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 <[log in to unmask]>:
>
>> 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
>
>
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