Ligand’s Partition to the Lipid Bilayer Should Be Accounted for When Estimating Their Affinity to Proteins

Abstract

Ligand-protein interactions are usually studied in complex media that also contain lipids. This is particularly relevant for membrane proteins that are always associated with lipid bilayers, but also for water-soluble proteins studied in in vivo conditions. This work addresses the following two questions: (i) How does the neglect of the lipid bilayer influence the apparent ligand-protein affinity? (ii) How can the intrinsic ligand-protein affinity be obtained? Here we present a framework to quantitatively characterize ligand-protein interactions in complex media for proteins with a single binding site. The apparent affinity obtained when following some often-used approximations is also explored, to establish these approximations’ validity limits and to allow the estimation of the true affinities from data reported in literature. It is found that an increase in the ligand lipophilicity or in the volume of the lipid bilayer always leads to a decrease in the apparent ligand-protein affinity, both for water-soluble and for membrane proteins. The only exceptions are very polar ligands (excluded from the lipid bilayer) and ligands whose binding affinity to the protein increases supralinearly with ligand lipophilicity. Finally, this work discusses which are the most relevant parameters to consider when exploring the specificity of membrane proteins.

Interaction of Hoechst 33342 with POPC Membranes at Different pH Values

“…The partition coefficients to the actual membranes or to representative model membranes must be used instead. This procedure must be followed whenever the association of solutes with membrane proteins is considered [94], as is the case for the interaction with the efflux transporter P-glycoprotein, of which Hoechst dyes are well-known substrates [13,14]. Failure to do so will lead to apparent affinities for the membrane proteins that do not reflect the interactions established between the ligand and the protein [95].…”

Permeation of a Homologous Series of NBD-Labeled Fatty Amines through Lipid Bilayers: A Molecular Dynamics Study

“…The localization of drugs on lipid bilayers might affect their interaction with drug-metabolizing cytochrome P450 (CYP) enzymes [ 14 ], and as a consequence affect the metabolism of drugs. Further, the localization and affinity to a membrane may play an important role in other biologically significant processes, such as interaction with other membrane proteins [ 15 , 16 , 17 , 18 ], and antioxidant inhibition of lipid peroxidation [ 19 , 20 , 21 ].…”