Re: [ccp4bb]: Ions in the internal protein cavities - addendum 3

[Bostjan Kobe <kobe@biosci.uq.edu.au>]

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>I do not think that it is impossible for an ion to occupy a well suited
>cavity in a protein that is folded to carry something in that cavity.
>Like hemoglobin.
>In the case we are talking about there is an elongated trimeric molecule
>formed by intertwined polypeptide chains with mostly hydrophobic filling
>and there is a plane of 3 Asps pointing to the axis surrounded by
>hydrophobics. It is possible that an ion migrated along the axis of the
>trimer but HOW on earth the protein folded so, that it had a
>non-neutralized +3 charge inside and waited till we start to crystallize
>it to suck something from the crystallization solution?
>
>Petr

Hi,

Fass et al. (1996) Nature Struct. Biol. 3, 465 used thermal denatiration
studies in presence of candidate ions, to identify a scatterer in the
middle of a coiled coil trimer. In their case (Moloney murine leukemia
virus envelope protein) the most likely candidate was a chloride. It is
surrounded by 3 Asn residues. Scatterers in similar environments have been
found in other trimeric coiled coils and are thought to stabilize the
structure and are presumably present in the structure since folding. In
your case of course you have Asps, and a negatively charged ion is less
likely. You could use similar methodology, in addition to looking at
anomalous signal, to shed light what your scatterer could be.

Best wishes,

Bostjan

Bostjan Kobe
Associate Professor
Wellcome Senior Research Fellow in Medical Science in Australia
Department of Biochemistry and Molecular Biology/Institute for Molecular
Bioscience
University of Queensland
Brisbane, Queensland 4072
Australia
Phone:	+61-7-3365-2132
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E-mail: kobe@biosci.uq.edu.au
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