Endoplasmic reticulum targeted AIE bioprobe as a highly efficient inducer of immunogenic cell death

Focused oxidative stress of the specific organelles(e.g., endoplasmic reticulum(ER) and mitochondrion) of cancer cells can boost the immunogenic cell death(ICD) effect for cancer immunotherapy. Herein, an ER-targeted bioprobe with aggregationinduced emission(AIE) characteristics(TPE-PR-FFKDEL) was rationally designed and synthesized by integrating a new AIE photosensitizer with ER targeting peptide, which has been demonstrated to be able to efficiently induce ER oxidative stress to evoke ICD. Compared with the photosensitizer hypericin that is well-known as an ER-targeted ICD inducer, TPE-PR-FFKDEL can lead to more robust emission of immunostimulatory damage-associated molecular patterns such as surface-exposed calreticulin, ATP secretion, and high-mobility group protein B1(HMGB1) and heat shock protein 70(HSP 70) expression.Furthermore, a range of immune responses are activated to protect mice from the attack of cancer cells in vivo.     

N-glycosylation of High Mobility Group Box 1 protein (HMGB1) modulates the interaction with glycyrrhizin: A molecular modeling study

High Mobility Group Box 1 protein (HMGB1) is an abundant protein with multiple functions in cells, acting as a DNA chaperone and damage-associated molecular pattern molecule. It represents an attractive target for the treatment of inflammatory diseases and cancers. The plant natural product glycyrrhizin (GLR) is a well-characterized ligand of HMGB1 and a drug used to treat diverse liver and skin diseases. The drug is known to bind to each of the two adjacent HMG boxes of the non-glycosylated protein. In cells, HMGB1 is N-glycosylated at three asparagine residues located in boxes A and B, and these N-glycans are essential for the nucleocytoplasmic transport of the protein. But the impact of the N-glycans on drug binding is unknown. Here we have investigated the effect of the N-glycosylation of HMGB1 on its interaction with GLR using molecular modelling, after incorporation of three N-glycans on a Human HMGB1 structure (PDB code 2YRQ). Sialylated bi-antennary N-glycans were introduced on the protein and exposed in a folded or an extended conformation for the drug binding study. The docking of the drug was performed using both 18α- and 18β-epimers of GLR and the conformations and potential energy of interaction (ΔE) of the different drug-protein complexes were compared. The N-glycans do not shield the drug binding sites on boxes A and B but can modulate the drug-protein interaction, via both direct and indirect effects. The calculations indicate that binding of 18α/β-GLR to the HMG box is generally reduced when the protein is N-glycosylated vs. the non-glycosylated protein. In particular, the N-glycans in an extended configuration significantly weaken the binding of GLR to box-B. The effects of the N-glycans are mostly indirect, but in one case a direct contact with the drug, via a carbohydrate-carbohydrate interaction, was observed with 18β-GLR bound to Box-B of glycosylated HMGB1. For the first time, it is shown (at least in silico) that N-glycosylation, one of the many post-translational modifications of HMGB1, can affect drug binding.     

Toll-like receptor 4 on islet β cells senses expression changes in high-mobility group box 1 and contributes to the initiation of type 1 diabetes

Type 1 diabetes mellitus is caused by the autoimmune destruction of β cells within the islets. In recent years, innate immunity has been proposed to play a key role in this process. High-mobility group box 1 (HMGB1), an inflammatory trigger in a number of autoimmune diseases, activates proinflammatory responses following its release from necrotic cells. Our aim was to determine the significance of HMGB1 in the natural history of diabetes in non-obese diabetic (NOD) mice. We observed that the rate of HMGB1 expression in the cytoplasm of islets was much greater in diabetic mice compared with non-diabetic mice. The majority of cells positively stained for toll-like receptor 4 (TLR4) were β cells; few α cells were stained for TLR4. Thus, we examined the effects of anti-TLR4 antibodies on HMGB1 cell surface binding, which confirmed that HMGB1 interacts with TLR4 in isolated islets. Expression changes in HMGB1 and TLR4 were detected throughout the course of diabetes. Our findings indicate that TLR4 is the main receptor on β cells and that HMGB1 may signal via TLR4 to selectively damage β cells rather than α cells during the development of type 1 diabetes mellitus.     

