satish at a.chem.upenn.edu
Mon Nov 28 15:47:56 EST 1994
In article <3bd5jd$fs1 at news.univ-rennes1.fr> MOREAUT at univ-tours.fr writes:
>I have a peptide substrate, the sequence of which is
>This peptide and a second one 4 residues longer at the N-ter side have
>been synthezised in order to study the specificity of a serine proteinase.
>The longest peptide is rapidly cleaved at the Arg/Ser bond as expected
>but the efficiency of cleavage (i.e the kcat/Km ratio) is reduced for
>the short peptide. My questions are:
>1/ which conformation of the Pro residue can we expect for such a short
>peptide i.e cis, trans or do both forms equilibrate?
>I know that cis forms of Pro sometimes occur in proteins but I do not
>know what happens for short peptides.
In globular, folded proteins, the trans form for a proline is favored
over the cis isomer by a ratio of 4:1. However, in random coils,
constraints favoring one isomer over another are released and an
equilibrium exists between the two isomers. The *rate* of isomerization
is very slow though.
>2/ if we have 80% of cis form in the short peptide, should we still have
>80% of cis form in the long peptide?
This can't be answered without doing some more work... for example, is the
longer peptide in a random coil or does it have some sort of secondary
>3/ is it possible that one form (i.e cis or trans) could be a better
>substrate than the other one for the protease?
Again, more data are necessary... for example, how many distinct subsites
are available in the enzyme active site for substrate binding (perhaps the
protease perfers longer peptides in general). I'd suppose one would have to
synthesize a similarly longer peptide without a pro and look at kcat/Km.
Anyway, here are a few references which may be of use:
1. Kelley and Richards, Biochemistry, 26, pp 6765-6774
2. Ramachandran and Mitra, J. Mol. Biol. 107, pp 85-92
3. Haas et al., Biopolymers, 17, pp. 11-31
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