Abstract
It is clear from the description of the workings of the living cell (Chapter 9) that the processes of life everywhere depend on interactions between molecules. From the base-pairing of nucleic acids, to the formation of the bilayer lipid membranes enclosing organelles and cells, through to the protein-protein interactions building up supramolecular complexes serving structural ends, or for carrying out reactions, the regulation of gene expression by transcription factors binding to promotors, the operation of the immune system—the list seems to be almost endless—one observes the molecules of life linked together in a web of interactions. The set of all these interactions, i.e. a list of all the molecules, associated with all the other molecules with which some kind of transient association is found, consitutes the interactome.
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References
Remarkable specificity is achievable, see e.g. the episematic process described by Popescu Misevic.
The dehydron (q.v.) is an underwrapped (i.e. under-desolvated) hydrogen bond and is a key determinant of protein affinity.
See e.g. Ramsden (1984, 1986).
Hydrogen bonding is a special example of Lewis acid-base (AB), or electron donor-acceptor (da) interactions.
E.g. Ramsden Dreier; see Ramsden Grätzel for a nonbiological example of dimensional reduction from three to two dimensions.
See Ramsden (1994) for a comprehensive survey of all these and others.
A popular way to avoid the bioincompatibility of the gold or silver surface of the transducer required with SPR has been to coat it with a thick (’ 200 nm) layer of a biocompatible polysaccharide such as dextran, which forms a hydrogel, to which the target protein is bound. Unfortunately this drastically changes the transport properties of the solution in the vicinity of the target (bound) protein (see the paper by Schuck), which can lead to errors of up to several orders of magnitude in apparent binding constants (via a differential effect on k a and kd). Furthermore such materials interact very strongly (via hydrogen bonds) with water, altering its hydrophilicity, with concomitant drastic changes to protein affinity, leading to further, possibly equally large, distortions in binding constant via its link to the free energy of interaction, i.e. AG = —RT 1n K.
A similar problem is posed by the olfactory system.
Percus et al.
Except near the end of the process, when a and b become very small.
Jeong et al.
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© 2004 Kluwer Academic Publishers
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Ramsden, J.J. (2004). Interactions. In: Bioinformatics: An Introduction. Computational Biology, vol 3. Springer, Dordrecht. https://doi.org/10.1007/978-1-4020-2950-9_14
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DOI: https://doi.org/10.1007/978-1-4020-2950-9_14
Publisher Name: Springer, Dordrecht
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