Multiple dimeric structures and strand-swap dimerization of E-cadherin in solution visualized by high-speed atomic force microscopy.

Classical cadherins play key roles in cell-cell adhesion. The adhesion process is thought to comprise mainly two steps: X-dimer and strand-swap (SS-) dimer formation of the extracellular domains (ectodomains) of cadherins. The dimerization mechanism of this two-step process has been investigated for type I cadherins, including E-cadherin, of classical cadherins, whereas other binding states also have been proposed, raising the possibility of additional binding processes required for the cadherin dimerization. However, technical limitations in observing single-molecule structures and their dynamics have precluded the investigation of the dynamic binding process of cadherin. Here, we used high-speed atomic force microscopy (HS-AFM) to observe full-length ectodomains of E-cadherin in solution and identified multiple dimeric structures that had not been reported previously. HS-AFM revealed that almost half of the cadherin dimers showed S- (or reverse S-) shaped conformations, which had more dynamic properties than the SS- and X-like dimers. The combined HS-AFM, mutational, and molecular modeling analyses showed that the S-shaped dimer was formed by membrane-distal ectodomains, while the binding interface was different from that of SS- and X-dimers. Furthermore, the formation of the SS-dimer from the S-shaped and X-like dimers was directly visualized, suggesting the processes of SS-dimer formation from S-shaped and X-dimers during cadherin dimerization.

Enhanced Nonradiative Charge Recombination in Microfiber-Based Bismuthene.

After the first report of a graphene-based passive mode-locking ultrafast fiber laser, two-dimensional materials as efficient saturable absorbers offer a new horizon in ultrafast fiber laser. However, the interactions on atomic scale between these two-dimensional materials and fiber and the fiber effect on the carrier dynamics have not been realized. To figure out the exact role of fiber and the carrier dynamics affected by the fiber substrate related to ultrafast photonics, bismuthene, a newly reported 2D quantum material used in a passive mode-locking fiber laser, deposited on α-quartz has been investigated. We surprisingly found that the α-quartz substrate can strongly accelerate the nonradiative electron-hole recombination of bismuthene in theory, and the transient absorption spectra of bismuthene on normal glass and α-quartz further verify the substrate effect on carrier dynamics of bismuthene. The discovery provides new thinking about substrate effect to regulate the performance of ultrafast mode-locking fiber lasers as well as ultrafast photonics.

Dynamic Interactions Between Brilliant Green and MscL Investigated by Solid-State NMR Spectroscopy and Molecular Dynamics Simulations.

The mechanosensitive ion channel of large conductance (MscL) is a promising template for the development of new antibiotics due to its high conservation and uniqueness to microbes. Brilliant green (BG), a triarylmethane dye, has been identified as a new antibiotic targeted MscL. However, the detailed binding sites to MscL and the dynamic pathway of BG through the MscL channel remain unknown. Here, the dynamic interactions between BG and MscL were investigated using solid-state NMR spectroscopy and molecule dynamics (MD) simulations. Residue site-specific binding sites of BG to the MscL channel were identified by solid-state NMR. In addition, MD simulations revealed that BG conducts through the MscL channel via residues along the inner surface of the pore sequentially, in which the strong hydrophobic interactions between BG and hydrophobic residues F23 and I27 in the hydrophobic gate region of the MscL channel are major restrictions. Particularly, it was demonstrated that BG activates the MscL channel by reducing the hydrophobicity of the F23 in the gate region by water molecules that are bound to BG. Taken together, these simulations and experimental data provide novel insights into the dynamic interactions between BG and MscL, based on which new hydrophobic antibiotics and adjuvants targeting MscL can be developed.

Nuclear Quantum Effects on the Charge-Density Wave Transition in NbX2 (X = S, Se).

Understanding the origin of charge-density wave (CDW) instability is important for manipulating novel collective electronic states. Many layered transition metal dichalcogenides (TMDs) share similarity in the structural and electronic instability, giving rise to diverse CDW phases and superconductivity. It is still puzzling that even isostructural and isoelectronic TMDs show distinct CDW features. For instance, bulk NbSe2 exhibits CDW order at low temperature, while bulk NbS2 displays no CDW instability. The CDW transitions in single-layer NbS2 and NbSe2 are also different. In the classic limit, we investigate the electron correlation effects on the dimensionality dependence of the CDW ordering. By performing ab initio path integral molecular dynamics simulations and comparative analyses, we further revealed significant nuclear quantum effects in these systems. Specifically, the quantum motion of sulfur anions significantly reduces the CDW transition temperature in both bulk and single-layer NbS2, resulting in distinct CDW features in the NbS2 and NbSe2 systems.

