Development of an FeII Complex Exhibiting Intermolecular Proton Shifting Coupled Spin Transition.

In this study, we investigated reversible intermolecular proton shifting (IPS) coupled with spin transition (ST) in a novel FeII complex. The host FeII complex and the guest carboxylic acid anion were connected by intermolecular hydrogen bonds (IHBs). We extended the intramolecular proton transfer coupled ST phenomenon to the intermolecular system. The dynamic phenomenon was confirmed by variable-temperature single-crystal X-ray diffraction, neutron crystallography, and infrared spectroscopy. The mechanism of IPS was further validated using density functional theory calculations. The discovery of IPS-coupled ST in crystalline molecular materials provides good insights into fundamental processes and promotes the design of novel multifunctional materials with tunable properties for various applications, such as optoelectronics, information storage, and molecular devices.

Phase Separation and Aggregation of α-Synuclein Diverge at Different Salt Conditions.

The coacervation and structural rearrangement of the protein alpha-synuclein (αSyn) into cytotoxic oligomers and amyloid fibrils are considered pathological hallmarks of Parkinson's disease. While aggregation is recognized as the key element of amyloid diseases, liquid-liquid phase separation (LLPS) and its interplay with aggregation have gained increasing interest. Previous work showed that factors promoting or inhibiting amyloid formation have similar effects on phase separation. Here, we provide a detailed scanning of a wide range of parameters including protein, salt and crowding concentrations at multiple pH values, revealing different salt dependencies of aggregation and phase separation. The influence of salt on aggregation under crowded conditions follows a non-monotonic pattern, showing increased effects at medium salt concentrations. This behavior can be elucidated through a combination of electrostatic screening and salting-out effects on the intramolecular interactions between the N-terminal and C-terminal regions of αSyn. By contrast, we find a monotonic salt dependence of phase separation due to the intermolecular interaction. Furthermore, we observe the time evolution of the two distinct assembly states, with macroscopic fibrillar-like bundles initially forming at medium salt concentration but subsequently converting into droplets after prolonged incubation. The droplet state is therefore capable of inhibiting aggregation or even dissolving the aggregates through a variety of heterotypic interactions, thus preventing αSyn from its dynamically arrested state.

Photo-induced valence tautomerism and polarization switching in mononuclear cobalt complexes with an enantiopure chiral ligand.

Light-induced polarization switchable molecular materials have attracted attention for decades owing to their potential remote manipulation and ultrafast responsiveness. Here we report a valence tautomeric (VT) complex with an enantiopure chiral ligand. By a suitable choice of counter anions, a significant improvement in photoconversion has been demonstrated, leading to novel photo-responsive polarization switching materials.

Electrically Detectable Photoinduced Polarization Switching in a Molecular Prussian Blue Analogue.

Light, a nondestructive and remotely controllable external stimulus, effectively triggers a variety of electron-transfer phenomena in metal complexes. One prime example includes using light in molecular cyanide-bridged [FeCo] bimetallic Prussian blue analogues, where it switches the system between the electron-transferred metastable state and the system's ground state. If this process is coupled to a ferroelectric-type phase transition, the generation and disappearance of macroscopic polarization, entirely under light control, become possible. In this research, we successfully executed a nonpolar-to-polar phase transition in a trinuclear cyanide-bridged [Fe2Co] complex crystal via directional electron transfer. Intriguingly, by exposing the crystal to the wavelength of light─785 nm─without any electric field─we can drive this ferroelectric phase transition to completely depolarize the crystal, during which a measurable electric current response can be detected. These discoveries signify an important step toward the realization of fully light-controlled ferroelectric memory devices.

Magnetoelectricity Enhanced by Electron Redistribution in a Spin Crossover [FeCo] Complex.

Molecular-based magnetoelectric materials are among the most promising materials for next-generation magnetoelectric memory devices. However, practical application of existing molecular systems has proven difficult largely because the polarization change is far lower than the practical threshold of the ME memory devices. Herein, we successfully obtained an [FeCo] dinuclear complex that exhibits a magnetic field-induced spin crossover process, resulting in a significant polarization change of 0.45 µC cm-2. Mössbauer spectroscopy and theoretical calculations suggest that the asymmetric structural change, coupled with electron redistribution, leads to the observed polarization change. Our approach provides a new strategy toward rationally enhancing the polarization change.

Integrative epigenome profiling of 47XXY provides insights into whole genomic DNA hypermethylation and active chromatin accessibility.

