Effects of sucrose on conformational equilibria and fluctuations within the native-state ensemble of proteins

Protein Science

Volumn 12, Issue 6, 2003, Pages 1252-1261

  Kim, Yong Sung ^a   Jones, Latoya S ^a,e   Dong, Aichun ^b   Kendrick, Brent S ^c   Chang, Byeong S ^c   Manning, Mark C ^a   Randolph, Theodore W ^d   Carpenter, John F ^a  

^a UNIVERSITY OF COLORADO   (United States)

^b UNIVERSITY OF NORTHERN COLORADO   (United States)

^c AMGEN INC   (United States)

^d UCB 450   (United States)

^e UNIVERSITY OF KANSAS   (United States)

Author keywords

Conformational dynamics; Hydrogen deuterium exchange; Osmolytes; Preferential exclusion; Thermodynamic stability

Indexed keywords

CYTOCHROME C; DEUTERIUM; GUANIDINE; HYDROGEN; PANCREATIC RIBONUCLEASE; PROTEIN; SUCROSE;

ARTICLE; CIRCULAR DICHROISM; CONCENTRATION RESPONSE; ENERGY; FACTORIAL ANALYSIS; NONHUMAN; OSMOLALITY; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN FOLDING; REACTION TIME; STRUCTURE ANALYSIS; THERMODYNAMICS; THERMOSTABILITY;

ANIMALS; CATTLE; CIRCULAR DICHROISM; CYTOCHROMES C; DEUTERIUM; HORSES; HYDROGEN; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEINS; RIBONUCLEASE, PANCREATIC; RIBONUCLEASES; SPECTROPHOTOMETRY, INFRARED; SUCROSE; THERMODYNAMICS;

BOVINAE; EQUUS CABALLUS;

EID: 0037907487     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.0242603     Document Type: Article

References (47)

