Hello everyone,
Roger Murphy mentioned a software (Peptide Companion from CoshiSoft, San
Diego) that has a predictive algorithm for looking for possible problem
sequences. Unfortunately, when I found the Website I discovered that it was
for PCs not MACs. Does anyone know of a similar program for MACs ?
Thank you,
Rebecca
Rebecca P. Ettling
Biotechnology Resource Laboratory
Protein Sequencing and Peptide Synthesis Facility
Medical University of South Carolina
173 Ashley Avenue, Room 733D BSB
Charleston, SC 29403
Tel.: (843) 792-1271
Fax: (843) 792-1264
--------------------------------------
Date: 7/16/98 9:26 PM
To: Rebecca Ettling
From: Roger Murphy
Dear Leo,
I have used Greg Fields' "Reagent K" for many years with great success
(ref. King et al., Int. J. Pept. Prot. Res., 36, 255-266, 1990), except
where only tBu groups need to be removed, in which case straight 95% TFA/5%
water works fine.
With regard to your sequences, you should get a copy of a program like
Peptide Companion (from CoshiSoft, San Diego), which has a predictive
algorithm for looking for possible problem sequences. I've always found it
to be a useful guide. Generally, long stretches of hydrophobic residues
will cause aggregation problems, particulalrly multi-Ala sequences. These
problems usually are most pronounced 5-15 residues into the synthesis. The
Pro residues can actually be helpful in breaking up hydrophobic
interactions by putting a kink into the growing peptide chains, but too
many Pros will be a problem in themselves.
If you haven't got a copy already, I would suggest you ask your local
Novabiochem agent for a copy of their Catalogue & Peptide Synthesis
Handbook - it has a great section of technical notes on synthesis, and it's
free!
Hope all this helps - if you're really desperate you could send me the
sequences you've been asked to look at, and I'll run them through Peptide
Companion myself. That's not a general invitation to everyone to do so
though!
Good luck and best wishes,
Roger
At 08:45 AM 16-07-98 -0300, you wrote:
>Dear all,
>
> I've used a final deprotection protocol for Fmoc Pept Synthesis for
>several years and now, i'm having some problems in deprotecting PMC
>group from Arg and some tBu from other aminoacids like Ser, Cys or
>Thr, identified in Mass Spec.
> I always used TFA: Anisol: EDT: Water at 85: 5: 3: 7 (and in
>presence of Cys, i use TIS at 5%) for 6-8 hs (is that too long?),
>then i extract it with ACOH 95%.
> Have someone faced some problems like this also? How could i solve
>it? Changing some scavengers or deprotection time, would help? Is it
>some problem with some of the deprotection reagents?
>
>
>another question:
>
>i'm (still) not a peptide synthesizer expert, and i'm having a
>"priviledge" to choose some peptides to synthesize. Actually i
>received a big list of peptides (9-15 aa) to be done and i can
>"eliminate" some of them that, by overlooking to the sequence, would
>be "more difficult" to be synthesized. What sequences would you
>eliminate first? I know that some sequences, changing the protocol
>would make them "easier" to be done.
> Anyways, when you look at a sequence of aminoacids, what sequences
>makes you "scared"? For example, penta-alanines, long sequences of
>hydrophobic aminoacids, presence of prolines etc.
>
> For both questions, any sugestions, coments and critics will be very
>welcomed. Thank you in advance,
>
>Leo
>
>----------------------------------------------------------
>Leo Kei Iwai - Chemist
>Dept of Biophysics
>Escola Paulista de Medicina - EPM - UNIFESP
>Lab of Transplant Immunology
>Instituto do Coracao - Incor - FMUSP
>----------------------------------------------------------
>
Roger Murphy, Ph.D.
Biological Production Facility
Ludwig Institute for Cancer Research
Austin & Repatriation Medical Centre
Studley Road,
Heidelberg, Vic. 3084
Australia.
Tel 61-3-94965463
Fax 61-3-94965436
Email murphy_r@licre.ludwig.edu.au
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