The guidance and adhesion protein FLRT2 dimerizes in cis via dual small-X3-small transmembrane motifs

MINFLUX Nanoscopy: A "Brilliant" Technique Promising Major Breakthrough

MINFLUX nanoscopy relies on the localization of single fluorophores with expected ~ 2 nm precision in 3D mapping, roughly one order of magnitude better than standard stimulated emission depletion microscopy or stochastic optical reconstruction microscopy. This "brilliant" technique takes advantage of specialized localization principles and algorithms that require only dim fluorescence signals with a minimum flux of photons; hence the name follows. With this level of performance, MINFLUX imaging and tracking should allow for the routine study of biological processes down to the molecular scale, revealing previously unresolved details in cell structures, such as the organization of calcium channels in muscle cells or the clustering of receptors in synapses. Whereas the high localization precision is definitely a strength of the MINFLUX technique, limitations and challenges also exist, especially in the labeling procedures aiming at appropriate density and on/off switching kinetics. This primer presents some significant results achieved with MINFLUX so far and highlights specific operational procedures crucial for this technique.

MINFLUX nanoscopy: Visualising biological matter at the nanoscale level

Since its introduction in 2017, MINFLUX nanoscopy has shown that it can visualise fluorescent molecules with an exceptional localisation precision of a few nanometres. In this overview, we provide a brief insight into technical implementations, fluorescent marker developments and biological studies that have been conducted in connection with MINFLUX imaging and tracking. We also formulate ideas on how MINFLUX nanoscopy and derived technologies could influence bioimaging in the future. This insight is intended as a general starting point for an audience looking for a brief overview of MINFLUX nanoscopy from theory to application.

Resolving Conformational Plasticity in Mammalian Cells with High-Resolution Fluorescence Tools

Investigating protein dynamic structural changes is fundamental for understanding protein function, drug discovery, and disease mechanisms. Traditional studies of protein dynamics often rely on investigations of purified systems, which fail to capture the complexity of the cellular environment. The intracellular milieu imposes distinct physicochemical constraints that affect macromolecular interactions and dynamics in ways not easily replicated in isolated experimental setups. We discuss the use of fluorescence resonance energy transfer, fluorescence anisotropy, and minimal photon flux imaging technologies to address these challenges and directly investigate protein conformational dynamics in mammalian cells. Key findings from the application of these techniques demonstrate their potential to reveal intricate details of protein conformational plasticity. By overcoming the limitations of traditional in vitro methods, these approaches offer a more accurate and comprehensive understanding of protein function and behavior within the complex environment of mammalian cells.

Dynamic pre-structuration of lipid nanodomain-segregating remorin proteins

Remorins are multifunctional proteins, regulating immunity, development and symbiosis in plants. When associating to the membrane, remorins sequester specific lipids into functional membrane nanodomains. The multigenic protein family contains six groups, classified upon their protein-domain composition. Membrane targeting of remorins occurs independently from the secretory pathway. Instead, they are directed into different nanodomains depending on their phylogenetic group. All family members contain a C-terminal membrane anchor and a homo-oligomerization domain, flanked by an intrinsically disordered region of variable length at the N-terminal end. We here combined molecular imaging, NMR spectroscopy, protein structure calculations and advanced molecular dynamics simulation to unveil a stable pre-structuration of coiled-coil dimers as nanodomain-targeting units, containing a tunable fuzzy coat and a bar code-like positive surface charge before membrane association. Our data suggest that remorins fold in the cytosol with the N-terminal disordered region as a structural ensemble around a dimeric anti-parallel coiled-coil core containing a symmetric interface motif reminiscent of a hydrophobic Leucine zipper. The domain geometry, the charge distribution in the coiled-coil remorins and the differences in structures and dynamics between C-terminal lipid anchors of the remorin groups provide a selective platform for phospholipid binding when encountering the membrane surface.

