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Nanodiscs provide an excellent system for the structure-function investigation of membrane proteins. Its direct advantage lies in presenting a water-soluble form of an otherwise hydrophobic molecule, making it amenable to a plethora of solution techniques. Nuclear magnetic resonance is one such high-resolution approach that looks at the structure and dynamics of a protein with atomic level precision. Recently, there has been a breakthrough in making nanodiscs more susceptible for structure determination by solution NMR, yet it still remains to become the preferred choice for a membrane mimetic. In this practical review, we provide a general discourse on nanodisc and its application to solution NMR. We also offer potential solutions to remediate the technical challenges associated with nanodisc preparation and the choice of proper experimental set-ups. Along with discussing several structural applications, we demonstrate an alternative use of nanodiscs for functional studies, where we investigated the phosphorylation of a cell surface receptor, integrin. This is the first successful manifestation of observing activated receptor phosphorylation in nanodisc through NMR. We additionally present an on-column method for nanodisc preparation with multiple strategies and discuss the potential use of alternative nanoscale phospholipid bilayer systems like styrene maleic acid lipid disc and saposin-A lipoprotein disc.

A plethora of membrane proteins are found along the cell surface and on the convoluted labyrinth of membranes surrounding organelles. Since the advent of various structural biology techniques, a sub-population of these proteins has become accessible to investigation at near-atomic resolutions. The predominant bona fide methods for structure solution, X-ray crystallography and cryo-EM, provide high resolution in three-dimensional space at the cost of neglecting protein motions through time. Though structures provide various rigid snapshots, only an amorphous mechanistic understanding can be inferred from interpolations between these different static states. In this review, we discuss various techniques that have been utilized in observing dynamic conformational intermediaries that remain elusive from rigid structures. More specifically we discuss the application of structural techniques such as NMR, cryo-EM and X-ray crystallography in studying protein dynamics along with complementation by conformational trapping by specific binders such as antibodies. We finally showcase the strength of various biophysical techniques including FRET, EPR and computational approaches using a multitude of succinct examples from GPCRs, transporters and ion channels.

The major outer sheath protein (MOSP) is a prominent constituent of the cell envelope of Treponema denticola (TDE) and one of its principal virulence determinants. Bioinformatics predicts that MOSP consists of N- and C-terminal domains, MOSP N and MOSP C . Biophysical analysis of constructs refolded in vitro demonstrated that MOSP C , previously shown to possess porin activity, forms amphiphilic trimers, while MOSP N forms an extended hydrophilic monomer. In TDE and E. coli expressing MOSP with a PelB signal sequence (PelB-MOSP), MOSP C is OM-embedded and surface-exposed, while MOSP N resides in the periplasm. Immunofluorescence assay, surface proteolysis, and novel cell fractionation schemes revealed that MOSP in TDE exists as outer membrane (OM) and periplasmic trimeric conformers; PelB-MOSP, in contrast, formed only OM-MOSP trimers. Although both conformers form hetero-oligomeric complexes in TDE, only OM-MOSP associates with dentilisin. Mass spectrometry (MS) indicated that OM-MOSP interacts with proteins in addition to dentilisin, most notably, oligopeptide-binding proteins (OBPs) and the β-barrel of BamA. MS also identified candidate partners for periplasmic MOSP, including TDE1658, a spirochete-specific SurA/PrsA ortholog. Collectively, our data suggest that MOSP destined for the TDE OM follows the canonical BAM pathway, while formation of a stable periplasmic conformer involves an export-related, folding pathway not present in E. coli .

Gasdermin D (GSDMD) is the common effector for cytokine secretion and pyroptosis downstream of inflammasome activation and was previously shown to form large transmembrane pores after cleavage by inflammatory caspases to generate the GSDMD N-terminal domain (GSDMD-NT) 1 – 10 . Here we report that GSDMD Cys191 is S -palmitoylated and that palmitoylation is required for pore formation. S -palmitoylation, which does not affect GSDMD cleavage, is augmented by mitochondria-generated reactive oxygen species (ROS). Cleavage-deficient GSDMD (D275A) is also palmitoylated after inflammasome stimulation or treatment with ROS activators and causes pyroptosis, although less efficiently than palmitoylated GSDMD-NT. Palmitoylated, but not unpalmitoylated, full-length GSDMD induces liposome leakage and forms a pore similar in structure to GSDMD-NT pores shown by cryogenic electron microscopy. ZDHHC5 and ZDHHC9 are the major palmitoyltransferases that mediate GSDMD palmitoylation, and their expression is upregulated by inflammasome activation and ROS. The other human gasdermins are also palmitoylated at their N termini. These data challenge the concept that cleavage is the only trigger for GSDMD activation. They suggest that reversible palmitoylation is a checkpoint for pore formation by both GSDMD-NT and intact GSDMD that functions as a general switch for the activation of this pore-forming family. Gasdermin D Cys191 is S -palmitoylated, and palmitoylation is required for pore formation.

