The effect of the Glu342Lys mutation in α1-antitrypsin on its structure, studied by molecular modelling methods.

• Authors: Grzegorz Jezierski , Marta Pasenkiewicz-Gierula
• Languages of publication: EN

Abstracts

EN

The structure of native α1-antitrypsin, the most abundant protease inhibitor in human plasma, is characterised primarily by a reactive loop containing the centre of proteinase inhibition, and a β-sheet composed of five strands. Mobility of the reactive loop is confined as a result of electrostatic interactions between side chains of Glu342 and Lys290, both located at the junction of the reactive loop and the β structure. The most common mutation in the protein, resulting in its inactivation, is Glu342→Lys, named the Z mutation. The main goal of this work was to investigate the influence of the Z mutation on the structure of α1-antitrypsin. Commonly used molecular modelling methods have been applied in a comparative study of two protein models: the wild type and the Z mutant. The results indicate that the Z mutation introduces local instabilities in the region of the reactive loop. Moreover, even parts of the protein located far apart from the mutation region are affected. The Z mutation causes a relative change in the total energy of about 3%. Relatively small root mean square differences between the optimised structures of the wild type and the Z mutant, together with detailed analysis of 'conformational searching' process, lead to the hypothesis that the Z mutation principally induces a change in the dynamics of α1-antitrypsin.

Keywords

EN

serpins; protein structure; energy minimisation; molecular dynamics simulation

• Publisher: Polish Biochemical Society
• Journal: Acta Biochimica Polonica
• Year: 2001
• Volume: 48
• Issue: 1
• Pages: 65-75

Dates

published

2001

revised

2001-01-26

received

2001-01-8

accepted

2001-02-6

Contributors

author

Grzegorz Jezierski

• Biophysics Department, Institute of Molecular Biology, Jagiellonian University, Kraków, Poland

author

Marta Pasenkiewicz-Gierula

• Biophysics Department, Institute of Molecular Biology, Jagiellonian University, Kraków, Poland

