Invisible States Research Articles

Measuring Diffusion Constants of Invisible Protein Conformers by Triple‐Quantum 1H CPMG Relaxation Dispersion

AbstractProteins are not locked in a single structure but often interconvert with other conformers that are critical for function. When such conformers are sparsely populated and transiently formed they become invisible to routine biophysical methods, however they can be studied in detail by NMR spin‐relaxation experiments. Few experiments are available in the NMR toolkit, however, for characterizing the hydrodynamic properties of invisible states. Herein we describe a CPMG‐based experiment for measuring translational diffusion constants of invisible states using a pulsed‐field gradient approach that exploits methyl 1H triple‐quantum coherences. An example, involving diffusion of a sparsely populated and hence invisible unfolded protein ensemble is presented, without the need for the addition of denaturants that tend to destroy weak interactions that can be involved in stabilizing residual structure in the unfolded state.

Classical phase transitions in a one-dimensional short-range spin model

Ising’s solution of a classical spin model famously demonstrated the absence of a positive-temperature phase transition in one-dimensional equilibrium systems with short-range interactions. No-go arguments established that the energy cost to insert domain walls in such systems is outweighed by entropy excess so that symmetry cannot be spontaneously broken. An archetypal way around the no-go theorems is to augment interaction energy by increasing the range of interaction. Here we introduce new ways around the no-go theorems by investigating entropy depletion instead. We implement this for the Potts model with invisible states. Because spins in such a state do not interact with their surroundings, they contribute to the entropy but not the interaction energy of the system. Reducing the number of invisible states to a negative value decreases the entropy by an amount sufficient to induce a positive-temperature classical phase transition. This approach is complementary to the long-range interaction mechanism. Alternatively, subjecting positive numbers of invisible states to imaginary or complex fields can trigger such a phase transition. We also discuss potential physical realisability of such systems.

Unlocking a Diazirine Long-Lived Nuclear Singlet State via Photochemistry: NMR Detection and Lifetime of an Unstabilized Diazo-Compound

Diazirines are important for photoaffinity labeling, and their photoisomerization is relatively well-known. This work shows how hyperpolarized NMR spectroscopy can be used to characterize an unstable diazo-compound formed via photoisomerization of a 15N2-labeled silyl-ether-substituted diazirine. This diazirine is prepared in a nuclear spin singlet state via catalytic transfer of spin order from para-hydrogen. The active hyperpolarization catalyst is characterized to provide insight into the mechanism. The photochemical isomerization of the diazirine into the diazo-analogue allows the NMR invisible nuclear singlet state of the parent compound to be probed. The identity of the diazo-species is confirmed by trapping with N-phenyl maleimide via a cycloaddition reaction to afford bicyclic pyrazolines that also show singlet state character. The presence of singlet states in the diazirine and the diazo-compound is validated by comparison of experimental nutation behavior with theoretical simulation. The magnetic state lifetime of the diazo-compound is determined as 12 ± 1 s in CD3OD solution at room temperature, whereas its chemical lifetime is measured as 100 ± 5 s by related hyperpolarized NMR studies. Indirect evidence for the generation of the photoproduct para-N2 is presented.

Decorrelating Kinetic and Relaxation Parameters in Exchange Saturation Transfer NMR: A Case Study of N-Terminal Huntingtin Peptides Binding to Unilamellar Lipid Vesicles.

