Sung Lun Lin and Arash Zarrine-Afsar contributed equally to this work.
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The osmolyte trimethylamine-N-oxide stabilizes the Fyn SH3 domain without altering the structure of its folding transition state
Article first published online: 6 JAN 2009
DOI: 10.1002/pro.52
Copyright © 2009 The Protein Society
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How to Cite
Lin, S. L., Zarrine-Afsar, A. and Davidson, A. R. (2009), The osmolyte trimethylamine-N-oxide stabilizes the Fyn SH3 domain without altering the structure of its folding transition state. Protein Science, 18: 526–536. doi: 10.1002/pro.52
Publication History
- Issue published online: 23 FEB 2009
- Article first published online: 6 JAN 2009
- Accepted manuscript online: 6 JAN 2009 12:00AM EST
- Manuscript Accepted: 17 DEC 2008
- Manuscript Revised: 15 DEC 2008
- Manuscript Received: 31 OCT 2008
Funded by
- Canadian Institutes of Health Research. Grant Number: MOP-13609
References
- 1, ( 1979) Counteraction of urea destabilization of protein structure by methylamine osmoregulatory compounds of elasmobranch fishes. Biochem J 183: 317–323.
- 2, , , , ( 1982) Living with water stress: evolution of osmolyte systems. Science 217: 1214–1222.
- 3, ( 1982) Mechanism of stabilization of proteins by glycerol and sucrose. Seikagaku 54: 1255–1259.
- 4, ( 1983) Preferential interactions of proteins with solvent components in aqueous amino acid solutions. Arch Biochem Biophys 224: 169–177.
- 5, ( 1984) The mechanism of action of Na glutamate, lysine HCl, and piperazine-N,N′-bis(2-ethanesulfonic acid) in the stabilization of tubulin and microtubule formation. J Biol Chem 259: 4979–4986.
- 6, ( 1985) Mechanism of poly(ethylene glycol) interaction with proteins. Biochemistry 24: 6756–6762.
- 7, ( 1985) The stabilization of proteins by osmolytes. Biophys J 47: 411–414.
- 8, , ( 1990) Preferential interactions determine protein solubility in three-component solutions: the MgCl2 system. Biochemistry 29: 1914–1923.
- 9( 1993) The control of protein stability and association by weak interactions with water: how do solvents affect these processes? Annu Rev Biophys Biomol Struct 22: 67–97.
- 10, ( 1994) Why do some organisms use a urea-methylamine mixture as osmolyte? Thermodynamic compensation of urea and trimethylamine N-oxide interactions with protein. Biochemistry 33: 12695–12701.
- 11, , , , ( 2000) Osmolyte-induced changes in protein conformational equilibria. Biopolymers 53: 293–307.Direct Link:
- 12, ( 2001) Second virial coefficients as a measure of protein–osmolyte interactions. Protein Sci 10: 12–16.Direct Link:
- 13( 2003) Protein stability in mixed solvents: a balance of contact interaction and excluded volume. Biophys J 85: 108–125.
- 14, ( 1995) The peptide backbone plays a dominant role in protein stabilization by naturally occurring osmolytes. Biochemistry 34: 12884–12891.
- 15, ( 1997) A naturally occurring protective system in urea-rich cells: mechanism of osmolyte protection of proteins against urea denaturation. Biochemistry 36: 9101–9108.
- 16, , ( 1998) Osmolyte-driven contraction of a random coil protein. Proc Natl Acad Sci USA 95: 9268–9273.
- 17, ( 2001) The osmophobic effect: natural selection of a thermodynamic force in protein folding. J Mol Biol 310: 955–963.
- 18, , ( 2003) Osmolyte effects on kinetics of FKBP12 C22A folding coupled with prolyl isomerization. J Mol Biol 330: 851–866.
- 19, , , ( 2008) Osmolyte effect on the stability and folding of a hyperthermophilic protein. Proteins 71: 110–118.Direct Link:
- 20, ( 2004) Osmolytes induce structure in an early intermediate on the folding pathway of barstar. J Biol Chem 279: 40303–40313.
- 21, , , ( 1989) Mapping the transition state and pathway of protein folding by protein engineering. Nature 340: 122–126.
- 22, ( 1998) Mutagenesis of a buried polar interaction in an SH3 domain: sequence conservation provides the best prediction of stability effects. Biochemistry 37: 16172–16182.
- 23, , , , , ( 1998) The folding kinetics and thermodynamics of the Fyn-SH3 domain. Biochemistry 37: 2529–2537.
- 24, , ( 2002) Hydrophobic core packing in the SH3 domain folding transition state. Nat Struct Biol 9: 126–130.
- 25, , ( 2002) Protein folding kinetics beyond the phi value: using multiple amino acid substitutions to investigate the structure of the SH3 domain folding transition state. J Mol Biol 320: 389–402.