References

• 1. Holaday, S.K., Martin, B.M., Fletcher, P.L. & Krishna, N.R. (2000) NMR solution structure of butantoxin. Arch. Biochem. Biophys. 379, 18-27.
• 2. Gettins, P.G.W., Patston, P.A. & Olson, S.T. (1996) Serpins: Structure, Function and Biology; pp. 1, 111, 177. Chapman & Hall, R.G. Landes and Austin, Texas.
• 3. Parmar, J.S. & Lomas, D.A. (2000) α1-Antitrypsin deficiency, the serpinopathies and conformational disease. J. R. Coll. Physicians. Lond. 34, 295-300.
• 4. Elliott, P.R., Pei, X.Y., Dafforn, T.R. & Lomas, D.A. (2000) Topography of a 2.0 Å structure of α1-antitrypsin reveals targets for rational drug design to prevent conformational disease. Protein. Sci. 9, 1274-1281.
• 5. Lomas, D.A. (2000) Loop-sheet polymerization: The mechanism of α1-antitrypsin deficiency. Respir. Med. 94, S3-S6.
• 6. Sivasothy, P., Dafforn, T.R., Gettins, P.G. & Lomas, D.A. (2000) Pathogenic α1-antitrypsin polymers are formed by reactive loop-β-sheet A linkage. J. Biol. Chem. 275, 33663-33668.
• 7. Loebermann, H., Tokuoka, R., Deisenhofer, J. & Huber, R. (1984) Human α1-proteinase inhibitor. Crystal structure analysis of two crystal modifications, molecular model and preliminary analysis of the implications for function. J. Mol. Biol. 177, 531-556.
• 8. Elliott, P.R., Abrahams, J. & Lomas, D.A. (1998) Wild-type α1-antitrypsin is in the canonical inhibitory conformation. J. Mol. Biol. 275, 419-425.
• 9. Mahadeva, R., Chang, W.S., Dafforn, T.R., Oakley, D.J., Foreman, R.C., Calvin, J., Wight, D.G. & Lomas, D.A. (1999) Heteropolymerization of S, I, and Z α1-antitrypsin and liver cirrhosis. J. Clin. Invest. 103, 999-1006.
• 10. Elliott, P.R., Bilton, D. & Lomas, D.A. (1998) Lung polymers in Z α1-antitrypsin deficiency-related emphysema. Am. J. Respir. Cell. Mol. Biol. 18, 670-674.
• 11. Carrell, R.W., Lomas, D.A., Sidhar, S. & Foreman, R. (1996) α1-Antitrypsin deficiency. A conformational disease. Chest 110, 243S-247S.
• 12. Lomas, D.A., Evans, D.L., Finch, J.T. & Carrell, R.W. (1992) The mechanism of Z α1-antitrypsin accumulation in the liver. Nature 357, 605-607.
• 13. Yu, M., Lee, K.N. & Kim, J. (1995) The Z type variation of human α1-antitrypsin causes a protein folding defect. Nat. Struct. Biol. 2, 363-367.
• 14. Lomas, D.A., Evans, D.L., Stone, S.R., Chang, W.S. & Carrell, R.W. (1993) Effect of the Z mutation on the physical and inhibitory properties of α1-antitrypsin. Biochemistry 32, 500-508.
• 15. Dunstone, M.A., Dai, W., Whisstock, J.C., Rossjohn, J., Pike, R.N., Feil, S.C., Le Bonniec, B.F., Parker, M.W. & Bottomley, S.P. (2000) Cleaved antitrypsin polymers at atomic resolution. Protein Sci. 9, 417-420.
• 16. Huntington, J.A., Pannu, N.S., Hazes, B., Read, R.J., Lomas, D.A. & Carrell, R.W. (1999) A 2.6 Å structure of a serpin polymer and implications for conformational disease. J. Mol. Biol. 293, 449-455.
• 17. Dafforn, T.R., Mahadeva, R., Elliott, P.R., Sivasothy, P. & Lomas, D.A. (1999) A Kinetic mechanism for the polymerization of α1-antitrypsin. J. Biol. Chem. 274, 9548-9555.
• 18. Koloczek, H., Banbula, A., Salvesen G.S. & Potempa, J. (1996) Serpin α1-proteinase inhibitor probed by intrinsic tryptophan fluorescence spectroscopy. Protein Sci. 5, 2226-2235.
• 19. Carrell, R.W., Stein, P.E., Fermi, G. & Wardell, M.R. (1994) Biological implications of a 3Å structure of dimeric antithrombin. Structure 2, 257-270.
• 20. Jorgensen, W.L. & Tirado-Rives, J. (1988) The OPLS potential functions for proteins. Energy minimizations for crystals of cyclic peptides and crambin. J. Am. Chem. Soc. 110, 1657-1666.
• 21. Ryckaert, J.-P., Ciccotti G. & Berendsen, H.J.C. (1977) Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes. J. Comp. Phys. 23, 327-341.
• 22. Berendsen, H.J.C., Postma, J.P.M., van Gunsteren, W.F., DiNola, A. & Haak, J.R. (1984) Molecular dynamics with coupling to an external bath. J. Chem. Phys. 81, 3684-3690.
• 23. Pearlman, D.A., Case, D.A., Caldwell, J.C., Seibel, G.L., Singh, U.C., Weiner, P. & Kollman, P.A. (1991) AMBER 4.0. University of California, San Francisco.
• 24. Tejero, R., Bassolino-Klimas, D., Bruccoleri, R.E. & Montelione, G.T. (1996) Simulated annealing with restrained molecular dynamics using CONGEN. Protein Sci. 5, 578-592.
• 25. Li, H., Tejero, R., Monleon, D., Bassolino- Klimas, D., Abate-Shen, C., Bruccoleri, R.E. & Montelione, G.T. (1997) Homology modeling using simulated annealing of restrained molecular dynamics and conformational search calculations with CONGEN. Protein Sci. 6, 956-970.
• 26. BIOSYM/MSI (1997, 1998) Molecular Simulations, San Diego, California.
• 27. Kabsch, W. & Sander, Ch. (1983) Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22, 2577-2637.