Prediction of the most favorable configuration in protein-membrane interactions based on computational calculations.

DIEGO F. VALLEJO; FERNANDO ZAMARREÑO; DIEGO M.A. GUÉRIN; J. RAUL GRIGERA; MARCELO D. COSTABEL

Trieste

Conferencia; 2nd Conference on Drug Development for the Third World: From Computational Molecular Biology to Experimental Approaches.; 2009

ICTP, ICS-UNIDO (Trieste) y INFM-DEMOCRITOS (Trieste)

To estimate the importance of the non-specific electrostatic energy in the ACBP-membrane interaction, we computationally modeled the interaction of HgACBP with both anionic and neutral membranes. Acyl-CoA binding proteins (ACBPs) are highly conserved 10 kDa cytosolic proteins that bind medium- and long-chain acyl-CoA esters. They act as intracellular carriers of acyl-CoA and play a role in acyl-CoA metabolism, gene regulation, acyl-CoA-mediated cell signaling, transport-mediated lipid synthesis, membrane trafficking and also, ACBPs were indicated as a possible inhibitor of diazepam binding to the GABAA receptor . To compute the Free Electrostatic Energy of Binding (dE ), we used the Finite Difference Poisson Boltzmann Equation (FDPB) method as implemented in APBS. In the most energetically favorable orientation, ACBP brings charged residues Lys18 and Lys50 and hydrophobic residues Met46 and Leu47 into membrane surface proximity. This conformation suggests that these four ACBP amino acids are most likely to play a leading role in the ACBP-membrane interaction and ligand intake. Thus, we propose that long range electrostatic forces are the first step in the interaction mechanism between ACBP and membranes.