Reconstitution of the Cytb5–CytP450 Complex in Nanodiscs for Structural Studies using NMR Spectroscopy

Cytochrome P450s (P450s) are a superfamily of enzymes responsible for the catalysis of a wide range of substrates. Dynamic interactions between full‐length membrane‐bound P450 and its redox partner cytochrome b₅ (cytb₅) have been found to be important for the enzymatic activity of P450. However, the stability of the circa 70 kDa membrane‐bound complex in model membranes renders high‐resolution structural NMR studies particularly difficult. To overcome these challenges, reconstitution of the P450–cytb₅ complex in peptide‐based nanodiscs, containing no detergents, has been demonstrated, which are characterized by size exclusion chromatography and NMR spectroscopy. In addition, NMR experiments are used to identify the binding interface of the P450–cytb₅ complex in the nanodisc. This is the first successful demonstration of a protein–protein complex in a nanodisc using NMR structural studies and should be useful to obtain valuable structural information on membrane‐bound protein complexes.     

Contact between the β1 and β2 Segments of α‐Synuclein that Inhibits Amyloid Formation

Conversion of the intrinsically disordered protein α‐synuclein (α‐syn) into amyloid aggregates is a key process in Parkinson’s disease. The sequence region 35–59 contains β‐strand segments β1 and β2 of α‐syn amyloid fibril models and most disease‐related mutations. β1 and β2 frequently engage in transient interactions in monomeric α‐syn. The consequences of β1–β2 contacts are evaluated by disulfide engineering, biophysical techniques, and cell viability assays. The double‐cysteine mutant α‐synCC, with a disulfide linking β1 and β2, is aggregation‐incompetent and inhibits aggregation and toxicity of wild‐type α‐syn. We show that α‐syn delays the aggregation of amyloid‐β peptide and islet amyloid polypeptide involved in Alzheimer’s disease and type 2 diabetes, an effect enhanced in the α‐synCC mutant. Tertiary interactions in the β1–β2 region of α‐syn interfere with the nucleation of amyloid formation, suggesting promotion of such interactions as a potential therapeutic approach.     

Supramolecular Protein Assemblies in the Nucleus of Human Cells

Genetically encoded supramolecular protein assemblies (SMPAs) are induced to form in living cells by combination of distinct self‐assembly properties. A single fusion construct contains genes encoding the heavy chain (H) of human ferritin and the citrine fluorescent protein, the latter exposing a weak dimerization interface, as well as a nuclear localization signal. Upon expression in HeLa cells, in vivo confocal fluorescence and differential interference contrast imaging revealed extended SMPA structures exclusively in the nuclei. Assemblies were typically round and took alveolar, shell‐like, or hybrid structure. Transmission electron microscopy revealed a crystalline packing. Site‐specific mutagenesis of the citrine dimerization interface clarified the mechanism of SMPA formation. The constituent proteins retained their activity in iron binding and fluorescence emission, thus suggesting a general strategy for formation of synthetic cellular bodies with specific biochemical function.     

Direct Targeting of Rab‐GTPase–Effector Interactions

Small GTPases are molecular switches using GDP/GTP alternation to control numerous vital cellular processes. Although aberrant function and regulation of GTPases are implicated in various human diseases, direct targeting of this class of proteins has proven difficult, as GTPase signaling and regulation is mediated by extensive and shallow protein interfaces. Here we report the development of inhibitors of protein–protein interactions involving Rab proteins, a subfamily of GTPases, which are key regulators of vesicular transport. Hydrocarbon‐stapled peptides were designed based on crystal structures of Rab proteins bound to their interaction partners. These modified peptides exhibit significantly increased affinities and include a stapled peptide (StRIP3) that selectively binds to activated Rab8a and inhibits a Rab8a–effector interaction in vitro.     

Structural Mapping of a Chaperone–Substrate Interaction Surface

NMR spectroscopy is used to detect site‐specific intermolecular short‐range contacts in a membrane–protein–chaperone complex. This is achieved by an “orthogonal” isotope‐labeling scheme that permits the unambiguous detection of intermolecular NOEs between the well‐folded chaperone and the unfolded substrate ensemble. The residues involved in these contacts are part of the chaperone–substrate contact interface. The approach is demonstrated for the 70 kDa bacterial Skp‐tOmpA complex.     

