Abstract
We have developed a computer program for the rapid assessment of the primary structure differences between a protein of unknown sequence and a homologous known protein. Both proteins are reduced, alkylated, and digested with the same hydrolytic agent. The unfractionated peptide mixtures are submitted to automatic sequence analysis. Based on the knowledge of the reference sequence, the program utilizes the analysis data to identify all the potential peptides present in the two mixtures, determining their primary structure, homology degree, and molecular weight calculated both as integer MH+ and average mass variables. These fingerprints allow the user to easily identify the structural differences between the two proteins and clarify possible doubts by a mass spectrometric analysis of the two mixtures. In order to verify the utility of the program, we provide an application example using the already reported data of two homologous proteins.
Similar content being viewed by others
REFERENCES
Biemann, K. (1980). In Biochemical Applications of Mass Spectrometry (Waller, G. R. ed.), Wiley, New York, pp. 469–525.
Cannon, L. E., and Lovins, R. E. (1972). Anal. Biochem. 46, 33–44.
Caporale, C., Carrano, L., Nitti, G., Poerio, E., Pucci P., and Buonocore V. (1991). Protein Seq. Data Anal. 4, 3–8.
Caporale, C., Caruso, C., Petrilli, P., Sepe, C., Poerio, E., and Buonocore, V. (1993). Protein Seq. Data Anal. 5, 337–344.
Caporale, C., Sepe, C., Caruso, C., Petrilli, C., and Buonocore, V. (1994). Comput. Appl. Biosci. 10, 489–494.
Caporale, C., Sepe, C., Caruso, C., Pucci, P., and Buonocore, V. (1996a). FEBS Lett. 393, 241–247.
Caporale, C., Garzillo, A. M. V., Caruso, C., and Buonocore, V. (1996b). Phytochemistry 41, 385–393.
Caporale, C., Sepe, C., Caruso, C., Garzillo, A. M. V., and Buonocore, V. (1996c). Comput. Appl. Biosci. 12, 81–88.
Caporale, C., Caruso, C., and Buonocore, V. (1996d). J. Protein Chem. 15, 405–412.
Cottrell, J. S. (1994). Peptide Res. 7, 115–124.
Erickson, B. J., and Jardine, I. (1986). Biomed. Environ. Mass. Spectrom. 13, 343–346.
Fairwell, T., Barnes, W. T., Richards, F. F., and Lovins, R. E. (1970). Biochemistry 9, 2260–2267.
Fernandez-de-Cossio, J., Gonzalez, J., and Besada, V. (1995). Comput. Appl. Biosci. 11, 427–434.
Griffin, P. R., MacCoss, M. J., Eng, J. K., Blevins, R. A., Aaronson, J. S., and Yates, J. R., III (1995). Rapid Commun. Mass Spectrom. 9, 1546–1551.
Henzel, W. J., Billeci, T. M., Stults, J. T., Wong, S. C., Grimley, C., and Watanabe, C. (1993). Proc. Natl. Acad. Sci. USA 90, 5011–5015.
Herlihy, W. C., and Biemann, K. (1981). Biomed. Mass. Spectrom. 8, 70–77.
James, P., Quadroni, M., Carafoli, E., and Gonnet, G. (1993). Biochem. Biophys. Res. Commun. 195, 58–64.
James, P., Quadroni, M., Carafoli, E., and Gonnet, G. (1994). Protein Sci. 3, 1347–1350.
Johnson, R. S., and Walsh, K. A. (1992). Protein Sci. 1, 1083–1091.
Kitagishy, T., Hong, Y., and Shimonishi, Y. (1981). Int. J. Peptide Protein Res. 17, 436–443.
Kitagishy, T., Hong, Y., Takao, T., Aimoto, S., and Shimonishi, Y. (1982). Bull. Chem. Soc. Jpn. 55, 575–580.
Mann, M., and Wilm, M. (1994). Anal. Chem. 66, 4390–4399.
Mann, M., Hojrup, P., and Roepstorff, P. (1993). Biol. Mass Spectrom. 22, 338–345.
Matsuo, T., Matsuda, H., and Katakuse, I. (1981). Biomed. Mass. Spectrom. 8, 137–143.
Mortz, E., O'Conrior, P. B., Roepstorff, P., Kelleher, N. L., Wood, T. D., McLafferty, F. W., and Mann, M. (1996). Proc. Natl. Acad. Sci. USA 93, 8264–8267.
Pappin, D., Hojrup, P., and Bleasby, A. (1993). Curr. Biol. 3, 327–332.
Patterson, S. D., and Aebersold, R. (1995). Electrophoresis 16, 1791–1814.
Petrilli, P., Sepe, C., and Pucci, P. (1991). Biol. Mass. Spectrom. 20, 115–120.
Petrilli, P., Caporale, C., and Caruso, C. (1994). Int. J. Pept. Protein Res. 43, 201–204.
Shimonishi, Y., Hong, Y., Katakuse, I., and Hara, S. (1981). Bull. Chem. Soc. Jpn. 54, 3069–3075.
Yates, J. R. (1996). Meth. Enzymol. 271, 351–377.
Yates, J. R., Speicher, S., Griffin, P. R., and Hunkapiller, T. (1993). Anal. Biochem. 214, 397–408.
Yates, J. R., III, Eng, J. K., McCormack A. L., and Schieltz, D. (1995). Anal. Chem. 67, 1426–1436.
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
Caporale, C., Sepe, C., Caruso, C. et al. A Computer Program to Compare Sequence Fingerprints of Homologous Proteins for the Rapid Assessment of Their Primary Structure Differences. J Protein Chem 17, 867–873 (1998). https://doi.org/10.1023/A:1020742721725
Published:
Issue Date:
DOI: https://doi.org/10.1023/A:1020742721725