Giant Molecule Research Articles

The effect of a permanent dipole moment on the polar molecule cavity quantum electrodynamics**Project supported by the Strategic Priority Research Program of the Chinese Academy of Sciences (Grant No. XDB01010200), the Hundred Talents Program of the Chinese Academy of Sciences (Grant No. Y321311401), the National Natural Science Foundation of China (Grant Nos. 61475139, 11347147, and 11247014), the National Basics Research

A dressed-state perturbation theory beyond the rotating wave approximation (RWA) is presented to investigate the interaction between a two-level electronic transition of polar molecules and a quantized cavity field. Analytical expressions can be explicitly derived for both the ground- and excited-state-energy spectrums and wave functions of the system, where the contribution of permanent dipole moments (PDM) and the counter-rotating wave term (CRT) can be shown separately. The validity of these explicit results is discussed by comparison with the direct numerical simulation. Compared to the CRT coupling, PDM results in the coupling of more dressed states and the energy shift is proportional to the square of the normalized permanent dipole difference, and a greater Bloch–Siegert shift can be produced in the giant dipole molecule cavity QED. In addition, our method can also be extended to the solution of the two-level atom Rabi model Hamiltonian beyond the RWA.

太陽電池パネル並びに合わせガラスの解体とリサイクルを中心とした「半導体の熱活性」(TASC: Thermal Activation of Semiconductors)技術の最近の進歩

Thermal activation of semiconductors (TASC) is our novel technology characterized by radical propagation in giant molecules, allowing us to decompose any polymers, in an instant, into H2O and CO2. The present phenomenon has successfully been applied to complete decomposition of VOC (volatile organic compound), or to elimination of polymer matrix in composites to recover valuables, for example, decomposition and recovery of FRPs (fiber reinforced plastic), repair of partially damaged FRPs, reclaim of rare-earth powder from resin-bonded magnets, disassembly and recycling of solar panels and laminated glass. The TASC technology dates back to our accidental finding that significant oxidative properties appear in semiconductors when heated at about 350-500 ℃ while quite inactive at room temperature. The oxidative effect (i.e. removal of bonded electrons) has been interpreted as arising from thermally generated defect electrons (“hole”) formed in the valence band of semiconductors. This triggers the decomposition of polymers by creating unstable radicals. Then, the radicals propagate, just like a domino effect or chain reaction, throughout the polymer to make the whole polymer unstable, resulting in the fragmentation of the giant molecule into small pieces such as ethylene and propane. Finally, the fragmented molecules react with oxygen in air to give H2O and CO2 (i.e. complete combustion). This process caused by radical propagation is compared to the reverse reaction of “radical polymerization”. The present overview describes the recent advances in TASC technology with major focus on the disassembly and recycling of solar panels and laminated glass.

Production of trilobite Rydberg molecule dimers with kilo-Debye permanent electric dipole moments

Permanent electric dipole moments are important for understanding symmetry breaking in molecular physics, control of chemical reactions, and realization of strongly correlated many-body quantum systems. However, large molecular permanent electric dipole moments are challenging to realize experimentally. We report the observation of ultralong-range Rydberg molecules with bond lengths of ~100 nanometers and kilo-Debye permanent electric dipole moments that form when an ultracold ground-state cesium (Cs) atom becomes bound within the electronic cloud of an extended Cs electronic orbit. The electronic character of this hybrid class of "trilobite" molecules is dominated by degenerate Rydberg manifolds, making them difficult to produce by conventional photoassociation. We used detailed coupled-channel calculations to reproduce their properties quantitatively. Our findings may lead to progress in ultracold chemistry and strongly correlated many-body physics.

