Automatic determination of disulfide bridges in proteins

Journal of Laboratory Automation

Volumn 17, Issue 6, 2012, Pages 408-416

  Sokolowska, Izabela ^a   Wetie, Armand G Ngounou ^a   Woods, Alisa G ^a   Darie, Costel C ^a  

^a CLARKSON UNIVERSITY   (United States)

Author keywords

Disulfide bridges; LC MS MS; MALDI MS; Mass spectrometry; Protein structure

Indexed keywords

AMINO ACIDS; CHROMATOGRAPHY; COVALENT BONDS; ELECTROPHORESIS; MASS SPECTROMETRY; PEPTIDES; SODIUM DODECYL SULFATE; SODIUM METALLOGRAPHY;

DISULFIDE BRIDGE; LC-MS/MS; MALDI-MS; NANO LIQUID CHROMATOGRAPHY; PROTEIN STRUCTURES; QUADRUPOLE-TIME OF FLIGHTS; SODIUM DODECYL SULFATE-POLYACRYLAMIDE GEL ELECTROPHORESIS; TERTIARY STRUCTURE OF PROTEINS;

SULFUR COMPOUNDS;

DATA ANALYSIS; DATA DEPENDENT ANALYSIS; DISULFIDE BOND; ELECTROSPRAY MASS SPECTROMETRY; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; INFORMATION DEPENDENT ANALYSIS; LABORATORY AUTOMATION; MASS SPECTROMETRY; MATRIX ASSISTED LASER DESORPTION IONIZATION MASS SPECTROMETRY; MOLECULAR SIZE; MOLECULAR WEIGHT; NANOLIQUID CHROMATOGRAPHY TANDEM MASS SPECTROMETRY; POLYACRYLAMIDE GEL ELECTROPHORESIS; PROTEIN ANALYSIS; PROTEIN DEGRADATION; PROTEIN DENATURATION; PROTEIN PROCESSING; QUADRUPOLE TIME OF FLIGHT MICRO MASS SPECTROMETRY; REVIEW; TANDEM MASS SPECTROMETRY; TWO DIMENSIONAL ELECTROPHORESIS; ULTRA PERFORMANCE LIQUID CHROMATOGRAPHY; CHEMICAL ANALYSIS; CHEMISTRY; LIQUID CHROMATOGRAPHY; METHODOLOGY;

DISULFIDE; PROTEIN;

AUTOMATION, LABORATORY; CHEMISTRY TECHNIQUES, ANALYTICAL; CHROMATOGRAPHY, LIQUID; DISULFIDES; ELECTROPHORESIS, POLYACRYLAMIDE GEL; PROTEINS; TANDEM MASS SPECTROMETRY;

EID: 84873985630     PISSN: 22110682     EISSN: 22110690     Source Type: Journal    
DOI: 10.1177/2211068212454737     Document Type: Review

References (50)

