Computational studies of colicin insertion into membranes: The closed state

Abstract

Colicins are water-soluble toxins that, upon interaction with membranes, undergo a conformational change, insert, and form pores in them. Pore formation activity is localized in a bundle of 10 α-helices named the pore-forming domain (PFD). There is evidence that colicins attach to the membrane via a hydrophobic hairpin embedded in the core of the PFD. Two main models have been suggested for the membrane-bound state: penknife and umbrella, differing in regard to the orientation of the hydrophobic hairpin with respect to the membrane. The arrangement of the amphipathic helices has been described as either a compact three-dimensional structure or a two-dimensional array of loosely interacting helices on the membrane surface. Using molecular dynamics simulations with an implicit membrane model, we studied the structure and stability of the conformations proposed above for four colicins. We find that colicins are initially driven towards the membrane by electrostatic interactions between basic residues and the negatively charged membrane surface. They do not have a unique binding orientation, but in the predominant orientations the central hydrophobic hairpin is parallel to the membrane. In the inserted state, the estimated free energy tends to be lower for the compact arrangements of the amphipathic helix, but the more expanded ones are in better agreement with experimental distance distributions. The difference in energy between penknife and umbrella conformations is small enough for equilibrium to exist between them. Elongation of the hydrophobic hairpin helices and membrane thinning were found unable to produce stabilization of the transmembrane configuration of the hydrophobic hairpin.

Implicit membrane treatment of buried charged groups: Application to peptide translocation across lipid bilayers

“…One first performs calculations for a range of membrane thicknesses (T) to compute the effective energy W as a function of T. An estimate of the membrane deformation free energy ΔG def as a function of T is then added to the resulting energies and the thickness that minimizes the sum of W and ΔG def is selected as the optimal result [40]. As in previous work [41], we use the spring model proposed by Andersen and coworkers [42] to estimate the membrane deformation free energy. According to this model, the deformation free energy can be calculated as Δ G def = H · (Δ T ) 2 , where ΔT stands for the deformation of the membrane and H is the spring constant that can be determined using the equation: $$H=H^{\ast }{\left(\frac{K_a}{K_a^{\ast }}\right)}^{\nu }{\left(\frac{K_c}{K_c^{\ast }}\right)}^{\mu }$$…”

Protein-fluctuation-induced water-pore formation in ion channel voltage-sensor translocation across a lipid bilayer membrane

“…For example, the MD simulation studies of the insertion of α-helices into the membrane and stability of α-helices in the membrane have been reported [73][74][75][76]. Although these studies have provided insightful information about the specific or generalized ion channels, the details of colicin Ia have not been studied with MD simulations largely due to the lack of experimental structural and dynamic information of the ion channel's membrane-bound states [77]. Nevertheless, in this work, we compared simulation results to the experimental findings to develop a molecular level picture of peptide translocation across lipid membrane while forming an active ion channel.…”

“…The umbrella conformation of the Cdomain ( Figure 1B) is used as the starting configuration of colicin Ia due to its reported lowest free energy amongst all the accessible conformations [77]. The DPhPC lipid bilayer model is constructed and simulated as discussed above.…”

In Situ Electrochemical and PM-IRRAS Studies of Colicin E1 Ion Channels in the Floating Bilayer Lipid Membrane

“…2 A plethora of biophysical studies have been conducted on colicin E1, including fluorescence resonance energy transfer, 3,4 solidstate NMR spectroscopy, 5 and molecular dynamics simulations. 6 These investigations revealed key insights into the closed-channel state, where the hydrophobic helices VIII and IX insert into the nonpolar core of the lipid bilayer to form a hydrophobic hairpin, while the other eight helices are embedded in the membrane interfacial layer. The colicin E1 ion channels open at the negative transmembrane potentials, 7 in which seven helices insert into the hydrophobic region of the bilayer to form ion-selective pores.…”

“…The X-ray crystallographic structure of the colicin E1 C-domain consists of 10 α-helices, in which helices VIII and IX are highly hydrophobic . A plethora of biophysical studies have been conducted on colicin E1, including fluorescence resonance energy transfer, , solid-state NMR spectroscopy, and molecular dynamics simulations . These investigations revealed key insights into the closed-channel state, where the hydrophobic helices VIII and IX insert into the nonpolar core of the lipid bilayer to form a hydrophobic hairpin, while the other eight helices are embedded in the membrane interfacial layer.…”