Gating of ß-Barrel Protein Pores, Porins, and Channels: An Old Problem with New Facets.

ß barrels are ubiquitous proteins in the outer membranes of mitochondria, chloroplasts, and Gram-negative bacteria. These transmembrane proteins (TMPs) execute a wide variety of tasks. For example, they can serve as transporters, receptors, membrane-bound enzymes, as well as adhesion, structural, and signaling elements. In addition, multimeric ß barrels are common structural scaffolds among many pore-forming toxins. Significant progress has been made in understanding the functional, structural, biochemical, and biophysical features of these robust and versatile proteins. One frequently encountered fundamental trait of all ß barrels is their voltage-dependent gating. This process consists of reversible or permanent conformational transitions between a large-conductance, highly permeable open state and a low-conductance, solute-restrictive closed state. Several intrinsic molecular mechanisms and environmental factors modulate this universal property of ß barrels. This review article outlines the typical signatures of voltage-dependent gating. Moreover, we discuss recent developments leading to a better qualitative understanding of the closure dynamics of these TMPs.

Self-Diffusion in Confined Water: A Comparison between the Dynamics of Supercooled Water in Hydrophobic Carbon Nanotubes and Hydrophilic Porous Silica.

Confined liquids are model systems for the study of the metastable supercooled state, especially for bulk water, in which the onset of crystallization below 230 K hinders the application of experimental techniques. Nevertheless, in addition to suppressing crystallization, confinement at the nanoscale drastically alters the properties of water. Evidently, the behavior of confined water depends critically on the nature of the confining environment and the interactions of confined water molecules with the confining matrix. A comparative study of the dynamics of water under hydrophobic and hydrophilic confinement could therefore help to clarify the underlying interactions. As we demonstrate in this work using a few representative results from the relevant literature, the accurate assessment of the translational mobility of water molecules, especially in the supercooled state, can unmistakably distinguish between the hydrophilic and hydrophobic nature of the confining environments. Among the numerous experimental methods currently available, we selected nuclear magnetic resonance (NMR) in a field gradient, which directly measures the macroscopic translational self-diffusion coefficient, and quasi-elastic neutron scattering (QENS), which can determine the microscopic translational dynamics of the water molecules. Dielectric relaxation, which probes the re-orientational degrees of freedom, are also discussed.

[Illuminating the nanoscopic world of viruses by fluorescence super-resolution microscopy]. / Apport de la microscopie de fluorescence super-résolue : dans l'intimité des virus !

The recent revolution in optical fluorescence microscopy, supported by the optimization of both spatial resolution and acquisition speed, led to the ability to visualize nano-scaled objects. Currently, the use of a new generation of super-resolution fluorescence microscopes coupled to improved fluorescent probes gives the possibility to study the replicative cycle of viruses in living cells, at the single-virus and molecule level. In this review, after a brief chronological description of these new approaches, we highlight several examples of super-resolution microscopies that have allowed to revisit our understanding of several human viruses and of host-pathogen interactions.

Illuminating the nanoscopic world of viruses by fluorescence super-resolution microscopy.

The recent revolution in optical fluorescence microscopy, supported by the optimization of both spatial resolution and acquisition speed, led to the ability to visualize nano-scaled objects. Currently, the use of a new generation of super-resolution fluorescence microscopes coupled to improved fluorescent probes gives the possibility to study the replicative cycle of viruses in living cells, at the single-virus and molecule level. In this review, after a brief chronological description of these new approaches, we highlight several examples of super-resolution microscopies that have allowed to revisit our understanding of several human viruses and of host-pathogen interactions.

The mechanism of pulsed electric field (PEF) targeting location on the spatial conformation of pine nut peptide.

