Peripheral Membrane Proteins: Promising Therapeutic Targets across Domains of Life

Abstract

Membrane proteins can be classified into two main categories-integral and peripheral membrane proteins-depending on the nature of their membrane interaction. Peripheral membrane proteins are highly unique amphipathic proteins that interact with the membrane indirectly, using electrostatic or hydrophobic interactions, or directly, using hydrophobic tails or GPI-anchors. The nature of this interaction not only influences the location of the protein in the cell, but also the function. In addition to their unique relationship with the cell membrane, peripheral membrane proteins often play a key role in the development of human diseases such as African sleeping sickness, cancer, and atherosclerosis. This review will discuss the membrane interaction and role of periplasmic nitrate reductase, CymA, cytochrome c, alkaline phosphatase, ecto-5'-nucleotidase, acetylcholinesterase, alternative oxidase, type-II NADH dehydrogenase, and dihydroorotate dehydrogenase in certain diseases. The study of these proteins will give new insights into their function and structure, and may ultimately lead to ground-breaking advances in the treatment of severe diseases.

Keywords: GPI-anchored proteins; drug targets; electrostatic interactions; human diseases; hydrophobic membrane anchor; peripheral membrane proteins.

Figure 1

Different types of membrane proteins shown in the cell membrane. Integral membrane proteins are shown to span the entire membrane (Escherichia coli ATP synthase as example). Peripheral membrane proteins can be categorized into two subtypes: proteins that only associate with the membrane via electrostatic or hydrophobic interactions (Caldalkalibacillus thermarum type-II NADH dehydrogenase as example), and proteins that anchor themselves in the lipid bilayer using a hydrophobic segment that does not span the entire membrane (Desulfovibrio vulgaris NrfH as example). 3D structural cartoons of E. coli ATP synthase (PDB:5T4Q) [4], D. vulgaris NrfH (PDB:2J7A) [5], Shewanella frigidimarina flavocytochrome c₃ (PDB:1Y0P) [6], and C. thermarum NDH-2 (PDB:6BDO) [7] were rendered with PyMol and the figure compiled in BioRender.com [8].

Figure 2

Schematic overview of Nap enzyme encoded from the nap operon. The different subunits (A, B, C, and D) are represented according to their location in the cell. Subunits NapA, NapB, NapC, and NapD are conserved across different species such as Cupriavidus necator, Rhodobacter sphaeroides, and Thiospaera pantotropha. The 3D structural cartoon of the C. necator NapAB (PDB:3ML1) [48] was rendered using PyMol and the figure compiled in BioRender.com [8].

Figure 3

A cross-section of the cytoplasmic membrane of S. oneidensis showing the electron pathway for the reduction of CymA. Example pathway starting from formate oxidation (by formate dehydrogenase) to the electron transfer between MQH₂ and CymA, to NapAB. 3D structural cartoons of the Escherichia coli formate dehydrogenase (PDB:1KQG) [56], the Desulfovibrio vulgaris NrfH (PDB:2J7A) [5], and the Shewanella frigidimarina flavocytochrome c₃ (PDB:1Y0P) [6] were rendered with PyMol and the figure compiled in BioRender.com [8].

Figure 4

Schematic representation of a GPI-anchored protein. The GPI-anchored protein (GPI-AP) is anchored to the head group of a phosphatidylinositol (PI) lipid via a GPI anchor. This anchor has a conserved core domain consisting of ethanolamine-PO₄-6Manα1-2Manα1-6Manα1-4GlcNα1-6myo-inositol-1-PO₄-lipid [64]. The mannose, glucosamine, and inositol groups are represented by black, green, and red aromatic rings, respectively.

Figure 5

Schematic overview of the human ecto-5′-nucleotidase. In contrast to the monomeric bacterial enzymes, eukaryotic e5NT exists and functions as a non-covalent homodimer. Open and closed conformations represented as reported in [73]. 3D structural cartoons of the Homo sapiens CD73 (PDB:4H2B and PDB:4H2I) [74,75] were rendered with PyMol and the figure compiled using BioRender.com [8].

Figure 6

Complex III, complex IV and cytochrome c in the electron transport chain. Electrons coming from complex I and II are transferred to ubiquinone (Q) in the membrane. Subsequently, the electrons are transferred to complex III, cytochrome c, and complex IV, which eventually incorporates the electrons in water. 3D structural cartoons of the Homo sapiens cytochrome bc₁ (PDB:5XTE) [89], the Homo sapiens cytochrome c oxidase (PDB:5Z62) [90], and the yeast cytochrome c (PDB:4Q5P) [91] were rendered using PyMol and the figure compiled using BioRender.com [8].

Figure 7

Schematic overview of the locations and reactions of both DHODH families. The two DHODH families are visualized with their respective location in the cell. Family 1 DHODH uses O₂, fumarate, or NAD⁺ as electron acceptors. Family 2 uses ubiquinone (Q) as an electron acceptor, which gets reduced to QH₂. 3D structural cartoons showing the Family 1 DHODH from Trypanosoma brucei (PDB:5XFV) [106], and the Family 2 DHODH from Plasmodium falciparum (PDB:6VTN) [107] were rendered with PyMol and the figure compiled using BioRender.com [8].

Figure 8

The reactions catalyzed by DHODH and a schematic overview of the proposed system to analyze the activity of DHODH. (A) DHODH catalyzes the oxidation of dihydroorotate (DHO) to orotate. The two electrons that are removed in that reaction are transferred to coenzyme Q via a flavin mononucleotide (FMN). (B) The activity of DHODH could be monitored using a planar tethered lipid bilayer system, homologous to that reported in Godoy-Hernandez et al., (2019). In this system, a gold electrode is connected to a cell membrane containing the DHODH enzyme. QH₂ that is generated after the reduction of coenzyme Q by DHODH is regenerated at the gold electrode. The two electrons coming from that reaction will generate a current in the electrode. 3D structural cartoons showing the Homo sapiens DHODH (PDB:2PRH) [109] were rendered using PyMol and the figure compiled using BioRender.com [8].