Probing protein structure and dynamics by second-derivative ultraviolet absorption analysis of cation-π interactions

Protein Science

Volumn 15, Issue 10, 2006, Pages 2228-2243

  Lucas, Laura H ^a,b   Ersoy, Baran A ^a,c   Kueltzo, Lisa A ^a,d   Joshi, Sangeeta B ^a   Brandau, Duane T ^a   Thyagarajapuram, Nagarajan ^a   Peek, Laura J ^a   Middaugh, C Russell ^a  

^a UNIVERSITY OF KANSAS   (United States)

^b PROCTER AND GAMBLE COMPANY   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d UNIVERSITY OF COLORADO   (United States)

Author keywords

Aromatic amino acids; Cation interactions; Dynamics; Peak shift; Protein structure; Second derivative UV spectra; Side chains

Indexed keywords

AROMATIC AMINO ACID; BENZENE DERIVATIVE; BENZYL DERIVATIVE; CATION; LITHIUM ION; RIBONUCLEASE T1; SODIUM CHLORIDE; SODIUM ION; SOLVENT;

ARTICLE; CHEMICAL ANALYSIS; DYNAMICS; ENTHALPY; PH; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN INTERACTION; PROTEIN STRUCTURE; SPECTRAL SENSITIVITY; TEMPERATURE; ULTRAVIOLET SPECTROPHOTOMETRY;

ACETYLATION; AMINO ACIDS, AROMATIC; CATIONS; ELECTRONS; METALS; MOLECULAR STRUCTURE; PROTEIN CONFORMATION; PROTEINS; SPECTROPHOTOMETRY, ULTRAVIOLET;

EID: 33749318250     PISSN: 09618368     EISSN: 1469896X     Source Type: Journal    
DOI: 10.1110/ps.062133706     Document Type: Article

References (56)