Interaction of fumigaclavine C with High Mobility Group Box 1 protein (HMGB1) and its DNA complex: A computational approach

The fumigaclavines represent a small group of clavine-type alkaloids produced by the pathogenic fungus Aspergillus fumigatus. The leading compound in the family is fumigaclavine C (Fm-C) endowed with potent anti-inflammatory properties. Fm-C represses the production of several inflammatory cytokines in cells via a mechanism implicating a reduced nucleo-cytoplasmic transport and extracellular export of the alarmin protein HMGB1, through a direct drug-protein interaction, and a down-regulation of HMGB1 expression. We have investigated the interaction of Fm-C with HMGB1 using two complementary forms of the HMG-box protein, in its free and DNA-bound configurations, using molecular modeling. We identified up to six potential binding sites for Fm-C in the vicinity of the B-box of HMGB1, with the site designated Lys-103 being the most favored and maintained when the protein is bound to a 16-base pair DNA oligonucleotide. Structure-binding relationships have been explored through the comparison of the HMGB1-binding properties of fumigaclavines A, B and C, and the related alkaloid lysergic acid diethylamide (LSD). Both the C-9 acetyl group and C-2 dimethylallyl side chain of Fm-C contribute importantly to the protein interaction. LSD appears also to form stable complexes with free HMGB1. According to the calculated empirical energies of interaction (ΔE), the compounds rank in the order: Fm-C ∼ LSD < Fm-A < Fm-B, for binding to HMGB1. The study helps to better comprehend the mechanism of action of Fm-C, and its anti-inflammatory and anticancer properties.     

On the existence of a global molecular network enmeshing the whole central nervous system: physiological and pathological implications

Proteins are endowed with the "Lego property", i.e., the capability of steric fitting with other proteins to form high molecular weight complexes with emergent functions. These interactions may occur both as horizontal molecular networks at the plasma membrane level and as vertical molecular networks, i.e., towards the extra- and/or intracellular side of the cell. The present paper broadens this view by proposing the existence of three dimensional molecular networks, mainly made by proteins and carbohydrates, which might interact with each other at boundaries of compartments such as plasma membranes to form a "global molecular network" (GMN) that pervades the intra- as well as the extra-cellular environment of the entire central nervous system. The GMN is a potentially plastic structure regulated through several means. For example, its extra-cellular part is under the remodeling action of the matrix metalloproteinases. The proposal of a GMN has physiological and pathological implications. In primis, classical synaptic transmission, gap junctions and volume transmission signals by modulating GMN could importantly contribute to the "binding phenomenon", i.e. the phase synchronization of firing rates in far-located neuronal cortical groups. Secondly, alterations in protein conformation could alter the GMN organization and hence the neuronal network morphology and function. This could lead to the formation of abnormal protein aggregates such as amyloid plaques and neurofibrillary tangles, which, in turn, might affect the GMN function and/or the reciprocal interactions between its parts especially at the boundaries between compartments.     

Glycyrrhizin binds to high-mobility group box 1 protein and inhibits its cytokine activities

High-mobility group box 1 protein (HMGB1) is a nuclear component, but extracellularly it serves as a signaling molecule involved in acute and chronic inflammation, for example in sepsis and arthritis. The identification of HMGB1 inhibitors is therefore of significant experimental and clinical interest. We show that glycyrrhizin, a natural anti-inflammatory and antiviral triterpene in clinical use, inhibits HMGB1 chemoattractant and mitogenic activities, and has a weak inhibitory effect on its intranuclear DNA-binding function. NMR and fluorescence studies indicate that glycyrrhizin binds directly to HMGB1 (K(d) approximately 150 microM), interacting with two shallow concave surfaces formed by the two arms of both HMG boxes. Our results explain in part the anti-inflammatory properties of glycyrrhizin, and might direct the design of new derivatives with improved HMGB1-binding properties.     

