Abstract
This conference is dedicated to examining new methods for the isolation and characterization of proteins. One extremely effective method for the characterization of a new protein involves the comparison of its amino acid sequence with the sequences of previously determined proteins. Although: this method is not new (but dates back to the early days of protein sequencing methodology), the wealth of information available is only recently being fully appreciated. The rapid increase in the accumulation of sequence data, owing to recombinant DNA technology, has greatly heightened interest in this area and has made large database searching a much more fruitful enterprise. The primary structures of well over 3, 000 proteins containing almost three quarters of a million residues are now known, more than double what was known just 5 years ago.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
L. T. Hunt and M. O. Dayhoff, Evolution of chromosomal proteins, in: “Macromolecular Sequences in Systematic and Evolutionary Biology,” M. Goodman, ed., Plenum, New York (1982).
J. Downward, Y. Yarden, E. Mayes, G. Scrace, N. Totty, P. Stockwell, A. Ullrich, J. Schlessinger, and M. D. Waterfield, Close similarity of epidermal growth factor receptor and v-erb-B oncogene protein sequences, Nature 307: 521 (1984).
A. Ullrich, L. Coussens, J. S. Hayflick, T. J. Dull, A. Gray, A. W. Tam, J. Lee, Y. Yarden, T. A. Libermann, J. Schlessinger, J. Downward, E. L. V. Mayes, N. Whittle, M. D. Waterfield, and P. H. Seeburg, Human epidermal growth factor receptor cDNA sequence and aberrant expression of the amplified gene in A431 epidermoid carcinoma cells, Nature 309: 418 (1984).
W. C. Barker and M. O. Dayhoff, Viral src gene products are related to the catalytic chain of mammalian cAMP-dependent protein kinase, Proc. Nat. Acad. Sci. USA 79: 2836 (1982).
M. L. Privalsky, R. Ralston, and J. M. Bishop, The membrane glycoprotein encoded by the retroviral oncogene v-erb-B is structurally related to tyrosine-specific protein kinases, Proc. Nat. Acad. Sci. USA 81: 704 (1984),
G. Naharro, K. C. Robbins, and E. P. Reddy, Gene product of v-fgr one: hybrid protein containing a portion of actin and a tyrosine-specific protein kinase, Science 223: 63 (1984).
T. Gilmore, J.E. DeClue, and G. S. Martin, Protein phosphorylation at tyrosine is induced by the v-erbB gene product in vivo and in vitro, Cell 40: 609 (1985).
R. M. Kris, I. Lax, W. Gullick, M. D. Waterfield, A. Ullrich, M. Fridkin, and J. Schlessinger, Antibodies against a synthetic peptide as a probe for the kinase activity of the avian EGF receptor and v-erb-B protein, Cell 40: 619 (1985).
M. O. Dayhoff, R.M. Schwartz, H. R. Chen, W. C. Barker, L. T. Hunt, and B. C. Orcutt, Nucleic acid sequence database, DNA 1: 51 (1981).
B. C. Orcutt, D. G. George, J. A. Fredrickson, and M. O. Dayhoff, Nucleic acid sequence database computer system, Nucl. Acids Res. 10: 157 (1982).
B. C. Orcutt, D. G. George, and M. O. Dayhoff, Protein and nucleic acid sequence database systems, Annu. Rev. Biophys. Bioeng. 12: 419 (1983).
M. O. Dayhoff, R. V. Eck, M. A. Chang, and M. R. Sochard, “Atlas of Protein Sequence and Structure 1965,” National Biomedical Research Foundation, Silver Spring, MD (1965).
R. V. Eck and M. O. Dayhoff, “Atlas of Protein Sequence and Structure 1966,” National Biomedical Research Foundation, Silver Spring, MD (1966).
M. O. Dayhoff, ed., “Atlas of Protein Sequence and Structure,” Vol. 5, National Biomedical Research Foundation, Washington (1972).
M. O. Dayhoff, ed., “Atlas of Protein Sequence and Structure,” Vol. 5, Suppl. 3, National Biomedical Research Foundation, Washington (1979).
M. O. Dayhoff, P. J. McLaughlin, W. C. Barker, and L. T. Hunt, Evolution of sequences within protein superfamilies, Naturwissenschaften 62: 154 (1975).
