Engineering domain-swapped binding interfaces by mutually exclusive folding

Journal of Molecular Biology

Volumn 416, Issue 4, 2012, Pages 495-502

  Ha, Jeung Hoi ^a   Karchin, Joshua M ^a   Walker Kopp, Nancy ^a   Huang, Li Shar ^a   Berry, Edward A ^a   Loh, Stewart N ^a  

^a State University of New York Upstate Medical University: College of Medicine   (United States)

Author keywords

barnase; protein folding; protein switch; self assembly; ubiquitin

Indexed keywords

BARNASE; MONOMER; UBIQUITIN;

ARTICLE; BINDING AFFINITY; NONHUMAN; OLIGOMERIZATION; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN STRUCTURE;

EID: 84857356493     PISSN: 00222836     EISSN: 10898638     Source Type: Journal    
DOI: 10.1016/j.jmb.2011.12.050     Document Type: Article

References (26)

1. Gronenborn A.M. Protein acrobatics in pairs-dimerization via domain swapping Curr. Opin. Struct. Biol. 19 2009 39 49
2. Bennett M.J., Schlunegger M.P., and Eisenberg D. 3D domain swapping: a mechanism for oligomer assembly Protein Sci. 4 1995 2455 2468
3. Bennett M.J., Choe S., and Eisenberg D. Domain swapping: entangling alliances between proteins Proc. Natl Acad. Sci. USA 91 1994 3127 3131 (Pubitemid 24130188)
4. Newcomer M.E. Protein folding and three-dimensional domain swapping: a strained relationship? Curr. Opin. Struct. Biol. 12 2002 48 53 (Pubitemid 34142720)
5. Takeichi M. Morphogenetic roles of classic cadherins Curr. Opin. Cell Biol. 7 1995 619 627
6. Patel S.D., Chen C.P., Bahna F., Honig B., and Shapiro L. Cadherin-mediated cell-cell adhesion: sticking together as a family Curr. Opin. Struct. Biol. 13 2003 690 698 (Pubitemid 37522144)
7. Harrison O.J., Bahna F., Katsamba P.S., Jin X., Brasch J., and Vendome J. Two-step adhesive binding by classical cadherins Nat. Struct. Mol. Biol. 17 2010 348 357
8. Ciatto C., Bahna F., Zampieri N., VanSteenhouse H.C., Katsamba P.S., and Ahlsen G. T-cadherin structures reveal a novel adhesive binding mechanism Nat. Struct. Mol. Biol. 17 2010 339 347
9. Miloushev V.Z., Bahna F., Ciatto C., Ahlsen G., Honig B., and Shapiro L. Dynamic properties of a type II cadherin adhesive domain: implications for the mechanism of strand-swapping of classical cadherins Structure 16 2008 1195 1205
10. Liu Y., and Eisenberg D. 3D domain swapping: as domains continue to swap Protein Sci. 11 2002 1285 1299 (Pubitemid 34547201)
11. Bennett M.J., Sawaya M.R., and Eisenberg D. Deposition diseases and 3D domain swapping Structure 14 2006 811 824 (Pubitemid 43674098)
12. Nagarkar R.P., Hule R.A., Pochan D.J., and Schneider J.P. Domain swapping in materials design Biopolymers 94 2010 141 155
13. Banta S., Wheeldon I.R., and Blenner M. Protein engineering in the development of functional hydrogels Annu. Rev. Biomed. Eng. 12 2010 167 186
14. Kuhlman B., O'Neill J.W., Kim D.E., Zhang K.Y., and Baker D. Conversion of monomeric protein L to an obligate dimer by computational protein design Proc. Natl Acad. Sci. USA 98 2001 10687 10691 (Pubitemid 32878682)
15. Radley T.L., Markowska A.I., Bettinger B.T., Ha J.H., and Loh S.N. Allosteric switching by mutually exclusive folding of protein domains J. Mol. Biol. 332 2003 529 536 (Pubitemid 37075979)
16. Cutler T., and Loh S.N. Thermodynamic analysis of an antagonistic folding-unfolding equilibrium between two protein domains J. Mol. Biol. 371 2007 308 316 (Pubitemid 47048284)
17. Cutler T., Mills B.M., Lubin D.J., Chong L.T., and Loh S.N. Effect of interdomain linker length on an antagonistic folding-unfolding equilibrium between two protein domains J. Mol. Biol. 386 2009 854 868
18. Ha J.H., Butler J.S., Mitrea D.M., and Loh S.N. Modular enzyme design: regulation by mutually exclusive protein folding J. Mol. Biol. 357 2006 1058 1062 (Pubitemid 43357972)
19. Mills B.M., and Chong L.T. Molecular simulations of mutually exclusive folding in a two-domain protein switch Biophys. J. 100 2011 756 764
20. Geiser M., Cebe R., Drewello D., and Schmitz R. Integration of PCR fragments at any specific site within cloning vectors without the use of restriction enzymes and DNA ligase Biotechniques 31 2001 88 92 (Pubitemid 32645915)
21. Khorasanizadeh S., Peters I.D., and Roder H. Evidence for a three-state model of protein folding from kinetic analysis of ubiquitin variants with altered core residues Nat. Struct. Biol. 3 1996 193 205 (Pubitemid 26045008)
22. Clarke J., Henrick K., and Fersht A.R. Disulfide mutants of barnase I: changes in stability structure assessed by biophysical methods and X-ray crystallography J. Mol. Biol. 254 1995 493 504
23. Otwinowski Z., and Minor W. Processing of X-ray diffraction data collected in oscillation mode Methods Enzymol. 276 1997 307 326 (Pubitemid 27085611)
24. Adams P.D., Afonine P.V., Bunkóczi G., Chen V.B., Davis I.W., and Echols N. PHENIX: a comprehensive Python-based system for macromolecular structure solution Acta Crystallogr., Sect. D: Biol. Crystallogr. 66 2010 213 221
25. Bottomley S.P. The folding pathway of alpha1-antitrypsin: avoiding the unavoidable Proc. Am. Thorac. Soc. 7 2010 404 407
26. Peng Q., and Li H. Direct observation of tug-of-war during the folding of a mutually exclusive protein J. Am. Chem. Soc. 131 2009 13347 13354