FREE-ENERGY SIMULATION STUDIES OF THE BINDING-SPECIFICITY OF MANNOSE-BINDING PROTEIN

Free energy simulations and standard molecular mechanics calculations have been used to examine the binding specificity of the C-type lectin rat mannose-binding protein. This protein, which is important in infl ammation and immunoglobin-independent immune response, recognizes and binds to mannose and high-mannose oligosaccharides but not to galactos e. Molecular dynamics simulations were used to estimate the free energ y difference between these two sugars in aqueous solution and in the b inding site of the protein. While the simulations found mannose to be favored over galactose, interactions with the solvent tended to favor galactose: The calculated binding free energy difference for these two sugars to MBP was 3.1 kcal/mol favoring mannose, approximately twice the experimental value. An estimate of the resolution into components found that enthalpy favored mannose but that entropy favored galactose , a reversal of the situation in solution. From standard MD simulation s, the galactose was found to rotate in the binding site away from the mannose orientation found in crystallographic studies.