Bradford assays and lysozymes

[J. S. John]

In our biochem techniques class, we did some protein assays on BSA and
Lysozyme. In the Bradford assay of lysozyme, the response was low. The
professor told us this would happen and we're to research on why it is
so. I'm still doing research on this but I have some questions.

Where can I find more detailed information about the MW, structure,
and amino acid sequence of lysozyme. I found a site that gives me the
sequence:
http://lysozyme.co.uk/lysozyme-sequence.php

It gives the amino acids as letter abbreviations. I also found another
site that converts the letters in 3-letter abbreviations and also
gives the frequency:
http://www.molbiol.ru/eng/scripts/01_17.html
http://www.molbiol.ru/eng/scripts/01_18.html

However, the mass this program gives is much less than the one on
http://lysozyme.co.uk/
Where can I get solid, non contradicting information?

Thanks very much

[Nathan McCorkle]

The masses are going to be different for each sequence that differs, its a protein not a molecule of set molecular weight

the link to BRENDA here has a lot of listings of the different sequences known... you're gonna have to give your prof a range or an average:

http://en.wikipedia.org/wiki/Lysozyme

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Nathan McCorkle
Rochester Institute of Technology
College of Science, Biotechnology/Bioinformatics

[J. S. John]

On Thu, Feb 4, 2010 at 2:54 PM, Nathan McCorkle <nmz...@gmail.com> wrote:
> The masses are going to be different for each sequence that differs, its a
> protein not a molecule of set molecular weight
>
> the link to BRENDA here has a lot of listings of the different sequences
> known... you're gonna have to give your prof a range or an average:
> http://en.wikipedia.org/wiki/Lysozyme

Actually, thats not the thing. I was only comparing MW to make sure I
was looking at the right stuff. What I really need is to find the
percentage of each of the amino acids in the structure. From some
research, I have learned that Coomassie binds more readily to charged
amino acids with arginine providing most to the interaction.

I looked at the chick lysozyme and it seemed to have a low percentage
of arginine. I also looked at the BSA sequence and it doesn't have too
high Arg percentage(~5) compared to lysozyme. Too much confusing
information.

This is the stuff they should be teaching us in school.

[Nathan McCorkle]

Seems like an easy program to write if you know a little programming... you could just loop through each character in the amino acid sequence string and have a counter for each AA letter... have either a bunch of if statements, or a switch block.

There has got to be a program out there already... hmm, if not, i could whip up some web-based thingy.

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[J. S. John]

On Fri, Feb 5, 2010 at 12:10 AM, Nathan McCorkle <nmz...@gmail.com> wrote:
> Seems like an easy program to write if you know a little programming... you
> could just loop through each character in the amino acid sequence string and
> have a counter for each AA letter... have either a bunch of if statements,
> or a switch block.
> There has got to be a program out there already... hmm, if not, i could whip
> up some web-based thingy.
>

I did find that program to online.
http://www.molbiol.ru/eng/scripts/01_17.html
http://www.molbiol.ru/eng/scripts/01_18.html

However, I wasn't sure if I had the right sequences

[Tom Randall]

http://mobyle.pasteur.fr/cgi-bin/portal.py
Under programs go to Protein > Composition and use the tool wordcount,
will work for proteins as well as DNA, gives an aa count.

More protein related tools under Sequence > Protein > Composition

On Feb 5, 12:10 am, Nathan McCorkle <nmz...@gmail.com> wrote:
> Seems like an easy program to write if you know a little programming... you
> could just loop through each character in the amino acid sequence string and
> have a counter for each AA letter... have either a bunch of if statements,
> or a switch block.
>
> There has got to be a program out there already... hmm, if not, i could whip
> up some web-based thingy.
>

> On Thu, Feb 4, 2010 at 6:14 PM, J. S. John <phillyj...@gmail.com> wrote:
>

[Meredith L. Patterson]

On Thu, Feb 4, 2010 at 9:10 PM, Nathan McCorkle <nmz...@gmail.com> wrote:
> Seems like an easy program to write if you know a little programming... you
> could just loop through each character in the amino acid sequence string and
> have a counter for each AA letter... have either a bunch of if statements,
> or a switch block.
> There has got to be a program out there already... hmm, if not, i could whip
> up some web-based thingy.

There's a module in biopython that'll do it.

--mlp