1. Han, L.; Monne, M.; Okumura, H.; Schwend, T.; Cherry, A. L.; Flot, D.; Matsuda, T.; Jovine, L. Cell 2010, 143(3), 404-415.
2. Tie, J. K.; Mutucumarana, V. P.; Straight, D. L.; Carrick, K. L.; Pope, R. M.; Stafford, D. W. J. Biol. Chem. 2003, 278(46), 45468-45475.
3. Wedemeyer, W. J.; Welker, E.; Narayan, M.; Scheraga, H. A. Biochemistry 2000, 39(15), 4207-4216.
4. Clauser, K. R.; Baker, P.; Burlingame, A. L. Anal. Chem. 1999, 71(14), 2871-2882.
5. Jones, M. D.; Patterson, S. D.; Lu, H. S. Anal. Chem. 1998, 70(1), 136-143.
6. Crimmins, D. L.; Saylor, M.; Rush, J.; Thoma, R. S. Anal. Biochem. 1995, 226(2), 355-361.
7. Patterson, S. D.; Katta, V. Anal. Chem. 1994, 66(21), 3727-3732.
8. Boja, E. S.; Hoodbhoy, T.; Garfield, M.; Fales, H. M. Biochemistry 2005, 44(50), 16445-16460.
9. Darie, C. C.; Biniossek, M. L.; Jovine, L.; Litscher, E. S.; Wassarman, P. M. Biochemistry 2004, 43(23), 7459-7478.
10. Yonezawa, N.; Nakano, M. Biochem. Biophys. Res. Commun. 2003, 307(4), 877-882.
11. Boja, E. S.; Hoodbhoy, T.; Fales, H. M.; Dean, J. J. Biol. Chem. 2003, 278(36), 34189-34202.
12. Darie, C. C.; Litscher, E. S.; Wassarman, P. M. Structure, Processing, and Polymerization of Rainbow Trout Egg Vitelline Envelope Proteins; Springer-Verlag: Düsseldorf, Germany, 2008.
13. Darie, C. C.; Janssen, W. G.; Litscher, E. S.; Wassarman, P. M. Biochim. Biophys. Acta 2008, 1784(2), 385-392.
14. Darie, C. C.; Biniossek, M. L.; Winter, V.; Mutschler, B.; Haehnel, W. FEBS J. 2005, 272(11), 2705-2716.
15. Darie, C. C.; Biniossek, M. L.; Gawinowicz, M. A.; Milgrom, Y.; Thumfart, J. O.; Jovine, L.; Litscher, E. S.; Wassarman, P. M. J. Biol. Chem. 2005, 280(45), 37585-37598.
16. Medzihradszky, K. F.; Bohlen, C. J. J. Am. Soc. Mass Spectrom. 2012, 23(5), 923-934.
17. Caliskan, F.; Quintero-Hernandez, V.; Restano-Cassulini, R.; Batista, C. V.; Zamudio, F. Z.; Coronas, F. I.; Possani, L. D. Toxicon 2012, 59(3), 408-415.
18. van der Linde, K.; Gutsche, N.; Leffers, H. M.; Lindermayr, C.; Muller, B.; Holtgrefe, S.; Scheibe, R. Plant Physiol. Biochem. 2011, 49(9), 946-957.
19. Stefanescu, R.; Born, R.; Moise, A.; Ernst, B.; Przybylski, M. J. Am. Soc. Mass Spectrom. 2011, 22(1), 148-157.
20. Rosa, R. D.; Santini, A.; Fievet, J.; Bulet, P.; Destoumieux-Garzon, D.; Bachere, E. PloS One 2011, 6(9), e25594.
21. Peigneur, S.; Billen, B.; Derua, R.; Waelkens, E.; Debaveye, S.; Beress, L.; Tytgat, J. Biochem. Pharmacol. 2011, 82(1), 81-90.
22. Knipp, M.; Taing, J. J.; He, C. J. Inorganic Biochem. 2011, 105(11), 1405-1412.
23. Chevreux, G.; Tilly, N.; Bihoreau, N. Anal. Biochem. 2011, 415(2), 212-214.
24. Brgles, M.; Kurtovic, T.; Halassy, B.; Allmaier, G.; Marchetti-Deschmann, M. J. Mass Spectrom. 2011, 46(2), 153-162.
25. Abbas, N.; Rosso, J. P.; Ceard, B.; Belghazi, M.; Lebrun, R.; Bougis, P. E.; Martin-Eauclaire, M. F. Peptides 2011, 32(5), 911-919.
26. Jovine, L.; Darie, C. C.; Litscher, E. S.; Wassarman, P. M. Annu. Rev. Biochem. 2005, 74, 83-114.
