The fact that you only see a peak when reduced/alkylated of course
indicates that the SH is unmodified, so the amino group is the only other
candidate. Is there a chance that you might have N-methyl Cys? (Some
bacterial pili have N-MePhe, for at least one proven example.) With
N-alkylation you still couple and cleave, but get a later elution,
naturally. This could be an especially tempting possibility if you see
preview of the second residue in cycle 1, since there is some spontaneous
cyclization of coupled secondary amines during coupling conditions,
revealing residue 2. Other reason
As to Trp-O, I once saw something I attributed to that (no proof!),
running ~14+ min (=shortly after Tyr) with Trp coming at ~18+ min. I
believe that both peaks were detected. This was a peptide with several
Trp, and more was seen with the one later in sequence.
Regards,
John
At 12:08 PM 3/1/99 -0800, you wrote:
>Dear Colleagues,
>
>can anybody think of reason why an N-terminal cysteine looks like a
tryptophane
>during N-terminal sequence analysis?
>
>We are expecting a Cys in the first cycle but we see a blank (that would
match
>the Cys suspicion) or a Trp upon reduction alone or upon reduction &
alkylation
>(using 4-VP). A Cys residue a little down the sequence comes out as
expected as
>pyridylethylcysteine residue indicating that the chemical reaction worked
fine.
>Asking the same question from a different angle: how does an oxidized Trp
>behave on the sequencer?
>
>Thanks for all your help, Kristine
>
>
>Kristine Swiderek
>Assoc. Research Director, Biological Structure
>ZymoGenetics, Inc.
>1201 Eastlake Ave. E
>Seattle, WA 98102
>Phone: (206)515-4901
>Fax: (206)442-6608
>e-mail: swiderek@zgi.com
>
>
John Hempel, PhD Ph (412) 624 0161
University of Pittsburgh FAX (412) 624 4759
Department of Biological Sciences
Pittsburgh PA 15260 email: hempel@psc.edu
http://www.pitt.edu/~biology/faculty/hempel.html