Stability and dynamics of the porcine odorant-binding protein

Biochemistry

Volumn 46, Issue 39, 2007, Pages 11120-11127

  Staiano, Maria ^a   D'Auria, Sabato ^a   Varriale, Antonio ^a   Rossi, Mose' ^a   Marabotti, Anna ^b   Fini, Carlo ^c   Stepanenko, Olesya V ^d   Kuznetsova, Irina M ^d   Turoverov, Konstantin K ^d  

^a INSTITUTE OF PROTEIN BIOCHEMISTRY   (Italy)

^b CNR   (Italy)

^c UNIVERSITY OF PERUGIA   (Italy)

^d INSTITUTE OF CYTOLOGY   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

BOUND WATER MOLECULES; FLUORESCENCE ANALYSIS; PORCINE ODORANT BINDING PROTEINS; UV CIRCULAR DICHROISM MEASUREMENTS;

DENATURATION; FLUORESCENCE; FREE ENERGY; HYDROCHLORIC ACID;

PROTEINS;

BINDING PROTEIN; GUANIDINE; LYSINE; PORCINE ODORANT BINDING PROTEIN; UNCLASSIFIED DRUG;

ARTICLE; CIRCULAR DICHROISM; DYNAMICS; ENERGY; FLUORESCENCE; FLUORESCENCE SPECTROSCOPY; NONHUMAN; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN DENATURATION; PROTEIN FOLDING; PROTEIN STABILITY; SWINE;

ANIMALS; CIRCULAR DICHROISM; GUANIDINE; PROTEIN DENATURATION; PROTEIN STRUCTURE, TERTIARY; RECEPTORS, ODORANT; SPECTROMETRY, FLUORESCENCE; SWINE; THERMODYNAMICS; TRYPTOPHAN;

SUS;

EID: 34848923766     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi7008129     Document Type: Article

References (42)

