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Protein-lipid interactions

Lipids and proteins are essential in a living organism. Proteins, as one of the most abundant macromolecules of life, have great diversity of functions ranging from catalyzing vital biological reactions to transporting nutrients. Likewise, lipids also have integral roles such as storing energy or being a major component of a membrane [7]. Despite their individual importance, interaction of these two molecules can provide functions that would not be possible individually. The greatest number of these interactions are seen in membranes, which are composed of a wide variety of lipids and proteins. Biological membranes separate the contents of the cell and many organelles from their surroundings and they define the shape of the cell, but it is the interaction of lipids and proteins that give an enormous amount of additional features to a membrane, rendering it much more than a mere barrier. 

Background

The biological membrane is the predominant structure where protein-lipid interactions occur. Proteins found in a biological membrane have important roles in cell signaling, transduction and transportation and the lipid bilayer is the framework where all these processes take place, thus lipids are an important part of protein function [5]. One of the common ways of classifying protein-lipid interactions is done as shown below:

Lipids in a biological membrane can be divided into three general groups [5]. 

  1. Bulk lipids: The lipids that form the bulk of the membrane without a contact with the membrane proteins are named bulk lipids.
  2. Annular Lipids: Some lipids surround the membrane proteins and interact relatively non-specifically with them. These lipids are called the annular lipids due to being similar to an annular shell.
  3. Non-annular lipids: These lipids interact specifically with some membrane proteins, virtually like a co-factor, and they are buried inside the protein structure.

Different proteins present in the membrane are summarized in figure 1 depending on their location.

Figure 1: A cartoon illustration showing different membrane proteins

Effect of Viscosity of the Membrane

The movement of any molecule or part of a molecule inside the membrane is influenced by the fluidity of this environment [5]. Every molecule experiences a frictional drag force during their movement inside the lipid bilayer structure of a biological membrane, and resistance of the fluid to this motion can be expressed in terms of the viscosity. Movement of a protein in the membrane is dictated by the frictional resistance and the molecular restoring forces acting on it. A fluorescence polarization anisotropy study on rotation of tryptophan (Trp) residues showed that motion of Trp was affected by the viscosity of the lipid environment for small scale motion, and the amplitude of this motion increased with the temperature as the viscosity decreased. However, after certain amplitudes the motion was confined by the surrounding peptide environment [11]. Another important aspect has also been revealed by molecular dynamics simulations. It has been illustrated that the effect of solvent viscosity on the protein motion is important when the protein is directly contacting the solvent molecules and if the rate of motion of protein is comparable to the dynamics of the solvent environment. In other words, high frequency motion of a protein that does not overlap the solvent motion does not depend on its viscosity [2]. Lipids are important in this context because viscosity of a biological membrane is mainly influenced by the types of lipids present as the lipid composition is one of the main determinants of the fluidity (see the main phase transitions for more information on membrane fluidity).

Effect of Membrane Curvature 

Dynamic curvature of plasma or intercellular membrane can be dictated by the interactions between proteins and lipids. In fact, cells can employ various mechanisms to sense curvature as a way to create regions of active membrane trafficking. Lipid composition is a major influence on membrane curvature based on their chemical properties and/or the size of their headgroup. Presence of certain lipids are key to interact with certain peripheral membrane proteins in order to induce a necessary curvature. For example phosphoinositides are required for budding of clathrin-coated vesicles as the required machinery can specifically bind to these lipids. The reason for this is that the headgroup of phosphoinosites can easily allow the formation of a curvature [8]. Another study illustrated that NSA4(1-48), a key transmembrane protein that mediates replication of Dengue virus (a mosquito born single positive-stranded RNA virus), has affinity to convex face of highly curved regions of synthetic bilayer vesicles as monitored by circular dichroism spectroscopy [4]. Some of the other well understood ways that lipid-protein interaction relates to curvature of the membrane are discussed in membrane curvature in detail

Effect of Changes in Membrane Thickness 

An important feature of lipids that can influence protein function is the thickness of the bilayer. As shown in figure 1, the hydrophobic thickness describes the region between two opposite head groups of the phospholipids in either leaflet of the bilayer. Transmembrane proteins need to match this hydrophobic thickness of the acyl chains for two reasons. First, acyl chains as well as hydrophobic groups of the membrane proteins do not form hydrogen bonds with water, and tend to minimize their contact with it as this is thermodynamically more favorable (see hydrophobic effect). When the hydrophobic thickness does not match, the phenomena called hydrophobic mismatch occurs. In order to minimize the exposure of hydrophobic parts of the lipid bilayer and transmembrane proteins to the aqueous environment, the bilayer can distort in various ways. It can stretch (Figure 2), compress, or even tilt.

Figure 2: Streching of a lipid bilayer to match the hydrophobic thickness of the protein (green).

Furthermore, the membrane proteins can aggregate (Figure 3) to minimize the area exposed to water [3]. In addition to being thermodynamically favorable, avoiding exposure of a transmembrane protein to aqueous environment is also important for optimal function because the hydrophobic side chains of the protein can change conformation when they contact water, distorting their native structure, and causing functional loss. The studies on these membrane distortions done with model membranes (artificial bilayers), show that the thickness of the acyl chain region is an essential part of protein function. For instance, sarcoplasmic reticulum Ca-ATPase, which is a protein important in calcium regulation in muscles, was shown to be greatly affected by the number of the carbons in the acyl chain, which determines the hydrophobic thickness of the membrane [10]. In addition, molecular dynamics simulations showed the possibility of protein aggregation (Figure 3) due to hydrophobic mismatch [11]. 