Dark state exchange saturation transfer (DEST) and lifetime line-broadening (Δ R2, the difference in the measured transverse relaxation rates for the observable species in the presence and absence of exchange with a species characterized by very large intrinsic transverse relaxation rates) have proven to be powerful NMR tools for studying exchange phenomena between a NMR visible species and a high-molecular weight, "dark", NMR invisible state. However, in the exchange regime, where the transverse spin relaxation rates in the bound state ( R2bound) are smaller than the strength of the DEST saturation radio frequency field, typically corresponding to systems below ∼6 MDa, the combination of DEST and Δ R2 data, while sufficient to define the apparent association rate constant, cannot unambiguously determine the population of the bound state pB and R2bound values independently. We show that the latter exchange and relaxation parameters can be decorrelated by the measurement of the maximal value of the contribution of the fast-relaxing magnetization component to the total NMR signal, Cfastmax, an observable that is directly proportional to pB. When integrated into the analysis of DEST/Δ R2 data, Cfastmax provides an indispensable source of information for quantitative studies of exchange involving high-molecular-weight dark states. We demonstrate the utility of this approach by investigating the binding kinetics of two huntingtin exon-1-derived peptides to small unilamellar lipid vesicles (SUV), ∼ 31 nm in diameter and 4.3 MDa in molecular weight. The interaction of the N-terminal amphiphilic domain of huntingtin exon-1 with membrane surfaces promotes polyglutamine-mediated aggregation and, as such, is thought to play a role in the etiology of Huntington's disease, an autosomal dominant fatal neurodegenerative condition. The first peptide comprises the 16-residue N-terminal amphiphilic domain (httNT) alone, while the second contains an additional seven residue polyglutamine tract at the C-terminus (httNTQ7). At a peptide-to-lipid molar ratio of 1:4, the population of peptide bound to the SUV surface is substantial, ∼ 7-8%, while exchange between the free and SUV-bound peptide is slow on the relaxation time-scale ( kex ∼ 200 s-1). The last two C-terminal residues of httNT and the last 9 of httNTQ7 remain flexible in the SUV-bound form due to transient detachment from the lipid surface that occurs on a time-scale several-fold faster than binding.

Search for invisible decays of ω and ϕ with J/ψ data at BESIII

Using a data sample of $(1310.6 \pm 7.0)\times 10^6$ $J/\psi$ events collected with the BESIII detector operating at the BEPCII collider, we perform the first experimental search for invisible decays of a light vector meson ($V=\omega,\phi$) via $J/\psi \to V \eta$ decays. The decay of $\eta \to \pi^+\pi^-\pi^0$ is utilized to tag the $V$ meson decaying into the invisible final state. No evidence for a significant invisible signal is observed, and the upper limits on the ratio of branching fractions at the 90\% confidence level are determined to be $\frac{\mathcal{B}(\omega \rightarrow \rm{invisible})}{\mathcal{B}(\omega \to \pi^+\pi^-\pi^0)} < 8.1 \times 10^{-5}$ and $\frac{\mathcal{B}(\phi \to \rm{invisible})}{\mathcal{B}(\phi \to K^+K^-)} < 3.4\times 10^{-4}$. By using the world average values of $\mathcal{B}(\omega \to \pi^+\pi^-\pi^0)$ and $\mathcal{B}(\phi\to K^+K^-)$, the upper limits on the decay branching fractions at the $90\%$ confidence level are set as $\mathcal{B}(\omega \to \rm{invisible})< 7.3 \times 10^{-5}$ and $\mathcal{B}(\phi \to \rm{invisible})< 1.7\times 10^{-4}$, respectively.

Primary Gastric Small Cell Carcinoma: A Case Identified as a Large Subepithelial Tumor from Invisible State in 6 Months.

Primary gastric small cell carcinoma (GSCC) is one of the gastroenteropancreatic neuroendocrine tumors. It is a rare cancer with a very aggressive behavior and a poor prognosis because of the high rate of metastases. It is usually found in far advanced stage. We experienced a case of GSCC which had developed into a large subepithelial tumor (SET) from invisible state in a short period. A 65-year-old man consulted our hospital because of early gastric cancer. He underwent endoscopic submucosal dissection for the early gastric cancer at high body posterior wall. After 6 months, the follow-up endoscopy showed a large newly developed SET-like lesion with central ulceration at the gastric cardia. Endoscopic biopsy revealed GSCC. Total gastrectomy was performed. One out of the 26 perigastric lymph nodes had a metastasis. He received 6 cycles of adjuvant chemotherapy with etoposide and cisplatin. He is still in good health 12 months after operation.