1. Flower, D. R., North, A. C., and Sansom, C. E. (2000) The lipocalin protein family: structural and sequence overview, Biochim. Biophys. Acta 1482, 9-24.
2. Nygren, P. A., and Skerra, A. (2004) Binding proteins from alternative scaffolds, J. Immunol. Methods 290, 3-28.
3. Skerra, A. (2000) Lipocalins as a scaffold, Biochim. Biophys. Acta 1482, 337-350.
4. Schlehuber, S., and Skerra, A. (2005) Lipocalins in drug discovery: from natural ligand-binding proteins to "anticalins", Drug Discovery Today 10, 23-33.
5. Korndorfer, I. P., Schlehuber, S., and Skerra, A. (2003) Structural mechanism of specific ligand recognition by a lipocalin tailored for the complexation of digoxigenin, J. Mol. Biol. 330, 385-396.
6. Tegoni, M., Pelosi, P., Vincent, F., Spinelli, S., Campanacci, V., Grolli, S., Ramoni, R., and Cambillau, C. (2000) Mammalian odorant binding proteins, Biochim. Biophys. Acta 1482, 229-240.
7. Tegoni, M., Ramoni, R., Bignetti, E., Spinelli, S., and Cambillau, C. (1996) Domain swapping creates a third putative combining site in bovine odorant binding protein dimer, Nat. Struct. Biol. 3, 863-867.
8. Bianchet, M. A., Bains, G., Pelosi, P., Pevsner, J., Snyder, S. H., Monaco, H. L., and Amzel, L. M. (1996) The three-dimensional structure of bovine odorant binding protein and its mechanism of odor recognition, Nat. Struct. Biol. 3, 934-939.
9. Spinelli, S., Ramoni, R., Grolli, S., Bonicel, J., Cambillau, C., and Tegoni, M. (1998) The structure of the monomeric porcine odorant binding protein sheds light on the domain swapping mechanism, Biochemistry 37, 7913-7918.
10. Dal Monte, M., Andreini, I., Revoltella, R., and Pelosi, P. (1991) Purification and characterization of two odorant-binding proteins from nasal tissue of rabbit and pig, Comp. Biochem. Physiol. B 99, 445-451.
11. Turoverov, K. K., Biktashev, A. G., Dorofeiuk, A. V., and Kuznelsova, I. M. (1998) A complex of apparatus and programs for the measurement of spectral, polarization and kinetic characteristics of fluorescence in solution, Tsitologiia 40, 806-817.
12. Turoverov, K. K., and Kuznetsova, I. M. (2003) Intrinsic fluorescence of actin, J. Fluoresc. 13, 41-57.
13. Marquardt, D. W. (1963) An algorithm for least-squares estimation of nonlinear parameters, J. Soc. Ind. Appl. Math. 11, 431-441.
14. Eftink, M. R. (1991) Fluorescence quenching: theory and applications, in Topics in fluorescence spectroscopy (Lakowicz, J. R., Ed. ) Vol. 2, pp 53-120, Plenum Press, New York and London.
15. Berman, H., Henrick, K., Nakamura, H., and Markley, J. L. (2007) The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data, Nucleic Acids Res. 35, D301-D303.
16. Turoverov, K. K., Kuznetsova, I. M., and Zaitsev, V. N. (1985) The environment of the tryptophan residue in Pseudomonas aeruginosa azurin and its fluorescence properties, Biophys. Chem. 23, 79-89.
17. Kuznetsova, I. M., and Turoverov, K. K. (1998) What determines the characteristics of the intrinsic UV-fluorescence of proteins? Analysis of the properties of the microenvironment and features of the localization of their tryptophan residues, Tsitologiia 40, 747-762.
18. Forster, Th. (1960) Transfer mechanisms of electronic excitation energy, Rad. Res. Suppl. 2, 326-339.
19. Dale, R. E., and Eisinger, J. (1974) Intramolecular distances determined by energy transfer. Dependence on orientational freedom of donor and acceptor, Biopolymers 13, 1573-1605.
20. Eisinger, J., Feuer, B., and Lamola, A. A. (1969) Intramolecular singlei excitation transfer. Applications to polypeptides, Biochemistry 8, 3908-3915.
21. Lindahl, E., Hess, B., and van der Spoel, D. (2001) GROMACS 3.0: a package for molecular simulation and trajectory analysis, J. Mol Model. 7, 306-317.
22. van der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E., and Berendsen, H. J. C.(2005) GROMACS: Fast, Flexible and Free, J. Comput. Chem. 26, 1701-1718.
23. Jorgensen, W. L., Maxwell, S., and Tirado-Rives, J. (1996) Development and testing of the OPLS All-Atom Force Field on conformational energetics and properties of organic liquids, J. Am. Chem. Soc. 118, 11225-11236.
24. Kaminski, G. A., Friesner, R. A., Tirado-Rives, J., and Jorgensen, W. L. (2001) Evaluation and reparametrization of the OPLS-AA Force Field for proteins via comparison with accurate quantum chemical calculations on peptides, J. Phys. Chem. B 105, 6474-6487.
25. Berendsen, H. J. C., Postma, J. P. M., van Gunsteren, W. F., and Hermans, J. (1981) in Intermolecular Forces (Pullman, B., Ed.) p 331, D. Reidel Publishing Company, Dordrecht.
26. Hess, B., Bekker, H., Berendsen, H. J. C., and Fraaije, J. G. E. M. (1997) LINCS: A linear constraint solver for molecular simulations, J. Comput. Chem. 18, 1463-1472.
27. Berendsen, H. J. C., Postma, J. P. M., Di Nola, A., and Haak, J. R. (1984) MD with coupling to an external bath, J. Phys. Chem. 81, 3684-3690.
28. Essmann, U., Perera, L., Berkowitz, M. L., Darden, T., Lee, H., and Pedersen, L. G. (1995) A smooth particle mesh Ewald method, J. Chem. Phys. 103, 8577-8593.
29. Humphrey, W., Dalke, A., and Schulten, K. (1996) VMD: Visual Molecular Dynamics, J. Mol. Graphics 14, 33-38.
30. Grinvald, A., and Steinberg, I. Z. (1976) The fluorescence decay of tryptophan residues in native and denatured proteins, Biochim. Biophys. Acta 427, 663-678.
31. Stepanenko, O. V., Marabotti, A., Kuznetsova, I. M., Turoverov, K. K., Fini, C., Varriale, A., Staiano, M., Rossi, M., and D'Auria, S. Hydrophobic interactions and ionic networks play an important role in thermal stability and denaturation mechanism of the porcine odorant binding protein, Proteins, in press.
32. Kuznetsova, I. M., Turoverov, K. K., and Uversky, V. N. (2004) Use of the phase diagram method to analyze the protein unfolding-refolding reactions: fishing out the "invisible" intermediates, J. Proteome Res. 3, 485-494.
33. D'Auria, S., Staiano, M., Kuznetsova, I. M., and Turoverov, K. K. (2005) The combined use of fluorescence spectroscopy and X-ray crystallography greatly contributes to elucidating structure and dynamics of proteins, Rev. Fluoresc. 25-61.
34. Merritt, E. A., and Bacon, D. J. (1977) Raster 3-D: Photorealistic molecular graphics, Methods Enzymol. 277, 505-524.
35. Pan, C. P., Barkley, M. D. (2004) Conformational effects on tryptophan fluorescence in cyclic hexapeptides, Biophys. J. 86, 3828-3835.
36. Pan, C. P., Callis, P. R., and Barkley, M. D. (2006) Dependence of tryptophan emission wavelength on conformation in cyclic hexapeptides, J. Phys. Chem. B. 110, 7009-7016.
37. Chen, Y., and Barkley, M. D. (1998) Toward understanding tryptophan fluorescence in proteins, Biochemistry 37, 9976-9982.
38. Vivian, J. T., and Callis, P. R. (2001) Mechanisms of tryptophan fluorescence shifts in proteins, Biophys. J. 80, 2093-2109.
39. Szabo, A. G., and Faerman, C. (1992) Dilemma of correlating fluorescence quantum yields and intensity decay times in single-tryptophan mutant proteins, Proc. SPIE 1640, 70-80.
40. Axelsen, P. H., and Prendergast, F. G. (1989) Molecular dynamics of tryptophan in ribonuclease-T1. II. Correlations with fluorescence, Biophys. J. 56, 43-66.
41. Nolting, B. (1999) Protein Folding Kinetics, in Biophysical Methods, p 145, Springer-Verlag, Berlin-Heidelberg.
42. Parisi, M., Mazzini, A., Sorbi, R. T., Ramoni, R., Grolli, S., and Favilla, R. (2003) Unfolding and refolding of porcine odorant binding protein in guanidinium hydrochloride: equilibrium studies at neutral pH, Biochim. Biophys. Acta 1652, 115-125.