Savvas Savvides wrote:
Indeed, but wouldn't consideration of micelle size affect our
estimation of the number of molecules in the asu, in some cases
significantly?
Good point- I think now that is taken into account by just saying
"membrane proteins tend to have a high solvent content" and taking
that into consideration when you guess the number of molecules.
But it would be nice to account for the detergent explicitly.
Say by analyzing detergent content of the crystals, or in some
ideal cases neutron diffraction with perdeuterated detergent.
The crystal packing of some membrane proteins shows that they tend to
pack as "potatoes in space" with relatively few protein-protein
contacts and with detergent micelles presumably providing the rest of
the crystal packing interactions. That also explains the often
significant diffraction anisotropy observed in such crystals. One
classic example is the prototypical potassium channel structure (KCSA)
(PDB entry 1bl8).
I'll have to look at KCSA again. I've been assuming the micelle is too
fluid and solvent-like to make any kind of a crystal contact, but it
occupies space holding the molecules apart and preventing real crystal
contacts. This was the rationale behind Michel's use of "small
amphiphiles" to replace the bulky micelle, and antibody fragments to
bridge the gap and provide hydrophilic areas for contact.
Savvas
Quoting Edward Berry <[EMAIL PROTECTED]>:
I would use a very general definition for "solvent",
including disordered detergent and lipids.
As you know in many cases ordered detergents and lipids
have been modeled in the coordinates, so they are part of
the model not the solvent. In some cases I think waters
should be included in the model not solvent- say for
structural waters buried in the protein at least.
Ed
Savvas Savvides wrote:
Dear colleagues,
in estimating the solvent content of membrane protein crystals it
would only seem reasonable that micelle size should also be taken
into account. Depending on the aggregation number and MW of a given
detergent, the concentation of detergent used, and the buffer
conditions, one may have micelles on the order of 15-25 kDa or even
35-50 kDa for detergents with alkyl chains of more than 10 carbons.
However, when I took a look in a handful of papers reporting
Matthews' numbers for membrane protein crystals, it became apparent
that only the protein MW is used in such estimates. I am
beginning to wonder if one should even bother reporting a Matthews
number for a membrane protein crystal given the uncertainties
surrounding size and role of micelles in crystal packing.
Any thoughts on this?
best wishes
Savvas