Polar domain structural evolution under electric field and temperature in the (Bi0.5Na0.5)TiO3‐0.06BaTiO3 piezoceramics

AbstractLead‐free bismuth sodium titanate and related compounds are of great interest as promising candidates for piezoelectric applications. However, the full understanding of this family of materials is still a challenge partly because of their structural complexity and different behaviors with or without the application of an external electric field. Here, piezoresponse force microscopy is used to gain insight into the mesoscopic‐scale domain structure of the morphotropic phase boundary (MPB) composition of (1‐x)Bi0.5Na0.5TiO3‐xBaTiO3 solid solution at x = 0.06 (abbreviated as BNT‐6BT). The evolution of the domains with the changes of the electric field and temperature has been thoroughly examined in conjunction with the crystal structure analysis and dielectric studies. It is found that ferroelectric domains with size of hundreds of nanometers are embedded in a relaxor state without visible domains on a mesoscopic scale, which are considered to contribute to the tetragonal and cubic phases in the material, respectively. Temperature‐independent domain configuration is observed in the unpoled sample from room temperature to 200°C. While, temperature‐dependent domain configuration is observed in the poled sample. The homogenously poled state breaks into the mixed domain configuration containing polydomain structure and invisible state around the so‐called depoling temperature. The structural changes on different length scales are also discussed. This work provides an in‐depth understanding of the structural and domain changes under an electric field and the temperature‐dependent domain evolution in both unpoled and poled states in the BNT‐BT solid solution of the MPB composition.

NMR probing of invisible excited states using selectively labeled RNAs.

Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion NMR experiments are invaluable for probing sparsely and transiently populated biomolecular states that cannot be directly detected by traditional NMR experiments and that are invisible by other biophysical approaches. A notable gap for RNA is the absence of CPMG experiments for measurement of methine base 1H and methylene C5' chemical shifts of ribose moieties in the excited state, partly because of complications from homonuclear 13C-13C scalar couplings. Here we present site-specific 13C labeling that makes possible the design of pulse sequences for recording accurate 1H-13C MQ and SQ CPMG experiments for ribose methine H1'-C1' and H2'-C2', base and ribose 1H CPMG, as well as a new 1H-13C TROSY-detected methylene (CH2) C5' CPMG relaxation pulse schemes. We demonstrate the utility of these experiments for two RNAs, the A-Site RNA known to undergo exchange and the IRE RNA suspected of undergoing exchange on microseconds to millisecond time-scale. We anticipate the new labeling approaches will facilitate obtaining structures of invisible states and provide insights into the relevance of such states for RNA-drug interactions.

Exploring methods to expedite the recording of CEST datasets using selective pulse excitation

Chemical Exchange Saturation Transfer (CEST) has emerged as a powerful tool for studies of biomolecular conformational exchange involving the interconversion between a major, visible conformer and one or more minor, invisible states. Applications typically entail recording a large number of 2D datasets, each of which differs in the position of a weak radio frequency field, so as to generate a CEST profile for each nucleus from which the chemical shifts of spins in the invisible state(s) are obtained. Here we compare a number of band-selective CEST schemes for speeding up the process using either DANTE or cosine-modulated excitation approaches. We show that while both are essentially identical for applications such as 15N CEST, in cases where the probed spins are dipolar or scalar coupled to other like spins there can be advantages for the cosine-excitation scheme.

Resolving biomolecular motion and interactions by R2 and R1ρ relaxation dispersion NMR.

Among the tools of structural biology, NMR spectroscopy is unique in that it not only derives a static three-dimensional structure, but also provides an atomic-level description of the local fluctuations and global dynamics around this static structure. A battery of NMR experiments is now available to probe the motions of proteins and nucleic acids over the whole biologically relevant timescale from picoseconds to hours. Here we focus on one of these methods, relaxation dispersion, which resolves dynamics on the micro- to millisecond timescale. Key biological processes that occur on this timescale include enzymatic catalysis, ligand binding, and local folding. In other words, relaxation-dispersion-resolved dynamics are often closely related to the function of the molecule and therefore highly interesting to the structural biochemist. With an astounding sensitivity of ∼0.5%, the method detects low-population excited states that are invisible to any other biophysical method. The kinetics of the exchange between the ground state and excited states are quantified in the form of the underlying exchange rate, while structural information about the invisible excited state is obtained in the form of its chemical shift. Lastly, the population of the excited state can be derived. This diversity in the information that can be obtained makes relaxation dispersion an excellent method to study the detailed mechanisms of conformational transitions and molecular interactions. Here we describe the two branches of relaxation dispersion, R2 and R1ρ, discussing their applicability, similarities, and differences, as well as recent developments in pulse sequence design and data processing.

