Membrane Protein Complex Subunit Research Articles

Multicolor fluorescence-based screening toward structural analysis of multiprotein membrane complexes.

Structures of membrane protein complexes provide a wealth of information on their biological function, the interplay among their subunits, and on ligand binding. Structural genomics of multiprotein membrane complexes seek to deliver structural information ideally of most of these complexes. Models of abundant native membrane protein complexes have been proposed from X-ray crystallography or single-particle cryo-EM. However, most of the remaining membrane protein complexes persist in very low copy numbers per cell and cannot be isolated from their native source without tremendous efforts. Therefore, heterologous expression systems are continually being developed to overproduce membrane protein complexes in various host cells of bacterial or eukaryotic origin. Still, only a small fraction of membrane proteins is suitable for structure determination due to poor expression levels, misfolding and aggregation, complex heterogeneity, imbalanced stoichiometry, and difficulties in solubilization as well as stabilization of the complexes. Powerful tools are therefore necessary to identify the correct expression host and to validate extraction and purification strategies for a given membrane protein complex at the earliest time point. Here, we discuss a fluorescence-based screening approach particularly tailored for the handy and sensitive analysis of the production and purification process for multiprotein membrane complexes. Multicolor fluorescence-detection size-exclusion chromatography provides a powerful readout system and allows quantitative monitoring of the production of critical single subunits of membrane protein complexes. The approach facilitates the tracking of improvements during sample optimization for monodispersity, balanced stoichiometry, and stability of multisubunit membrane protein complexes.

Perfusion reversed-phase high-performance liquid chromatography for protein separation from detergent-containing solutions: An alternative to gel-based approaches

Detergents are frequently used for the solubilization of membrane proteins during and after purification steps. Unfortunately some of these detergents impair chromatographic separations and mass spectrometry (MS) analysis. Perfusion reversed-phase high-performance liquid chromatography (RP–HPLC) using POROS materials is suited for separating intact proteins solubilized by detergents due to the particles’ highly diffusive pores and chemical stability. In this article, the use of perfusive reversed-phase material packed into small inner diameter capillary columns is presented as a cheap, rapid, and efficient method for the removal of different types of detergents from protein solutions. The ability to purify and separate the subunits of membrane protein complexes with self-packed capillary columns is exemplified for bovine cytochrome bc1 complex. Even highly hydrophobic subunits can be detected in collected fractions by intact mass measurements and identified after proteolytic digestion and matrix-assisted laser desorption/ionization tandem MS (MALDI MS/MS). The comparison with a gel-based approach shows that this method is a valuable alternative for purification and separation of intact proteins with subsequent MS analysis and that hydrophobic proteins are even better represented in the LC-based approach.

Structure of the Whole Cytosolic Region of ATP-Dependent Protease FtsH

An ATP-dependent protease, FtsH, digests misassembled membrane proteins in order to maintain membrane integrity and digests short-lived soluble proteins in order to control their cellular regulation. This enzyme has an N-terminal transmembrane segment and a C-terminal cytosolic region consisting of an AAA+ ATPase domain and a protease domain. Here we present two crystal structures: the protease domain and the whole cytosolic region. The cytosolic region fully retains an ATP-dependent protease activity and adopts a three-fold-symmetric hexameric structure. The protease domains displayed a six-fold symmetry, while the AAA+ domains, each containing ADP, alternate two orientations relative to the protease domain, making "open" and "closed" interdomain contacts. Apparently, ATPase is active only in the closed form, and protease operates in the open form. The protease catalytic sites are accessible only through a tunnel following from the AAA+ domain of the adjacent subunit, raising a possibility of translocation of polypeptide substrate to the protease sites through this tunnel.

Detection of phosphorylated subunits by combined LA–ICP–MS and MALDI–FTICR–MS analysis in yeast mitochondrial membrane complexes separated by blue native/SDS-PAGE

We report on the identification of phosphorylated subunits of yeast mitochondrial ATPase using a novel screening technique in combination with BN/SDS-PAGE. Protein complexes present in yeast mitochondrial membranes were separated in their native state in the first dimension and their subunit composition was resolved by SDS-PAGE in the second dimension. Laser ablation inductively coupled plasma mass spectrometry (LA–ICP–MS) was used to rapidly screen for the presence of phosphorus in the subunits. The detection limits of elements investigated in selected protein spots are in the low μg g −1 concentration range. Sulfur was used as the internal standard element for quantification. Phosphorus was detected in two of the proteins, that were identified by matrix-assisted laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry (MALDI–FTICR–MS) as subunits Atp1p and Atp2p of the ATPase. These results were confirmed by Western blot analysis using antibodies directed against phosphorylated amino acids. The combination of LA–ICP–MS and MALDI–FTICR–MS with BN/SDS-PAGE provides a fast and sensitive tool for structure analysis of phosphorus and metal-containing subunits of membrane protein complexes.

Hide and run

Arginine-based endoplasmic reticulum (ER)-localization signals are sorting motifs that are involved in the biosynthetic transport of multimeric membrane proteins. After their discovery in the invariant chain of the major histocompatibility complex class II, several hallmarks of these signals have emerged. They occur in polytopic membrane proteins that are subunits of membrane protein complexes; the presence of the signal maintains improperly assembled subunits in the ER by retention or retrieval until it is masked as a result of heteromultimeric assembly. A distinct consensus sequence and their position independence with respect to the distal termini of the protein distinguish them from other ER-sorting motifs. Recognition by the coatomer (COPI) vesicle coat explains ER retrieval. Often, di-leucine endocytic signals occur close to arginine-based signals. Recruitment of 14-3-3 family or PDZ-domain proteins can counteract ER-localization activity, as can phosphorylation. This, and the occurrence of arginine-based signals in alternatively spliced regions, implicates them in the regulated surface expression of multimeric membrane proteins in addition to their function in quality control.

C3 receptors on macrophages.

The complement receptors on macrophage are responsible for their binding and ingestion of opsonized targets. The two established receptors are CR1, which recognizes C3b, and CR3, which recognizes iC3b, the natural product of C3b from cleavage by the complement control protein factor I and its cofactors. CR1 belongs to a group of proteins that contain a structural element characterized by its size of 60-65 amino acids, and four conservatively positioned cysteines, which engage in a self-contained 1-3, 2-4 disulphide arrangement. This structural unit is called SCR (short consensus repeat) and is found in the complement proteins C1r, C1s, C2, factor B, factor H, C4BP, DAF, MCP and CR2, each of which interacts with some cleavage products of C3 and/or C4. CR1 has 30 SCR units accounting for its entire extracellular structure. It has a transmembrane segment and a small cytoplasmic domain. CR3 is a heterodimer containing an alpha and beta subunit held together by non-covalent forces. The beta subunit is also found in the two leukocyte antigens, LFA-1 and p150,95, which have alpha subunits distinct from that of CR3. The beta subunit contains 56 cysteine residues, 42 of which lie in a span of 256 residues immediately adjacent to the transmembrane segment. It shares extensive sequence homology with subunits of membrane protein complexes that bind fibronectin and vitronectin, implicating that they all belong to an extended set of surface adhesion molecules not restricted to the immune system. p150,95 is also expressed on macrophages and it has iC3b binding activity. It also shares some functional properties with CR3 as an adhesion surface molecule.