Re: [ccp4bb] Protein Color

- Protein crystallography

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: Protein color
From: Palm palm {- at -} UNI-GREIFSWALD {- dot -} DE
Date: 2008-09-05

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Subject: Re: Protein Color
From: Roger Rowlett rrowlett {- at -} MAIL {- dot -} COLGATE {- dot -} EDU
Date: 2008-09-05

Subject: Re: Protein Color
From: Nathaniel Echols nathaniel {- dot -} echols {- at -} GMAIL {- dot -} COM
Date: 2008-09-05

>
> I am working with a protein that turns a yellowish-brown color when it is
> concentrated to around 2 mg/ml or higher in a small volume (a few hundred
> uL). I was wondering if the protein bound a metal or other prosthetic
> group that would give it this color? The protein's color somewhat
> resembles iron binding proteins, but there is no peak in the 400 nm range
> that would suggest heme, and an iron sulfur cluster is not that likely
> since there are only five cysteines in the protein. Proteins with
> structures homologous to the one I am studying bind magnesium, but are not
> know to bind other metals.

This does not rule out other metals, though. For instance, protein kinases
in eukaryotes always use magnesium, but the ones in TB - which are nearly
identical in global structure (with > 30% sequence identity) and appear to
be enzymatically similar - use manganese instead, as do several other TB
homologs of magnesium-binding proteins. This is a quirk of TB's physiology
but there are certainly other protein families (glyoxalases, dioxygenases)
that vary in metal preference depending on organism and substrate
preference. I don't know if Mn would cause that color (although some Mn
compounds are brown or orange-brown); however, there are many ligands that
could. Heme will also change color depending on iron oxidation state, and
possibly local chemical environment. Endogenously purified full-length E.
coli catalase, for instance, is green, but a common proteolytic fragment
(from the same prep) is yellow-brown.

Any information about what this color might
> suggest about the protein or how I could analyze possible bound metals or
> prosthetic groups using only a small amount of protein would be helpful.
>

Mass spec, obviously; if it's a metal, ICP-AES may be more effective, but
I'm not sure how much protein you need. You can also use X-ray fluorescence
to identify metals, but as far as I know this requires a synchrotron.
Sometimes the visual light spectrum alone is enough to tell you what's
there, but it can be difficult to cross-reference this with published data
since (AFAIK) there is no online database of spectra.

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: Protein color
From: Palm palm {- at -} UNI-GREIFSWALD {- dot -} DE
Date: 2008-09-05

Next message:
Subject: Re: Protein Color
From: Roger Rowlett rrowlett {- at -} MAIL {- dot -} COLGATE {- dot -} EDU
Date: 2008-09-05