СТРУКТУРНЫЕ ОСОБЕННОСТИ И СТАБИЛЬНОСТЬ ПРОМЕЖУТОЧНЫХ СОСТОЯНИЙ КАРБОКСИАНГИДРАЗЫ
Аннотация и ключевые слова
Аннотация (русский):
Карбоксиангидраза представляет собой однодоменный глобулярный белок, в нативном состоянии которого преобладает β-структура. В данной работе проведено исследование равновесного разворачивания апоформы карбоксиангидразы понижением рН. Показано, что денатурация белка кислым рН представляет собой переход между тремя состояниями N → I1→ I2. Добавление мочевины к I2 приводит к его разворачиванию до развернутого состояния I2 → U. С помощью аппроксимации переходов равновесного разворачивания белка понижением рН и мочевиной удалось провести оценку стабильностей нативного и двух промежуточных состояний карбоксиангидразы. Описанный подход может быть использован в дальнейшем для исследования влияния аминокислотных замен на сворачивание данного белка. Также в работе были исследованы структурные особенности конформационных состояний карбоксиангидразы, полученные результаты позволили сделать вывод, что состояние I1 находится в составе ассоциатов и содержит ненативные α-спиральные участки.

Ключевые слова:
карбоксиангидраза, сворачивание белка, промежуточное состояние, равновесное разворачивание, круговой дихроизм
Список литературы

1. Kolb V.A., Makeyev E.V., Spirin A.S. Folding of firefly luciferase during translation in a cell-free system. EMBO J., 1994, vol. 13, pp. 3631-3637.; DOI: https://doi.org/10.1002/j.1460-2075.1994.tb06670.x; EDN: https://elibrary.ru/ZUONSG

2. Dill K.A., MacCallum J.L. The protein-folding problem, 50 years on. Science, 2012, vol. 338, pp. 1042-1046.; DOI: https://doi.org/10.1126/science.1219021; EDN: https://elibrary.ru/RJHPAL

3. Anfinsen C.B. The formation and stabilization of protein structure. Biochem. J., 1972, vol. 128, pp. 737-749.

4. Honig B. Protein folding: from the Levintal paradox to structure prediction. J. Mol. Biol., 1999, vol. 293, pp. 283-293.; DOI: https://doi.org/10.1006/jmbi.1999.3006; EDN: https://elibrary.ru/KPIPAF

5. Privalov P.L., Khechinashvili N.N. A thermodynamic approach to the problem of stabilization of globular protein structure: a calorimetric study. J. Mol. Biol., 1974, vol. 86, pp. 665-684.; DOI: https://doi.org/10.1016/0022-2836(74)90188-0; EDN: https://elibrary.ru/ZYDMRD

6. Privalov P.L. Intermediate states in protein folding. J. Mol. Biol., 1996, vol. 258, pp. 707-725.; DOI: https://doi.org/10.1006/jmbi.1996.0280; EDN: https://elibrary.ru/YBQLHQ

7. Brockwell D.J., Radford S.E. Intermediates: ubiquitous species on folding energy landscapes? Curr. Opin. Struct. Biol., 2007, vol. 17, pp. 30-37.

8. Baldwin R.L., Rose G.D. Is protein folding hierarchic? I. Local structure and peptide folding. Trends Biochem. Sci., 1999, vol. 24, pp. 26-33.

9. Calamai M., Chiti F., Dobson C.M. Amyloid fibril formation can proceed from different conformations of a partially unfolded protein. Biophys. J., 2005, vol. 89, pp. 4201-4210.; DOI: https://doi.org/10.1529/biophysj.105.068726; EDN: https://elibrary.ru/MJARHT

10. Apetri A.C., Surewicz K., Surewicz W.K. The effect of disease-associated mutations on the folding pathway of human prion protein. J. Biol. Chem., 2004, vol. 279, pp. 18008-18014.

11. Dolgikh D.A., Gilmanshin R.I., Brazhnikov E.V., Bychkova V.E., Semisotnov G.V., Venyaminov S., Ptitsyn O.B. Alpha-lactalbumin: Compact state with fluctuating tertiary structure? FEBS Letters, 1981, vol. 136, pp. 311-315.; DOI: https://doi.org/10.1016/0014-5793(81)80642-4; EDN: https://elibrary.ru/XUNCMH

12. Ptitsyn O.B., Pain R.H., Semisotnov G.V., Zerovnik E., Razgulyaev O.I. Evidence for a molten globule state as a general intermediate in protein folding. FEBS Letters, 1990, vol. 262, pp. 20-24.; DOI: https://doi.org/10.1016/0014-5793(90)80143-7; EDN: https://elibrary.ru/XVTSBM

13. Naiyer A., Hassan M.I., Islam A., Sundd M., Ahmad F. Structural characterization of MG and pre-MG states of proteins by MD simulations, NMR, and other techniques. J. Biomol. Struct. Dyn., 2015, vol. 33, pp. 2267-2284.; DOI: https://doi.org/10.1080/07391102.2014.999354; EDN: https://elibrary.ru/UUTKSR