Klinefelter syndrome (KS, 47XXY) is a disorder characterized by sex chromosomal aneuploidy, which may lead to changes in epigenetic regulations of gene expression. To define epigenetic architectures in 47XXY, we annotated DNA methylation in euploid males (46XY) and females (46XX), and 47XXY individuals using whole genome bisulfite sequencing (WGBS) and integrated chromatin accessbilty, and detected abnormal hypermethylation in 47XXY. Furthermore, we detected altered chromatin accessibility in 47XXY, in particular in chromosome X, using Assay for Transposase-Accessible Chromatin sequencing (ATAC-seq) in cultured amniotic cells. Our results construct the whole genome-wide DNA methylation map in 47XXY, and provide new insights into the early epigenomic dysregulation resulting from an extra chromosome X in 47XXY.

Interpreting Transient Interactions of Intrinsically Disordered Proteins.

The flexible nature of intrinsically disordered proteins (IDPs) gives rise to a conformational ensemble with a diverse set of conformations. The simplest way to describe this ensemble is through a homopolymer model without any specific interactions. However, there has been growing evidence that the conformational properties of IDPs and their relevant functions can be affected by transient interactions between specific and even nonlocal pairs of amino acids. Interpreting these interactions from experimental methods, each of which is most sensitive to a different distance regime referred to as probing length, remains a challenging and unsolved problem. Here, we first show that transient interactions can be realized between short fragments of charged amino acids by generating conformational ensembles using model disordered peptides and coarse-grained simulations. Using these ensembles, we investigate how sensitive different types of experimental measurements are to the presence of transient interactions. We find methods with shorter probing lengths to be more appropriate for detecting these transient interactions, but one experimental method is not sufficient due to the existence of other weak interactions typically seen in IDPs. Finally, we develop an adjusted polymer model with an additional short-distance peak which can robustly reproduce the distance distribution function from two experimental measurements with complementary short and long probing lengths. This new model can suggest whether a homopolymer model is insufficient for describing a specific IDP and meets the challenge of quantitatively identifying specific, transient interactions from a background of nonspecific, weak interactions.

Relative survival analysis of gynecological cancers in an urban district of Shanghai during 2002-2013.

OBJECTIVE: Appraisal of cancer survival is essential for cancer control, but studies related to gynecological cancer are scarce. Using cancer registration data, we conducted an in-depth survival analysis of cervical, uterine corpus, and ovarian cancers in an urban district of Shanghai during 2002-2013. MATERIALS AND METHODS: The follow-up data of gynecological cancer from the Changning District of Shanghai, China, were used to estimate the 1-5-year observed survival rate (OSR) and relative survival rate (RSR) by time periods and age groups during 2002-2013. Age-standardized relative survival rates estimated by the international cancer survival standards were calculated during 2002-2013 to describe the prognosis of cervical, uterine corpus, and ovarian cancers among women in the district. RESULTS: In total, 1307 gynecological cancer cases were included in the survival analysis in the district during 2002-2013. Among gynecological cancers, the 5-year OSRs and RSRs of uterine corpus cancer were highest (5-year OSR 84.40%, 5-year RSR 87.67%), followed by those of cervical cancer (5-year OSR 73.58%, 5-year RSR 75.91%), and those of ovarian cancer (5-year OSR 53.89%, 5-year RSR 55.90%). After age adjustment, the 5-year relative survival rates of three gynecological cancers were 71.23%, 80.11%, and 43.27%, respectively. CONCLUSION: The 5-year relative survival rate did not show a systematic temporal trend in cervical cancer, uterine cancer, or ovarian cancer. The prognosis in elderly patients was not optimistic, and this needs a more advanced strategy for early diagnosis and treatment. The age structure of gynecological cancer patients in the district tended to be younger than the standardized age, which implies that more attention to the guidance and health education for the younger generation is needed.

Biophysical and Integrative Characterization of Protein Intrinsic Disorder as a Prime Target for Drug Discovery.

Protein intrinsic disorder is increasingly recognized for its biological and disease-driven functions. However, it represents significant challenges for biophysical studies due to its high conformational flexibility. In addressing these challenges, we highlight the complementary and distinct capabilities of a range of experimental and computational methods and further describe integrative strategies available for combining these techniques. Integrative biophysics methods provide valuable insights into the sequence-structure-function relationship of disordered proteins, setting the stage for protein intrinsic disorder to become a promising target for drug discovery. Finally, we briefly summarize recent advances in the development of new small molecule inhibitors targeting the disordered N-terminal domains of three vital transcription factors.

Incorporation of D2O-Induced Fluorine Chemical Shift Perturbations into Ensemble-Structure Characterization of the ERalpha Disordered Region.