In this study, the pine nut peptides, Lys-Asp-His-Cyc-His (KDHCH), was used as the molecule dynamics (MD) simulations subject, which has been proved that the antioxidant activity was improved after pulse electric field (PEF) treatment and the secondary structure was changed as the circular dichroism (CD) results showed. In the present study, we applied the MD simulation to discover the mechanism of the antioxidant activity improvement. The MD results showed that with the PEF treatment of 15 kV/cm, the oxygen atoms of KDHCH changed a lot, especially the atoms No.32 and No.63, of which the distance difference value was -3.02 nm, compared with the 0 kV/cm PEF treatment. The result showed an approach trend between residues Lys-and His-and the α-C atom of Lys, Cys-and His-all got closer after the PEF treatment, which means the structure became tight after the PEF treatment. However, the results of 45 kV/cm PEF treatment presented more effects on the change of KDHCH. The calculations of oxygen atoms show an approach trend between residues Lys, Asp-and His. The α-C atom of Lys, Cys-and His-all got closer after the PEF treatment, which means the structure became tight after the PEF treatment and proved the results of the calculations of the oxygen atoms. The structures of PEF treated and untreated peptide samples were measured by 1D and 2D nuclear magnetic resonance (NMR) in order to verify the results of the molecular dynamics simulations. The 8.37-8.40 ppm (-NH- in chain) and 8.84-8.88 ppm (-NH- in chain) appeared left shift, while at the 8.45-8.47 ppm (-NH- in chain) occurred a right shift. The 7.82 ppm (-NH- in imidazole ring) on His-shifted left after PEF treatment, which reached 7.84 ppm by the 1D-1H NMR spectroscopy. Moreover, the long-range connectivity between -NHα (8.78 ppm) on 2H-ASP and -CHα (2.72 ppm) on 1H-LYS; -SH (2.50 ppm) on 4H-CYS and -OH (3.53 ppm) on 5H-HIS all appeared in spectra of the PEF treatment sample. This study will also be helpful to further mechanism exploration.

High-affinity RNA binding by a hyperthermophilic single-stranded DNA-binding protein.

Single-stranded DNA-binding proteins (SSBs), including replication protein A (RPA) in eukaryotes, play a central role in DNA replication, recombination, and repair. SSBs utilise an oligonucleotide/oligosaccharide-binding (OB) fold domain to bind DNA, and typically oligomerise in solution to bring multiple OB fold domains together in the functional SSB. SSBs from hyperthermophilic crenarchaea, such as Sulfolobus solfataricus, have an unusual structure with a single OB fold coupled to a flexible C-terminal tail. The OB fold resembles those in RPA, whilst the tail is reminiscent of bacterial SSBs and mediates interaction with other proteins. One paradigm in the field is that SSBs bind specifically to ssDNA and much less strongly to RNA, ensuring that their functions are restricted to DNA metabolism. Here, we use a combination of biochemical and biophysical approaches to demonstrate that the binding properties of S. solfataricus SSB are essentially identical for ssDNA and ssRNA. These features may represent an adaptation to a hyperthermophilic lifestyle, where DNA and RNA damage is a more frequent event.

Symmetry breaking in the early mammalian embryo: the case for quantitative single-cell imaging analysis.

In recent years, advances in imaging probes, cutting-edge microscopy techniques and powerful bioinformatics image analysis have markedly expanded the imaging toolbox available to developmental biologists. Apart from traditional qualitative studies, embryonic development can now be investigated in vivo with improved spatiotemporal resolution, with more detailed quantitative analyses down to the single-cell level of the developing embryo. Such imaging tools can provide many benefits to investigate the emergence of the asymmetry in the early mammalian embryo. Quantitative single-cell imaging has provided a deeper knowledge of the dynamic processes of how and why apparently indistinguishable cells adopt separate fates that ensure proper lineage allocation and segregation. To advance our understanding of the mechanisms governing such cell fate decisions, we will need to address current limitations of fluorescent probes, while at the same time take on challenges in image processing and analysis. New discoveries and developments in quantitative, single-cell imaging analysis will ultimately enable a truly comprehensive, multi-dimensional and multi-scale investigation of the dynamic morphogenetic processes that work in concert to shape the embryo.

Mapping Full Conformational Transition Dynamics of Intrinsically Disordered Proteins Using a Single-Molecule Nanocircuit.

