Molecular Mechanism for Gramicidin Dimerization and Dissociation in Bilayers of Different Thickness

Abstract

Membrane protein functions can be altered by subtle changes in the host lipid bilayer physical properties. Gramicidin channels have emerged as a powerful system for elucidating the underlying mechanisms of membrane protein function regulation through changes in bilayer properties, which are reflected in the thermodynamic equilibrium distribution between nonconducting gramicidin monomers and conducting bilayer-spanning dimers. To improve our understanding of how subtle changes in bilayer thickness alter the gramicidin monomer and dimer distributions, we performed extensive atomistic molecular dynamics simulations and fluorescence-quenching experiments on gramicidin A (gA). The free-energy calculations predicted a nonlinear coupling between the bilayer thickness and channel formation. The energetic barrier inhibiting gA channel formation was sharply increased in the thickest bilayer (1,2-dierucoyl-sn-glycero-3-phosphocholine). This prediction was corroborated by experimental results on gramicidin channel activity in bilayers of different thickness. To further explore the mechanism of channel formation, we performed extensive unbiased molecular dynamics simulations, which allowed us to observe spontaneous gA dimer formation in lipid bilayers. The simulations revealed structural rearrangements in the gA subunits and changes in lipid packing, as well as water reorganization, that occur during the dimerization process. Together, the simulations and experiments provide new, to our knowledge, insights into the process and mechanism of gramicidin channel formation, as a prototypical example of the bilayer regulation of membrane protein function.

Assessing the Perturbing Effects of Drugs on Lipid Bilayers Using Gramicidin Channel-Based In Silico and In Vitro Assays

“…The simulations unveiled that the tested drug molecules shift the gA dimer versus monomer equilibrium by non-specifically perturbing the lipid–gA interactions, and the perturbing effects are more pronounced in the thick bilayer than in the thin bilayer. These simulation and experimental approaches, and the unveiled molecular mechanism, open up for an approach to identify PAINS-like molecules, 4 , 31 , 32 which are promiscuous modifiers of membrane protein function, and for safety assessment in drug design and development.…”

Shorter Antibacterial Peptide Having High Selectivity for E. coli Membranes and Low Potential for Inducing Resistance

“…In general, AMP–membrane interactions are complex, requiring biophysical analysis. Several approaches have been used for extracting such information; isothermal titration calorimetry (ITC), bioinformatics simulations and NMR have revealed very precise information about AMP-membrane interactions [ 47 , 66 , 67 , 85 , 86 , 87 , 88 ]. For example, NMR has revealed interactions altering membrane curvature leading to its disruption for peptides such as those derived from magainin and LL-37 [ 9 , 10 , 88 , 89 , 90 ].…”

Calculating the Effect of Membrane Thickness on the Lifetime of the Gramicidin A Channel: A Landmark

“…In this issue of the Biophysical Journal, Sun et al (1) report the results of a remarkable molecular dynamics (MD) study about the effect of membrane thickness on the dimerization and dissociation of the gramicidin A (gA) dimer channel. Although MD simulations of biomolecular systems of fantastical complexity are becoming almost commonplace, this work deserves our attention.…”

“…Since then, there has been a steady progress in simulation algorithms, numerical methods, and computer software and hardware. The allatom force field, which was used by Sun et al (1), was first introduced in the 1990s and was refined for more than 20 years (9)(10)(11)(12)(13).…”

“…In retrospect, it took almost 50 years to bridge the classic experimental measurements showing that the lifetime of the gA channel depends on membrane thickness with the MD simulations of Sun et al (1), which account quantitatively for this observation. In its historical context, this landmark study offers a sobering lesson regarding the pace of fundamental research and the perseverance that is required to move forward, but it also gives us the chance to acknowledge the great advances that have been accomplished in computational biophysics during this period.…”