Structural characterization of intrinsically disordered proteins (IDPs) requires a concerted effort between experiments and computations by accounting for their conformational heterogeneity. Given the diversity of experimental tools providing local and global structural information, constructing an experimental restraint-satisfying structural ensemble remains challenging. Here, we use the disordered N-terminal domain (NTD) of the estrogen receptor alpha (ERalpha) as a model system to combine existing small-angle X-ray scattering (SAXS) and hydroxyl radical protein footprinting (HRPF) data and newly acquired solvent accessibility data via D2O-induced fluorine chemical shifting (DFCS) measurements. A new set of DFCS data for the solvent exposure of a set of 12 amino acid positions were added to complement previously acquired HRPF measurements for the solvent exposure of the other 16 nonoverlapping amino acids, thereby improving the NTD ensemble characterization considerably. We also found that while choosing an initial ensemble of structures generated from a different atomic-level force field or sampling/modeling method can lead to distinct contact maps even when the same sets of experimental measurements were used for ensemble-fitting, comparative analyses from these initial ensembles reveal commonly recurring structural features in their ensemble-averaged contact map. Specifically, nonlocal or long-range transient interactions were found consistently between the N-terminal segments and the central region, sufficient to mediate the conformational ensemble and regulate how the NTD interacts with its coactivator proteins.

Incorporating second-tier genetic screening for multiple acyl-CoA dehydrogenase deficiency.

BACKGROUND: Newborn screening (NBS) for multiple acyl-CoA dehydrogenase deficiency (MADD) has poor sensitivity. This study aimed to evaluate the feasibility of incorporating second-tier genetic screening for MADD. METHODS: A total of 453,390 newborns were screened for inherited metabolic disorders using tandem mass spectrometry from January 2017 to May 2022. A matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) assay was developed to identify 23 common ETFDH variants and used for second-tier screening of MADD. RESULTS: Overall, 185 newborns with suspected MADD received second-tier genetic screening. Thirty-three (17.8 %) newborns with positive results, of which 7 were homozygotes, 5 were compound heterozygotes, 21 were heterozygotes. Further genetic analysis revealed that 6 of the 21 newborns had a second ETFDH variant. Therefore, 18 patients were finally diagnosed with MADD, with a positive predictive value of 9.73 %. The detection rate and diagnostic rate of MALDI-TOF MS assay were 83.33 % and 66.67 %, respectively. Thus the incidence of MADD in our population was estimated at 1:25,188. Nine different ETFDH variants were identified in MADD patients. The most common ETFDH variant being c.250G > A with an allelic frequency of 47.22 %, followed by c.524G > A (13.89 %) and c.998A > G (13.89 %). All patients had elevation of multiple acylcarnitines at NBS. However, seven patients had normal acylcarnitine levels and two patients showed mild elevation of only two acylcarnitines during the recall review. CONCLUSION: We have established a high throughput MALDI-TOF MS assay for MADD screening. Half of the MADD patients would not be detected under conventional screening protocols. Incorporating second-tier genetic screening into the current NBS could improve the performance of MADD NBS.

Macroscopic Polarization Change of Mononuclear Valence Tautomeric Cobalt Complexes Through the Use of Enantiopure Ligand.

The crystallization of a complex having electron transfer properties in a polar space group can induce the polarization switching of a crystal in a specific direction, which is attractive for the development of sensors, memory devices, and capacitors. Unfortunately, the probability of crystallization in a polar space group is usually low. Noticing that enantiopure compounds crystallize in Sohncke space groups, this paper reports a strategy for the molecular design of non-ferroelectric polarization switching crystals based on the use of intramolecular electron transfer and chirality. In addition, this paper describes the synthesis of a mononuclear valence tautomeric (VT) cobalt complex bearing an enantiopure ligand. The introduction of enantiomer enables the crystallization of the complex in the polar space group (P21 ). The polarization of the crystals along the b-axis direction is not canceled out and the VT transition is accompanied by a change in the macroscopic polarization of the polar crystal. Polarization switching via electron transfer is realized at around room temperature.

Incidence, Mortality Features and Lifetime Risk Estimation of Digestive Tract Cancers in an Urban District of Shanghai, China.

