Affinity of rhodopsin to raft enables the aligned oligomer formation from dimers: Coarse-grained molecular dynamics simulation of disk membranes

Abstract

24 The visual photopigment protein rhodopsin (Rh) is a typical G protein-coupled receptor 25 (GPCR) that initiates the phototransduction cascade in retinal disk membrane of 26 rod-photoreceptor cells. Rh molecule has a tendency to form dimer, and the dimer tends 27 to form rows, which is suggested to heighten phototransduction efficiency in 28 single-photon regime. In addition, the dimerization confers Rh an affinity for lipid raft, 29 i.e. raftophilicity. However, the mechanism by which Rh-dimer raftophilicity 30 contributes to the organization of the higher order structure remains unknown. In this 31 study, we performed coarse-grained molecular dynamics simulations of a disk 32 membrane model containing unsaturated lipids, saturated lipids with cholesterol, and 33 Rh-dimers. We described the Rh-dimers by two-dimensional particle populations where 34 the palmitoyl moieties of each Rh exhibits raftophilicity. We simulated the structuring 35 of Rh in a disk for two types of Rh-dimer, i.e., the most and second most stable Rh 36 dimers, which exposes the raftophilic regions at the dimerization-interface (H1/H8 37 dimer) and two edges away from the interface (H4/H5 dimer), respectively. Our 38 simulations revealed that only the H1/H8 dimer could form a row structure. A small 39 number of raftophilic lipids recruited to and intercalated in a narrow space between 40 H1/H8 dimers stabilize the side-by-side interaction between dimers in a row. Our results 41 implicate that the nano-sized lipid raft domains act as a "glue" to organize the long row 42 structures of Rh-dimers. 43 44 INTRODUCTION 45 The visual pigment rhodopsin (Rh) initiates the phototransduction cascade in vertebrate 46 disk membranes of rod photoreceptor cells. Rh is a prototypical seven-transmembrane 47 G protein-coupled receptor (GPCR) and is highly concentrated in the disk membrane, 48 occupying approximately 30% of the total disk membrane area [1,2]. 49Similar to many other GPCRs, Rh is doubly palmitoylated (C16:0) at the 50 C-terminus of the juxta-membrane eighth-helix (H8) [3]. The tandem palmitoyls are 51 known to be a robust raft-targeting signal for membrane proteins [4][5][6][7][8][9]. However, 52 despite having two palmitoyls, Rh prefers polyunsaturated phospholipids because of its 53 rough intramembrane surface, which is similar to other membrane proteins [10,11].54 Thus, rhodopsin is inherently a non-raftophilic (raftophobic) membrane protein.55 Nevertheless, dimerization, which is stabilized by the binding of the cognate G protein 56 transducin, confers a high lipid raft affinity (raftophilicity) for Rh , i.e., the di-palmitoyl 57 modification at the C-terminus of H8 is prerequisite for the dimerization-dependent 58 raftophilicity of Rh [12]. Single-and semi-multimolecular observations on rhodopsin 59 dynamics in retinal disk have revealed that the oligomerization-induced raftophilicity of 60 Rh promotes spontaneous formation of raftophilic Rh-clusters [13]. 61 The organization and dynamics of Rh in the disk membrane have long been 62 debate...

A hybrid stochastic/deterministic model of single photon response and light adaptation in mouse rods

“…We further tested the effect of a dynamic scaffolding of rhodopsin and transducin, postulated in previous in silico [8] , [9] , [10] and in vitro [5] , [7] studies, which has been integrated in recent mechanistic descriptions of the phototransduction cascade [5] , [11] . Rhodopsin assembles into tracks of dimers in disk membranes thereby providing a platform for pre-assembling with transducin in the dark state [5] .…”

“…Previous simulations suggested that the dynamic pre-assembly would not perturb the kinetics of photoresponses, although the analysis did not consider spatial constraints and was not performed in a stochastic framework [7] . The kinetics of this process in the context of the identified supramolecular organization of rhodopsin in tracks of dimers has been recently investigated [5] , [11] . In the present simulations, we did not observe any change in the kinetics of the photoresponse, neither an acceleration nor a slowing down, when we incorporated parameters describing the pre-assembled state in the model.…”

“…First, the GPCR rhodopsin is spatially ordered in track-like structures in the membrane of rod outer segment disks, and is thereby more restricted in its diffusion than previously thought [4] , [5] , [6] . Furthermore, in dark-adapted conditions, about 30% of transducin molecules might pre-assemble with rhodopsin [7] , [8] , which could facilitate the light-triggered activation process in such a spatially ordered system [9] , [10] , [11] , even though a contribution by Schöneberg et al [12] questioned the significance of this phenomenon for efficient signaling, thus originating a debate on the physiological role of the pre-assembly [13] , [14] . Lastly, it has been recently proposed that the main effector in the cascade is not single-, but double-activated PDE [15] , which would reduce the continuous noise in darkness by suppressing the spurious signal of spontaneous transducin activation [16] .…”