Gasdermin D (GSDMD) is the common effector for cytokine secretion and pyroptosis downstream of inflammasome activation by forming large transmembrane pores upon cleavage by inflammatory caspases. Here we report the surprising finding that GSDMD cleavage is not sufficient for its pore formation. Instead, GSDMD is lipidated by S-palmitoylation at Cys191 upon inflammasome activation, and only palmitoylated GSDMD N-terminal domain (GSDMD-NT) is capable of membrane translocation and pore formation, suggesting that palmitoylation licenses GSDMD activation. Treatment by the palmitoylation inhibitor 2-bromopalmitate and alanine mutation of Cys191 abrogate GSDMD membrane localization, cytokine secretion, and cell death, without affecting GSDMD cleavage. Because palmitoylation is formed by a reversible thioester bond sensitive to free thiols, we tested if GSDMD palmitoylation is regulated by cellular redox state. Lipopolysaccharide (LPS) mildly and LPS plus the NLRP3 inflammasome activator nigericin markedly elevate reactive oxygen species (ROS) and GSDMD palmitoylation, suggesting that these two processes are coupled. Manipulation of cellular ROS by its activators and quenchers augment and abolish, respectively, GSDMD palmitoylation, GSDMD pore formation and cell death. We discover that zDHHC5 and zDHHC9 are the major palmitoyl transferases that mediate GSDMD palmitoylation, and when cleaved, recombinant and partly palmitoylated GSDMD is 10-fold more active in pore formation than bacterially expressed, unpalmitoylated GSDMD, evidenced by liposome leakage assay. Finally, other GSDM family members are also palmitoylated, suggesting that ROS stress and palmitoylation may be a general switch for the activation of this pore-forming family.Competing Interest StatementThe authors have declared no competing interest.

Several membrane proteins, comprising of either α-helical or β-barrel structures have been successfully studied in vitro using several membrane mimetic systems. Nanodiscs, a new class of discoidal nanoscale lipoprotein complex have been used extensively in the present study to investigate different membrane proteins. We begin by delineating the development of small (D7) nanodiscs through its rigorous characterization and demonstrate advantages in solution NMR applications. In addition, we show the development of an on-column method to generate nanodiscs through the selective use of variable protein tags. D7 discs have been further used to visualize the downstream phosphorylation events of activated integrin β3 through Src kinase. The C-terminal domains, TprC and MOSPC, two β-barrel membrane porins, were shown to trimerize when visualized through negatively stained transmission electron microscopy images in nanodiscs. The periplasmic and membrane conformers of native MOSP in Treponema denticola was established along with the partial identification of their multimeric complexes through a series of immuno-chemical experiments. Also discussed are two specific studies which revisit previously published papers where, (a) the direction of the cytoplasmic tail of integrin β3bound to the SH3 domain of Src kinase was shown to be in the reverse orientation w.r.t the published crystal structure; and (b) PLIC proteins, [Protein Linking the cell membrane (IAP/CD47) to the Cytoskeleton] was shown to be involved in proteasomal degradation with no binding ability to the cytoplasmic tail of CD47. Small angle X-ray scattering studies of BTN3A1, an immune modulator, revealed the rearrangement of the intracellular cytoplasmic B30.2 domain with respect to the juxta membrane region in the presence of a phosphoantigen HMBPP. Lastly, a novel finding is briefly described involving orthlogs of TamB, a component of the transloaction and assembly module system, comprising of the TamA-TamB complex in proteobacteria, interacting with BamA (Beta-barrel assembly machinery protein A) in bacterial diderms where TamA is absent.