Natural history data for young subjects with Sanfilippo syndrome type B (MPS IIIB)

Among the tools of structural biology, NMR spectroscopy is unique in that it not only derives a static three-dimensional structure, but also provides an atomic-level description of the local fluctuations and global dynamics around this static structure. A battery of NMR experiments is now available to probe the motions of proteins and nucleic acids over the whole biologically relevant timescale from picoseconds to hours. Here we focus on one of these methods, relaxation dispersion, which resolves dynamics on the micro- to millisecond timescale. Key biological processes that occur on this timescale include enzymatic catalysis, ligand binding, and local folding. In other words, relaxation-dispersion-resolved dynamics are often closely related to the function of the molecule and therefore highly interesting to the structural biochemist. With an astounding sensitivity of ∼0.5%, the method detects low-population excited states that are invisible to any other biophysical method. The kinetics of the exchange between the ground state and excited states are quantified in the form of the underlying exchange rate, while structural information about the invisible excited state is obtained in the form of its chemical shift. Lastly, the population of the excited state can be derived. This diversity in the information that can be obtained makes relaxation dispersion an excellent method to study the detailed mechanisms of conformational transitions and molecular interactions. Here we describe the two branches of relaxation dispersion, R2 and R1ρ, discussing their applicability, similarities, and differences, as well as recent developments in pulse sequence design and data processing.

Міфологія рахування: концепти «четвертий» і «п’ятий» у традиційній картині світу слов’ян (на матеріалі лікувально-обрядових текстів)

Introduction . The subject of the space mythology is an important part of the mythological picture of the world, which explains the existence of different concepts of interpretation of its semantics and confirms the relevance of the problem studied. Purpose . Unlike other numbers, the mythology of the semantic pair of “four-five” has not been practically studied. In some articles, there are only fragmentary references to the meaning of these numbers in the mythological picture of the world of the Slavs. The study of the mythology of the number is a difficult task, so it is advisable to divide this issue into separate parts. In this aspect, the symbols of geometric figures, in particular the “circle”, “rectangle” and “angle”, make a special interest. Results . In the mythological picture of the world, the “four” is the numerical equivalent of Claude Levi-Strauss’ “wild / domestic” opposition, as evidenced by the parameters of natural and cultural objects, particularly rounded shapes of trees, lakes, mountains, and rectangular outlines of fields, buildings, and household objects. Association of “cultural” and therefore “correct”, “reliable”, and “wild” - “irregular” and “conflict”, explains semantic logic of dual rites of protection and expulsion of the disease. In the “four sides” protection there is a concentration of force in the centre, which explains the symbols of the cross, icon, and ritual rectangular objects. Instead, the expulsion is accompanied by the rejection of “alien” / “harmful” with further “worldwide” distribution / sending “to the four winds”. In contrast to the “space” four, the number “five” is associated with time, as indicated by the five phases of the moon, four of which are visible, and the one is invisible. Invisible state brings down the image of the moon, and hence the five, to the other world. In this case, the five seems to “dematerialize” the four, because it involves the existence of an invisible reality, mixed with transformational and transitive processes. Hence the five objects in protective rites are used as attributes of not destruction, but disappearance of the antagonist, its transition / return to the invisible state. The boundary characteristics of the five put it in line with other transitional numbers - seven and twelve, indicating the completeness of the lunar and solar cycles. The invisible state of the fifth element, its association with darkness and death, allows changing the quality of an object, turning it into new, sometimes opposite forms (a wolf turns into a lynx, just as an old man becomes a young one). It is possible that this is the Christian interpretation of the five, which becomes the symbol of the resurrection. The semantics of the number “five” is important as well in organizing the mythological picture of the world as a sign of a four-dimensional space with a fixed fifth centre. Hence, the five-member organization of sacred buildings, for example pagan pantheons, which visually resemble a pentagram, or residential rectangular spaces with centre in the middle.