Intrinsically disordered proteins (IDPs) are emerging therapeutic targets for human diseases. However, probing their transient conformations remains challenging because of conformational heterogeneity. To address this problem, we developed a biosensor using a point-functionalized silicon nanowire (SiNW) that allows for real-time sampling of single-molecule dynamics. A single IDP, N-terminal transactivation domain of tumor suppressor protein p53 (p53TAD1), was covalently conjugated to the SiNW through chemical engineering, and its conformational transition dynamics was characterized as current fluctuations. Furthermore, when a globular protein ligand in solution bound to the targeted p53TAD1, protein-protein interactions could be unambiguously distinguished from large-amplitude current signals. These proof-of-concept experiments enable semiquantitative, realistic characterization of the structural properties of IDPs and constitute the basis for developing a valuable tool for protein profiling and drug discovery in the future.

Visualization, Quantification, and Statistical Evaluation of Dynamics for DNA-Binding Proteins in Bacteria by Single-Molecule Tracking.

All DNA-binding proteins in vivo exist as a population of freely diffusing molecules and of DNA-bound molecules. The molecules bound to DNA can be split into specifically/tightly and nonspecifically bound proteins. Single-molecule tracking (SMT) is a method allowing to visualize protein dynamics in living cells, revealing their behavior in terms of mode of motion, diffusion coefficient/speed, change of dwell times, and unveiling preferred subcellular sites of dwelling. Bleaching-type SMT or fluorescent protein-tagged SMT involves rapid laser-induced bleaching of most fluorophore-labeled molecules. The remaining single fluorescent proteins are then continuously tracked. The trajectories of several fluorescent molecules per cell for a population of cells are analyzed and combined to permit a robust analysis of average behavior of single molecules in live cells, including analyses of protein dynamics in mutant cells or cells exposed to changes in environmental conditions.In this chapter, we describe the preparation of Bacillus subtilis cells, the recording of movies of those cells expressing a monomeric variant of a yellow fluorescent protein (mNeonGreen) fused to a protein of choice, and the subsequent curation of the movie data including the statistical analysis of the protein dynamics. We present a short overview of the analysis program SMTracker 2.0, highlighting its ability to analyze SMT data by non-expert scientists.

Molecule Dynamics Simulation of the Effect of Oxidative Aging on Properties of Nitrile Rubber.

The effects of oxidative aging on the static and dynamic properties of nitrile rubber at the molecular scale were investigated by molecular dynamics simulation. The aged nitrile rubber models were constructed by introducing hydroxyl groups and carbonyl groups into rubber molecular chains to mimic oxidative aging. The static and dynamic properties of the unaged and aged nitrile rubber under different conditions were evaluated by mean square displacement, self-diffusion coefficients, hydrogen bond, fractional free volume, radial distribution function, cohesive energy density and solubility parameter. The results show that the elevated temperature intensified significantly the mobility of rubber molecular chains and fractional free volume, while the compressive strain displayed the opposite effect resulting in packing and rearrangement of rubber chains. The introduction of hydroxyl groups and carbonyl groups enhanced the polarity, intermolecular interactions, the volume and rigidity of molecular chains, implying weaker mobility of molecular chains as compared to unaged models. The compressive strain and oxidative aging both decreased the fractional free volume, which inhibited gaseous and liquid diffusion into the rubber materials, and slowed down the oxidative aging rate. This study provides insights to better understand the effect of molecular changes due to oxidative aging on the structural and dynamic properties of rubber materials at the molecular level.

Network pharmacology-based predictions of active components and pharmacological mechanisms of Artemisia annua L. for the treatment of the novel Corona virus disease 2019 (COVID-19).

BACKGROUND: Novel Corona Virus Disease 2019 (COVID-19) is closely associated with cytokines storms. The Chinese medicinal herb Artemisia annua L. (A. annua) has been traditionally used to control many inflammatory diseases, such as malaria and rheumatoid arthritis. We performed network analysis and employed molecular docking and network analysis to elucidate active components or targets and the underlying mechanisms of A. annua for the treatment of COVID-19. METHODS: Active components of A. annua were identified through the TCMSP database according to their oral bioavailability (OB) and drug-likeness (DL). Moreover, target genes associated with COVID-19 were mined from GeneCards, OMIM, and TTD. A compound-target (C-T) network was constructed to predict the relationship of active components with the targets. A Compound-disease-target (C-D-T) network has been built to reveal the direct therapeutic target for COVID-19. Molecular docking, molecular dynamics simulation studies (MD), and MM-GBSA binding free energy calculations were used to the closest molecules and targets between A. annua and COVID-19. RESULTS: In our network, GO, and KEGG analysis indicated that A. annua acted in response to COVID-19 by regulating inflammatory response, proliferation, differentiation, and apoptosis. The molecular docking results manifested excellent results to verify the binding capacity between the hub components and hub targets in COVID-19. MD and MM-GBSA data showed quercetin to be the more effective candidate against the virus by target MAPK1, and kaempferol to be the other more effective candidate against the virus by target TP53. We identified A. annua's potentially active compounds and targets associated with them that act against COVID-19. CONCLUSIONS: These findings suggest that A. annua may prevent and inhibit the inflammatory processes related to COVID-19.