Making a molecular fossil lookalike

Molecular Physics Atoms are generally compact objects. However, if one of the electrons orbiting the nucleus is given an extra boost of energy so that it's barely still attached, you get a much larger Rydberg atom. Booth et al. created an even more exotic species: a giant molecule consisting of a regular cesium atom bound within a Rydberg atom of the same element. The molecules are named “trilobites” because their electronic density visually resembles fossils of these extinct marine creatures. Science , this issue p. [99][1] [1]: /lookup/volpage/348/99?iss=6230

Single-Molecule FRET Reveals Hidden Complexity in a Protein Energy Landscape

SummaryHere, using single-molecule FRET, we reveal previously hidden conformations of the ankyrin-repeat domain of AnkyrinR, a giant adaptor molecule that anchors integral membrane proteins to the spectrin-actin cytoskeleton through simultaneous binding of multiple partner proteins. We show that the ankyrin repeats switch between high-FRET and low-FRET states, controlled by an unstructured “safety pin” or “staple” from the adjacent domain of AnkyrinR. Opening of the safety pin leads to unravelling of the ankyrin repeat stack, a process that will dramatically affect the relative orientations of AnkyrinR binding partners and, hence, the anchoring of the spectrin-actin cytoskeleton to the membrane. Ankyrin repeats are one of the most ubiquitous molecular recognition platforms in nature, and it is therefore important to understand how their structures are adapted for function. Our results point to a striking mechanism by which the order-disorder transition and, thereby, the activity of repeat proteins can be regulated.

Asymmetric Organic–Inorganic Hybrid Giant Molecule: Hierarchical Smectic Phase Induced from POSS Nanoparticles by Addition of Nematic Liquid Crystals

Spontaneous vertical alignment (VA) of a nematic liquid crystal medium, 4-cyano-4′-heptyloxybiphenyl (7OCB), was successfully achieved by directely adding a small amount of cyanobiphenyl monosubstituted polyhedral oligomeric silsesquioxane (POSS-CB) giant molecules [Kim, D.-Y.; Kim, S.; Lee, S.-A; Choi, Y.-E.; Yoon, W.-J.; Kuo, S.-W.; Hsu, C.-H.; Huang, M.; Lee, S. H.; Jeong, K.-U. J. Phys. Chem. C 2014, 118, 6300–6306]. The cyanobiphenyl moiety chemically attached to the pristine POSS improved the initial solubility with the 7OCB molecules and alleviated the macroscopic aggregates. However, the phase behavior and structural evolution of the finely tuned POSS-CB giant molecules with 7OCB are still open questions. Based on the thermal, microscopic, and scattering experiments, it was realized that the POSS-based giant molecules strongly interacted with host 7OCB at a molecular level and induced the layered structure. The POSS groups in the POSS-CB giant molecules were laterally close-packed to create the st...

RRS-PBC: a molecular approach for periodic systems

Technically, when dealing with a perfect crystal, methods in k-(reciprocal) space that impose periodic boundary conditions (PBC) in conjunction with plane-wave basis sets are widely used. Chemists, however, tend to think of a solid as a giant molecule, which offers a molecular way to describe a solid by using a finite cluster model (FCM). However, FCM may fail to simulate a perfect crystal due to its inevitable boundary effects. We propose an RRS-PBC method that extracts the k-space information of a perfect crystalline solid out of a reduced real space (RRS) of an FCM. We show that the inevitable boundary effects in an FCM are eliminated naturally to achieve converged high-quality band structures.

Spin dynamics of the giant polyoxometalate molecule {Mn40W224} studied by NMR

7Li nuclear magnetic resonance (NMR) studies have been performed to investigate magnetic properties and spin dynamics of Mn3+ (S = 2) spins in the giant polyoxometalate molecule {Mn40W224}. The 7Li-NMR line width is proportional to the external magnetic field H as expected in a paramagnetic state above 3 K. Below this temperature the line width shows a sudden increase and is almost independent of H, which indicates freezing of the local Mn3+ spins. The temperature dependence of T1 for both 1H and 7Li reveals slow spin dynamics at low temperatures, consistent with spin freezing. The slow spin dynamics is also evidenced by the observation of a peak of 1/T2 around 3 K, where the fluctuation frequency of spins is of the order of ∼200 kHz. An explicit form of the temperature dependence of the fluctuation frequency of Mn3+ spins is derived from the nuclear relaxation data.