1. Bai, Y., Sosnick, T.R., Mayne, L., and Englander, S.W. 1995. Protein folding intermediates: Native-state hydrogen exchange. Science 269: 192-197.
2. Barksdale, A.D. and Rosenberg, A. 1983. Acquisition and interpretation of hydrogen exchange data from peptides, polymers, and proteins. Methods Biochem. Anal. 28: 1-111.
3. Burg, M.B., Kwon, E.D., and Peters, E.M. 1996. Glycerophosphocholine and betaine counteract the effect of urea on pyruvate kinase. Kidney Int. Suppl. 57: S100-S104.
4. Burg, M.B., Peters, E.M., Bohren, K.M., and Gabbay, K.H. 1999. Factors affecting counteraction by methylamines of urea effects on aldose reductase. Proc. Natl. Acad. Sci. 96: 6517-6522.
5. Catanzano, F., Giancola, C., Graziano, G., and Barone, G. 1996. Temperature-induced denaturation of ribonuclease S: A thermodynamic study. Biochemistry 35: 13378-13385.
6. Chakshusmathi, G., Ratnaparkhi, G.S., Madhu, P.K., and Varadarajan, R. 1999. Native-state hydrogen-exchange studies of a fragment complex can provide structural information about the isolated fragments. Proc. Natl. Acad. Sci. 96: 7899-7904.
7. de Jongh, H.H., Goormaghtigh, E., and Ruysschaert, J.M. 1995. Tertiary stability of native and methionine-80 modified cytochrome c detected by proton-deuterium exchange using on-line Fourier transform infrared spectroscopy. Biochemistry 34: 172-179.
8. DePaz, R.A., Barnett, C.C., Dale, D.A., Carpenter, J.F., Gaertner, A.L., and Randolph, T.W. 2000. The excluding effects of sucrose on a protein chemical degradation pathway: Methionine oxidation in subtilisin. Arch. Biochem. Biophys. 384: 123-132.
9. Dong, A., Huang, P., and Caughey, W.S. 1990. Protein secondary structures in water from second-derivative amide I infrared spectra. Biochemistry 29: 3303-3308.
10. Dong, A., Prestrelski, S.J., Allison, S.D., and Carpenter, J.F. 1995. Infrared spectroscopic studies of lyophilization- and temperature-induced protein aggregation. J. Pharm. Sci. 84: 415-424.
11. Dong, A., Hyslop, R.M., and Pringle, D.L. 1996. Differences in conformational dynamics of ribonucleases A and S as observed by infrared spectroscopy and hydrogen-deuterium exchange. Arch. Biochem. Biophys. 333: 275-281.
12. Elöve, G.A., Bhuyan, A.K., and Roder, H. 1994. Kinetic mechanism of cytochrome c folding: Involvement of the heme and its ligands. Biochemistry 33: 6925-6935.
13. Fields, P.A., Wahlstrand, B.D., and Somero, G.N. 2001. Intrinsic versus extrinsic stabilization of enzymes: The influence of solutes and temperature on A4-lactate dehydrogenase orthologs from warm-adapted and cold-adapted marine fishes. Eur. J. Biochem. 268: 4497-4505.
14. Foord, R.L. and Leatherbarrow, R.J. 1998. Effect of osmolytes on the exchange rates of backbone amide hydrogens in proteins. Biochemistry 37: 2969-2978.
15. Frauenfelder, H., Sligar, S.G., and Wolynes, P.G. 1991. The energy landscapes and motions of proteins. Science 254: 1598-1603.
16. Garcia-Perez, A. and Burg, M.B. 1991. Renal medullary organic osmolytes. Physiol. Rev. 71: 1081-1115.
17. Goux, W.J. and Hooker, T.M. 1980. Chirooptical properties of proteins. 1. Near-ultraviolet circular dichroism of ribonuclease-S. J. Am. Chem. Soc. 102: 7080-7087.
18. Haris, P.I., Lee, D.C., and Chapman, D. 1986. A Fourier transform infrared investigation of the structural differences between ribonuclease A and ribonuclease S. Biochim. Biophys. Acta 874: 255-265.
19. Hutcheon, G.A., Parker, M.C., and Moore, B.D, 2000. Measuring enzyme motility in organic media using novel H-D exchange methodology. Biotechnol. Bioeng. 70: 262-269.
20. Huyghues-Despointes, B.M., Scholtz, J.M., and Pace, C.N. 1999. Protein conformational stabilities can be determined from hydrogen exchange rates. Nat. Struct. Biol. 6: 910-912.
21. Hvidt, A. and Nielsen, S.O. 1966. Hydrogen exchange in proteins. Adv. Protein Chem. 21: 287-386.
22. Johnson Jr., W.C. 1986. Circular dichroism and its empirical application to biopolymers. Methods Biochem. Anal. 31: 61-163.
23. Karplus, M. and McCammon, J.A. 1983. Dynamics of proteins: Elements and function. Annu. Rev. Biochem. 52: 263-300.
24. Kendrick, B.S., Chang, B.S., Arakawa, T., Peterson, B., Randolph, T.W., Manning, M.C., and Carpenter, J.F. 1997. Preferential exclusion of sucrose from recombinant interleukin-I receptor antagonist: Role in restricted conformational mobility and compaction of native state. Proc. Natl. Acad. Sci. 94: 11917-11922.