Lys716 in the transmembrane domain of yeast mitofusin Fzo1 modulates anchoring and fusion

Outer mitochondrial membrane fusion, a vital cellular process, is mediated by mitofusins. However, the underlying molecular mechanism remains elusive. We have performed extensive multiscale molecular dynamics simulations to predict a model of the transmembrane (TM) domain of the yeast mitofusin Fzo1. Coarse-grained simulations of the two TM domain helices, TM1 and TM2, reveal a stable interface, which is controlled by the charge status of residue Lys716. Atomistic replica-exchange simulations further tune our model, which is confirmed by a remarkable agreement with an independent AlphaFold2 (AF2) prediction of Fzo1 in complex with its fusion partner Ugo1. Furthermore, the presence of the TM domain destabilizes the membrane, even more if Lys716 is charged, which can be an asset for initiating fusion. The functional role of Lys716 was confirmed with yeast experiments, which show that mutating Lys716 to a hydrophobic residue prevents mitochondrial fusion.

Coarse-Graining the Recognition of a Glycolipid by the C-Type Lectin Mincle Receptor

Macrophage inducible Ca2+-dependent lectin (Mincle) receptor recognizes Mycobacterium tuberculosis glycolipids to trigger an immune response. This host membrane receptor is thus a key player in the modulation of the immune response to infection by M. tuberculosis and has emerged as a promising target for the development of new vaccines against tuberculosis. The recent development of the Martini 3 force field for coarse-grained (CG) molecular modeling allows the study of interactions of soluble proteins with small ligands which was not typically modeled well with the previous Martini 2 model. Here, we present a refined approach detailing a protocol for modeling interactions between a glycolipid and its receptor at a CG level using the Martini 3 force field. Using this approach, we studied Mincle and identified critical parameters governing ligand recognition, such as loop flexibility and the regulation of hydrophobic groove formation by calcium ions. In addition, we assessed ligand affinity using free energy perturbation calculations. Our results offer mechanistic insight into the interactions between Mincle and glycolipids, providing a basis for the rational design of molecules targeting this type of membrane receptors.

Photoactivatable Xanthone (PaX) Dyes Enable Quantitative, Dual Color, and Live-Cell MINFLUX Nanoscopy

The single-molecule localization concept MINFLUX has triggered a reevaluation of the features of fluorophores for attaining nanometer-scale resolution. MINFLUX nanoscopy benefits from temporally controlled fluorescence ("on"/"off") photoswitching. Combined with an irreversible switching behavior, the localization process is expected to turn highly efficient and quantitative data analysis simple. The potential in the recently reported photoactivable xanthone (PaX) dyes is recognized to extend the list of molecular switches used for MINFLUX with 561 nm excitation beyond the fluorescent protein mMaple. The MINFLUX localization success rates of PaX560, PaX+560, and mMaple are quantitatively compared by analyzing the effective labeling efficiency of endogenously tagged nuclear pore complexes. The PaX dyes prove to be superior to mMaple and on par with the best reversible molecular switches routinely used in single-molecule localization microscopy. Moreover, the rationally designed PaX595 is introduced for complementing PaX560 in dual color 561 nm MINFLUX imaging based on spectral classification and the deterministic, irreversible, and additive-independent nature of PaX photoactivation is showcased in fast live-cell MINFLUX imaging. The PaX dyes meet the demands of MINFLUX for a robust readout of each label position and fill the void of reliable fluorophores dedicated to 561 nm MINFLUX imaging.

Transmembrane dimers of type 1 receptors sample alternate configurations: MD simulations using coarse grain Martini 3 versus AlphaFold2 Multimer

Structures and dynamics of transmembrane (TM) receptor regions are key to understanding their signaling mechanism across membranes. Here we examine configurations of TM region dimers, assembled using the recent Martini 3 force field for coarse-grain (CG) molecular dynamics simulations. At first glance, our results show only a reasonable agreement with ab initio predictions using PREDDIMER and AlphaFold2 Multimer and with nuclear magnetic resonance (NMR)-derived structures. 5 of 11 CG TM structures are similar to the NMR structures (within <3.5 Å root-mean-square deviation [RMSD]) compared with 10 and 9 using PREDDIMER and AlphaFold2, respectively (with 8 structures of the later within 1.5 Å). Surprisingly, AlphaFold2 predictions are closer to NMR structures when the 2001 instead of 2020 database is used for training. The CG simulations reveal that alternative configurations of TM dimers readily interconvert with a predominant population. The implications for transmembrane signaling are discussed, including for the development of peptide-based pharmaceuticals.