Lesson 9
Membrane Proteins
Proteins are classified as soluble or membrane proteins. Soluble proteins reside in the aqueous environment of the cell and fold such that their hydrophobic residues are buried in the core of the protein so that they are excluded from interacting with the polar water molecules. Membrane proteins, on the other hand, bury their hydrophobic residues within a lipid bilayer. This lesson focuses on membrane proteins (which the Columbus Lab specializes in).
Membrane proteins are encoded by about 20-30% of an organism’s genome and serve a wide range of functions including as receptors, transporters, and enzymes. Over half of current pharmaceuticals target membrane proteins, yet they constitute less than 2% of known protein structures in the protein data bank (PDB). This disparity comes from the difficulty in studying membrane proteins due to the need to reconstitute the protein in a membrane mimetic. For example, the first soluble protein structure of myoglobin was determined by X-ray crystallography in 1958 (Kendrew et al.), but it took until 1985 for the first membrane protein structure to be determined (Deisenofer et al.). However, recent advances in membrane protein expression and purification, crystallography, NMR, and cryo-EM techniques have resulted in an accelerated pace for membrane protein structural and functional characterization in recent years.
Types of Membrane Proteins
Membrane proteins can be further classified as 1) integral membrane proteins or 2) membrane associated or peripheral membrane proteins.
Integral membrane proteins completely transverse the lipid bilayer and serve a variety of functions including ion transport, cell signaling, nutrient intake, and as membrane bound enzymes. The majority of integral membrane proteins are made of one (bitopic) or more (polytopic) alpha-helices (orange in figure below). These proteins generally have hydrophobic residues in the transmembrane region and hydrophilic residues outside of the membrane. Beta-barrel proteins are integral membrane proteins made up of 8-26 antiparallel beta-strands that twist to form a closed barrel structure, most with hydrophobic residues positioned toward the membrane and hydrophilic or hydrophobic residues toward the interior (blue in figure below).
Peripheral membrane proteins are proteins which interact with the membrane, but do not completely transverse it (green in the figure below). Such membrane interactions could be through an amphipathic alpha-helix perpendicular to the membrane, an electrostatic or ionic interaction with the lipid headgroups, or by an interaction with a covalently bound lipid. Peripheral membrane proteins play important physiological roles including in bacterial virulence, nutrient uptake, cell signaling, antibiotic resistance, and triggering innate immune responses.
Membrane proteins are structurally and functionally diverse. Read this excerpt from Molecular Biology of the Cell (4th edition) for more information.
Membrane Mimics
When membrane proteins are studied, a membrane mimic must be used to recapitulate the membrane environment. This membrane mimic must shield the hydrophobic transmembrane resides of the membrane protein from the surrounding aqueous environment. Membrane mimics include micelles, bicelles, nano discs, amphipoles, lipodisqs (or SMALPs), and liposomes. Each mimetic has its own advantages and disadvantages, but the consequences of the mimetic on protein fold and function is still largely unknown (and is a focus of the Columbus lab). Read section 2: Membrane mimetic systems commonly used in solution NMR studies of membrane proteins (Liang and Tamm, 2018) for a description of each of these membrane mimics. Micelle and bicelle mimetics are very commonly used and are schematically shown below.
Review questions from Module 1: Why do micelles form a spherical shape while bicelles form a disc shape? Why is it favorable for membrane proteins to reside in a membrane-like environment?
Assignment: This week we will have another journal club to give you more experience reading scientific literature. This paper is a nice wrap up for Module 2 as it describes protein structure, protein function, membrane proteins, and introduces activity assays which we will talk more about in lesson 13. It also describes the protein (LspA) for which we have been analyzing the sequence of in this module.
I will email out this paper (Vogeley et al., 2016) as it is not freely available online.