Decoy solutions

Forsten, K. E., and Lauffenburger, D. A., Autocrine ligand binding to cell receptors Mathematical analysis of competition by solution decoys. Biophys. J. 61, 1 (1992a). 

The volume of protein extract solution was adjusted to 5.0 ml with a phosphate reaction buffer consisting of 20 mM phosphates at pH 7.4 and then incubated with 5.0 mg ultra clean carbon/cellobiose core (0.5 ml of stock solution) at 4o C for 24 hours. The final colloid consisted of carbon ceramic particulates coated with a layer of cellobiose and a more superficial layer of adsorbed HIV proteins. These colloidal ceramic viral decoys were prepared for use by clearing unadsorbed material by ultrafiltration dialysis with a stir cell [Filtron, Northborough, MA] mounted with a 100 kd filter and flushed with 100 ml of sterile phosphate buffered saline (injection grade) at 4°C under a N2 pressure head of 10 psi. 

The stability of each decoy structure is determined by the sum of the intra-complex energy and the solvation free energy A//. Figure 6.3 shows A// and (Ec + A/i) against RMSDj for the IPPE complex. The complex structures with low RMSDj have smaller E that the other decoys, and with addition of the solvation term, the (E + Afi) value for the equilibrium structure in solution becomes distinctively the smallest. The right structure for IPPE can thus be singled out from Fig. 6.3. It should be noted that the crystal structure is a close but not the right one in solution. The protein structure in solution deviates from that in crystal t3q)icaUy by a few A. 

---