Size-exclusion chromatography in structural analysis of intrinsically disordered proteins

Methods in Molecular Biology

Volumn 896, Issue , 2012, Pages 179-194

  Uversky, Vladimir N ^a,b  

^a UNIVERSITY OF SOUTH FLORIDA   (United States)

^b INSTITUTE FOR BIOLOGICAL INSTRUMENTATION   (Russian Federation)

Author keywords

Coil like; Compaction; Gel filtration chromatography; Gel permeation chromatography; Hydrodynamic dimensions; Induced folding; Intrinsically disordered protein; Molecular mass; Molten globule; Pre molten globule; Size exclusion chromatography

Indexed keywords

PROTEIN; SYNUCLEIN;

ARTICLE; CALIBRATION; CHEMISTRY; GEL CHROMATOGRAPHY; HUMAN; HYDRODYNAMICS; METHODOLOGY; PROTEIN FOLDING;

CALIBRATION; CHROMATOGRAPHY, GEL; HUMANS; HYDRODYNAMICS; PROTEIN FOLDING; PROTEINS; SYNUCLEINS;

EID: 84865346866     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-4614-3704-8_11     Document Type: Article

References (47)

1. Tanford C (1968) Protein denaturation. Adv Protein Chem 23:121-282
2. Uversky VN (1993) Use of fast protein sizeexclusion liquid chromatography to study the unfolding of proteins which denature through the molten globule. Biochemistry 32:13288-13298
3. Uversky VN (1994) Gel-permeation chromatography as a unique instrument for quantitative and qualitative analysis of protein denaturation and unfolding. Int J Bio-Chromatogr 1:103-114
4. Uversky VN (2003) Protein folding revisited. A polypeptide chain at the folding-misfoldingnonfolding cross-roads: which way to go? Cell Mol Life Sci 60:1852-1871
5. Porath J, Flodin P (1959) Gel filtration: a method for desalting and group separation. Nature 183:1657-1659
6. Porath J (1968) Molecular sieving and adsorption. Nature 218:834-838
7. Andrews P (1965) The gel-filtration behaviour of proteins related to their molecular weights over a wide range. Biochem J 96:595-606
8. Ackers GK (1967) Molecular sieve studies of interacting protein systems. I. Equations for transport of associating systems. J Biol Chem 242:3026-3034
9. Ackers GK (1970) Analytical gel chromatography of proteins. Adv Protein Chem 24:343-446
10. le Maire M, Ghazi A, Moller JV, Aggerbeck LP (1987) The use of gel chromatography for the determination of sizes and relative molecular masses of proteins. Interpretation of calibration curves in terms of gel-pore-size distribution. Biochem J 243:399-404
11. Le Maire M, Aggerbeck LP, Monteilhet C, Andersen JP, Moller JV (1986) The use of high-performance liquid chromatography for the determination of size and molecular weight of proteins: a caution and a list of membrane proteins suitable as standards. Anal Biochem 154:525-535
12. Potschka M(1987) Universal calibration of gel permeation chromatography and determination of molecular shape in solution. Anal Biochem 162:47-64
13. Corbett RJ, Roche RS (1984) Use of highspeed size-exclusion chromatography for the study of protein folding and stability. Biochemistry 23:1888-1894
14. Fish WW, Reynolds JA, Tanford C (1970) Gel chromatography of proteins in denaturing solvents. Comparison between sodium dodecyl sulfate and guanidine hydrochloride as denaturants. J Biol Chem 245:5166-5168
15. Corbett RJ, Roche RS (1983) The unfolding mechanism of thermolysin. Biopolymers 22:101-105
16. Endo S, Saito Y, Wada A (1983) Denaturantgradient chromatography for the study of protein denaturation: principle and procedure. Anal Biochem 131:108-120
17. Lau SY, Taneja AK, Hodges RS (1984) Synthesis of a model protein of defined secondary and quaternary structure. Effect of chain length on the stabilization and formation of twostranded alpha-helical coiled-coils. J Biol Chem 259:13253-13261
18. Brems DN, Plaisted SM, Havel HA, Kauffman EW, Stodola JD, Eaton LC, White RD (1985) Equilibrium denaturation of pituitary-and recombinant-derived bovine growth hormone. Biochemistry 24:7662-7668
19. Gupta BB (1983) Determination of native and denatured milk proteins by high-performance size exclusion chromatography. J Chromatogr 282:463-475
20. Uversky VN, Semisotnov GV, Pain RH, Ptitsyn OB (1992) 'All-or-none' mechanism of the molten globule unfolding. FEBS Lett 314:89-92
21. Uversky VN, Ptitsyn OB (1994) "Partly folded" state, a new equilibrium state of protein molecules: four-state guanidinium chloride-induced unfolding of beta-lactamase at low temperature. Biochemistry 33:2782-2791
22. Uversky VN, Ptitsyn OB (1996) Further evidence on the equilibrium "pre-molten globule state": four-state guanidinium chlorideinduced unfolding of carbonic anhydrase B at low temperature. J Mol Biol 255:215-228
