Self organization of membrane proteins via dimerization
Introduction
Many proteins form hetero- or homodimers, but why? For example, a large number of G-protein coupled receptors (GPCRs) are able to form homo- and heterodimers (reviewed in [1], [2]), but the reason for this dimerization remains elusive. In most cases, dimerization of GPCRs does not directly correlate with the receptor's signaling state, as some receptors form dimers in the active state while others form dimers in the inactive state. It has been suggested that dimerization influences receptor cross-talk or desensitization, but the mechanism for this interaction is not currently known [3], [4]. Similarly, receptor dimerization not directly related to signaling is common in other signal transduction pathways. For example, recent findings have suggested that dimerization of the epidermal growth factor receptor is independent and separable from receptor signaling [5]. Similarly, the bacterial receptor Tar [6], human nerve growth factor receptor [7], and the bacterial and plant Photosystem II proteins [8] are all able to reversibly form dimers in the membrane, but the reasons for these interactions are largely unknown.
Here we propose a diffusion-limited mechanism by which receptor dimerization can drive the formation of oligomer-like clusters. We further demonstrate that such clusters could affect physiological processes such as cross-talk.
It is important to distinguish the one-to-one process of dimerization from non-specific oligomerization. GPCRs, like other membrane bound receptors, contain residues that mediate the specific protein–protein binding events that permit dimerization [9]. As a result of these specific interface sites, when a dimer is formed between two receptors, the binding face is covered, thereby disallowing any additional bonds to form. Therefore, receptors with only one specific binding site can only form dimers and cannot form stable larger structures such as trimers or oligomers. In contrast, non-specific oligomerization or aggregation takes place when proteins have many, non-specific binding sites, such as when a protein is denatured or misfolded. This process of non-specific oligomerization can be adequately simulated using condensed matter models, such as hard spheres interacting via a Leonard–Jones or square well potential [10]. Similarly, non-specific lattice-gas models of dimer–dimer interactions have also been proposed [11]. Specific dimerization, in contrast, cannot be described this way because once a dimer is formed, the effective attractive potential of the dimer for other particles drops to zero.
Therefore, although dimerization is common in biology, new models are needed to understand the physiological role of dimerization. For example, how does dimerization affect protein localization in the membrane? How does this dimerization-induced organization in turn affect cellular processes, such as signal transduction? In this work we use computer simulations to address both these questions.
We hypothesize that dimerization could have long-range ordering effects via a partner switching mechanism shown in Fig. 1. In this view, each protein competes to bind with its neighbors before they move too far apart to interact. If the partner switching is fast relative to the diffusion rate, then the proteins can effectively share a single bond between multiple proteins and in doing so form clusters of proteins that extend beyond a dimer pair. By modifying the localization of proteins in the membrane, dimerization could provide an elegantly simple way to control access of signaling elements to each other, thereby affecting signaling related processes such as receptor cross-talk.
The findings of this study suggest that GPCRs can exhibit dimerization-induced oligomerization like that shown in Fig. 1, and that such organization can in turn affect receptor signaling. This finding is in agreement with a number of unexplained experimental results relating to receptor cross talk and GPCR cluster size.
Section snippets
Methods
In developing a model for protein dimerization in the membrane, we strove to keep the model as simple as possible such that the effects of dimerization alone could be studied. In this spirit, we approximated proteins as hard disks with a single binding site. The processes that govern the dimerization rate of two adjacent proteins, such as protein rotation within the membrane and the reaction rate of two aligned proteins, were collapsed into a single, intrinsic dimerization rate constant, kdimer
Results
The results of the simulations follow from simplest to more complicated. Under the simplest conditions, dimerization of only one species was simulated under a wide range of kmono and kdimer values to see if an oligomer regime could be detected. Next, simulations were performed with the addition of a second, inert species to better simulate conditions in the real cell membrane. Finally, we explore the effects of homo- and heterodimerization with two receptor species. Together these results give
Dimerization of a single species
The results in Fig. 2 describe a situation in which the dimerization of a single species can organize receptors into clusters. This finding is physiologically relevant because GPCRs likely have the ability to exist in the monomer gas, dimer gas, or oligomer regimes depending on their dimerization kinetics and diffusion coefficients. Dimerization kinetics could be altered by the presence or absence of ligands, which has been experimentally demonstrated to regulate the dimerization state of some
Acknowledgements
This work was supported by a Whitaker Foundation Fellowship, NIH Training Grant # GM08353 (P.J.W.), and NIH R01 GM62930-01 (J.J.L.).
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