The problem is that micelle shape/size depends on many factors such as ionic strength, pH, temperature etc (this also depends on the particular detergent). So, even if one would take the ROUGH estimate of the amount of detergent associated with the protein from gel filtration/light scattering experiments, more likely than not this would not correspond to the amount of detergent associated with the protein in the crystal. So a "micelle-corrected" Vm value would still have a large degree of uncertainty and would not really help narrowing down the number of molecules/AU.
Bert van den Berg University of Massachusetts Medical School Program in Molecular Medicine Biotech II, 373 Plantation Street, Suite 115 Worcester MA 01605 Phone: 508 856 1201 (office); 508 856 1211 (lab) e-mail: [EMAIL PROTECTED] http://www.umassmed.edu/pmm/faculty/vandenberg.cfm -----Original Message----- From: CCP4 bulletin board on behalf of Savvas Savvides Sent: Sun 9/23/2007 4:55 AM To: [email protected] Subject: Re: [ccp4bb] Solvent content of membrane protein crystals Indeed, but wouldn't consideration of micelle size affect our estimation of the number of molecules in the asu, in some cases significantly? 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). 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
