O-GlcNAcylation promotes pancreatic tumor growth by regulating malate dehydrogenase 1.

Oncogenic Kras-activated pancreatic ductal adenocarcinoma (PDAC) cells highly rely on an unconventional glutamine catabolic pathway to sustain cell growth. However, little is known about how this pathway is regulated. Here we demonstrate that Kras mutation induces cellular O-linked ß-N-acetylglucosamine (O-GlcNAc), a prevalent form of protein glycosylation. Malate dehydrogenase 1 (MDH1), a key enzyme in the glutamine catabolic pathway, is positively regulated by O-GlcNAcylation on serine 189 (S189). Molecular dynamics simulations suggest that S189 glycosylation on monomeric MDH1 enhances the stability of the substrate-binding pocket and strengthens the substrate interactions by serving as a molecular glue. Depletion of O-GlcNAcylation reduces MDH1 activity, impairs glutamine metabolism, sensitizes PDAC cells to oxidative stress, decreases cell proliferation and inhibits tumor growth in nude mice. Furthermore, O-GlcNAcylation levels of MDH1 are elevated in clinical PDAC samples. Our study reveals that O-GlcNAcylation contributes to pancreatic cancer growth by regulating the metabolic activity of MDH1.

In silico design and validation of high-affinity RNA aptamers targeting epithelial cellular adhesion molecule dimers.

Nucleic acid aptamers hold great promise for therapeutic applications due to their favorable intrinsic properties, as well as high-throughput experimental selection techniques. Despite the utility of the systematic evolution of ligands by the exponential enrichment (SELEX) method for aptamer determination, complementary in silico aptamer design is highly sought after to facilitate virtual screening and increased understanding of important nucleic acid-protein interactions. Here, with a combined experimental and theoretical approach, we have developed two optimal epithelial cellular adhesion molecule (EpCAM) aptamers. Our structure-based in silico method first predicts their binding modes and then optimizes them for EpCAM with molecular dynamics simulations, docking, and free energy calculations. Our isothermal titration calorimetry experiments further confirm that the EpCAM aptamers indeed exhibit enhanced affinity over a previously patented nanomolar aptamer, EP23. Moreover, our study suggests that EP23 and the de novo designed aptamers primarily bind to EpCAM dimers (and not monomers, as hypothesized in previous published works), suggesting a paradigm for developing EpCAM-targeted therapies.

Binding patterns and dynamics of double-stranded DNA on the phosphorene surface.

Phosphorene, a monolayer of black phosphorus, has emerged as one of the most promising two-dimensional (2D) nanomaterials for various applications in the post-graphene-discovery period due to its highly anisotropic structure and novel properties. In order to apply phosphorene in biomedical fields, it is crucial to understand how it interacts with biomolecules. Herein, we use both molecular dynamics (MD) simulations and experimental techniques to investigate the interactions of phosphorene with a dsDNA segment. Our results reveal that dsDNA can form a stable binding on the phosphorene surface through the terminal base pairs and adopt an upright orientation regardless of its initial configurations. Moreover, the binding strength of dsDNA with phosphorene is found to be mild and does not cause significant distortion in the internal structure of dsDNA. This phenomenon is attributed to the weaker dispersion interaction between dsDNA and phosphorene. Further analysis of the free energy profile calculated by the umbrella sampling technique suggests that the puckered surface morphology significantly reduces the adsorption free energy of DNA bases to phosphorene. Compared to graphene, phosphorene is found to show a milder attraction to DNA, which is confirmed by our electrophoresis experiments. We believe that these findings provide valuable insight into the molecular interactions between phosphorene and dsDNA which may prompt further investigation of phosphorene for future biomedical applications.

Directional extraction and penetration of phosphorene nanosheets to cell membranes.

Recently, phosphorene, a novel two-dimensional nanomaterial with a puckered surface morphology, was shown to exhibit cytotoxicity, but its underlying molecular mechanisms remain unknown. Herein, using large scale molecular dynamics simulations, we show that phosphorene nanosheets can penetrate into and extract large amounts of phospholipids from the cell membranes due to the strong dispersion interaction between phosphorene and lipid molecules, which would reduce cell viability. The extracted phospholipid molecules are aligned along the wrinkle direction of the phosphorene nanosheet because of its unique puckered structure. Our results also reveal that small phosphorene nanosheets penetrate into the cell membrane in a specific direction which is determined by the size and surface topography of phosphorene and the thickness of the membrane. These findings might shed light on understanding phosphorene's cytotoxicity and would be helpful for the future potential biomedical applications of phosphorene, such as biosensors and antibacterial agents.