Stability comparison of four lipases and catalytic mechanism during the synthesis of 1,3-di-oleic-2-medium chain triacylglycerols in a trace water-in-oil system: Experimental analyses and computational simulations.

In the present study, a kind of structured lipids, namely 1,3-di-oleic-2-medium chain (OMO) triacylglycerols, were synthesized through lipase-catalyzed reactions using coconut oil and rapeseed acid as materials in a trace water-in-oil system. Experimental analysis and computational simulations were undertaken to compare the stability of four lipases including Lipozyme RMIM, Lipozyme TLIM, Novozym 435, and Aspergillus oryzae immobilized lipase (AOIM), and illustrate catalytic mechanism of Novozym 435 during the synthesis of OMO. Fourier transform infrared and molecular dynamics simulation results demonstrated that a decrease in ordered structure (α-helix and ß-sheet) led to a reduction in enzyme activity. Compared with Lipozyme RMIM and Novozym 435, Lipozyme TLIM and AOIM exhibited better stability due to a short-chain lid in TLIM, which covers activity sites, and hydrogen bonds formed between activity center of AOIM and water. Among four lipases, AOIM exhibited best catalytic performance: a OMO yield of 30.7% at 3 hr and a good stability of long term (48 hr). Density functional theory results demonstrated that specifically, during the synthesis of OMO triacylglycerol, the addition of Novozym 435 (derived from Candida antarctica lipase B, CALB) substantially lowered reaction barriers (64.4 KJ/mol with CALB vs. 332.7 KJ/mol with no lipase), aiding in the generation of OMO because of the formations of transitional tetrahedral intermediates. A trace water-in-oil system was a green and efficient alternative for lipase-catalyzed production of OMO, and this study provided crucial insights into the stability/instability and catalytic mechanisms of lipase in the synthesis of structured lipids. PRACTICAL APPLICATIONS: We compared the stability of Lipozyme RMIM, Lipozyme 435, Lipozyme TLIM, and AOIM during the synthesis of the OMO triacylglycerols in a trace water-in-oil system, where exhibited a high catalytic activity of lipase in water-oil interface. AOIM had the highest stability and showed the best catalytic performance due to the formation of hydrogen bonds. Besides, for the first time, the transition tetrahedral structure was revealed in the enzymatic synthesis of medium- and long-chain triacylglycerols. This study provides a rational approach to compare lipase stability and a possible hint to choose appropriate enzyme in a specific catalytic condition.

A Singular Molecule-to-Molecule Transformation on Video: The Bottom-Up Synthesis of Fullerene C60 from Truxene Derivative C60H30.

Singular reaction events of small molecules and their dynamics remain a hardly understood territory in chemical sciences since spectroscopy relies on ensemble-averaged data, and microscopic scanning probe techniques show snapshots of frozen scenes. Herein, we report on continuous high-resolution transmission electron microscopic video imaging of the electron-beam-induced bottom-up synthesis of fullerene C60 through cyclodehydrogenation of tailor-made truxene derivative 1 (C60H30), which was deposited on graphene as substrate. During the reaction, C60H30 transformed in a multistep process to fullerene C60. Hereby, the precursor, metastable intermediates, and the product were identified by correlations with electron dose-corrected molecular simulations and single-molecule statistical analysis, which were substantiated with extensive density functional theory calculations. Our observations revealed that the initial cyclodehydrogenation pathway leads to thermodynamically favored intermediates through seemingly classical organic reaction mechanisms. However, dynamic interactions of the intermediates with the substrate render graphene as a non-innocent participant in the dehydrogenation process, which leads to a deviation from the classical reaction pathway. Our precise visual comprehension of the dynamic transformation implies that the outcome of electron-beam-initiated reactions can be controlled with careful molecular precursor design, which is important for the development and design of materials by electron beam lithography.

Single-molecule enzymatic reaction dynamics and mechanisms of GPX3 and TRXh9 from Arabidopsis thaliana.