1. Adams, P.D., Loh, A.P., and Oswald, R.E. 2004. Backbone dynamics of an oncogenic mutant of Cdc42Hs shows increased flexibility at the nucleotide-binding site. Biochemistry 43: 9968-9977.
2. Balestrieri, C., Colonna, G., Giovane, A., Irace, G., and Servillo, L. 1978. Second-derivative spectroscopy of proteins. Eur. J. Biochem. 90: 433-440.
3. _. 1980. Second-derivative spectroscopy of proteins: Studies on tyrosyl residues. Anal. Biochem. 106: 49-54.
4. Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., and Bourne, P.E. 2000. The Protein Data Bank. Nucleic Acids Res. 28: 235-242.
5. Bohórquez, H.J., Obregón, M., Cárdenas, C., Llanos, E., Suárez, C., Villaveces, J.L., and Patarroyo, M.E. 2003. Electronic energy and multi-polar moments characterize amino acid side chains into chemically related groups. J. Phys. Chem. A 107: 10090-10097.
6. Derrick, T., Grillo, A.O., Vitharana, S.N., Jones, L., Rexroad, J., Shah, A., Perkins, M., Spitznagel, T.M., and Middaugh, C.R. 2006. Effect of polyanions on the structure and stability of RepiferminTM (Keratinocyte Growth Factor-2). J. Pharm. Sci. (in press).
7. De Swarte, J., De Vos, S., Langhorst, U., Steyaert, J., and Loris, R. 2001. The contribution of metal ions to the conformational stability of ribonuclease T1: Crystal versus solution. Eur. J. Biochem. 268: 3993-4000.
8. Donovan, J.W. 1969. Ultraviolet absorption. In Physical principles and techniques of protein chemistry (ed. S.J. Leach). Part A, pp. 101-170. Academic Press, New York.
9. _. 1973. Ultraviolet difference spectroscopy-new techniques and applications. Methods Enzymol. 27: 497-525.
10. Dougherty, D.A. 1996. Cation-π interactions in chemistry and biology: A new view of benzene, Phe, Tyr, and Trp. Science 271: 163-168.
11. Edsall, J.T. and McKenzie, H.A. 1978. Water and proteins. I. The significance and structure of water; its interaction with electrolytes and non-electrolytes. Adv. Biophys. 10: 137-207.
12. Edwards, K.L.T., Kueltzo, L.A., Fisher, M.T., and Middaugh, C.R. 2001. Complex effects of molecular chaperones on the aggregation and refolding of fibroblast growth factor-1. Arch. Biochem. Biophys. 393: 14-21.
13. Fasano, M., Orsale, M., Melino, S., Nicolai, E., Forlani, F., Rosato, N., Cicero, D., Pagani, S., and Paci, M. 2003. Surface changes and role of buried water molecules during the sulfane sulfur transfer in Rhodanese from Azotobacter vinelandii: A fluorescence quenching and nuclear magnetic relaxation dispersion spectroscopic study. Biochemistry 42: 8550-8557.
14. Faucon, J.F., Dufourcq, J., and Lussan, C. 1979. The self-association of melittin and its binding to lipids. An intrinsic fluorescence polarization study. FEBS Lett. 102: 187-190.
15. Gallivan, J.P. and Dougherty, D.A. 1999. Cation-π interactions in structural biology. Proc. Natl. Acad. Sci. 96: 9459-9464.
16. Ghose, A.K., Viswanadhan, V.N., and Wendoloski, J.J. 1998. Prediction of hydrophobic (lipophilic) properties of small organic molecules using fragmental methods: An analysis of ALOGP and CLOGP methods. J. Phys. Chem. A 102: 3762-3772.
17. Giese, A.T. and French, C.S. 1955. The analysis of overlapping spectral absorption bands by derivative spectrophotometry. Appl. Spectrosc. 9: 78-96.
18. Grum, F., Paine, D., and Zoeller, L. 1972. Derivative absorption and emission spectrophotometry. Appl. Opt. 11: 93-98.
19. Harris, D.C. 1995. Quantitative chemical analysis. W.H. Freeman and Company, New York.
20. Hofmeister, F. 1888. Zur lehre von der wirkung der salze. Arch. Exp. Pathol. Pharmakol. 24: 247-260.
21. Ichikawa, T. and Terada, H. 1977. Second derivative spectrophotometry as an effective tool for examining phenylalanine residues in proteins. Biochim. Biophys. Acta 494: 267-270.
22. _. 1979. Estimation of state and amount of phenylalanine residues in proteins by second derivative spectrophotometry. Biochim. Biophys. Acta 580: 120-128.
23. Ito, M. 1960. Ultraviolet absorption study of the molecular association of phenols. J. Mol. Spectrosc. 4: 125-143.
24. Keniry, M.A. and Carver, J.A. 2002. NMR spectroscopy of large proteins. Ann. Rep. NMR Spectrosc. 48: 31-69.
25. Kielland, J. 1937. Individual activity coefficients of ions in aqueous solutions. J. Am. Chem. Soc. 59: 1675-1678.
26. Kueltzo, L.A. and Middaugh, C.R. 2003. Structural characterization of bovine granulocyte colony stimulating factor: Effect of temperature and pH. J. Pharm. Sci. 92: 1793-1804.
27. Kueltzo, L.A., Ersoy, B., Ralston, J.P., and Middaugh, C.R. 2003. Derivative absorbance spectroscopy and protein phase diagrams as tools for comprehensive protein characterization: A bGCSF case study. J. Pharm. Sci. 92: 1805-1820.
28. Kunz, W., Henle, J., and Ninham, B.W. 2004. Zur lehre von der wirkung der salze' (About the science of the effect of salts): Franz Hofmeister's historical papers. Curr. Opin. Coll. Interface Sci. 9: 19-37.
