Re: [DIYbio] Re: Molecular Dynamics

Are you saying that sometimes the way proteins crystallize isn't how

they are in situ,

We must face this possibility. For example, many hemoglobine PDBs
turn out to be of improbable or unimportant conformation, and they have
to rewrite the book on how oxygen storage works with hemoglobine.
50 years of research down the drain!

T. Yonetani, M. Laberge: ''Protein dynamics explain the allosteric behaviors of hemoglobin.'' In: ''Biochimica et biophysica acta.'' 1784, 9, September 2008, 1146–1158. doi:10.1016/j.bbapap.2008.04.025. PMID 18519045. PMC 2668241. (Review).

Kanaori K, Tajiri Y, Tsuneshige A, Ishigami I, Ogura T, Tajima K, Neya S, Yonetani T. "T-quaternary structure of oxy human adult hemoglobin in the presence of two allosteric effectors, L35 and IHP." Biochim Biophys Acta. 2011 Oct;1807(10):1253-61. Epub 2011 Jun 15. PMID 21703224

Citation from abstract:
Therefore, the widely held assumptions of the structure-function correlation of Hb - [the deoxy-state]=[the T-quaternary structure]=[the low O(2)-affinity state] and [the oxy-state]=[the R-quaternary structure]=[the high O(2)-affinity state] and the O(2)-affiny of Hb being regulated by the T/R-quaternary structural transition - are no longer sustainable.

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