Explicit Spatiotemporal Simulation of Receptor-G Protein Coupling in Rod Cell Disk Membranes

Abstract

Dim-light vision is mediated by retinal rod cells. Rhodopsin (R), a G-protein-coupled receptor, switches to its active form (R(∗)) in response to absorbing a single photon and activates multiple copies of the G-protein transducin (G) that trigger further downstream reactions of the phototransduction cascade. The classical assumption is that R and G are uniformly distributed and freely diffusing on disk membranes. Recent experimental findings have challenged this view by showing specific R architectures, including RG precomplexes, nonuniform R density, specific R arrangements, and immobile fractions of R. Here, we derive a physical model that describes the first steps of the photoactivation cascade in spatiotemporal detail and single-molecule resolution. The model was implemented in the ReaDDy software for particle-based reaction-diffusion simulations. Detailed kinetic in vitro experiments are used to parametrize the reaction rates and diffusion constants of R and G. Particle diffusion and G activation are then studied under different conditions of R-R interaction. It is found that the classical free-diffusion model is consistent with the available kinetic data. The existence of precomplexes between inactive R and G is only consistent with the data if these precomplexes are weak, with much larger dissociation rates than suggested elsewhere. Microarchitectures of R, such as dimer racks, would effectively immobilize R but have little impact on the diffusivity of G and on the overall amplification of the cascade at the level of the G protein.

Spatial and Temporal Aspects of Signaling by G-Protein–Coupled Receptors

“…In principle, any step within the sequence of conformational conversions described above could be affected and modulate the overall speed of G-protein activation. A possible scenario would be that one of the binding partners is held in a supramolecular structure, from or in which it is slowly made available for interaction (Schöneberg et al, 2014). This is reminiscent of recent work on rhodopsin, which has resulted in dramatically different simulated activation rates of G t , depending on the localization of the activating R* within or outside rows of dimers of the receptor (Gunkel et al, 2015).…”

ReaDDyMM: Fast Interacting Particle Reaction-Diffusion Simulations Using Graphical Processing Units

“…Typical proteins can be simulated with timesteps of~1 ns (4), such that a coarse-grained simulation of a bacterial cytosol segment (using r ¼ 50%, N ¼ 4733, n ¼ 1000, and t ¼ 1 ns) would require 3 h, 20 min/ms simulation time using 4733 particles, or approximately three days per ms simulation time using 100,000 particles (for comparison, Escherichia coli has 3,000,000 protein copies in total). Many signal-transduction processes, such as phototransduction or neurotransmission, are governed by slowly diffusing membrane or membrane-associated proteins permitting timesteps of~10 ns (5). The protein volume density is low in such simulations; using r ¼ 10%, N ¼ 1000, n ¼ 1000, and t ¼ 10 ns would require~6 h for 1 s of simulation time.…”

“…These timescales facilitate the study of very fast processes, such as the activation phase in phototransduction requiring~200 ms of simulation time with 1000 slowly-diffusing particles (5). To access a wider range of biological phenomena and larger simulation systems, a significant speedup is needed.…”

Particle-based membrane model for mesoscopic simulation of cellular dynamics

“…The particles in such models typically represent entire proteins, protein domains or metabolites, and thus represent a spatial resolution of a few nanometers. Despite the success of such models in simulating cellular signal transduction processes 28,[30][31][32] , these approaches are missing membrane mechanics in order to be able to model signaling at biomembranes. In spite of the extensive research on membrane models, there is arguably no readily usable model at the same scale, that is suited to be integrated into such a particle-based reaction-diffusion framework.…”