Membrane Proteins

Key Concepts

Membrane proteins are essential for most processes occurring at biological membranes. They interact with lipid bilayers in several ways and can be classified based on their association and structural features.

• Integral, peripheral, and amphitropic proteins are the main types of membrane-associated proteins.

• Some proteins are anchored by covalent attachment to lipids.

• Integral membrane proteins can span the bilayer using α-helices or β-sheets.

• The amino acid sequence can sometimes predict structural features of membrane proteins.

Functions of Membranes and Membrane Proteins

Biological membranes and their proteins serve several critical functions:

• Permeability Barriers:

  • Regulate molecular and ionic composition of cells and organelles.

  • Channels and pumps act as selective transport systems.

  • Electrical polarization due to ion concentration differences.

• Information Processing:

  • Signal reception by specific protein receptors (binding).

  • Transmission and transduction of signals via protein conformational changes.

• Energy Conversion:

  • Ordered arrays of enzymes organize sequential reactions.

  • Photosynthesis: conversion of light energy to chemical bond energy.

  • Oxidative phosphorylation: oxidation of fuel molecules to provide chemical bond energy.

Classification and Types of Membrane Proteins

Integral, Peripheral, and Amphitropic Proteins

• Integral proteins: Embedded in the bilayer through hydrophobic interactions.

• Peripheral proteins: Interact with integral proteins or lipid head groups, mostly by polar interactions.

• Amphitropic proteins: Reversibly associate with the membrane.

Structural Basis of Membrane Protein-Bilayer Interactions

• Transmembrane α-helices: Helices long enough to span the bilayer, with hydrophobic surfaces interacting with the lipid core.

• Transmembrane β-strands: Membranes can be spanned by β-sheets, forming β-barrels.

• Hydrophobic surfaces: Some proteins interact with the bilayer via hydrophobic areas but do not span it.

• Covalent attachment of hydrophobic "anchor": Soluble proteins can be tethered to membranes by covalent attachment of a hydrophobic group.

Additional info: The absence of hydrogen-bonding groups inside the bilayer limits the types of structure that can exist there. Membrane proteins must satisfy their own hydrogen-bonding groups.

Types of Integral Membrane Proteins

• Monotopic: Interact with only a single leaflet of the membrane via small hydrophobic domains.

• Bitopic: Span the bilayer once, extending on either surface, with a single hydrophobic sequence.

• Polytopic: Cross the membrane several times, with multiple hydrophobic sequences (~20 residues each) forming transmembrane α-helices.

Examples

• Glycophorin: A bitopic protein in red blood cells with a single transmembrane helix and extensive glycosylation on the extracellular side.

• Bacteriorhodopsin: A polytopic protein with 7 transmembrane helices, functioning as a proton pump in halophilic bacteria.

• SARS-CoV-2 spike protein and ACE2 receptor: Both are integral membrane proteins involved in viral entry.

Predicting Transmembrane Domains

Hydropathy and Sequence Analysis

The primary sequence of a protein can be used to predict transmembrane helices using hydropathy plots and transfer free energy calculations.

• Hydropathy plot: Graphs the hydrophobicity of amino acid residues over a window (typically 20 residues).

• Transfer free energy ():

  • indicates transfer from membrane to water is favorable.

  • Transfer free energy is a measure of hydropathy (hydrophilicity or hydrophobicity).

• Criterion level: A window above the criterion level suggests (but does not prove) the presence of a transmembrane helix.

Table: Polarity Scale for Identifying Transmembrane Helices

Additional info: Hydrophobic residues (e.g., Phe, Ile, Leu, Val) are favored in transmembrane regions.

Distribution of Amino Acids in Integral Proteins

• Charged residues (Lys, Arg, Glu, Asp) are typically found at the membrane interface.

• Aromatic residues (Tyr, Trp) are often located at the boundary between the hydrophobic core and the polar head groups.

Transmembrane β-Sheets and β-Barrel Proteins

Transmembrane β-Sheets

• Some integral membrane proteins use β-sheets to span the bilayer.

• β-strand: 3.5 Å distance between Cβ atom positions.

• Whole bilayer: ~40 Å, 11-12 residues; hydrocarbon core: ~30 Å, 9 residues.

β-Barrel Membrane Proteins

• Form closed β-sheets (β-barrels) that create channels in the membrane.

• Strands are not oriented perpendicular to the membrane; more than 9 residues are typically required to span it.

• Found in outer membranes of bacteria, mitochondria, and chloroplasts.

Porin Proteins

• Porins form hydrophilic pores for the passage of sugars and other polar metabolites.

• Distribution of hydrophilic and hydrophobic residues in the β-barrel structure allows selective transport.

• Topology: β-strands alternate pointing into the barrel interior and outward, creating a polar interior.

Hydropathy Plot for Porin

Hydropathy plots for β-barrel proteins do not reveal obvious transmembrane regions, making topology prediction more difficult than for α-helical proteins.

Examples of Membrane β-Barrels

• FepA (iron transport)

• OmpLA (phospholipase)

• Maltoporin (sugar transport)

• TolC (export of toxins)

• α-Hemolysin toxin (lysis of cells)

Lipid-Anchored (Lipid-Linked) Proteins

Structure and Function

• Proteins can be anchored to the membrane by covalently attached lipids (e.g., palmitoyl, myristoyl, GPI anchors).

• The type of lipid anchor can direct the protein to specific regions of the membrane and to either the inside or outside surface.

Membrane Microdomains and Rafts

Protein Clustering in Rafts

• Membrane proteins can cluster with lipids in microdomains called rafts, enriched in sphingolipids and cholesterol.

• Rafts can comprise up to 50% of the membrane and are important for organizing membrane proteins, especially receptors.

Caveolae

• Caveolae are local regions of the plasma membrane that form indentations in the cell surface.

• Formed in cholesterol-rich rafts by the protein caveolin, which bends the membrane.

• Increase surface area and provide room for membrane proteins involved in signaling.

Membrane Curvature, Fusion, and Fission

Curvature by Proteins

• Proteins such as caveolin and those with BAR domains can induce membrane curvature.

• Curvature is important for processes such as vesicle formation, trafficking, and fusion.

Membrane Fusion and Fission

• Curvature facilitates fusion of membranes (e.g., vesicle trafficking, exocytosis, endocytosis, viral infection, fusion of sperm and egg).

• Delivery of vesicle contents is essential for cell signaling, nutrient uptake, and export of factors.

Vesicle Fusion by SNARE Proteins

• SNARE proteins mediate vesicle fusion, crucial for neurotransmission and other cellular processes.

Summary Table: Types of Membrane Proteins

Key Equations

• Transfer Free Energy: Negative indicates favorable transfer from membrane to water.

Conclusion

Membrane proteins are diverse in structure and function, playing critical roles in transport, signaling, and energy conversion. Their study is essential for understanding cellular processes and developing biomedical applications.