• Jeremy J. Ramsden
Part of the Computational Biology book series (COBO, volume 3)


The proteome is the ensemble of expressed proteins in a cell, and proteomics is the study of that ensemble, i.e. the identification and determination of amounts, locations and interactions of all the proteins. The tasks of proteomics are summarized in figure 13.1.


Laser Desorption Ionization Expression Space Phage Population Anionic Detergent Sodium Dodecyl Sulphate Detergent Sodium Dodecyl Sulphate 
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  1. 1.
    Northern blotting allows detection of specific RNA sequences. RNA is fractionated by agarose gel electorphoresis, followed by transfer (blotting) to a membrane support, followed by hybridization with known DNA or RNA probes.Google Scholar
  2. 2.
    The same principle (cf. Southern blotting compared with Northern) If one is trying to determine whether certain genes are present in a bacterial culture (for example), the array should be coated with patches of complementary nucleic acid sequences. The DNA is extracted from the bacteria, subjected to some rudimentary purification, separated into single strands, and usually cut into fragments using restriction enzymes, and then poured over the microarray.Google Scholar
  3. 3.
    Fodor et al.Google Scholar
  4. 4.
    This is known as isoelectric point (i.e.p.), or pI, or point of zero charge (p.z.c.).Google Scholar
  5. 5.
    Linderstrpm-Lang worked out a method of taking these correlations into account; his formula works practically as well as more sophisticated approaches (including explicit numerical simulation by Brownian dynamics) and is much simpler and more convenient to calculate (see Ramsden et al. (1995) for an application example).Google Scholar
  6. 6.
    See Patel Weber for a review.Google Scholar
  7. 7.
    The N-terminal of the protein is derivatized with phenylisothiocyanate to form a phenylthiocarbamate peptide, and the first amino acid is cleaved by strong acid resulting in its anilothiazolinone derivative plus the protein minus its first N-terminal amino acid. The anilothiazolinone derivative is converted to the stabler phenylthiohydantoin for subsequent HPLC identification.Google Scholar
  8. 8.
    See Chem. Rev. 103 (2003), no 2. 9Developed by Aebersold (Gygi et al.).Google Scholar
  9. 9.
    As an alternative way to prepare receptors, the phage display technique invented by Dyax is very useful. The gene for the coat protein expressed abundantly on the surface of a bacteriophage virus is modified by adding a short sequence coding for an oligopeptide to one end. Typically a large number (— 100) of random oligonucleotides are synthesized and incorporated (one per phage) into the virus gene. The phages are then allowed to multiply by infecting a host virus; the random peptide is expressed in abundance on the coat of the phage along with the regular coat protein. The phage population is then exposed to an immobilized target (e.g. a protein). Any phage (a single one suffices) whose peptide interacts with the target during this screening is retained and is then also expressed in abundance on the coat of the phage. The phage population is then exposed to an immobilized target (e.g. a protein). Any phage (a single one suffices) whose peptide interacts with the target during this screening is retained and recovered, and then multiplied in bacteria.Google Scholar
  10. 10.
    See Vohradskÿ Ramsden, Ramsden Vohradskÿ.Google Scholar
  11. 11.
    Groups of operons controlled by a single transcription factor are called regulons, groups of regulons modulons.Google Scholar
  12. 12.
    After Vohradskÿ.Google Scholar

Copyright information

© Kluwer Academic Publishers 2004

Authors and Affiliations

  • Jeremy J. Ramsden
    • 1
  1. 1.Cranfield UniversityCranfieldUK

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