Asymmetric Organic–Inorganic Hybrid Giant Molecule: Cyanobiphenyl Monosubstituted Polyhedral Oligomeric Silsesquioxane Nanoparticles for Vertical Alignment of Liquid Crystals

For liquid crystal (LC) alignment, polyhedral oligomeric silsesquioxanes (POSS) can be considered as one of the promising candidates for the formation of vertical alignment (VA) of LC. However, because of their poor compatibility and weak interaction with LC hosts, the pristine POSS are highly aggregate themselves in the LC media and create the macroscopic particles, resulting in severe light scatterings. To overcome this barrier, we proposed and successfully synthesized the cyanobiphenyl monosubstituted POSS giant molecule (abbreviated as POSS-CBP1), which showed an excellent dispersion in nematic (N) LC media and formed the perfect VA of LC without using conventional polymer-based VA layers. On the basis of the systematic experiments and careful analysis, we realized that the cyanobiphenyl moiety chemically attached to the pristine POSS with an alkyl chain can significantly improve the initial solubility and interaction with LC media but finely tune POSS-CBP1 to gradually diffuse onto the substrate of L...

Small Heat Shock Proteins Prevent Titin Aggregation-Induced Stiffening in Human Myocytes

During stretch of myocytes, mechanically active domains of the giant elastic titin molecule become unfolded. Unfolded proteins typically expose previously buried hydrophobic sites and are under risk to aggregate and lose their function. As for titin, it is unclear whether domain unfolding leads to aggregation and functional impairment. Here we consider that small heat shock proteins (sHSPs), which are abundantly expressed in myocytes, could help prevent titin aggregation. Various sHSPs, including HSP27 and αB-crystallin, are known to translocate under stress conditions preferentially to the sarcomeres, especially the elastic I-band region, where the titin springs are located. We find that HSP27 and αB-crystallin share binding sites on the titin springs, associating with immunoglobulin-like domain (Ig) containing regions, but not with the intrinsically disordered PEVK-domain. In sarcomeres, sHSP-binding to titin occurs independent of the presence of actin filaments and is enhanced by stretch. The titin spring elements behave in vitro mainly as monomers. However, unfolded Ig regions aggregate in vitro, preferentially under acidic conditions, whereas αB-crystallin protects against aggregation. Disordered titin spring regions do not aggregate. Single human cardiomyocytes in which titin Ig unfolding is promoted reveal elevated stiffness under acidic stress, but HSP27 or αB-crystallin suppress this stiffening. The two sHSPs do not bind to the sarcomeres of stretched cardiomyocytes expressing very compliant titin (Ig domain-unfolding probability very low), but localize to the I-band region in stretched cardiomyocytes expressing stiff titin (Ig domain-unfolding probability high). In diseased human muscle/heart tissue both sHSPs associate with the titin springs, in contrast to cytosolic/Z-disk locations in healthy muscle/heart. We conclude that aggregation of unfolded titin Ig domains under stress conditions would stiffen myocytes, but sHSPs translocating to these domains prevent titin aggregation and cell stiffening.

3P126 転写調節タンパク質STPRは長鎖DNAを塩基配列非特異的に折り畳む(05B. 核酸:相互作用・複合体,ポスター,第52回日本生物物理学会年会(2014年度))

3P126 転写調節タンパク質STPRは長鎖DNAを塩基配列非特異的に折り畳む(05B. 核酸:相互作用・複合体,ポスター,第52回日本生物物理学会年会(2014年度))

Formation of Regular Stripes of Chemically Converted Graphene on Hydrophilic Substrates

Chemically converted graphene (CCG), from a chemistry point of view, is a giant molecule with a unique two-dimensional (2D) configuration. The availability of CCG dispersion provides a range of scalable methods to assemble graphene-based materials but brings the challenge of understanding and control of the CCG morphology in solution processing. In this study, we found that, similar to conventional colloidal systems (e.g., spherical particles or polymers), a 2D sheet of CCG can be transferred from its aqueous dispersion to solid substrates in the form of highly regular stripe patterns by evaporation-driven deposition. The width and spacing can be defined by the concentration of the CCG dispersion and the properties of the substrate (e.g., roughness and surface charge). Furthermore, the high resolution AFM images illustrate that both 2D flattened and highly wrinkled CCG can be formed in each individual stripe, depending on the location across the stripe. The in situ optical observation of the stripe formation indicates that the morphological change of CCG may occur in the crowded meniscus of the drying front.

