3D-proteine structure: Homology modeling versus X-ray chrystallography
crebeiz at UIUC.EDU
Wed Feb 1 10:16:54 EST 1995
>> . . . I wonder
>> however, about the relationship of a laboratory-grown crystal of a
>> membrane-bound solubilized protein to the native protein in situ.
>> Constantin A. Rebeiz
>> 240 A, PABL
>> 1201 W. Gregory
>> Univ. Illinois, Urbana, IL 61801
>True, many of us do -- but at least we know the real fold of that
>polypeptide under at least one set of conditions.
>It is often not mentioned that the "folding problem" is actually the
>prediction of the structure of a particular sequence in a particular
>environment. If this were not so, proteins would not denature, and
>we know that some of them are very sensitive to things like pH,
>temperature, salt, . . .
>This makes the "folding problem" something more than an exercise in
>pattern detection and matching.
>Lynn Ten Eyck
>teneyck at sdsc.edu
In that case the debate that has been going in this forum, on on the
relative merits of X-ray data versus 3D-modeling is trivial since neither of
the two techniques can be related with absolute certainty to the state of a
protein in situ. I must add however that twith this uncertainty in mind,
dynamic 3D-modeling (amber) and docking techniques for example, do permit
the derivation of additional 3D-models derived from a homology model,
which may be more compatible with known experimental data. In other words
the dynamic choices offered by 3D-modeling which are not offered by the more
rigid X-ray data, should not be iognored or minimized.
Constantin A. Rebeiz
240 A, PABL
1201 W. Gregory
Univ. Illinois, Urbana, IL 61801
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