- 26, , , , , ( 2004) Dramatic acceleration of protein folding by stabilization of a nonnative backbone conformation. Proc Natl Acad Sci USA 101: 7954–7959.
- 27, , ( 2007) Protein folding kinetics provides a context-independent assessment of beta-strand propensity in the Fyn SH3 domain. J Mol Biol 373: 764–774.
- 28, , ( 2005) The family feud: do proteins with similar structures fold via the same pathway? Curr Opin Struct Biol 15: 42–49.
- 29, ( 1997) Folding dynamics of the src SH3 domain. Biochemistry 36: 15685–15692.
- 30, ( 1999) The folding transition state between SH3 domains is conformationally restricted and evolutionarily conserved. Nat Struct Biol 6: 1010–1016.
- 31, , , , , ( 1999) Experiment and theory highlight role of native state topology in SH3 folding. Nat Struct Biol 6: 1016–1024.
- 32, , ( 2000) Long-range order in the src SH3 folding transition state. Proc Natl Acad Sci USA 97: 7084–7089.
- 33, , ( 2003) The relationship between conservation, thermodynamic stability, and function in the SH3 domain hydrophobic core. J Mol Biol 333: 641–655.
- 34, , , , , , ( 2008) Theoretical and experimental demonstration of the importance of specific nonnative interactions in protein folding. Proc Natl Acad Sci USA 105: 9999–10004.
- 35, , , ( 2001) Dramatic stabilization of an SH3 domain by a single substitution: roles of the folded and unfolded states. J Mol Biol 307: 913–928.
- 36( 1998) How do small single-domain proteins fold? Fold Des 3: R81–R91.
- 37, ( 1993) Application of physical organic chemistry to engineered mutants of proteins: Hammond postulate behavior in the transition state of protein folding. Proc Natl Acad Sci USA 90: 7814–7818.
- 38, ( 2003) Hammond behavior versus ground state effects in protein folding: evidence for narrow free energy barriers and residual structure in unfolded states. J Mol Biol 327: 867–884.
- 39, ( 1991) Protein engineering in analysis of protein folding pathways and stability. Methods Enzymol 202: 82–112.
- 40, ( 2003) Measuring the stability of partly folded proteins using TMAO. Protein Sci 12: 1522–1529.Direct Link:
- 41, ( 1998) Trifluoroethanol promotes helix formation by destabilizing backbone exposure: desolvation rather than native hydrogen bonding defines the kinetic pathway of dimeric coiled coil folding. Biochemistry 37: 14613–14622.
- 42
- 43, ( 1999) Does trifluoroethanol affect folding pathways and can it be used as a probe of structure in transition states? Nat Struct Biol 6: 831–835.
- 44, , , , , ( 2000) Evidence concerning rate-limiting steps in protein folding from the effects of trifluoroethanol. Nat Struct Biol 7: 58–61.
- 45, , ( 1995) Denaturant m values and heat capacity changes: relation to changes in accessible surface areas of protein unfolding. Protein Sci 4: 2138–2148.Direct Link:
- 46, , ( 2005) Osmolyte trimethylamine-N-oxide does not affect the strength of hydrophobic interactions: origin of osmolyte compatibility. Biophys J 89: 858–866.
- 47, ( 2005) Interactions of trimethylamine N-oxide and water with cyclo-alanylglycine. J Phys Chem B 109: 24142–24151.
- 48, ( 2007) Mixed osmolytes: the degree to which one osmolyte affects the protein stabilizing ability of another. Protein Sci 16: 293–298.Direct Link:
- 49, ( 2007) The influence of urea and trimethylamine-N-oxide on hydrophobic interactions. J Phys Chem B 111: 7932–7933.
- 50, ( 2004) Additive transfer free energies of the peptide backbone unit that are independent of the model compound and the choice of concentration scale. Biochemistry 43: 1329–1342.
- 51, ( 2005) Predicting the energetics of osmolyte-induced protein folding/unfolding. Proc Natl Acad Sci USA 102: 15065–15068.
- 52, ( 2006) Osmolyte-induced protein folding free energy changes. Proteins 63: 290–296.Direct Link:
- 53, , ( 2005) Counteracting osmolyte trimethylamine N-oxide destabilizes proteins at pH below its pKa. Measurements of thermodynamic parameters of proteins in the presence and absence of trimethylamine N-oxide. J Biol Chem 280: 11035–11042.
- 54, , , , ( 1995) How to measure and predict the molar absorption coefficient of a protein. Protein Sci 4: 2411–2423.Direct Link:
- 55, ( 2004) The analysis of protein folding kinetic data produced in protein engineering experiments. Methods 34: 41–50.
- 56, ( 1998) Baseline length and automated fitting of denaturation data. Protein Sci 7: 1262–1263.Direct Link: