Cathepsin B & Synthetic Substrates
Simon M. Brocklehurst
smb at bioch.ox.ac.uk
Tue May 28 12:59:30 EST 1996
Louis Hom wrote:
> So I've been looking at a viral protease that is homologous to the
> cathepsins, and has the substrate specificity of cathepsin B (i.e., it
> prefers an Arg 2 aa's N-terminal to the site of cleavage). The researchers
> used Z-Arg-Arg-MCA and some other synthetic substrates to demonstrate this.
> What sort of puzzles me is why these experiments almost always use
> Z-Arg-X-MCA rather than Z-Lys-X-MCA. After all, the crystal structure
> suggests a preference for the positive charge of Arg more than, say, its
> shape. Any ideas? Is there some esoteric quirk involving difficulty in
A couple of points...
It is much easier to synthesise alpha-N-acyl-Arg derivatives than the
corresponding Lys ones-because of acylation of epsilon NH2 as well as alpha
And of course, some enzymes, eg trypsin, do not discriminate between R and
K (at P1). Others however _DO_ discriminate. I don't at what level you've
looked at the crystal structure - but discrimination can depend on subtle
features of the geometry of the enzyme subsite and the position of the D/E
within in it.
In other words, if you're looking at the structure and saying, "well there's
the subsite, and there's a negative charge at the bottom," then that's not close
to being enough information to form an opinion as to whether K or R or either
derivatives should be recognised.
Hope this helps a bit...
| ,_ o Simon M. Brocklehurst,
| / //\, Oxford Centre for Molecular Sciences, Department of Biochemistry,
| \>> | University of Oxford, Oxford, UK.
| \\, E-mail: smb at bioch.ox.ac.uk | WWW: http://www.ocms.ox.ac.uk/~smb/
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