Computing membrane-AQP5-phosphatidylserine binding affinities with hybrid steered molecular dynamics approach

Mechanism of Reversible Peptide-Bilayer Attachment: Combined Simulation and Experimental Single-Molecule Study

The binding of peptides and proteins to lipid membrane surfaces is of fundamental importance for many membrane-mediated cellular processes. Using closely matched molecular dynamics simulations and atomic force microscopy experiments, we study the force-induced desorption of single peptide chains from phospholipid bilayers to gain microscopic insight into the mechanism of reversible attachment. This approach allows quantification of desorption forces and decomposition of peptide-membrane interactions into energetic and entropic contributions. In both simulations and experiments, the desorption forces of peptides with charged and polar side chains are much smaller than those for hydrophobic peptides. The adsorption of charged/polar peptides to the membrane surface is disfavored by the energetic components, requires breaking of hydrogen bonds involving the peptides, and is favored only slightly by entropy. By contrast, the stronger adsorption of hydrophobic peptides is favored both by energy and by entropy and the desorption forces increase with increasing side-chain hydrophobicity. Interestingly, the calculated net adsorption free energies per residue correlate with experimental results of single residues, indicating that side-chain free energy contributions are largely additive. This observation can help in the design of peptides with tailored adsorption properties and in the estimation of membrane binding properties of peripheral membrane proteins.

Factors affecting the interactions between beta-lactoglobulin and fatty acids as revealed in molecular dynamics simulations

Beta-lactoglobulin (BLG), a bovine dairy protein, is a promiscuously interacting protein that can bind multiple hydrophobic ligands. Fatty acids (FAs), common hydrophobic molecules bound to BLG, are important sources of fuel for life because they yield large quantities of ATP when metabolized. The binding affinity increases with the length of the ligands, indicating the importance of the van der Waals (vdW) interactions between the hydrocarbon tail and the hydrophobic calyx of BLG. An exception to this rule is caprylic acid (OCA) which is two-carbon shorter but has a stronger binding affinity than capric acid. Theoretical calculations in the current literature are not accurate enough to shed light on the underlying physics of this exception. The computed affinity values are greater for longer fatty acids without respect for the caprylic exception and those values are generally several orders of magnitude away from the experimental data. In this work, we used hybrid steered molecular dynamics to accurately compute the binding free energies between BLG and the five saturated FAs of 8 to 16 carbon atoms. The computed binding free energies agree well with experimental data not only in rank but also in absolute values. We gained insights into the exceptional behavior of caprylic acid in the computed values of entropy and electrostatic interactions. We found that the electrostatic interaction between the carboxyl group of caprylic acid and the two amino groups of K60/69 in BLG is much stronger than the vdW force between the OCA's hydrophobic tail and the BLG calyx. This pulls OCA to the top of the beta barrel where it is easier to fluctuate, giving rise to greater entropy of OCA at the binding site.