Glutathione peroxidases (GPXs) regulate the levels of reactive oxygen species in cells and tissues. During the redox cycling, the plant GPX is regenerated by thioredoxins (TRXs) as reductant rather than glutathione as the electron donor. However, the direct experimental observation on the interaction dynamics between GPXs and TRXs has not been reported, and the redox mechanism is unclear. In this work, the protein interactions between oxidized AtGPX3 and reduced AtTRXh9 have been studied using single-molecule fluorescence resonance energy transfer (smFRET). The obtained results indicate there are four processes in these two protein interaction, including biological recognition, binding, intermediate and unbinding state. Two enzymatic reaction intermediate states have been identified in the dissociation of AtGPX3-AtTRXh9 complex from binding to unbinding state, suggesting two types of interaction pathways and intermediate complexes. In particular, the dynamical study reveals that the redox reaction between oxidized AtGPX3 and reduced AtTRXh9 is realized through the forming and breaking of disulfide bonds via the active sites of Cys4 and Cys57 in AtTRXh9. These findings are of significant for deep understanding the redox reaction and mechanism between GPXs and TRXs enzymes, and studying other protein dynamics at single-molecule level.

Super-Resolution Microscopy and Single-Molecule Tracking Reveal Distinct Adaptive Dynamics of MreB and of Cell Wall-Synthesis Enzymes.

The movement of filamentous, actin-like MreB and of enzymes synthesizing the bacterial cell wall has been proposed to be highly coordinated. We have investigated the motion of MreB and of RodA and PbpH cell wall synthesis enzymes at 500 ms and at 20 ms time scales, allowing us to compare the motion of entire MreB filaments as well as of single molecules with that of the two synthesis proteins. While all three proteins formed assemblies that move with very similar trajectory orientation and with similar velocities, their trajectory lengths differed considerably, with PbpH showing shortest and MreB longest trajectories. These experiments suggest different on/off rates for RodA and PbpH at the putative peptidoglycan-extending machinery (PGEM), and during interaction with MreB filaments. Single molecule tracking revealed distinct slow-moving and freely diffusing populations of PbpH and RodA, indicating that they change between free diffusion and slow motion, indicating a dynamic interaction with the PGEM complex. Dynamics of MreB molecules and the orientation and speed of filaments changed markedly after induction of salt stress, while there was little change for RodA and PbpH single molecule dynamics. During the stress adaptation phase, cells continued to grow and extended the cell wall, while MreB formed fewer and more static filaments. Our results show that cell wall synthesis during stress adaptation occurs in a mode involving adaptation of MreB dynamics, and indicate that Bacillus subtilis cell wall extension involves an interplay of enzymes with distinct binding kinetics to sites of active synthesis.

Bond Dissociation and Reactivity of HF and H2O in a Nano Test Tube.

Molecular motion and bond dissociation are two of the most fundamental phenomena underpinning the properties of molecular materials. We entrapped HF and H2O molecules within the fullerene C60 cage, encapsulated within a single-walled carbon nanotube (X@C60)@SWNT, where X = HF or H2O. (X@C60)@SWNT represents a class of molecular nanomaterial composed of a guest within a molecular host within a nanoscale host, enabling investigations of the interactions of isolated single di- or triatomic molecules with the electron beam. The use of the electron beam simultaneously as a stimulus of chemical reactions in molecules and as a sub-angstrom resolution imaging probe allows investigations of the molecular dynamics and reactivity in real time and at the atomic scale, which are probed directly by chromatic and spherical aberration-corrected high-resolution transmission electron microscopy imaging, or indirectly by vibrational electron energy loss spectroscopy in situ during scanning transmission electron microscopy experiments. Experimental measurements indicate that the electron beam triggers homolytic dissociation of the H-F or H-O bonds, respectively, causing the expulsion of the hydrogen atoms from the fullerene cage, leaving fluorine or oxygen behind. Because of a difference in the mechanisms of penetration through the carbon lattice available for F or O atoms, atomic fluorine inside the fullerene cage appears to be more stable than the atomic oxygen under the same conditions. The use of (X@C60)@SWNT, where each molecule X is "packaged" separately from each other, in combination with the electron microscopy methods and density functional theory modeling in this work, enable bond dynamics and reactivity of individual atoms to be probed directly at the single-molecule level.