Effect of Lipid Bilayer Composition on Membrane Protein Association

Aiswarya B. Pawar*; Xavier Prasanna*,†; Durba Sengupta*,†,1    * CSIR-National Chemical Laboratory, Pune, Maharashtra, India
† Academy of Scientific and Innovative Research, Pune, Maharashtra, India
1 Corresponding author: email address: d.sengupta@ncl.res.in

1 Introduction

The cell membrane is the primary barrier for the cell and is involved in the regulation of cellular information networks [1]. In its simplest form, the cell membrane can be considered as a bilayer of lipids exhibiting free lateral diffusion, as suggested by the fluid mosaic model [2]. With advances in experimental techniques, coupled with a better understanding of multicomponent lipid systems, a paradigm shift has been seen in this view of membrane. The cell membrane is no longer considered as a homogenous “sea of lipids” but suggested to exhibit asymmetrical distribution within and across the leaflets [3]. A diverse species of lipids such as saturated and unsaturated phospholipids, glycolipids and sphingolipids as well as cholesterol are present in cell membranes whose composition is dependent on cell type, stress conditions and even cellular age. The complexity in membrane composition is coupled to evidences pointing toward the presence of transient lipid “micro” or perhaps “nanodomains” which differ in composition and physical properties, such as fluidity and thickness [4]. A schematic representation of the cell membrane highlighting these features is shown in Fig. 1. Besides heterogeneity in nature of lipids, the cell membrane hosts a large population of diverse membrane proteins. The most abundant and best-studied membrane proteins which regulate several physiological processes include transmembrane receptors such as receptor tyrosine kinases (RTKs) (represented by the single transmembrane helices in Fig. 1) and G-protein coupled receptors (GPCRs) (corresponding to the multi-transmembrane protein in Fig. 1) [5, 6]. In addition, the cell membrane is intricately associated with the underlying cytoskeletal network [7] (shown by the green (gray mesh below the membrane in the print version) network in Fig. 1). The role of various membrane components in cellular function and how they interact together to function is still not clearly understood.

In this chapter, we discuss the interplay between membrane components—proteins, lipids, and cholesterol. The effect of proteins on the surrounding membrane and how in turn the bilayer modulates protein organization has been analyzed using a few interesting examples. We review the contribution of multiscale simulation studies in providing a molecular-level understanding of these processes. Two protein classes, single transmembrane helices that include the ErbB2 family and larger seven transmembrane proteins, GPCRs have been discussed in detail highlighting the membrane effects in protein association. And finally, a simple overview of the energetics of membrane organization is given.

1.1 Role of Membrane Protein Association in Function

Membrane proteins play important roles in several cellular processes and are involved in pathological mechanisms underlying various human diseases [8]. These proteins interact and associate with one another to form large multimers, several of which have physiological roles [9]. In a few cases, association confers function, while in others activity is regulated by their interaction with each other. A classical example involves the growth factor family (ErbB 1–4) belonging to the RTK class of membrane proteins that have been suggested to associate to an active dimer to initiate downstream signaling [10]. These associations are usually transient and the equilibrium between the multimers determines activity. Over expression of ErbB2, presumably leading to increased association have been shown to be oncogenic. Consequently, modulating transmembrane association can modify downstream signaling events and transmembrane peptides targeting ErbB2 have been recently shown to inhibit breast tumor growth and metastasis [11]. Another example of transmembrane association is the GPCR family in which super resolution experimental approaches have confirmed a dynamic equilibrium between various oligomeric species [12, 13]. Although the monomeric species have been shown to be sufficient for function [14], GPCR dimerization has been suggested to have both organizational and regulatory roles [15]. Since GPCRs represent important drug targets [16], the ability of these proteins to exist in several oligomeric states presents a new challenge for targeted drug therapy. An dominant role of lipids in shaping membrane-protein structure [17] and function [18, 19] is emerging, but its contribution to membrane protein organization is still less explored. The need arises to understand membrane protein association and evaluate the factors controlling association.

1.2 Protein Interactions Are Suggested to Be Sequence Dependent

Experimental approaches investigating membrane protein association suggest sequence specificity to be the major factor in driving interaction [20]. Sequence motifs such as the GxxxG motif have been identified as determinants of transmembrane helix association [21] and unique helical interfaces comprising of these residues have been proposed [22]. However, inhibition of protein association due to mutation of key residues “predicted” to be essential for protein–protein interaction, could be reverted back by a second mutation elsewhere along the transmembrane segment [23]. Further, quantitative estimates of transmembrane helix association [24] have revealed key differences from the previous estimates in detergent micelles [21, 25] and via indirect in vivo measurements [26]. Related studies have shown that the lipid bilayer modulates association through sequence-independent effects and membrane composition [27], and fluidity [28] have been suggested to play important roles in helix association.

Similarly for GPCRs, unique dimer interfaces have been proposed from experimental studies [29]. Crystal structure of oligomeric β1-adrenergic receptor revealed two distinct dimer conformations, suggesting the presence of multiple dimer interfaces [30]. Importantly, membrane composition has also been reported to influence structural organization of transmembrane proteins [31, 32]. It is becoming increasingly clear that “non-protein” contributions are significant in membrane protein organization. Even with current state-of-art technologies [33], experimental approaches are limited in their ability to probe the factors governing membrane protein association. The lack of a “molecular” level insight into the structure and underlying thermodynamics arises due to experimental limitations in structural resolution and lower time-scale sampling.

2 Computational Methods to Analyze...