Dithiane- and trithiane-based photolabile scaffolds for molecular recognition

[see structure]. A modular synthetic approach to novel dithiane- and trithiane-based photolabile molecular hosts equipped with elements of molecular recognition is developed. The approach provides ready access to a family of amino-derivatized photocleavable molecular systems capable of hydrogen-bonding-based recognition of biologically relevant molecules, e.g., ureas, barbiturates etc. These systems undergo efficient photofragmentation in the presence of external (e.g., benzophenone) or internal (e.g., nitropyridine) electron-transfer sensitizers.     

Changes in the secondary structure of HMGB1 protein bonded to DNA

The stage of noncooperative interaction of the chromosomal nonhistone protein HMGB1 with DNA has been studied by spectroscopic methods and gel retardation. It was found that complexation was accompanied by compaction of the DNA molecule over a wide range of protein/DNA ratios in the complex. A circular dichroism study showed that the binding with DNA changed the secondary structure of the HMGB1 protein. Changes in the structure of the protein start under the conditions of an excess of binding sites on DNA and end at a ratio of ∼40–50 base pairs per protein molecule, the α-helicity of HMGB1 in the complex increasing by 20% compared with the free state. It is believed that the change in the secondary structure of HMGB1 during the binding with DNA underlies the mechanisms of the various functions of this protein in the cell.     

Expression and Secretion of a CB4-1 scFv–GFP Fusion Protein by Fission Yeast

There is a rapidly growing demand for fluorescent single-chain Fv (scFv) antibody fragments for many applications. Yeasts have developed into attractive hosts for recombinant production of these functionalized proteins because they provide several advantages over prokaryotes and higher eukaryotes as expression systems, e.g., being capable of high-level secretion of heterologous proteins. In this study, we report Schizosaccharomyces pombe as a new host organism for secretory production of scFv-green fluorescent protein (GFP) fusions and compare it with previously described yeast expression systems. We cloned a plasmid for the expression and secretion of the anti-p24 (human immunodeficiency virus 1) CB4-1 scFv fused to GFP. After expression of the scFv–GFP fused to an N-terminal Cpy1 secretion signal sequence, fluorescence microscopy of living yeast cells indicated that the heterologous protein entered the secretory pathway. Western blot analysis of cell-free culture supernatants confirmed that the scFv–GFP was efficiently secreted with yields up to 5 mg/L. In addition, fluorescence measurements of culture supernatants demonstrated that the GFP moiety of the scFv–GFP protein is fully functional after secretion. Our data suggest that S. pombe has the potential for being used as alternative expression host in recombinant antibody fragment production by ensuring efficient protein processing and secretion.     

Using nanoelectrospray ion mobility spectrometry (GEMMA) to determine the size and relative molecular mass of proteins and protein assemblies: a comparison with MALLS and QELS

The determination of protein assembly size and relative molecular mass is currently of great importance in biochemical analysis. In particular, the technique of nanoelectrospray (nES) with a gas-phase electrophoretic mobility molecular analyzer (GEMMA) has received increased attention for such measurements. However, in order for the GEMMA technique to gain broader acceptance in protein analysis, it must be further evaluated and compared with other established bioanalytical techniques. In the present study, nES-GEMMA was evaluated for the analysis of a set of protein and protein complexes involved in the Sec and the bacterial type III secretion pathway of enteropathogenic Escherichia coli bacteria. The same set of proteins, isolated and purified using standard biochemical protocols, were also analyzed using multi-angle laser light scattering (MALLS) and quasi-elastic light scattering (QELS), following size exclusion chromatography. This allowed for direct comparisons between the three techniques. It was found that nES-GEMMA, in comparison to the more established MALLS and QELS techniques, offers several complementary advantages. It requires considerably less amount of material, i.e., nanogram vs. milligram amounts, and time per sample analysis, i.e., few minutes vs. tens of minutes. Whereas the determined size and relative molecular mass are similar between the compared methods, the electrophoretic diameters determined using nES-GEMMA seem to be systematically smaller compared to the hydrodynamic diameter derived by QELS. Some of the GEMMA technique disadvantages include its narrow dynamic range, limited by the fact that at elevated protein concentrations there is increased potential for the occurrence of nES-induced oligomers. Thus, it is preferred to analyze dilute protein solutions because non-specific oligomers are less likely to occur whereas biospecific oligomers remain detected. To further understand the formation of nES-oligomers, the effect of buffer concentration on their formation was evaluated. Also, nES-GEMMA is not compatible with all the buffers commonly used with MALLS and QELS. Overall, however, the nES-GEMMA technique shows promise as a high-throughput proteomics/protein structure tool.     

