Molecular dynamics simulations of adipocyte lipid-binding protein: effect of electrostatics and acyl chain unsaturation.
Molecular dynamics (MD) simulations have been performed on adipocyte lipid-binding protein, using the apo and holo forms, bound with stearic and oleic acid. The contribution of electrostatics to protein dynamics and ligand stabilization was assayed by perturbing the electrostatic charge of Arg106 and Arg126 (positive-->neutral) and the fatty acid (132H) headgroup (negative-->neutral). MD simulations for charged holo forms demonstrated significantly greater electrostatic binding energy and a more stabilized hydrogen bond network than simulations performed using neutral forms. Electrostatics, however, appeared to have little effect on fatty acid behavior, e.g., fluctuation of the dihedral head group; number of dihedral transitions within the acyl chain; and change in the end-to-end distance for fatty acid. Instead, fatty acid behavior appeared to be dictated by the presence or absence of an unsaturated bond within the acyl chain. A significantly greater number of transitions were observed during MD simulations in oleic than stearic acid. In addition, significantly greater fluctuation was observed for oleic acid, within the C2 headgroup and C9 and C11 dihedrals (which lie adjacent to the olefin bond of oleic acid). The dynamic behavior of the acyl chain may thereby be more a property of van der Waals contact, and the degree of acyl chain unsaturation, than a function of electrostatics. In the absence of fatty acid, an increase in distance between guanidino carbon centered atoms of Arg126 and Arg106 was observed during MD simulations of the charged apo form. This effect not observed with the neutral apo form or in any of the holo complexes and, presumbably, was a result of repulsion between the negatively charged arginine sidechains. Conserved waters reflected substantially lower mean-square displacement (msd) in all simulations, except the neutral apo form. This suggests that the presence of either charged amino acids or lipid provides increased order for water within the binding pocket. These results provide a dynamic perspective of the interactive nature within the FABP binding pocket regulated in a complex manner by the electrostatics within the binding cavity, acyl chain structure and behavior, and water energetics.
Rich
M R
MR
Department of Biology, New York University, New York 10003, USA.
Evans
J S
JS
D002352:Carrier Proteins / Q000737:chemistry*; D003198:Computer Simulation; D004560:Electricity; D050556:Fatty Acid-Binding Proteins; D005231:Fatty Acids, Unsaturated / Q000737:chemistry*; D008958:Models, Molecular; D008968:Molecular Conformation; D018996:Myelin P2 Protein / Q000737:chemistry*; D009363:Neoplasm Proteins; D019301:Oleic Acid; D009829:Oleic Acids / Q000737:chemistry; D013229:Stearic Acids / Q000737:chemistry
D002352:Carrier Proteins; D050556:Fatty Acid-Binding Proteins; D005231:Fatty Acids, Unsaturated; D018996:Myelin P2 Protein; D009363:Neoplasm Proteins; D009829:Oleic Acids; D013229:Stearic Acids; D019301:Oleic Acid; C031183:stearic acid