Figure 3: Aggregated proteins to minimize hydrophobic mismatch[13].

Protein-lipid Interactions in Molecular Terms

In addition to the interactions of lipids and proteins mediated by the physical changes in the lipid environment, it is good to consider lipid-protein interactions on a molecular level. Types of lipids that were defined previously interact differently with proteins. Figure 4 is a basic representation of the interaction of bulk lipids and annular lipids with a protein surface. Lipids present in the first shell, having a higher level of interaction and more restricted motion are the "annular lipids", while the second shell shows the bulk lipids.

Figure 4. Simple illustration of the interaction of annular and bulk lipids with the surface of a protein [6].

Annular lipids and proteins weakly interact through van der Waals, hydrogen bonding and/or electrostatic interactions. These weak interactions allow annular-lipids to be frequently exchanged with the lipids in the bulk bilayer, which implies that their interactions with proteins are fairly unspecific. The level of interactions between annular lipids, which are highly dynamic, is an ongoing area of research as it still is a challenging task to analyze their structure. One example of interactions of such lipids with membrane proteins suggest that charges of annular lipids are important in functioning of certain proteins. Accordingly, a type of ABC transporter protein, which can involve in diseases such as multidrug resistance, preferred interacting with phosphatidylglycerol, a negatively charged phospholipid, and not with phosphatidylethanolamine, a zwitterionic phospholipid suggesting the presence of higher affinity spots on the protein [1].

Unlike the other types of lipids, non-annular lipids interact specifically with proteins. These lipids are buried inside the protein, and are thought to be vital for optimal function. An example of such an interaction is found to be useful in bovine heart cytochrome c oxidase, on which 13 different types of lipids were suggested to have specific binding sites. It was also suggested that two palmitate tails of phosphatidylglycerols have a role in blocking O2 transfer pathway of this protein [12]. 

Experimental Methods Used to Study Lipid-Protein Interactions

Some of the techniques used to study physical properties of lipid environment interacting with the membrane proteins include fluorescence spectroscopy, and electron paramagnetic resonance (EPR). There are methods utilized to understand interactions in molecular terms based on resolving the three dimensional structures of proteins, which also helps clarify functions of some of the non-annular lipids [5]. X-Ray crystallographyNMR or EPR are among common tools analyzing lipid-protein interactions in molecular terms. Molecular dynamics simulations are another area of focus, that can help understand interactions of proteins and lipids both in molecular and physical terms.

References

  1. Bechara, C., Noll, A., Morgner, N., Degiacomi, M., Tampe, R., & Robinson, C. (2015). A Subset of Annular Lipids is linked to the Flippase Activity of an ABC Transporter. Biophysical Journal.
  2. C.L. Brooks, M. Karplus, Solvent effects on protein motion and protein effects on solvent motion, J. Mol. Biol. 208 (1989) 159–181.
  3. Faller, R., MCB/PBH 241 Course Lectures. 2015.
  4. Hung, Y., Schwarten, M., Schünke, S., Thiagarajan-Rosenkranz, P., Hoffmann, S., Sklan, E., Koenig, B. (2015). Dengue virus NS4A cytoplasmic domain binding to liposomes is sensitive to membrane curvature. Biochimica Et Biophysica Acta (BBA) - Biomembranes, 1119-1126.
  5. Lee, A. (2004). How lipids affect the activities of integral membrane proteins. Biochimica Et Biophysica Acta (BBA) - Biomembranes, 62-87.
  6. Lee, A. (2011). Biological membranes: The importance of molecular detail. Trends in Biochemical Sciences, 493-500.
  7. Lehninger, A. (1982). Principles of biochemistry. New York, N.Y.: Worth.
  8. Mcmahon, H., & Gallop, J. (2005). Membrane curvature and mechanisms of dynamic cell membrane remodelling. Nature, 590-596.
  9. M.M. Sperotto.A theoretical model for the association of amphiphilic transmembrane peptides in lipid bilayers. Eur. Biophys. J., 26 (1997), pp. 405–416
  10. Razvan, L., & Thomas, D. (1994). Effects of Membrane Thickness on the Molecular Dynamics and Enzymatic Activity of Reconstituted Ca-ATPase. Biochemistry, 33, 2912-2920.
  11. Rholam, M., Scarlata, S., & Weber, G. (1984). Frictional resistance to the local rotations of fluorophores in proteins. Biochemistry, 6793-6796.
  12. Shinzawa-Itoh, K. et al. (2007) Structures and physiological roles of 13 integral lipids of bovine heart cytochrome c oxidase. EMBO J. 26, 1713– 1725
  13. Hydrophobic mismatch. (2013, September 20). In Wikipedia, The Free Encyclopedia. Retrieved 21:05, May 13, 2015,from http://en.wikipedia.org/w/index.php?title=Hydrophobic_mismatch&oldid=573729778