Predicting the binding properties of cibacron blue F3GA in affinity separation systems.
The binding properties of cibacron blue F3GA (CB-F3GA) bound to a model NAD(P)H/FAD(H2)-dependent protein system, namely cytosolic quinone reductase (QR), was characterized by AMBER in an attempt to address the binding properties of immobilized CB-F3GA used in the separation of serum albumin. A favorable binding free energy of -4.52kcal/mol (KD=5.09 x 10(-4)kcal/mol) was determined for CB-F3GA binding by MM-PBSA method, which was found to be a ballpark estimate of empirical values reported in literature (DeltaG approximately -6kcal/mol). We propose that CB-F3GA primarily follows a class III binding motif in presence of FAD in the binding site of QR in solution, while a class II binding motif is observed in the crystal form. It was found that favorable van der Waals/hydrophobic interactions take place in the binding site making a major contribution to a favorably dominating enthalpy of binding (DeltaHtot=-25.87kcal/mol) as compared to a disfavorable binding entropy term (TDeltaStot=-21.35kcal/mol). Additional MM-PBSA experiments in the absence of FAD gave rise to a disfavorable binding free energy for CB in complex with QR, suggesting that FAD is an essential determinant of CB-F3GA binding. This is in contrast to an earlier observation of Denizli et al. on separation of human serum albumin (HSA) by immobilized CB-F3GA in the absence of FAD. Therefore, a class I binding model for CB-F3GA is proposed here to account for the efficient separation of HSA in affinity chromatography systems.
Dicle University, Department of Chemistry, Diyarbakir, Turkey.
Cenk A
CA
Andac
Muge
M
Andac
Adil
A
Denizli
D001665:Binding Sites; D002846:Chromatography, Affinity / Q000379:methods*; D003198:Computer Simulation; D006860:Hydrogen Bonding; D057927:Hydrophobic and Hydrophilic Interactions; D008956:Models, Chemical; D008958:Models, Molecular; D015394:Molecular Structure; D009243:NAD / Q000378:metabolism; D011808:Quinone Reductases / Q000378:metabolism; D012709:Serum Albumin / Q000302:isolation & purification; D055672:Static Electricity; D013816:Thermodynamics; D014227:Triazines / Q000737:chemistry* / Q000378:metabolism*
D012709:Serum Albumin; D014227:Triazines; D009243:NAD; C012842:Cibacron Blue F 3GA; D011808:Quinone Reductases