Witnessing Trauma through Discordant Chronology of Words in Yvonne Vera’s Under the Tongue

Yvonne Vera is a reformist writer of Zimbabwe who agitated the society to attend to serious issues in the life of a Zimbabwean woman. This paper will examine Yvonne Vera’s Under the Tongue in which representations of language of monologue contribute to the creation of an atmosphere in which the pain of female body is obviously felt. The legacies of colonialism and strategic policies of nationalism collaborate to facilitate the vulnerability of women thus contributing to their violation of rights and victimisation. It is a metaphorical representation of female resistance against violent male Zimbabwean society. The trauma of the victim is thoughtfully integrated into linguistic and symbolic systems aesthetically created by the writer. Using the discordant chronology of words of the female protagonist, Vera stylistically identifies the silence of a girl who is captive of flashbacks and intrusive thoughts but struggles to liberate herself from the discourse of pain. Restoration of confidence does take place with the power of language. By articulating a private experience of a victimised young girl, the writer reclaims the essential power of women’s speech and silences in the context of gendered nationalist ideology where sacrifices of women have been reduced to an invisible state by historiographers.

Opening up the Design Space of Neurofeedback Brain--Computer Interfaces for Children

Brain--computer interface applications (BCIs) utilizing neurofeedback (NF) can make invisible brain states visible in real time. Learning to recognize, modify, and regulate brain states is critical to all children's development and can improve learning, and emotional and mental health outcomes. How can we design usable and effective NF BCIs that help children learn and practice brain state self-regulation? Our contribution is a list of challenges for this emerging design space and a conceptual framework that addresses those challenges. The framework is composed of five interrelated strong concepts that we adapted from other design spaces. We derived the concepts reflectively, theoretically, and empirically through a design research process in which we created and evaluated a NF BCI, called Mind-Full , designed to help children living in Nepal who had suffered from complex trauma learn to self-regulate anxiety and attention. We add rigor to our derivation methodology by horizontally and vertically grounding our concepts, that is, relating them to similar concepts in the literature and instantiations in other artifacts. We illustrate the generative power of the concepts and the inter-relationships between them through the description of two new NF BCIs we created using the framework for urban and indigenous children with anxiety and attentional challenges. We then show the versatility of our framework by describing how it inspired and informed the conceptual design of three NF BCIs for different types of self-regulation: selective attention and working memory, pain management, and depression. Last, we discuss the contestability, defensibility, and substantiveness of our conceptual framework in order to ensure rigor in our research design process. Our contribution is a rigorously derived design framework that opens up this new and emerging design space of NF BCI's for children for other researchers and designers.

Exact solution of a classical short-range spin model with a phase transition in one dimension: The Potts model with invisible states

We present the exact solution of the 1D classical short-range Potts model with invisible states. Besides the q states of the ordinary Potts model, this possesses r additional states which contribute to the entropy, but not to the interaction energy. We determine the partition function, using the transfer-matrix method, in the general case of two ordering fields: h1 acting on a visible state and h2 on an invisible state. We analyse its zeros in the complex-temperature plane in the case that h1=0. When Imh2=0 and r≥0, these zeros accumulate along a line that intersects the real temperature axis at the origin. This corresponds to the usual “phase transition” in a 1D system. However, for Imh2≠0 or r<0, the line of zeros intersects the positive part of the real temperature axis, which signals the existence of a phase transition at non-zero temperature.

Prospects for rare and forbidden hyperon decays at BESIII

The study of hyperon decays at the Beijing Electron Spectrometer III (BESIII) is proposed to investigate the events of J/ψ decay into hyperon pairs, which provide a pristine experimental environment at the Beijing Electron–Positron Collider II. About 106–108 hyperons, i.e., Λ, Σ, Ξ, and Ω, will be produced in the J/ψ and ψ(2S) decays with the proposed data samples at BESIII. Based on these samples, the measurement sensitivity of the branching fractions of the hyperon decays is in the range of 10−5–10−8. In addition, with the known center-of-mass energy and “tag technique”, rare decays and decays with invisible final states can be probed.

Detection and imaging of thermochromic ink compounds in erasable pens using desorption electrospray ionization mass spectrometry.