Digestive tract cancers are the common cause of cancer deaths in both China and worldwide. This study aimed to describe the burden, recent trends and lifetime risks in the incidence and mortality of digestive tract cancers in an urban district of Shanghai, China. Our study extracted data on stomach, colon, rectum and liver cancers diagnosed in Changning District between 2010 and 2019 from the Shanghai Cancer Registry. We calculated age-standardized incidence and mortality rates, the risks of developing and dying from cancer, and the estimated annual percent changes. Between 2010 and 2019, 8619 new cases and 5775 deaths were registered with digestive tract cancers in the district. The age-standardized incidence rates (ASIRs) of liver cancer decreased steadily, whereas the ASIRs of stomach, colon and rectum cancers remained stable from 2010 to 2019. The age-standardized mortality rates (ASMRs) of stomach and liver cancers showed significant declining changes from 2010 to 2019 in both sexes, but that of colon and rectum cancers remained stable during the entire period. The risks of developing and dying from digestive tract cancers were substantially higher in men than women. The burden of digestive tract cancer and its disparities between sex and age group remain major public health challenges in urban Shanghai. To reduce the burden of digestive tract cancers, the government and researchers should develop and promote a healthy diet, organize a screening, and reduce the prevalence of smoking, alcohol drinking, and hepatitis B virus and hepatitis C virus infections.

Multiscale Transcriptomic Integration Reveals B-Cell Depletion and T-Cell Mistrafficking in Nasopharyngeal Carcinoma Progression.

Nasopharyngeal carcinoma (NPC), featured by Epstein-Barr virus (EBV) infection and regional epidemiology, is curable when detected early, but highly lethal at an advanced stage. The molecular mechanism of NPC progression toward a clinically uncontrollable stage remains elusive. In this study, we developed a novel computational framework to conduct multiscale transcriptomic analysis during NPC progression. The framework consists of four modules enabling transcriptomic analyses spanning from single-cell, bulk, microenvironment, to cohort scales. The bulk-transcriptomic analysis of 133 NPC or normal samples unraveled leading functional enrichments of cell-cycle acceleration, epithelial-mesenchymal transition, and chemokine-modulated inflammatory response during NPC progression. The chemokine CXCL10 in the NPC microenvironment, discovered by single-cell RNA sequencing data analysis, recruits cytotoxic T cells through interacting with its receptor CXCR3 at early but late stages. This T-cell mistrafficking was featured by the decline of cytotoxic T cells and the increase of regulatory T cells, accompanied with B-cell depletion confirmed by immunohistochemistry staining. The featured immunomodulatory chemokines were commonly upregulated in the majority of cancers associated with viral or bacterial infections.

Multivariate effects of pH, salt, and Zn2+ ions on Aß40 fibrillation.

Amyloid-ß (Aß) peptide aggregation plays a central role in the progress of Alzheimer's disease (AD), of which Aß-deposited extracellular amyloid plaques are a major hallmark. The brain micro-environmental variation in AD patients, like local acidification, increased ionic strength, or changed metal ion levels, cooperatively modulates the aggregation of the Aß peptides. Here, we investigate the multivariate effects of varied pH, ionic strength and Zn2+ on Aß40 fibrillation kinetics. Our results reveal that Aß fibrillation kinetics are strongly affected by pH and ionic strength suggesting the importance of electrostatic interactions in regulating Aß40 fibrillation. More interestingly, the presence of Zn2+ ions can further alter or even reserve the role of pH and ionic strength on the amyloid fibril kinetics, suggesting the importance of amino acids like Histidine that can interact with Zn2+ ions. Both pH and ionic strength regulate the secondary nucleation processes, however regardless of pH and Zn2+ ions, ionic strength can also modulate the morphology of Aß40 aggregates. These multivariate effects in bulk solution provide insights into the correlation of pH-, ionic strength- or Zn2+ ions changes with amyloid deposits in AD brain and will deepen our understanding of the molecular pathology in the local brain microenvironment.

Proteomics analysis of the effects for different salt ions in leaves of true halophyte Sesuvium portulacastrum.

Sesuvium portulacastrum is a true halophyte and shows an optimal development under moderate salinity with large amounts of salt ions in its leaves. However, the specific proteins in response to salt ions are remained unknown. In this study, comparative physiological and proteomic analyses of different leaves subject to NaCl, KCl, NaNO3 and KNO3 were performed. Chlorophyll content was decreased under the above four kinds of salt treatments. Starch and soluble sugar contents changed differently under different salt treatments. A total of 53 differentially accumulated proteins (DAPs) were identified by mass spectrometry. Among them, 13, 25, 26 and 25 DAPs were identified after exposure to KCl, NaCl, KNO3, and NaNO3, respectively. These DAPs belong to 47 unique genes, and 37 of them are involved in protein-protein interactions. These DAPs displayed different expression patterns after treating with different salt ions. Functional annotation revealed they are mainly involved in photosynthesis, carbohydrate and energy metabolism, lipid metabolism, and biosynthesis of secondary metabolites. Genes and proteins showed different expression profiles under different salt treatments. Enzyme activity analysis indicated P-ATPase was induced by KCl, NaCl and NaNO3, V-ATPase was induced by KCl and NaCl, whereas V-PPase activity was significantly increased after application of KNO3, but sharply inhibited by NaCl. These results might deepen our understanding of responsive mechanisms in the leaves of S. portulacastrum upon different salt ions.