PLEIAD/SIMC1/C5orf25, a Novel Autolysis Regulator for a Skeletal-Muscle-Specific Calpain, CAPN3, Scaffolds a CAPN3 Substrate, CTBP1

CAPN3/p94/calpain-3 is a skeletal-muscle-specific member of the calpain protease family. Multiple muscle cell functions have been reported for CAPN3, and mutations in this protease cause limb-girdle muscular dystrophy type 2A. Little is known about the molecular mechanisms that allow CAPN3 to be so multifunctional. One hypothesis is that the very rapid and exhaustive autolytic activity of CAPN3 needs to be suppressed by dynamic molecular interactions for specific periods of time. The previously identified interaction between CAPN3 and connectin/titin, a giant molecule in muscle sarcomeres, supports this assumption; however, the regulatory mechanisms of non-sarcomere-associated CAPN3 are unknown. Here, we report that a novel CAPN3-binding protein, PLEIAD [Platform element for inhibition of autolytic degradation; originally called SIMC1/C5orf25 (SUMO-interacting motif containing protein 1/chromosome 5open reading frame 25)], suppresses the protease activity of CAPN3. Database analyses showed that PLEIAD homologs, like CAPN3 homologs, are evolutionarily conserved in vertebrates. Furthermore, we found that PLEIAD also interacts with CTBP1 (C-terminal binding protein 1), a transcriptional co-regulator, and CTBP1 is proteolyzed in COS7 cells expressing CAPN3. The identified cleavage sites in CTBP1 suggested that it undergoes functional modification upon its proteolysis by CAPN3, as well as by conventional calpains. These results indicate that PLEIAD can shift its major function from CAPN3 suppression to CAPN3-substrate recruitment, depending on the cellular context. Taken together, our data suggest that PLEIAD is a novel regulatory scaffold for CAPN3, as reflected in its name.

Photo‐induced Free Radical Modification of Graphene

Graphene has stimulated enormous interest due to its intriguing structure and fascinating properties. The extremely high carrier mobility, mechanical flexibility, and optical transparency as well as the versatility for band structure engineering make graphene a promising candidate for next-generation carbon-based electronic devices. Graphene chemistry, the covalent functionalization of graphene as a 2D giant molecule, offers a promising direction to controllably tailor its properties through the introduction of various chemical decorations. One of the great challenges for graphene functionalization originates from its strong chemical stability, thus highly reactive chemical species are needed as the reactants. In recent years, novel photochemical approaches have been developed to achieve efficient graphene modification and bandgap modulation, following a general concept of "Photochemical Bandgap Engineering of Graphene". In this article, such kinds of photochemical graphene engineering are demonstrated, together with a brief discussion on the future directions, challenges, and opportunities in this fascinating research area.

Janus graphene from asymmetric two-dimensional chemistry

Janus materials have distinct surfaces on their opposite faces. Graphene, a two-dimensional giant molecule, provides an excellent candidate to fabricate the thinnest Janus discs and study the asymmetric chemistry of atomic-thick nanomembranes using covalent chemical functionalisation. Here we present the first experimental realisation of nonsymmetrically modified single-layer graphene--Janus graphene--which is fabricated by a two-step surface covalent functionalisation assisted by a poly(methyl methacrylate)-mediated transfer approach. Four types of Janus graphene are produced by co-grafting of halogen and aryl/oxygen-functional groups on each side. Chemical decorations on one side are found to be capable of affecting both chemical reactivity and physical wettability of the opposite side, indicative of communication between the two grafted groups. This novel asymmetric structure provides a platform for theoretical and experimental studies of two-dimensional chemistry and graphene devices with multiple functions.

Организация хромосом эукариот: от работ Н.К. Кольцова до наших дней

N. K. Kol'tsov ideas and views on the organization of eukaryotic chromosomes, including the notion of a giant hereditary molecule (genoneme) and its structural functional organization, are considered. Different approaches to chromosome studies are discussed, ranging from the examination of a chromosome as a stained cell organelle and the visualization of individual chromosomes in a living cell to the identification of topological domains of human and murine chromosomes using 3C and 5C technologies. The prospects of studies of chromosome organization using up-to-date methods of cytology, molecular biology, and bioinformatics are discussed.