Efficient quantification of the importance of contacts for the dynamical stability of proteins

Understanding the stability of the native state and the dynamics of a protein is of great importance for all areas of biomolecular design. The efficient estimation of the influence of individual contacts between amino acids in a protein structure is a first step in the reengineering of a particular protein for technological or pharmacological purposes. At the same time, the functional annotation of molecular evolution can be facilitated by such insight. Here, we use a recently suggested, information theoretical measure in biomolecular design - the Kullback-Leibler-divergence - to quantify and therefore rank residue-residue contacts within proteins according to their overall contribution to the molecular mechanics. We implement this protocol on the basis of a reduced molecular model, which allows us to use a well-known lemma of linear algebra to speed up the computation. The increase in computational performance is around 10(1)- to 10(4)-fold. We applied the method to two proteins to illustrate the protocol and its results. We found that our method can reliably identify key residues in the molecular mechanics and the protein fold in comparison to well-known properties in the serine protease inhibitor. We found significant correlations to experimental results, e.g., dissociation constants and Φ values.     

Fast and high resolution analysis of human serum transferrin by high performance isoelectric focusing in capillaries

Human serum transferrin is a mixture of isoforms (isoproteins) having different amounts of carbohydrates. Each isoform may exist in iron-free and iron-complexed molecular form. The genetic variations in different populations increase the number of combinations of the different forms of transferrin. To resolve the many components in transferrin preparations, the new high performance capillary technique was employed for isoelectric focusing. Iron-free transferrin and transferrin samples of known iron content were examined. The above method gives an exceptionally rapid analysis (within 15-25 min) of small amounts of samples (less than 1 microgram protein) and as good as or better resolution than other isoelectric focusing techniques previously used for transferrin analysis. By monitoring the focused protein zones at both 280 and 460 nm the molecular forms of transferrin (iron-free, monoferric and differic complexes) can easily be identified. Both steps of isoelectric focusing in capillaries (i.e., prefocusing and mobilization) can be used for analysis. We observed that chelating agents (e.g., carrier ampholytes, nitrilotriacetate) may release iron from microsyringes having metal pistons causing the formation of iron-transferrin complexes.     

Quantum chemical geometry optimizations in proteins using crystallographic raw data

A method is developed for the combination of quantum chemical geometry optimizations and crystallographic structure refinement. The method is implemented by integrating the quantum chemical software Turbomole with the crystallographic software Crystallography and NMR System (CNS), using three small procedures transferring information between the two programs. The program (COMQUM-X)is used to study the binding of the inhibitor N-methylmesoporphyrin to ferrochelatase, and we show that the method behaves properly and leads to an improvement of the structure of the inhibitor. It allows us to directly quantify in energy terms how much the protein distort the structure of the bound inhibitor compared to the optimum vacuum structure (4-6 kJ/mol). The approach improves the standard combined quantum chemical and molecular mechanics (QC/MM) approach by guaranteeing that the final structure is in accordance with experimental data (the reflections) and avoiding the risk of propagating errors in the crystal coordinates. The program can also be seen as an improvement of standard crystallographic refinement, providing an accurate empirical potential function for any group of interest. The results can be directly interpreted in standard crystallographic terms (e.g., R factors or electron density maps). The method can be used to interpret crystal structures (e.g., the protonation status of metal-bound water molecules) and even to locally improve them.     