Diffusion of a disordered protein on its folded ligand.

Intrinsically disordered proteins often form dynamic complexes with their ligands. Yet, the speed and amplitude of these motions are hidden in classical binding kinetics. Here, we directly measure the dynamics in an exceptionally mobile, high-affinity complex. We show that the disordered tail of the cell adhesion protein E-cadherin dynamically samples a large surface area of the protooncogene ß-catenin. Single-molecule experiments and molecular simulations resolve these motions with high resolution in space and time. Contacts break and form within hundreds of microseconds without a dissociation of the complex. The energy landscape of this complex is rugged with many small barriers (3 to 4 kBT) and reconciles specificity, high affinity, and extreme disorder. A few persistent contacts provide specificity, whereas unspecific interactions boost affinity.

Quantitative NMR Study of Insulin-Degrading Enzyme Using Amyloid-ß and HIV-1 p6 Elucidates Its Chaperone Activity.

Insulin-degrading enzyme (IDE) hydrolyzes monomeric polypeptides, including amyloid-ß (Aß) and HIV-1 p6. It also acts as a nonproteolytic chaperone to prevent Aß polymerization. Here we compare interactions of Aß and non-amyloidogenic p6 with IDE. Although both exhibited similar proteolysis rates, the binding kinetics to an inactive IDE characterized using relaxation-based NMR were remarkably different. IDE and Aß formed a sparsely populated complex with a lifetime of milliseconds in which a short hydrophobic cleavage segment of Aß was anchored to IDE. Strikingly, a second and more stable complex was significantly populated with a subsecond lifetime owing to multiple intermolecular contacts between Aß and IDE. By selectively sequestering Aß in this nonproductive complex, IDE likely increases the critical concentration required for fibrillization. In contrast, IDE and p6 formed a transient, submillisecond complex involving a single anchoring p6 motif. Modulation of intermolecular interactions, thus, allows IDE to differentiate between non-amyloidogenic and amyloidogenic substrates.

Salt-Dependent Conformational Changes of Intrinsically Disordered Proteins.

The flexible structure of an intrinsically disordered protein (IDP) is known to be perturbed by salt concentrations, which can be understood by electrostatic screening on charged amino acids. However, an IDP usually contains more uncharged residues that are influenced by the salting-out effect. Here we have parametrized the salting-out effect into a coarse-grained model using a set of Förster resonance energy transfer data and verified with experimental salt-dependent liquid-liquid phase separation (LLPS) of 17 proteins. The new model can correctly capture the behavior of 6 more sequences, resulting in a total of 13 when varying salt concentrations. Together with a survey of more than 500 IDP sequences, we conclude that the salting-out effect, which was considered to be secondary to electrostatic screening, is important for IDP sequences with moderately charged residues at physiological salt concentrations. The presented scheme is generally applicable to other computational models for capturing salt-dependent IDP conformations.

Using a sequence-specific coarse-grained model for studying protein liquid-liquid phase separation.

The formation of membraneless organelles (MLOs) via liquid-liquid phase separation (LLPS) of biomolecules is a topic that has garnered significant attention in the scientific community recently. Experimental studies have revealed that intrinsically disordered proteins (IDPs) may play a major role in driving the formation of these droplets via LLPS by forming multivalent interactions between amino acids. To quantify these interactions is an arduous task as it is difficult to investigate these interactions at the amino acid level using currently available experimental tools. It becomes necessary to complement experimental studies using appropriate computational methods such as coarse-grained models of IDPs that can allow one to simulate biomolecular LLPS using general-purpose hardware. Here, we summarize our coarse-grained modeling framework that uses a single bead per amino acid resolution and the co-existence sampling technique to study sequence-specific protein phase separation using molecular dynamics simulations. We further discuss the caveats and technicalities, which one must consider while using this method to obtain thermodynamic phase diagrams. To ease the learning curve, we provide our implementations of the coarse-grained potentials in the HOOMD-Blue simulation package and associated python scripts to run such simulations.