14. Hughson F.M., Wright P.E., Baldwin R.L. Structural characterization of a partly folded apomyoglobin intermediate. Science, 1990, vol. 249, pp. 1544-1548.; EDN: https://elibrary.ru/BHQEDD

15. Uversky V.N., Ptitsyn O.B. Further evidence on the equilibrium ‘pre-molten globule state’: Four-state guanidinium chloride-induced unfolding of carbonic anhydrase b at low temperature. J. Mol. Biol., 1996, vol. 255, pp. 215-228.; DOI: https://doi.org/10.1006/jmbi.1996.0018; EDN: https://elibrary.ru/GRQLJF

16. Uversky V.N., Ptitsyn O.B. ‘Partly folded’ state, a new equilibrium state of protein molecules: Four-state guanidinium chloride-induced unfolding of beta-lactamase at low temperature. Biochemistry, 1994, vol. 33, pp. 2782-2791.; DOI: https://doi.org/10.1021/bi00176a006; EDN: https://elibrary.ru/SIXZWI

17. Uversky V.N., Goto Y. Acid denaturation and anion-induced folding of globular proteins: multitude of equilibrium partially folded intermediates. Curr. Protein Pept. Let., 2009, vol. 10, pp. 447-455.

18. Neuweiler H., Doose S., Sauer M. A microscopic view of miniprotein folding: enhanced folding efficiency through formation of an intermediate. Proc. Natl. Acad. Sci. USA, 2005, vol. 102, pp. 16650-16655.

19. Forge V., Hoshino M., Kuwata K., Arai M., Kuwajima K., Batt C.A., Goto Y. Is folding of beta-lactoglobulin non-hierarchic? Intermediate with native-like beta-sheet and non-native alpha-helix. J. Mol. Biol., 2000, vol. 296, pp. 1039-1051.

20. Yang J.J., Yang H., Ye Y., Hopkins H.Jr., Hastings G. Temperature-induced formation of non-native intermediate state of the all beta-sheet protein CD2. Cell Biochem. Biophys., 2002, vol. 36, pp. 1-18.

21. Sakurai K., Fujioka S., Konuma T., Yagi M., Goto Y. A circumventing role for the non-native intermediate in the folding of β-lactoglobulin. Biochemistry, 2011, vol. 50, pp. 6498-6507.; DOI: https://doi.org/10.1021/bi200241a; EDN: https://elibrary.ru/OKWDEL

22. Friel C.T., Beddard G.S., Radford S.E. Switching two-state to three-state kinetics in the helical protein Im9 via the optimisation of stabilising non-native interactions by design. J. Mol. Biol., 2004, vol. 342, pp. 261-273.; DOI: https://doi.org/10.1016/j.jmb.2004.06.076; EDN: https://elibrary.ru/KFOZGJ

23. Uzawa T., Nishimura C., Akiyama S., Ishimori K., Takahashi S., Dyson H.J., Wright P.E. Hierarchical folding mechanism of apomyoglobin revealed by ultra-fast H/D exchange coupled with 2D NMR. Proc. Natl. Acsd. Sci. USA, 2008, vol. 105, pp. 13859-13864.

24. Maisuradze G.G., Zhou R., Liwo A., Xiao Y., Scheraga H.A. Effects of mutation, truncation, and temperature on the folding kinetics of WW domain. J. Mol. Biol., 2012, vol. 420, pp. 350-365.; DOI: https://doi.org/10.1016/j.jmb.2012.04.027; EDN: https://elibrary.ru/YACHHQ

25. Es-Haghi A., Shariatizi S., Ebrahim-Habibi A., Nemat-Gorgani M. Amyloid fibrillation in native and chemically-modified forms of carbonic anhydrase II: role of surface hydrophobicity. Biochim. Biophys. Acta, 2012, vol. 1824, pp. 468-477.

26. Gard D.K., Kundu B. Clues for divergent, polymorphic amyloidogenesisi through dissection of amyloid forming steps of bovine carbonic anhydrase and its critical amyloid forming stretch. Biochim. Biophys. Acta., 2016, vol. 1864, pp. 794-804.

27. Krishnamurthy V.M., Kaufman G.K., Urbach A.R., Gitlin I., Gudiksen K.L., Weibel D.B., Whitesides G.M. Carbonic anhydrase as a model for biophysical and physical-organic studies of proteins and protein-ligand binding. Chem. Rev., 2008, vol. 108, pp. 946-1051.; DOI: https://doi.org/10.1021/cr050262p; EDN: https://elibrary.ru/KYEUSO

28. Saito R., Sato T., Ikai A., Tanaka N. Structure of bovine carbonic anhydrase II at 1.95 A resolution. Acta Crystallogr. D. Biol. Crystallogr., 2004, vol. 60, pp. 792-795.

29. Uversky V.N., Ptitsyn O.B. Further evidence on the equilibrium “pre-molten globule state”: four-state guanidinum chloride-induced unfolding of carbonic anhydrase B at low temperature. J. Mol. Biol., 1996, vol. 255, pp. 215-228.; DOI: https://doi.org/10.1006/jmbi.1996.0018; EDN: https://elibrary.ru/GRQLJF

30. Bushmarina N.A., Kuznetsova I.M., Biktashev A.G., Turoverov K.K., Uversky V.N. Partially folded conformations in the folding pathway of bovine carbonic anhydrase II: a fluorescence spectroscopic analysis. Chembiochem., 2001, vol. 2, pp. 813-821.