Thermochromic ink pens are widely accessible worldwide and have gained popularity among the general public. These pens are very useful to undo mistakes while writing important documents or exams. They are also, however, misused in committing crimes such as counterfeiting checks or wills. Thus, the forensics community is in need of techniques that will allow these forgeries to be detected rapidly, reliably and conveniently. Thermochromic ink compounds were investigated using Desorption Electrospray Ionization (DESI) coupled with an LTQ mass spectrometer and Thin-Layer Chromatography (TLC). Tandem mass spectrometric analysis was conducted using Electrospray Ionization (ESI) coupled with an Orbitrap LTQ mass spectrometer performing Collision-Induced Dissociation (CID) for identification of ink traces. Chemical marker ions characteristic of the state of ink (visible or invisible) were identified and mapped in ink traces by the use of DESI-MS imaging. These ions can be employed by forensic experts as fingerprint markers in forged documents. The marker ions were also characterised by conducting tandem mass spectrometry using paper spray in an Orbitrap LTQ mass spectrometer. Specific chemical components yielding ions of m/z 400, 405, 615 and 786 were distinguished as only being apparent in the invisible and reappeared state of the ink. The absence of these compounds in the original state of the ink enabled their recognition as useful chemical determinants in detecting forgery. DESI-MSI was thus shown to be a very useful, convenient and reliable technique for detecting forgery in paper documents due to its fast and reproducible mode of analysis, with no sample preparation and minimal damage to the document under investigation. Copyright © 2017 John Wiley & Sons, Ltd.

Molecular Cross-Talk between Nonribosomal Peptide Synthetase Carrier Proteins and Unstructured Linker Regions.

Nonribosomal peptide synthetases (NRPSs) employ multiple domains separated by linker regions to incorporate substrates into natural products. During synthesis, substrates are covalently tethered to carrier proteins that translocate between catalytic partner domains. The molecular parameters that govern translocation and associated linker remodeling remain unknown. Here, we used NMR to characterize the structure, dynamics, and invisible states of a peptidyl carrier protein flanked by its linkers. We showed that the N-terminal linker stabilizes and interacts with the protein core while modulating dynamics at specific sites involved in post-translational modifications and/or domain interactions. The results detail the molecular communication between peptidyl carrier proteins and their linkers and could guide efforts in engineering NRPSs to obtain new pharmaceuticals.

Cross section and Higgs mass measurement with Higgsstrahlung at the CEPC **Supported by the Joint Funds of the NSFC (U1232105) and CAS Hundred Talent Program (Y3515540U1)

The Circular Electron Positron Collider (CEPC) is a future Higgs factory proposed by the Chinese high energy physics community. It will operate at a center-of-mass energy of 240–250 GeV. The CEPC will accumulate an integrated luminosity of 5 ab−1 over ten years of operation, producing one million Higgs bosons via the Higgsstrahlung and vector boson fusion processes. This sample allows a percent or even sub-percent level determination of the Higgs boson couplings. With GEANT4-based full simulation and a dedicated fast simulation tool, we have evaluated the statistical precisions of the Higgstrahlung cross section σZH and the Higgs mass mH measurement at the CEPC in the Z → μ+μ− channel. The statistical precision of σZH (mH) measurement could reach 0.97% (6.9 MeV) in the model-independent analysis which uses only the information from Z boson decays. For the standard model Higgs boson, the mH precision could be improved to 5.4 MeV by including the information from Higgs decays. The impact of the TPC size on these measurements is investigated. In addition, we studied the prospect of measuring the Higgs boson decaying into invisible final states at the CEPC. With the Standard Model ZH production rate, the upper limit of could reach 1.2% at 95% confidence level.

Search for D0 decays to invisible final states at Belle

We report the result from the first search for $D^0$ decays to invisible final states. The analysis is performed on a data sample of 924 $\rm{fb}^{-1}$ collected at and near the $\Upsilon(4S)$ and $\Upsilon(5S)$ resonances with the Belle detector at the KEKB asymmetric-energy $e^{+}e^{-}$ collider. The absolute branching fraction is determined using an inclusive $D^0$ sample, obtained by fully reconstructing the rest of the particle system including the other charmed particle. No significant signal yield is observed and an upper limit of $9.4\times 10^{-5}$ is set on the branching fraction of $D^0$ to invisible final states at 90\% confidence level.