. Biol. 286:257-265.
39. Viguera, A.-R., and L. Serrano. 1997. Loop length, intramolecular diffusion and protein folding. Nat. Struct. Biol. 4:939-946.
40. Hartley, R. W. 1993. Directed mutagenesis and barnase-barstar recognition. Biochemistry. 32:5978-5984.
41. Schreiber, G., and A. R. Fersht. 1993. Interaction of barnase with its polypeptide inhibitor barstar studied by protein engineering. Biochemistry. 32:5145-5150.
42. Jones, D. N. M., M. Bycroft, A. R. Fersht. 1993. Identification of the barstar binding site of barnase by NMR spectroscopy and hydrogen-deuterium exchange. FEBS Lett. 331:165-172.
43. Butler, J. S., D. M. Mitrea, S. N. Loh. 2009. Structural and thermodynamic analysis of a conformationally strained circular permutant of barnase. Biochemistry. 48:3497-3507.
44. Blois, T. M., H. Hong, J. U. Bowie. 2009. Protein unfolding with a steric trap. J. Am. Chem. Soc. 131:13914-13915.
45. Gront, D., S. Kmiecik, and A. Kolinski. 2007. Backbone building from quadrilaterals: a fast and accurate algorithm for protein backbone reconstruction from alpha carbon coordinates. J. Comput. Chem. 28:1593-1597.
46. De Lano, W. L. 2002. The PyMOL Molecular Graphics System, Ver. 1.2. De Lano Scientific, Palo Alto, CA.