25. Kendrick, B.S., Carpenter, J.F., Cleland, J.L., and Randolph, T.W. 1998. A transient expansion of the native state precedes aggregation of recombinant human interferon-γ. Proc. Natl. Acad. Sci. 95: 14142-14146.
26. Kim, K.-S., Fuchs, J.A., and Woodward, C.K. 1993. Hydrogen exchange identifies native-state motional domains important in protein folding. Biochemistry 32: 9600-9608.
27. Kim, Y.-S., Wall, J.S., Meyer, J., Murphy, C., Randolph, T.W., Manning, M.C., Solomon, A., and Carpenter, J.F. 2000. Thermodynamic modulation of light chain amyloid fibril formation. J. Biol. Chem. 275: 1570-1574.
28. Kim, Y.-S., Cape, S.P., Chi, E., Raffen, R., Wilkins-Stevens, P., Stevens, F.J., Manning, M.C., Randolph, T.W., Solomon, A., and Carpenter, J.F. 2001. Counteracting effects of renal solutes on amyloid fibril formation by immunoglobulin light chains. J. Biol. Chem. 276: 1626-1633.
29. Kim, Y.-S., Randolph, T.W., Stevens, F.J., and Carpenter, J.F. 2002. Kinetics and energetics of assembly, nucleation, and growth of aggregates and fibrils for an amyloidogenic protein: Insights into transition states from pressure, temperature, and co-solute studies. J. Biol. Chem. 277: 27240-27246.
30. Krishnan, S., Chi, E.Y., Webb, J.N., Chang, B.S., Shan, D., Goldenberg, M., Manning, M.C., Randolph, T.W., and Carpenter, J.F. 2002. Aggregation of granulocyte colony stimulating factor under physiological conditions: Characterization and thermodynamic inhibition. Biochemistry 41: 6422-6431.
31. Lee, J.C. and Timasheff, S.N. 1981. The stabilization of proteins by sucrose. J. Biol. Chem. 256: 7193-7201.
32. Mayo, S.L. and Baldwin, R.L. 1993. Guanidium chloride induction of partial unfolding in amide proton exchange in RNase A. Science 262: 873-876.
33. Miller, D.W. and Dill, K.A. 1995. A statistical mechanical model for hydrogen exchange in globular proteins. Protein Sci. 4: 1860-1873.
34. Nabedryk-Viala, E., Thiery, C., Calvet, P., and Thiery, J.M. 1976. Hydrogenisotope exchange of oxidized and reduced cytochrome c: A comparison of mass spectrometry and infrared methods. Eur. J. Biochem. 61: 253-258.
35. Neira, J.L., Sevilla, P., Menéndez, M., Bruix, M., and Rico, M. 1999. Hydrogen exchange in ribonuclease A and ribonuclease S: Evidence for residual structure in the unfolded state under native conditions. J. Mol. Biol. 285: 627-643.
36. Nonnenmacher, G., Viala, E., Thiery, J.M., and Calvet, P. 1971. A deuterium-hydrogen exchange study of inhibitor-induced conformational changes in ribonuclease A. Eur. J. Biochem. 21: 393-399.
37. Onuchic, J.N., Luthey-Schulten, Z., and Wolynes, P.G. 1997. Theory of protein folding: The energy landscape perspective. Annu. Rev. Phys. Chem. 48: 545-600.
38. Pace, C.N. 1986. Determination and analysis of urea and guanidine hydrochloride denaturation curves. Methods Enzymol. 131: 266-280.
39. Prestrelski, S.J., Tedeschi, N., Arakawa, T., and Carpenter, J.F. 1993. Dehydration-induced conformational transitions in proteins and their inhibition by stabilizers. Biophys. J. 65: 661-671.
40. Privalov, P.L. and Makhatadze, G.I. 1990. Heat capacity of proteins. II. Partial molar heat capacity of the unfolded polypeptide chain of proteins: Protein unfolding effects. J. Mol. Biol. 213: 385-391.
41. Sreerama, N. and Woody, R.W. 1993. A self-consistent method for the analysis of protein secondary structure from circular dichroism. Anal. Biochem. 209: 32-44.
42. Strickland, E.H. 1972. Interactions contributing to the tyrosyl circular dichroism bands of ribonuclease S and A. Biochemistry 11: 3465-3474.
43. Timasheff, S.N. 1998. Control of protein stability and reactions by weakly interacting cosolvents: The simplicity of the complicated. Adv. Protein Chem. 51: 355-432.
44. Wang, A., Robertson, A.D., and Bolen, D.W. 1995. Effects of a naturally occurring compatible osmolyte on the internal dynamics of ribonuclease A. Biochemistry 34: 15096-15104.
45. Webb, J.N., Webb, S.D., Cleland, J.L., Carpenter, J.F., and Randolph, T.W. 2001. Partial molar volume, surface area, and hydration changes for equilibrium unfolding and formation of aggregation transition state: High pressure and cosolute studies on recombinant human IFN-γ. Proc. Natl. Acad. Sci. 98: 7259-7264.
46. Wooll, J.O., Wrabl, J.O., and Hilser, V.J. 2000. Ensemble modulation as an origin of denaturant-independent hydrogen exchange in proteins. J. Mol. Biol. 301: 247-256.
47. Yancey, P.H., Clark, M.E., Hand, S.C., Bowlus, R.D., and Somero, G.N. 1982. Living with water-stress: Evolution of osmolyte systems. Science 217: 1214-1222.