Bacterial Analogs to Cholesterol Affect Dimerization of Proteorhodopsin and Modulates Preferred Dimer Interface

Abstract

Hopanoids, the bacterial analogues of sterols, are ubiquitous in bacteria and play a significant role in organismal survival under stressful environments. Unlike sterols, hopanoids have a high degree of variation in the size and chemical nature of the substituent attached to the ring moiety, leading to different effects on the structure and dynamics of biological membranes. While it is understood that hopanoids can indirectly tune membrane physical properties, little is known on the role that hopanoids may play in affecting the organization and behavior of bacterial membrane proteins. In this work we used coarse-grained molecular dynamics simulations to characterize the effects of two hopanoids, diploptene (DPT) and bacteriohopanetetrol (BHT), on the oligomerization of proteorhodopsin (PR) in a model membrane composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phophoethanolamine (POPE) and 1-palmitoyl-2-oleoyl-sn-3-phosphoglycerol (POPG). PR is a bacterial membrane protein that functions as a light-activated proton pump. We chose PR based on its ability to adopt a distribution of oligomeric states in different membrane environments. Furthermore, the efficiency of proton pumping in PR is intimately linked to its organization into oligomers. Our results reveal that both BHT and DPT indirectly affect dimerization by tuning membrane properties in a fashion that is concentration-dependent. Variation in their interaction with PR in the membrane-embedded and the cytoplasmic regions leads to distinctly different effects on the plasticity of the dimer interface. BHT has the ability to intercalate between monomers in the dimeric interface, whereas DPT shifts dimerization interactions via packing of the interleaflet region of the membrane. Our results show a direct relationship between hopanoid structure and lateral organization of PR, providing a first glimpse at how these bacterial analogues to eukaryotic sterols produce very similar biophysical effects within the cell membrane.

Hopanoid Hopene Locates in the Interior of Membranes and Affects Their Properties

“…Poger and Mark and Melo et al investigated the partitioning of HOP in POPC membranes, and found that HOP located in the midplane of the phospholipid bilayer even at proportions as low as 9%. This preferential location was also observed in POPE bilayers …”

“…The previous results indicate that HOP segregated from POPC even at proportions as low as 1%, forming three-dimensional aggregates and inducing less stiff and more expanded films. Bilayers provide a different environment than monolayers, and HOP could accumulate between POPC hemilayers as predicted by simulated experiments. − To test this, we prepared giant unilamellar vesicles (GUVs) composed of POPC and 20% HOP, as well as pure POPC, POPC and CHO, or POPC and DP for comparison.…”

“…We propose that in bilayers, very low percentages of HOP (lower than ∼1%) locate parallel to the POPC molecules, affecting the surface electrostatics and polar headgroup hydration and order. The excess HOP molecules locate between leaflets as proposed in studies using molecular dynamics simulations. − A scheme of the proposed structure is shown in Figure . These excess HOP molecules inside the membrane increase the average bilayer thickness, causing an increase in the bending rigidity and shear viscosity, and a moderate decrease in conductivity.…”

Relative Affinities of Protein-Cholesterol Interactions from Equilibrium Molecular Dynamics Simulations

“…PyLipID was also used to identify cholesterol binding sites using a community analysis approach to group residues which simultaneously interact with a bound cholesterol over the course of the trajectories. This method is described in detail elsewhere 53,54 and has been applied to a number of recent examples to characterise lipid binding sites and kinetics [55][56][57] . Since the residue composition of Sites A and B varied slightly with the % cholesterol present in the bilayer, we selected six residues from each site, contacts to which were maintained across all cholesterol concentrations and used these six residues in our subsequent analysis (Supplementary Fig.…”

Heliorhodopsin Evolution Is Driven by Photosensory Promiscuity in Monoderms

“…Microbial rhodopsins typically associate as oligomers in vivo , which is also the case with heliorhodopsins that are known to form dimers ( 5 , 22 ). Indeed, it has been demonstrated that lipid composition of the membrane can directly affect proteorhodopsin dimerization ( 23 ). The presence of MORN-repeats in HeRs exclusively within extreme haloalkaliphilic bacteria (class Dethiobacteria ) may be accounted for via their potential role in stabilizing HeR dimers in conditions of increased membrane fluidity (see Fig.…”