[RASMB] Hb tetramer

[Mattia Rocco]

Hi Mitra,

apologies for chiming in so late in the debate, but I was away. We have 
been modeling Hb as a part of an intensive testing effort for a paper that 
will be published in the AUC & HYDRO 2008 EBJ special issue Brookes et al., 
Eur. Biophys J., in press). Thus, we did some literature searches, and 
indeed the reported s(20,w) for HUMAN deoxy Hb is 4.34 S (Goers JW, 
Schumaker VN (1970). Differential sedimentation study on the dissociation 
and conformational change in hemoglobin. J Mol Biol 54: 125-129). However, 
when we CALCULATED the s(20,w) based on the 1HGA human deoxy Hb crystal 
structure, using the SOMO programs (Rai et al., Structure 13: 723-734, 
2005; Brookes et al., Eur Biophys J, in press), we get a 4.77 S value! 
That's VERY close to your actual value... while the agreement with  the 
Goers & Schumaker value was one of the worst in our testing of the SOMO 
method...  And, in case you're wondering, we used the Demoll et al. psv for 
the heme...

Perhaps it would be interesting to re-compute the value for an homology 
model of your Hb based on the human structure? (I assume that the true 
structure of your avian Hb isn't available).

Hope this helps - Mattia

At 02:19 PM 2/5/2009 -0600, mitrana at mail.utexas.edu wrote:
>Hello All
>
>After re-measuring the viscosity my current deoxy Hb S20,w value
>stands at ~4.82 right now. I don't think the inclusion of the v-bar of
>IHP is going to change this value much. This is still much higher than
>the 4.1 - 4.5 range of Hb tetramer that Allen mentions.
>
>The avian Hb D that I am working with has MW similar to BSA than human
>Hb - it's about 66500 Da. versus ~ 64500 for human Hb. Plus I don't
>think there is a lot of literature on s-values for avian Hb minor
>component - at least I can't seem to find it. The major component has
>S20,w values in the 4.1-4.5 range as expected and the Hb lysate shows
>similar values.
>
>I think the best step forward for me is to decrease the dithionite
>concentration to 1 mM and do the experiment. Make sure that excess
>dithionite is not doing anything funky to the Hb.
>
>Thanks for the discussion. BTW, I traced the 11 mM dithionite that I
>was using to this reference - Andersen, M. E. (1972) J. Biol. Chem.
>246, 4800-4806.
>
>Mitra
>
>
>
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