23. Withka J, Moncuse P, Baziotis A, Maskiewicz R (1987) Use of high-performance sizeexclusion, ion-exchange, and hydrophobic interaction chromatography for the measurement of protein conformational change and stability. J Chromatogr 398:175-202
24. Uversky VN, Li J, Fink AL (2001) Evidence for a partially folded intermediate in alphasynuclein fibril formation. J Biol Chem 276:10737-10744
25. Receveur-Brechot V, Bourhis JM, Uversky VN, Canard B, Longhi S (2006) Assessing protein disorder and induced folding. Proteins 62:24-45
26. Uversky VN, Li J, Souillac P, Millett IS, Doniach S, Jakes R, Goedert M, Fink AL (2002) Biophysical properties of the synucleins and their propensities to fibrillate: inhibition of alpha-synuclein assembly by beta-and gammasynucleins. J Biol Chem 277:11970-11978
27. Uversky VN, Gillespie JR, Millett IS, Khodyakova AV, Vasiliev AM, Chernovskaya TV, Vasilenko RN, Kozlovskaya GD, Dolgikh DA, Fink AL, Doniach S, Abramov VM (1999) Natively unfolded human prothymosin alpha adopts partially folded collapsed conformation at acidic pH. Biochemistry 38:15009-15016
28. Uversky VN, Permyakov SE, Zagranichny VE, Rodionov IL, Fink AL, Cherskaya AM,Wasserman LA, Permyakov EA (2002) Effect of zinc and temperature on the conformation of the gamma subunit of retinal phosphodiesterase: a natively unfolded protein. J Proteome Res 1:149-159
29. Meunier DM (1997) Molecular weight determinations. In: Settle F (ed) Handbook of instrumental techniques for analytical chemistry. Prentice-Hall, Inc., Upper Saddle River, NJ, pp 853-866
30. Ui N (1979) Rapid estimation of the molecular weights of protein polypeptide chains using high-pressure liquid chromatography in 6 M guanidine hydrochloride. Anal Biochem 97:65-71
31. Grossberg AY, Khohlov AR (1989) Statistical physics of macromolecules. Nauka, Moscow
32. Abramov VM, Vasiliev AM, Khlebnikov VS, Vasilenko RN, Kulikova NL, Kosarev IV, Ishchenko AT, Gillespie JR, Millett IS, Fink AL, Uversky VN (2002) Structural and functional properties of Yersinia pestis Caf1 capsular antigen and their possible role in fulminant development of primary pneumonic plague. J Proteome Res 1:307-315
33. Tcherkasskaya O, Davidson EA, Uversky VN (2003) Biophysical constraints for protein structure prediction. J Proteome Res 2:37-42
34. Tcherkasskaya O, Uversky VN (2001) Denatured collapsed states in protein folding: example of apomyoglobin. Proteins 44:244-254
35. Tcherkasskaya O, Uversky VN (2003) Polymeric aspects of protein folding: a brief overview. Protein Pept Lett 10:239-245
36. Uversky VN (2002) Natively unfolded proteins: a point where biology waits for physics. Protein Sci 11:739-756
37. Uversky VN (2002) What does it mean to be natively unfolded? Eur J Biochem 269:2-12
38. Ptitsyn OB (1995) Molten globule and protein folding. Adv Protein Chem 47:83-229
39. Ptitsyn OB, Bychkova VE, Uversky VN (1995) Kinetic and equilibrium folding intermediates. Philos Trans R Soc Lond B Biol Sci 348:35-41
40. Permyakov SE, Millett IS, Doniach S, Permyakov EA, Uversky VN (2003) Natively unfolded C-terminal domain of caldesmon remains substantially unstructured after the effective binding to calmodulin. Proteins 53:855-862
41. Uversky VN, Lee HJ, Li J, Fink AL, Lee SJ (2001) Stabilization of partially folded conformation during alpha-synuclein oligomerization in both purified and cytosolic preparations. J Biol Chem 276:43495-43498
42. Li BQ, Fu T, Gong WH, Dunlop N, Kung H, Yan Y, Kang J, Wang JM (2000) The flavonoid baicalin exhibits anti-inflammatory activity by binding to chemokines. Immunopharmacology 49:295-306
43. Ikezoe T, Chen SS, Heber D, Taguchi H, Koeffler HP (2001) Baicalin is a major component of PC-SPES which inhibits the proliferation of human cancer cells via apoptosis and cell cycle arrest. Prostate 49:285-292
44. Gao Z, Huang K, Xu H (2001) Protective effects of flavonoids in the roots of Scutellaria baicalensis Georgi against hydrogen peroxideinduced oxidative stress in HS-SY5Y cells. Pharmacol Res 43:173-178
45. Shieh DE, Liu LT, Lin CC (2000) Antioxidant and free radical scavenging effects of baicalein, baicalin and wogonin. Anticancer Res 20:2861-2865
46. Zhu M, Rajamani S, Kaylor J, Han S, Zhou F, Fink AL (2004) The flavonoid baicalein inhibits fibrillation of alpha-synuclein and disaggregates existing fibrils. J Biol Chem 279:26846-26857
47. Hong DP, Fink AL, Uversky VN (2008) Structural characteristics of alpha-synuclein oligomers stabilized by the flavonoid baicalein. J Mol Biol 383:214-223