29. Lakowicz, J.R., Maliwal, B.P., Cherek, H., and Balter, A. 1983. Rotational freedom of tryptophan residues in proteins and peptides. Biochemistry 22: 1741-1752.
30. Levine, R.L. and Federici, M.M. 1982. Quantitation of aromatic residues in proteins: Model compounds for second-derivative spectroscopy. Biochemistry 21: 2600-2606.
31. Lovejoy, B., Cascio, D., and Eisenberg, D. 1993. Crystal structure of canine and bovine granulocyte-colony stimulating factor (G-CSF). J. Mol. Biol. 234: 640-653.
32. Ma, J.C. and Dougherty, D.A. 1997. The cation-π interaction. Chem. Rev. 97: 1303-1324.
33. Mach, H. and Middaugh, C.R. 1994. Simultaneous monitoring of the environment of tryptophan, tyrosine, and phenylalanine residues in proteins by near-ultraviolet second-derivative spectroscopy. Anal. Biochem. 222: 323-331.
34. _. 1995. Interaction of partially structured states of acidic fibroblast growth factor with phospholipid membranes. Biochemistry 34: 9913-9920.
35. Mach, H., Thomson, J.A., Middaugh, C.R., and Lewis, R.L. 1991. Examination of phenylalanine microenvironments in proteins by second-derivative absorption spectroscopy. Arch. Biochem. Biophys. 287: 33-40.
36. Moriyama, Y. and Takeda, K. 2005. Protective effects of small amounts of bis(2-ethylhexyl)sulfosuccinate on the helical structures of human and bovine serum albumins in their thermal denaturations. Langmuir 21: 5524-5528.
37. Nar, H., Messerschmidt, A., van de Kamp, M., and Canters, G.W. 1991. Crystal structure analysis of oxidized Pseudomonas aeruginosa azurin at pH 5.5 and pH 9.0. A pH-induced conformational transition involves a peptide bond flip. J. Mol. Biol. 218: 427-447.
38. Padrós, E., Morros, A., Mañosa, J., and Duñach, M. 1982. The state of tyrosine and phenylalanine residues in proteins analyzed by fourth-derivative spectrophotometry. Eur. J. Biochem. 127: 117-122.
39. Poluektov, O.G., Utschig, L.M., Dalosto, S., and Thurnauer, M.C. 2003. Probing local dynamics of photosynthetic bacterial reaction center with a cysteine specific spin label. J. Phys. Chem. B 107: 6239-6244.
40. Rexroad, J., Wiethoff, C.M., Green, A.P., Kierstead, T.D., Scott, M.O., and Middaugh, C.R. 2003. Structural stability of adenovirus type 5. J. Pharm. Sci. 92: 665-678.
41. Rogers, D.M. and Hirst, J.D. 2003. Ab initio study of aromatic side chains of amino acids in gas phase and solution. J. Phys. Chem. A 107: 11191-11200.
42. + with the aromatic amino acids, phenylalanine, tyrosine, and tryptophan. J. Am. Chem. Soc. 126: 14600-14610.
43. +-glutamate dehydrogeanse from Thermus thermophilus HB8. J. Protein Chem. 22: 295-301.
44. + with Phe, Tyr, and Trp in the gas phase. J. Am. Soc. Mass Spectrom. 11: 1037-1046.
45. Shannon, R.D. 1976. Revised effective ionic radii and systematic studies of interatomic distances in halides and chalcogenides. Acta Crystallogr. A 32: 751-767.
46. Skoog, D.A., Holler, F.J., and Nieman, T.A. 1998. Principles of instrumental analysis.. Harcourt Brace and Company, Chicago.
47. Solli, N.J. and Herskovits, T.T. 1973. Solvent perturbation studies and analysis of protein and model compound data in denaturing organic solvents. Anal. Biochem. 54: 370-378.
48. Sugio, S., Kashima, A., Mochizuki, S., Noda, M., and Kobayashi, K. 1999. Crystal structure of human serum albumin at 2.5 Å resolution. Protein Eng. 12: 439-446.
49. Swain, A.L., Jaskolski, M., Housset, D., Rao, J.K., and Wlodawer, A. 1993. Crystal structure of Escherichia coli L-asparaginase, an enzyme used in cancer therapy. Proc. Natl. Acad. Sci. 90: 1474-1478.
50. Talbot, J.C., Dufourcq, J., de Bony, J., Faucon, J.F., and Lussan, C. 1979. Conformational change and self association of monomeric melittin. FEBS Lett. 102: 191-193.
51. Wetzel, R., Becker, M., Behlke, J., Billwitz, J., Boehm, S., Ebert, B., Hamann, J., Krumbiegel, J., and Lassman, G. 1980. Temperature behavior of human serum albumin. Eur. J. Biochem. 104: 469-478.
52. Woods, A.S. 2004. The mighty arginine, the stable quaternary amines, the powerful aromatics, and the aggressive phosphate: Their role in the noncovalent minuet. J. Proteome Res. 3: 478-484.
53. Yan, X., Watson, J., Ho, P.S., and Deinzer, M.L. 2004. Mass spectrometric approaches using electrospray ionization charge states and hydrogen-deuterium exchange for determining protein structures and their conformational studies. Mol. Cell. Proteomics 3: 10-23.
54. Yu, S., Mei, F.C., Le, J.C., and Cheng, X. 2004. Probing cAMP-dependent protein kinase holoenzyme complexes Iα and IIβ by FT-IR and chemical protein footprinting. Biochemistry 43: 1908-1920.
55. Yuan, Z., Zhao, J., and Wang, Z.-X. 2003. Flexibility analysis of enzyme active sites by crystallographic temperature factors. Protein Eng. 16: 109-114.
56. Zhang, Z. and Smith, D.L. 1993. Determination of amide hydrogen exchange by mass spectrometry: A new tool for protein structure elucidation. Protein Sci. 2: 522-531.