Raman Evidence of P53-DBD Disorder Decrease Upon Interaction with the Anticancer Protein Azurin

Overview

Journal Int J Mol Sci

Publisher MDPI

Specialties Biochemistry
Chemistry
Molecular Biology

Date 2019 Jun 27

PMID 31238511

Citations 8

Authors

Sara Signorelli

Salvatore Cannistraro

Anna Rita Bizzarri

Affiliations

Soon will be listed here.

Abstract

Raman spectroscopy, which is a suitable tool to elucidate the structural properties of intrinsically disordered proteins, was applied to investigate the changes in both the structure and the conformational heterogeneity of the DNA-binding domain (DBD) belonging to the intrinsically disordered protein p53 upon its binding to Azurin, an electron-transfer anticancer protein from . The Raman spectra of the DBD and Azurin, isolated in solution or forming a complex, were analyzed by a combined analysis based on peak inspection, band convolution, and principal component analysis (PCA). In particular, our attention was focused on the Raman peaks of Tyrosine and Tryptophan residues, which are diagnostic markers of protein side chain environment, and on the Amide I band, of which the deconvolution allows us to extract information about α-helix, β-sheet, and random coil contents. The results show an increase of the secondary structure content of DBD concomitantly with a decrease of its conformational heterogeneity upon its binding to Azurin. These findings suggest an Azurin-induced conformational change of DBD structure with possible implications for p53 functionality.

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References

Thomas Jr G . Raman spectroscopy of protein and nucleic acid assemblies. Annu Rev Biophys Biomol Struct. 1999; 28:1-27. DOI: 10.1146/annurev.biophys.28.1.1. View

Altose M, Zheng Y, Dong J, Palfey B, Carey P . Comparing protein-ligand interactions in solution and single crystals by Raman spectroscopy. Proc Natl Acad Sci U S A. 2001; 98(6):3006-11. PMC: 30597. DOI: 10.1073/pnas.061029598. View

Arp Z, Autrey D, Laane J, Overman S, Thomas Jr G . Tyrosine Raman signatures of the filamentous virus Ff are diagnostic of non-hydrogen-bonded phenoxyls: demonstration by Raman and infrared spectroscopy of p-cresol vapor. Biochemistry. 2001; 40(8):2522-9. DOI: 10.1021/bi0023753. View

Bell S, Klein C, Muller L, Hansen S, Buchner J . p53 contains large unstructured regions in its native state. J Mol Biol. 2002; 322(5):917-27. DOI: 10.1016/s0022-2836(02)00848-3. View

Tompa P . Intrinsically unstructured proteins. Trends Biochem Sci. 2002; 27(10):527-33. DOI: 10.1016/s0968-0004(02)02169-2. View

Yamada T, Goto M, Punj V, Zaborina O, Chen M, Kimbara K . Bacterial redox protein azurin, tumor suppressor protein p53, and regression of cancer. Proc Natl Acad Sci U S A. 2002; 99(22):14098-103. PMC: 137843. DOI: 10.1073/pnas.222539699. View

Goto M, Yamada T, Kimbara K, Horner J, Newcomb M, Das Gupta T . Induction of apoptosis in macrophages by Pseudomonas aeruginosa azurin: tumour-suppressor protein p53 and reactive oxygen species, but not redox activity, as critical elements in cytotoxicity. Mol Microbiol. 2003; 47(2):549-59. DOI: 10.1046/j.1365-2958.2003.03317.x. View

Punj V, Das Gupta T, Chakrabarty A . Bacterial cupredoxin azurin and its interactions with the tumor suppressor protein p53. Biochem Biophys Res Commun. 2003; 312(1):109-14. DOI: 10.1016/j.bbrc.2003.09.217. View

Maiti N, Apetri M, Zagorski M, Carey P, Anderson V . Raman spectroscopic characterization of secondary structure in natively unfolded proteins: alpha-synuclein. J Am Chem Soc. 2004; 126(8):2399-408. DOI: 10.1021/ja0356176. View

10.

Yamada T, Hiraoka Y, Ikehata M, Kimbara K, Avner B, Das Gupta T . Apoptosis or growth arrest: Modulation of tumor suppressor p53's specificity by bacterial redox protein azurin. Proc Natl Acad Sci U S A. 2004; 101(14):4770-5. PMC: 387323. DOI: 10.1073/pnas.0400899101. View

11.

Apiyo D, Wittung-Stafshede P . Unique complex between bacterial azurin and tumor-suppressor protein p53. Biochem Biophys Res Commun. 2005; 332(4):965-8. DOI: 10.1016/j.bbrc.2005.05.038. View

12.

Yamada T, Fialho A, Punj V, Bratescu L, Das Gupta T, Chakrabarty A . Internalization of bacterial redox protein azurin in mammalian cells: entry domain and specificity. Cell Microbiol. 2005; 7(10):1418-31. DOI: 10.1111/j.1462-5822.2005.00567.x. View

13.

Nar H, Messerschmidt A, Huber R, van de Kamp M, Canters G . Crystal structure of Pseudomonas aeruginosa apo-azurin at 1.85 A resolution. FEBS Lett. 1992; 306(2-3):119-24. DOI: 10.1016/0014-5793(92)80981-l. View

14.

Canadillas J, Tidow H, Freund S, Rutherford T, Ang H, Fersht A . Solution structure of p53 core domain: structural basis for its instability. Proc Natl Acad Sci U S A. 2006; 103(7):2109-14. PMC: 1413739. DOI: 10.1073/pnas.0510941103. View

15.

Ortiz C, Zhang D, Xie Y, Ribbe A, Ben-Amotz D . Validation of the drop coating deposition Raman method for protein analysis. Anal Biochem. 2006; 353(2):157-66. DOI: 10.1016/j.ab.2006.03.025. View

16.

Vousden K, Lane D . p53 in health and disease. Nat Rev Mol Cell Biol. 2007; 8(4):275-83. DOI: 10.1038/nrm2147. View

17.

De Grandis V, Bizzarri A, Cannistraro S . Docking study and free energy simulation of the complex between p53 DNA-binding domain and azurin. J Mol Recognit. 2007; 20(4):215-26. DOI: 10.1002/jmr.840. View

18.

Wen Z . Raman spectroscopy of protein pharmaceuticals. J Pharm Sci. 2007; 96(11):2861-78. DOI: 10.1002/jps.20895. View

19.

Uversky V, Oldfield C, Midic U, Xie H, Xue B, Vucetic S . Unfoldomics of human diseases: linking protein intrinsic disorder with diseases. BMC Genomics. 2009; 10 Suppl 1:S7. PMC: 2709268. DOI: 10.1186/1471-2164-10-S1-S7. View

20.

Funari G, Domenici F, Nardinocchi L, Puca R, DOrazi G, Bizzarri A . Interaction of p53 with Mdm2 and azurin as studied by atomic force spectroscopy. J Mol Recognit. 2009; 23(4):343-51. DOI: 10.1002/jmr.999. View