Self-assembly of a tetrahedral 58-nuclear barium vanadium oxide cluster

We report the synthesis and characterization of a molecular barium vanadium oxide cluster featuring high nuclearity and high symmetry. The tetrameric, 2.3 nm cluster H(5)[Ba(10)(NMP)(14)(H(2)O)(8)[V(12)O(33)](4)Br] is based on a bromide-centred, octahedral barium scaffold which is capped by four previously unknown [V(12)O(33)](6-) clusters in a tetrahedral fashion. The compound represents the largest polyoxovanadate-based heterometallic cluster known to date. The cluster is formed in organic solution and it is suggested that the bulky N-methyl-2-pyrrolidone (NMP) solvent ligands allow the isolation of this giant molecule and prevent further condensation to a solid-state metal oxide. The cluster is fully characterized using single-crystal XRD, elemental analysis, ESI mass spectrometry and other spectroscopic techniques.

Faradaurate Nanomolecules: A Superstable Plasmonic 76.3 kDa Cluster

Information on the emergence of the characteristic plasmonic optical properties of nanoscale noble-metal particles has been limited, due in part to the problem of preparing homogeneous material for ensemble measurements. Here, we report the identification, isolation, and mass spectrometric and optical characterization of a 76.3 kDa thiolate-protected gold nanoparticle. This giant molecule is far larger than any metal-cluster compound, those with direct metal-to-metal bonding, previously known as homogeneous molecular substances, and is the first to exhibit clear plasmonic properties. The observed plasmon emergence phenomena in nanomolecules are of great interest, and the availability of absolutely homogeneous and characterized samples is thus critical to establishing their origin.

Ahnak1 abnormally localizes in muscular dystrophies and contributes to muscle vesicle release

Ahnak1 is a giant, ubiquitously expressed, plasma membrane support protein whose function in skeletal muscle is largely unknown. Therefore, we investigated whether ahnak would be influenced by alterations of the sarcolemma exemplified by dysferlin mutations known to render the sarcolemma vulnerable or by mutations in calpain3, a protease known to cleave ahnak. Human muscle biopsy specimens obtained from patients with limb girdle muscular dystrophy (LGMD) caused by mutations in dysferlin (LGMD2B) and calpain3 (LGMD2A) were investigated for ahnak expression and localization. We found that ahnak1 has lost its sarcolemmal localization in LGMD2B but not in LGMD2A. Instead ahnak1 appeared in muscle connective tissue surrounding the extracellular site of the muscle fiber in both muscular dystrophies. The entire giant ahnak1 molecule was present outside the muscle fiber and did only partially colocalize with CD45-positive immune cell infiltration and the extracelluar matrix proteins fibronectin and collagenVI. Further, vesicles shedded in response to Ca2+ by primary human myotubes were purified and their protein content was analysed. Ahnak1 was prominently present in these vesicles. Electron microscopy revealed a homogenous population of vesicles with a diameter of about 150 nm. This is the first study demonstrating vesicle release from human myotubes that may be one mechanism underlying abnormally localized ahnak1. Taken together, our results define ahnak1 in muscle connective tissue as a novel feature of two genetically distinct muscular dystrophies that might contribute to disease pathology.Electronic supplementary materialThe online version of this article (doi:10.1007/s10974-011-9271-8) contains supplementary material, which is available to authorized users.

Crystallization and preliminary crystallographic analysis of an Ig-domain-encompassing fragment of the giant adhesion protein SiiE fromSalmonella enterica

Salmonella infections can be life-threatening. SiiE is a giant adhesion molecule of 5559 amino acids that is encoded in Salmonella pathogenicity island 4 (SPI4) and that promotes the initial contact between the pathogen and polarized epithelial cells in the intestine of the host. Starting from an engineered deletion version of SiiE (mini-SiiE; 97 kDa), limited proteolysis was used to reproducibly generate a 30 kDa fragment that readily crystallized. Mass spectrometry hints that this fragment spans the predicted Ig domains 50-52 of SiiE. Crystals of both native and selenomethionine-labelled protein could be obtained in space group C2 and diffraction data were recorded to a resolution of 1.85 Å.