31. Ptitsyn O.B., Pain R.H., Semisotnov G.V., Zerovnik E., Razgulyaev O.I. Evidence for a molten globule state as a general intermediate in protein folding. FEBS Lett., 1990, vol. 262, pp. 20-24.; DOI: https://doi.org/10.1016/0014-5793(90)80143-7; EDN: https://elibrary.ru/XVTSBM

32. Dolgikh D.A., Kolomiets A.P., Bolotina I.A., Ptitsyn O.B. ‘Molten-globule’ state accumulates in carbonic anhydrase folding. FEBS Lett., 1984, vol. 165, pp. 88-92.; DOI: https://doi.org/10.1016/0014-5793(84)80020-4; EDN: https://elibrary.ru/XLTBLW

33. Melnik B.S., Marchenkov V.V., Evdokimov S.R., Samatova E.N., Kotova N.V. Multy-state protein: determination of carbonic anhydrase free-energy landscape. Biochem. Biophys. Res. Commun., 2008, vol. 369, pp. 701-706.; DOI: https://doi.org/10.1016/j.bbrc.2008.02.096; EDN: https://elibrary.ru/LLBQUP

34. McCoy L.F. Jr, Rowe E.S., Wong K.P. Multiparameter kinetic study on the unfolding and refolding of bovine carbonic anhydrase B. Biochemistry, 1980, vol. 19, pp. 4736-4743.

35. Andersson D., Hammarstrom P., Carlsson U. Cofactor-induced refolding: refolding of molten globule carbonic anhydrase induced by Zn(II) and Co(II). Biochemistry, 2001, vol. 40, pp. 2653-2661.; DOI: https://doi.org/10.1021/bi000957e; EDN: https://elibrary.ru/LMLRHL

36. Laemmli U.K. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature, 1970, vol. 227, pp. 680-685.

37. Gill S.C., von Hippel P.H. Calculation of protein extinction coefficients from amino acid sequence data. Anal. Biochem., 1989, vol. 182, pp. 319-326.

38. Kawahara K., Tanford C. Viscosity and density of aqueous solutions of urea and guanidine hydrochloride. J. Biol. Chem., 1966, vol. 241, pp. 3228-3232.

39. Oliveberg M., Fersht A.R. Formation of electrostatic interactions on the protein-folding pathway. Biochemistry, 1996, vol. 35, pp. 2726-2737.

40. Jamin M., Geierstanger B., Baldwin R.L. The pKa of His-24 in the folding transition state of apomyoglobin. Proc. Natl. Acad. Sci., 2001, vol. 98, pp. 6127-6131.

41. Bolen D.W., Santoro M.M. Unfolding free energy changes determined by the linear extrapolation method. 2. Incorporation of delta G degrees N-U values in a thermodynamic cycle. Biochemistry, 1998, vol. 27, pp. 8069-8074.

42. Pace C.N. Determination and analysis of urea and guanidine hydrochloride denaturation curves. Methods Enzymol., 1986, vol. 131, pp. 266-280.; DOI: https://doi.org/10.1016/0076-6879(86)31045-0; EDN: https://elibrary.ru/XVFKRE

43. Kelly S.M., Price N.C. The use of circular dichroism in the investigation of protein structure and function. Curr. Protein Pept. Sci., 2000, vol. 1, pp. 349-384.

44. Semisotnov G.V., Rodionova N.A., Razgulyaev O.I., Uversky V.N., Gripas’ A.F., Gilmanshin R.I. Study of the “molten globule” intermediate state in protein folding by a hydrophobic fluorescent probe. Biopolymers, 1991, vol. 31, pp. 119-128.; DOI: https://doi.org/10.1002/bip.360310111; EDN: https://elibrary.ru/XYFRLP

45. Andrade M.A., Chacon P., Merelo J.J., Moran F. Evaluation of secondary structure of proteins from UV circular dichroism spectra using an unsupervised learning neural network. Protein Eng., 1993, vol. 6, pp. 383-390.; EDN: https://elibrary.ru/IVYNAN

46. Chen E., Everett M.L., Holzknecht Z.E., Holzknecht R.A., Lin S.S., Bowles D.E., Parker W. Short-lived alpha-helical intermediates in the folding of beta-sheet proteins. Biochemistry, 2010, vol. 49, pp. 5609-5619.; DOI: https://doi.org/10.1021/bi100288q; EDN: https://elibrary.ru/MXSRLX

47. Lim V.I. Structural principles of the globular organization of protein chains. A stereochemical theory of globular protein secondary structure. J. Mol. Biol., 1974, vol. 88, pp. 857-872.

48. Kumar T.A. CFSSP: Chou and Fasman secondary structure prediction server. Wide Spectrum, 2013, vol. 1, pp. 15-19.


Войти или Создать
* Забыли пароль?