A 3,2-Hydroxypyridinone-based Decorporation Agent that Removes Uranium from Bones In Vivo.

Searching for actinide decorporation agents with advantages of high decorporation efficiency, minimal biological toxicity, and high oral efficiency is crucial for nuclear safety and the sustainable development of nuclear energy. Removing actinides deposited in bones after intake is one of the most significant challenges remaining in this field because of the instantaneous formation of highly stable actinide phosphate complexes upon contact with hydroxyapatite. Here we report a hydroxypyridinone-based ligand (5LIO-1-Cm-3,2-HOPO) exhibiting stronger affinity for U(VI) compared with the reported tetradentate hydroxypyridinone ligands. This is further revealed by the first principles calculation analysis on bonding between the ligand and uranium. Both in vitro uranium removal assay and in vivo decorporation experiments with mice show that 5LIO-1-Cm-3,2-HOPO can remove uranium from kidneys and bones with high efficiencies, while the decorporation efficiency is nearly independent of the treatment time. Moreover, this ligand shows a high oral decorporation efficiency, making it attractive for practical applications.

Hydroxyl-Group-Dominated Graphite Dots Reshape Laser Desorption/Ionization Mass Spectrometry for Small Biomolecular Analysis and Imaging.

Small molecules play critical roles in life science, yet their facile detection and imaging in physiological or pathological settings remain a challenge. Matrix-assisted laser desorption ionization mass spectrometry (MALDI MS) is a powerful tool for molecular analysis. However, conventional organic matrices (CHCA, DHB, etc.) used in assisting analyte ionization suffer from intensive background noise in the mass region below m/z 700, which hinders MALDI MS applications for small-molecule detection. Here, we report that a hydroxyl-group-dominated graphite dot (GD) matrix overcomes limitations of conventional matrices and allows MALDI MS to be used in fast and high-throughput analysis of small biomolecules. GDs exhibit extremely low background noise and ultrahigh sensitivity (with limit of detection <1 fmol) in MALDI MS. This approach allows identification of complex oligosaccharides, detection of low-molecular-weight components in traditional Chinese herbs, and facile analysis of puerarin and its metabolites in serum without purification. Moreover, we show that the GDs provide an effective matrix for the direct imaging or spatiotemporal mapping of small molecules and their metabolites (m/z < 700) simultaneously at the suborgan tissue level. Density functional theory calculations further provide the mechanistic basis of GDs as an effective MALDI matrix in both the positive-ion and negative-ion modes. Collectively, our work uncovered a useful matrix which reshapes MALDI MS technology for a wide range of applications in biology and medicine.

Highly Sensitive and Selective Uranium Detection in Natural Water Systems Using a Luminescent Mesoporous Metal-Organic Framework Equipped with Abundant Lewis Basic Sites: A Combined Batch, X-ray Absorption Spectroscopy, and First Principles Simulation Investigation.

Uranium is not only a strategic resource for the nuclear industry but also a global contaminant with high toxicity. Although several strategies have been established for detecting uranyl ions in water, searching for new uranium sensor material with great sensitivity, selectivity, and stability remains a challenge. We introduce here a hydrolytically stable mesoporous terbium(III)-based MOF material compound 1, whose channels are as large as 27 Å × 23 Å and are equipped with abundant exposed Lewis basic sites, the luminescence intensity of which can be efficiently and selectively quenched by uranyl ions. The detection limit in deionized water reaches 0.9 µg/L, far below the maximum contamination standard of 30 µg/L in drinking water defined by the United States Environmental Protection Agency, making compound 1 currently the only MOF material that can achieve this goal. More importantly, this material exhibits great capability in detecting uranyl ions in natural water systems such as lake water and seawater with pH being adjusted to 4, where huge excesses of competing ions are present. The uranyl detection limits in Dushu Lake water and in seawater were calculated to be 14.0 and 3.5 µg/L, respectively. This great detection capability originates from the selective binding of uranyl ions onto the Lewis basic sites of the MOF material, as demonstrated by synchrotron radiation extended X-ray adsorption fine structure, X-ray adsorption near edge structure, and first principles calculations, further leading to an effective energy transfer between the uranyl ions and the MOF skeleton.