Probing the Lipid Annular Belt by Gas‐Phase Dissociation of Membrane Proteins in Nanodiscs

Interactions between membrane proteins and lipids are often crucial for structure and function yet difficult to define because of their dynamic and heterogeneous nature. Here, we use mass spectrometry to demonstrate that membrane protein oligomers ejected from nanodiscs in the gas phase retain large numbers of lipid interactions. The complex mass spectra that result from gas‐phase dissociation were assigned using a Bayesian deconvolution algorithm together with mass defect analysis, allowing us to count individual lipid molecules bound to membrane proteins. Comparison of the lipid distributions measured by mass spectrometry with molecular dynamics simulations reveals that the distributions correspond to distinct lipid shells that vary according to the type of protein–lipid interactions. Our results demonstrate that nanodiscs offer the potential for native mass spectrometry to probe interactions between membrane proteins and the wider lipid environment.     

Electrostatics and Intrinsic Disorder Drive Translocon Binding of the SRP Receptor FtsY

Integral membrane proteins in bacteria are co‐translationally targeted to the SecYEG translocon for membrane insertion via the signal recognition particle (SRP) pathway. The SRP receptor FtsY and its N‐terminal A domain, which is lacking in any structural model of FtsY, were studied using NMR and fluorescence spectroscopy. The A domain is mainly disordered and highly flexible; it binds to lipids via its N terminus and the C‐terminal membrane targeting sequence. The central A domain binds to the translocon non‐specifically and maintains disorder. Translocon targeting and binding of the A domain is driven by electrostatic interactions. The intrinsically disordered A domain tethers FtsY to the translocon, and because of its flexibility, allows the FtsY NG domain to scan a large area for binding to the NG domain of ribosome‐bound SRP, thereby promoting the formation of the quaternary transfer complex at the membrane.     

Bioorthogonal Probes for the Study of MDM2‐p53 Inhibitors in Cells and Development of High‐Content Screening Assays for Drug Discovery

To study the behavior of MDM2‐p53 inhibitors in a disease‐relevant cellular model, we have developed and validated a set of bioorthogonal probes that can be fluorescently labeled in cells and used in high‐content screening assays. By using automated image analysis with single‐cell resolution, we could visualize the intracellular target binding of compounds by co‐localization and quantify target upregulation upon MDM2‐p53 inhibition in an osteosarcoma model. Additionally, we developed a high‐throughput assay to quantify target occupancy of non‐tagged MDM2‐p53 inhibitors by competition and to identify novel chemical matter. This approach could be expanded to other targets for lead discovery applications.     

Accelerating the Association of the Most Stable Protein–Ligand Complex by More than Two Orders of Magnitude

The complex between the bacterial type 1 pilus subunit FimG and the peptide corresponding to the N‐terminal extension (termed donor strand, Ds) of the partner subunit FimF (DsF) shows the strongest reported noncovalent molecular interaction, with a dissociation constant (K_D) of 1.5×10^?20 m . However, the complex only exhibits a slow association rate of 330 m ^?1 s^?1 that limits technical applications, such as its use in affinity purification. Herein, a structure‐based approach was used to design pairs of FimGt (a FimG variant lacking its own N‐terminal extension) and DsF variants with enhanced electrostatic surface complementarity. Association of the best mutant FimGt/DsF pairs was accelerated by more than two orders of magnitude, while the dissociation rates and 3D structures of the improved complexes remained essentially unperturbed. A K_D value of 8.8×10^?22 m was obtained for the best mutant complex, which is the lowest value reported to date for a protein/ligand complex.     

Analysis of Interactions between the Epidermal Growth Factor Receptor and Soluble Ligands on the Basis of Single‐Molecule Diffusivity in the Membrane of Living Cells

We present a single‐molecule diffusional‐mobility‐shift assay (smDIMSA) for analyzing the interactions between membrane and water‐soluble proteins in the crowded membrane of living cells. We found that ligand–receptor interactions decreased the diffusional mobility of ErbB receptors and β‐adrenergic receptors, as determined by single‐particle tracking with super‐resolution microscopy. The shift in diffusional mobility was sensitive to the size of the water‐soluble binders that ranged from a few tens of kilodaltons to several hundred kilodaltons. This technique was used to quantitatively analyze the dissociation constant and the cooperativity of antibody interactions with the epidermal growth factor receptor and its mutants. smDIMSA enables the quantitative investigation of previously undetected ligand–receptor interactions in the intact membrane of living cells on the basis of the diffusivity of single‐molecule membrane proteins without ligand labeling.