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  • Title: Predicting the binding properties of cibacron blue F3GA in affinity separation systems.
    Author: Andac CA, Andac M, Denizli A.
    Journal: Int J Biol Macromol; 2007 Oct 01; 41(4):430-8. PubMed ID: 17675148.
    Abstract:
    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.
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