EGCG in Green Tea Induces Aggregation of HMGB1 Protein through Large Conformational Changes with Polarized Charge Redistribution.

As a major effective component in green tea, (-)-epigallocatechin-3-gallate (EGCG)'s potential benefits to human health have been widely investigated. Recent experimental evidences indicate that EGCG can induce the aggregation of HMGB1 protein, a late mediator of inflammation, which subsequently stimulates the autophagic degradation and thus provides protection from lethal endotoxemia and sepsis. In this study, we use molecular dynamics (MD) simulations to explore the underlying molecular mechanism of this aggregation of HMGB1 facilitated by EGCG. Our simulation results reveal that EGCG firmly binds to HMGB1 near Cys106, which supports previous preliminary experimental evidence. A large HMGB1 conformational change is observed, where Box A and Box B, two homogenous domains of HMGB1, are repositioned and packed together by EGCG. This new HMGB1 conformation has large molecular polarity and distinctive electrostatic potential surface. We suggest that the highly polarized charge distribution leads to the aggregation of HMGB1, which differs from the previous hypothesis that two HMGB1 monomers are linked by the dimer of EGCG. Possible aggregating modes have also been investigated with potential of mean force (PMF) calculations. Finally, we conclude that the conformation induced by EGCG is more aggregation-prone with higher binding free energies as compared to those without EGCG.

Simplified TiO2 force fields for studies of its interaction with biomolecules.

Engineered TiO2 nanoparticles have been routinely applied in nanotechnology, as well as in cosmetics and food industries. Despite active experimental studies intended to clarify TiO2's biological effects, including potential toxicity, the relation between experimentally inferred nanotoxicity and industry standards for safely applying nanoparticles remains somewhat ambiguous with justified concerns. Supplemental to experiments, molecular dynamics simulations have proven to be efficacious in investigating the molecular mechanism of a biological process occurring at nanoscale. In this article, to facilitate the nanotoxicity and nanomedicine research related to this important metal oxide, we provide a simplified force field, based on the original Matsui-Akaogi force field but compatible to the Lennard-Jones potentials normally used in modeling biomolecules, for simulating TiO2 nanoparticles interacting with biomolecules. The force field parameters were tested in simulating the bulk structure of TiO2, TiO2 nanoparticle-water interaction, as well as the adsorption of proteins on the TiO2 nanoparticle. We demonstrate that these simulation results are consistent with experimental data/observations. We expect that simulations will help to better understand the interaction between TiO2 and molecules.

Spatial profiling of protein hydrophobicity: native vs. decoy structures.

A recent study of 30 soluble globular protein structures revealed a quasi-invariant called the hydrophobic ratio. This invariant, which is the ratio of the distance at which the second order hydrophobic moment vanished to the distance at which the zero order moment vanished, was found to be 0.75 +/- 0.05 for 30 protein structures. This report first describes the results of the hydrophobic profiling of 5,387 non-redundant globular protein domains of the Protein Data Bank, which yields a hydrophobic ratio of 0.71 +/- 0.08. Then, a new hydrophobic score is defined based on the hydrophobic profiling to discriminate native-like proteins from decoy structures. This is tested on three widely used decoy sets, namely the Holm and Sander decoys, Park and Levitt decoys, and Baker decoys. Since the hydrophobic moment profiling characterizes a global feature and requires reasonably good statistics, this imposes a constraint upon the size of the protein structures in order to yield relatively smooth moment profiles. We show that even subject to the limitations of protein size (both Park & Levitt and Baker sets are small protein decoys), the hydrophobic moment profiling and hydrophobic score can provide useful information that should be complementary to the information provided by force field calculations.

Detecting native protein folds among large decoy sets with hydrophobic moment profiling.

A new hydrophobic score will be presented in this paper for detecting native-like folds from a large set of decoy structures. A recent paper (B. D. Silverman, PNAS 98, 4996, 2001) had revealed that for globular proteins there exists a relatively universal constant of 0.74 for a hydrophobic ratio, which is defined as the ratio of radii from the protein centroid at which the second order hydrophobic moment and the zero order moment vanishes. This paper further defines a new hydrophobic score which will be used to examine protein decoys, in particular, the Holm & Sander, Park & Levitt and Baker decoy sets. It will be shown that the hydrophobic score and profile shapes can provide useful information that should be complementary to the information provided by other procedures, such as free energy calculations.