Thermodynamic Protein Destabilization by GFP Tagging: A Case of Interdomain Allostery

Biophysical Journal

Volumn 109, Issue 6, 2015, Pages 1157-1162

  Sokolovski, Miri ^a   Bhattacherjee, Arnab ^a   Kessler, Naama ^a   Levy, Yaakov ^a   Horovitz, Amnon ^a  

^a WEIZMANN INSTITUTE OF SCIENCE   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

ENGRAIL PROTEIN, DROSOPHILA; ENHANCED GREEN FLUORESCENT PROTEIN; GREEN FLUORESCENT PROTEIN; HOMEODOMAIN PROTEIN; SOLUTION AND SOLUBILITY; TRANSCRIPTION FACTOR;

ALLOSTERISM; ANIMAL; CHEMISTRY; CIRCULAR DICHROISM; DROSOPHILA MELANOGASTER; ESCHERICHIA COLI; GENETICS; ISOLATION AND PURIFICATION; METABOLISM; MOLECULAR DYNAMICS; PROTEIN DENATURATION; PROTEIN STABILITY; PROTEIN TERTIARY STRUCTURE; SOLUTION AND SOLUBILITY; THERMODYNAMICS;

ALLOSTERIC REGULATION; ANIMALS; CIRCULAR DICHROISM; DROSOPHILA MELANOGASTER; ESCHERICHIA COLI; GREEN FLUORESCENT PROTEINS; HOMEODOMAIN PROTEINS; MOLECULAR DYNAMICS SIMULATION; PROTEIN DENATURATION; PROTEIN STABILITY; PROTEIN STRUCTURE, TERTIARY; SOLUTIONS; THERMODYNAMICS; TRANSCRIPTION FACTORS;

EID: 84941805051     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2015.04.032     Document Type: Article

References (31)

1. D. Ekman, and A.K. Björklund A. Elofsson Multi-domain proteins in the three kingdoms of life: orphan domains and other unassigned regions J. Mol. Biol. 348 2005 231 243
2. J.H. Han, and S. Batey J. Clarke The folding and evolution of multidomain proteins Nat. Rev. Mol. Cell Biol. 8 2007 319 330
3. R. Jaenicke Stability and folding of domain proteins Prog. Biophys. Mol. Biol. 71 1999 155 241
4. L.G. Randles, and S. Batey J. Clarke Distinguishing specific and nonspecific interdomain interactions in multidomain proteins Biophys. J. 94 2008 622 628
5. S. Bandi, S.M. Singh, and K.M. Mallela The C-terminal domain of the utrophin tandem calponin-homology domain appears to be thermodynamically and kinetically more stable than the full-length protein Biochemistry 53 2014 2209 2211
6. T.L. Radley, and A.I. Markowska S.N. Loh Allosteric switching by mutually exclusive folding of protein domains J. Mol. Biol. 332 2003 529 536
7. T. Hagai, and Y. Levy Ubiquitin not only serves as a tag but also assists degradation by inducing protein unfolding Proc. Natl. Acad. Sci. USA 107 2010 2001 2006
8. L.M. Luheshi, and C.M. Dobson Bridging the gap: from protein misfolding to protein misfolding diseases FEBS Lett. 583 2009 2581 2586
9. C.F. Wright, and S.A. Teichmann C.M. Dobson The importance of sequence diversity in the aggregation and evolution of proteins Nature 438 2005 878 881
10. E. Jacob, R. Unger, and A. Horovitz N-terminal domains in two-domain proteins are biased to be shorter and predicted to fold faster than their C-terminal counterparts Cell Reports 3 2013 1051 1056
11. D. Rivenzon-Segal, and S.G. Wolf A. Horovitz Sequential ATP-induced allosteric transitions of the cytoplasmic chaperonin containing TCP-1 revealed by EM analysis Nat. Struct. Mol. Biol. 12 2005 233 237
12. R.Y. Tsien Nobel lecture: constructing and exploiting the fluorescent protein paintbox Integr. Biol. (Camb) 2 2010 77 93
13. U. Mayor, and J.G. Grossmann A.R. Fersht The denatured state of Engrailed Homeodomain under denaturing and native conditions J. Mol. Biol. 333 2003 977 991
14. U. Mayor, and N.R. Guydosh A.R. Fersht The complete folding pathway of a protein from nanoseconds to microseconds Nature 421 2003 863 867
15. F. Jiang, and Y.D. Wu Folding of fourteen small proteins with a residue-specific force field and replica-exchange molecular dynamics J. Am. Chem. Soc. 136 2014 9536 9539
16. F. van den Ent, and J. Löwe RF cloning: a restriction-free method for inserting target genes into plasmids J. Biochem. Biophys. Methods 67 2006 67 74
17. T. Unger, and Y. Jacobovitch Y. Peleg Applications of the Restriction Free (RF) cloning procedure for molecular manipulations and protein expression J. Struct. Biol. 172 2010 34 44
18. D.A. Zacharias, and J.D. Violin R.Y. Tsien Partitioning of lipid-modified monomeric GFPs into membrane microdomains of live cells Science 296 2002 913 916
19. C. Clementi, H. Nymeyer, and J.N. Onuchic 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 2000 937 953
20. A. Azia, and Y. Levy Nonnative electrostatic interactions can modulate protein folding: molecular dynamics with a grain of salt J. Mol. Biol. 393 2009 527 542
21. O. Arviv, and Y. Levy Folding of multidomain proteins: biophysical consequences of tethering even in apparently independent folding Proteins 80 2012 2780 2798
22. A. Mor, G. Ziv, and Y. Levy Simulations of proteins with inhomogeneous degrees of freedom: The effect of thermostats J. Comput. Chem. 29 2008 1992 1998
23. S. Kumar, and D. Bouzida J.M. Rosenberg The weighted histogram analysis method for free-energy calculations on biomolecules. I. The method J. Comput. Chem. 13 1992 1011 1021
24. S.S. Cho, Y. Levy, and P.G. Wolynes P versus Q: structural reaction coordinates capture protein folding on smooth landscapes Proc. Natl. Acad. Sci. USA 103 2006 586 591
25. N.J. Greenfield, and G.D. Fasman Computed circular dichroism spectra for the evaluation of protein conformation Biochemistry 8 1969 4108 4116
26. U. Mayor, and C.M. Johnson A.R. Fersht Protein folding and unfolding in microseconds to nanoseconds by experiment and simulation Proc. Natl. Acad. Sci. USA 97 2000 13518 13522
27. D.C. Rees, and A.D. Robertson Some thermodynamic implications for the thermostability of proteins Protein Sci. 10 2001 1187 1194
28. A.D. Robertson, and K.P. Murphy Protein structure and the energetics of protein stability Chem. Rev. 97 1997 1251 1268
29. B. Ma, and C.J. Tsai R. Nussinov Dynamic allostery: linkers are not merely flexible Structure 19 2011 907 917
30. H.S. Chan, and Z. Zhang Z. Liu Cooperativity, local-nonlocal coupling, and nonnative interactions: principles of protein folding from coarse-grained models Annu. Rev. Phys. Chem. 62 2011 301 326
31. V. Sobolev, and A. Sorokine M. Edelman Automated analysis of interatomic contacts in proteins Bioinformatics 15 1999 327 332