27. Jovine, L.; Qi, H.; Williams, Z.; Litscher, E.; Wassarman, P. M. Nat. Cell Biol. 2002, 4(6), 457-461.
28. McDonagh, B. Methods Mol. Biol. 2009, 519, 305-310.
29. Sokolowska, I.; Woods, A. G.; Wagner, J.; Dorler, J.; Wormwood, K.; Thome, J.; Darie, C. C. Mass Spectrometry for Proteomics-based Investigation of Oxidative Stress and Heat Shock Proteins. In Oxidative Stress: Diagnostics and Therapy; American Chemical Society: Washington, DC, 2011.
30. Ali, S. A.; Alam, J. M.; Stoeva, S.; Schutz, J.; Abbasi, A.; Zaidi, Z. H.; Voelter, W. Toxicon 1999, 37(11), 1505-1520.
31. Batista, C. V.; del Pozo, L.; Zamudio, F. Z.; Contreras, S.; Becerril, B.; Wanke, E.; Possani, L. D. J. Chromatogr. B Anal. Technol. Biomed. Life Sci. 2004, 803(1), 55-66.
32. Fini, C.; Amoresano, A.; Andolfo, A.; D'Auria, S.; Floridi, A.; Paolini, S.; Pucci, P. Eur. J. Biochem. 2000, 267(16), 4978-4987.
33. Leinweber, B.; Barofsky, E.; Barofsky, D. F.; Ermilov, V.; Nylin, K.; Beckman, J. S. Free Rad. Biol. Med. 2004, 36(7), 911-918.
34. Martin, G.; Sorokine, O.; Moniatte, M.; Bulet, P.; Hetru, C.; Van Dorsselaer, A. Eur. J. Biochem. 1999, 262(3), 727-736.
35. Muller, A.; Solem, S. T.; Karlsen, C. R.; Jorgensen, T. O. Protein Expression Purification 2008, 62(2), 206-215.
36. Seppala, U.; Hagglund, P.; Wurtzen, P. A.; Ipsen, H.; Thorsted, P.; Lenhard, T.; Roepstorff, P.; Spangfort, M. D. J. Biol. Chem. 2005, 280(5), 3208-3216.
37. Solouki, T.; Emmett, M. R.; Guan, S.; Marshall, A. G. Anal. Chem. 1997, 69(6), 1163-1168.
38. Stehling, E. G.; da Silveira, W. D.; Campos, T. A.; Brocchi, M.; Pertinhez, T. A.; Spisni, A., Protein Expression Purification 2008, 57(1), 88-94.
39. Thiede, B.; Hohenwarter, W.; Krah, A.; Mattow, J.; Schmid, M.; Schmidt, F.; Jungblut, P. R. Methods 2005, 35(3), 237-247.
40. Trachsel, C.; Kampfer, U.; Bechtold, R.; Schaller, J.; Schurch, S. Anal. Biochem. 2009, 390(2), 103-108.
41. Wang, Y. J.; Hayes, T. K.; Holman, G. M.; Chavez, A. R.; Keeley, L. L. Peptides 2000, 21(4), 477-484.
42. Zvonok, N.; Williams, J.; Johnston, M.; Pandarinathan, L.; Janero, D. R.; Li, J.; Krishnan, S. C.; Makriyannis, A. J. Proteome Res. 2008, 7(5), 2158-2164.
43. Legowska, A.; Bulak, E.; Jaskiewicz, A.; Maluch, I.; Sieracki, M.; Wysocka, M.; Lesner, A.; Rolka, K. Protein Peptide Lett. 2010, 17(10), 1223-1227.
44. Chevalier, F.; Kelly, A. L. J. Agric. Food Chem. 2010, 58(12), 7437-7444.
45. Weber, W.; Buck, F.; Meyer, A.; Hilz, H. Biochem. Biophys. Res. Commun. 2009, 379(4), 1101-1106.
46. Trejo, S. A.; Lopez, L. M.; Caffini, N. O.; Natalucci, C. L.; Canals, F.; Aviles, F. X. Planta 2009, 230(2), 319-328.
47. Baumgartner, C.; Rejtar, T.; Kullolli, M.; Akella, L. M.; Karger, B. L. J. Proteome Res. 2008, 7(9), 4199-4208.
48. Colgrave, M. L.; Poth, A. G.; Kaas, Q.; Craik, D. J. Biopolymers 2010, 94(5), 592-601.
49. Darie, C. C.; Deinhardt, K.; Zhang, G.; Cardasis, H. S.; Chao, M. V.; Neubert, T. A. Proteomics 2011, 11(23), 4514-4528.
50. Sokolowska, I.; Woods, A. G.; Gawinowicz, M. A.; Roy, U.; Darie, C. C. J. Biol. Chem. 2012, 287(3), 1719-1733.