Quantitative Retention - Eluent Composition Relationships in Liquid Chromatography

Abstract

Mechanistic molecular models of liquid-liquid and liquid-solid equilibria are discussed for common types of liquid chromatography systems. In spite of the assumed simplifications (e.g., use of concentrations in the definition of equilibrium constants) the approximate formulas for retentioneluent composition relationships are satisfactory for the preliminary optimization of TLC and HPLC systems; the molecular structure of the solute is indirectly expressed by the equilibrium constants and slopes of the plots so that graphical analysis of the relationships may provide information about the chromatographed compounds. It is demonstrated that, depending on the system type, the R_M (log k') values are often a linear function of concentration of the modifier either in linear or in logarithmic scale.     

Oxidative Crosslinking of Peptides and Proteins: Mechanisms of Formation,Detection, Characterization and Quantification

Covalent crosslinks within or between proteins play a key role in determining the structure and function of proteins. Some of these are formed intentionally by either enzymatic or molecular reactions and are critical to normal physiological function. Others are generated as a consequence of exposure to oxidants (radicals, excited states or two-electron species) and other endogenous or external stimuli, or as a result of the actions of a number of enzymes (e.g., oxidases and peroxidases). Increasing evidence indicates that the accumulation of unwanted crosslinks, as is seen in ageing and multiple pathologies, has adverse effects on biological function. In this article, we review the spectrum of crosslinks, both reducible and non-reducible, currently known to be formed on proteins; the mechanisms of their formation; and experimental approaches to the detection, identification and characterization of these species.     

基于固体核磁共振方法的蛋白质组装体三维结构解析

蛋白质组装体广泛存在于生物体内,具有相关生物学功能或与人类的重要疾病密切相关。蛋白质组装体分子量大,通常难以溶解和结晶,限制了常用的结构研究手段如X射线晶体学和液体NMR等在其高分辨三维结构解析中的应用。固体核磁共振技术(ssNMR)在难溶、非结晶样品的三维结构解析中具有独特的优势,尤其随着固体NMR硬件包括高场磁体和高性能的探头、固体NMR多维脉冲实验技术和样品制备技术特别是同位素标记技术的快速发展,固体NMR已经成为了蛋白组装体三维结构解析的重要手段。在样品制备方法方面,强调了样品制备条件的优化对得到构象均一样品的重要性,以及丰富的同位素标记方法的使用对固体NMR谱图分辨率提高的重要作用。同时多种脉冲序列如质子驱动自旋扩散技术(PDSD),偶极辅助旋转共振技术(DARR),质子辅助重偶技术(PAR)或转移回波双共振技术(TEDOR)等的建立和发展为结构约束条件收集提供了基本的技术方法。此外,固体NMR与其它实验技术如扫描透射电镜(STEM),冷冻电镜(Cryo-EM)等和理论模拟方法的联用能显著地提高固体NMR的能力,从而能解析分子量更大、结构更复杂的蛋白质组装体的三维结构。本文以Aβ纤维和T3SS针状体的三维结构解析为例介绍固体NMR在蛋白质组装体结构研究的最新实验方法,重点介绍最新的距离约束条件获取的实验方法进展,以及固体NMR与其它实验和理论模拟研究手段的联用在蛋白质组装体结构解析上的最新进展,期望有助于读者对固体NMR技术在蛋白质组装体的三维结构解析方面的研究进展有所了解。     

Hofmeister salt effects on surface tension arise from partitioning of anions and cations between bulk water and the air-water interface

We apply a recently developed surface-bulk partitioning model to interpret the effects of individual Hofmeister cations and anions on the surface tension of water. The most surface-excluded salt (Na2SO4) provides a minimum estimate for the number of water molecules per unit area of the surface region of 0.2 H2O A-2. This corresponds to a lower bound thickness of the surface region of approximately 6 A, which we assume is a property of this region and not of the salt investigated. At salt concentrations < or = 1 m, single-ion partition coefficients Kp,i, defined relative to Kp,Na+ = Kp,SO42- = 0, are found to be independent of bulk salt concentration and additive for different salt ions. Semiquantitative agreement with surface-sensitive spectroscopy data and molecular dynamics simulations is attained. In most cases, the rank orders of Kp,i for both anions and cations follow the conventional Hofmeister series, qualitative rankings of ions based on their effects on protein processes (folding, precipitation, assembly). Most anions that favor processes that expose protein surface to water (e.g., SCN-), and hence must interact favorably with (i.e., accumulate at) protein surface, are also accumulated at the air-water interface (Kp >1, e.g., Kp,SCN- =1.6). Most anions that favor processes that remove protein surface from water (e.g., F-), and hence are excluded from protein surface, are also excluded from the air-water interface (Kp,F- = 0.5). The guanidinium cation, a strong protein denaturant and therefore accumulated at the protein surface exposed in unfolding, is somewhat excluded from the air-water surface (Kp,GuH+ = 0.7), but is much less excluded than alkali metal cations (e.g., Kp,Na+ identical with 0, Kp,K+ = 0.1). Hence, cation Kp values for the air-water surface appear shifted (toward exclusion) as compared with values inferred for interactions of these cations with protein surface.     