M. O. Dayhoff, The origin and evolution of protein superfamilies, Fed. Proc. 35: 2132 (1976).
M. O. Dayhoff, W. C. Barker, and L. T. Hunt, Establishing homologies in protein sequences, Methods Enzymol. 91: 524 (1983).
B. C. Orcutt and W. C. Barker, Searching the protein sequence database, Bull. Math. Biol. 46: 545 (1984).
M. S. Waterman, General methods of sequence comparison, Bull. Math. Biol. 46: 473 (1984).
D. Sankoff and J. B. Kruskal, eds., “Time Warps, String Edits, and Macromolecules: The Theory and practice of Sequence Comparison,” Addison-Wesley, Reading, MA (1983).
J. B. Kruskal, An overview of sequence comparison: time warps, string edits, and macromolecules, SIAM Rev. 25: 201 (1983).
S. B. Needleman and C. D. Wunsch, A general method applicable to the search for similarities in the amino acid sequence of two proteins, J. Mol. Biol. 48: 443 (1970).
P. H. Sellers, On the theory and computation of evolutionary distances, SIAM J. Appl. Math. 26: 787 (1974).
T. F. Smith, M. S. Waterman, and W. M. Fitch, Comparative biosequence metrics, J. Mol. Evol. 18: 38 (1981).
M. S. Waterman, Sequence alignments in the neighborhood of the optimum with general application to dynamic programming, Proc. Nat. Acad. Sci. USA 80: 3123 (1983).
W. R. Widger, W. A. Cramer, R. G. Herrmann, and A. Trebst, Sequence homology and structural similarity between cytochrome b of mitochondrial complex III and the chloroplast b6-f complex: Position of the cytochrome b hemes in the membrane, Proc. Nat. Acad. Sci. USA 81: 674 (1984).
R. M. Schwartz and M. O. Dayhoff, Matrices for detecting distant relationships, in: “Atlas of Protein Sequence and Structure,” Vol. 5, Suppl. 3, M. O. Dayhoff, ed., National Biomedical Research Foundation, Washington (1979).
D. F. Feng, M. S. Johnson, and R. F. Doolittle, Aligning amino acid sequences: comparison of commonly used methods, Mol. Evol. 21: 112 (1985).
A. J. Gibbs and G. A. Mclntyre, The diagram, a method for comparing sequences, its use with amino acjid and nucleotide sequences, Eur. Biochem. 16: 1 (1970).
A. D. McLachlan, Tests for comparing related amino-acid sequences. Cytochromec and cytochromec, J. Mol. Biol. 61: 409 (1971).
J. V. Maizel, Jr. and R. P. Lenk, Enhanced graphic matrix analysis of Inucleic acid and protein sequences, Proc. Nat. Acad. Sci. USA 78: 7665 (1981).
R. Staden, An interactive graphics program for comparing and aligning nucleic acid and amino acid sequences, Nucl. Acids Res. 10: 2951 (1982).
D. G. George, L.-S. L. Yeh, and W. C. Barker, Unexpected relationships between bacteriophage lambda hypothetical proteins and bacteriophage T4 tail-fiber proteins, Biochem. Biophys. Res. Commun. 115: 1061 (1983).
W. J. Wilbur and D. J. Lipman, Rapid similarity searches of nucleic acid and protein data banks, Proc. Nat. Acad. Sci. USA 80: 726 (1983).
W. J. Wilbur and D. J. Lipman, The context dependent comparison of biological sequences, SIAM J. Appl. Math. 44: 557 (1984).
D. J. Lipman and W. R. Pearson, Rapid and sensitive protein similarity searches, Science 227: 1435 (1985).
M. O. Dayhoff and B. C. Orcutt, Methods for identifying proteins by using partial sequences, Proc. Nat. Acad. Sci. USA 76: 2170
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 1987 Plenum Press, New York
About this chapter
Cite this chapter
George, D.G., Barker, W.C., Hunt, L.T. (1987). The Protein Identification Resource (PIR): An On-Line Computer System for the Characterization of Proteins Based on Comparisons with Previously Characterized Protein Sequences. In: L’Italien, J.J. (eds) Proteins. Springer, Boston, MA. https://doi.org/10.1007/978-1-4613-1787-6_44
Download citation
DOI: https://doi.org/10.1007/978-1-4613-1787-6_44
Publisher Name: Springer, Boston, MA
Print ISBN: 978-1-4612-9001-8
Online ISBN: 978-1-4613-1787-6
eBook Packages: Springer Book Archive