Involvement of protein kinase C epsilon in thyrotropin-releasing hormone-stimulated phosphorylation of the myristoylated alanine-rich C kinase substrate in rat pituitary clonal cells

We have shown previously that novel protein kinase Cepsilon (nPKCepsilon) plays a key role in the basal and thyrotropin-releasing hormone (TRH)-stimulated prolactin (PRL) secretion in rat pituitary GH4C1 cells (Akita et al., J. Biol. Chem. 1994, 269, 4653-4660). Here we examined the region downstream of nPKCepsilon activation in order to understand the molecular mechanism by which nPKCepsilon mediates TRH-induced signal transduction. Exposure of GH4C1 cells to TRH causes a stimulation of the phosphorylation of a p80 (Mr approximately 80 000, pI approximately 4.3) and two p19 (p19a and b; Mr approximately 19 000, pI approximately 5.6 and 5.5, respectively). Phorbol ester, a potent activator of protein kinase C (PKC), also enhances these phosphorylations, whereas bisindolylmaleimide I, a specific inhibitor of PKC, clearly inhibits the phosphorylation of p80. p80 and p19 were identified as myristoylated alanine-rich C kinase substrate (MARCKS) and stathmin, respectively, as assessed by their two-dimensional gel electrophoretic profiles and their stabilities to heat and acid treatment. In nPKCepsilon-overexpressing stable clones, the phosphorylated level of MARCKS but not stathmin was high in the resting state, and enhanced and sustained upon TRH stimulation, correlating with the increased activation of nPKCepsilon. TRH stimulates the release of MARCKS from the membrane/cytoskeletal fraction to the cytosol fraction. These results, taken together with previous data concerning PRL secretion, suggest that MARCKS, a regulatory component of the cytoskeletal architecture, is the major substrate of nPKCepsilon in vivo, and that its phosphorylation may regulate TRH-stimulated PRL secretion.     

Synthesis of Linear Poly(1-Benzyltrimethyleneimine) by the Hofmann Reaction of Poly(1-Cyanoethyltrimethyleneimine) Quaternized with Benzylbromide

The synthesis of a linear polymer having a tertiary amino group in a part of the main chain has been attempted by several methods. However, it was difficult for the linear polyamine to form because of the complicated reaction of the amino group. In the polymerization of weakly basic cyclic amines, e.g., 1-cyanoethylazetidine or 1-cyanoethylaziridine, high molecular weight polymers, poly-1-cyanoethyltrimethyleneimine (poly-CET) and poly-1-cyanoethyl-ethyleneimine (poly-CEE), were obtained. An attempt was made to convert poly-CET and poly-CEE into poly(l-benzylalkyleneimine)s (poly-BET and poly-BEE). Linear poly-BET was prepared by the alkylation of poly-CET (MW about 6000) with benzylbromide, followed by the elimination of the cyanoethyl group of polymer by heating. The poly-BET obtained was a white, greasy substance with a molecular weight of about 5000; its structure was determined by NMR spectroscopy. The cyanoethyl groups were replaced completely by benzyl groups. However, poly-BEE with a complete exchange to benzyl group was not obtained from poly-CEE due to the remaining cyanoethyl groups. Residual cyanoethyl groups replaced about 40% of the amino groups in poly-CEE.