Mutant p53 Sequestration of the MDM2 Acidic Domain Inhibits E3 Ligase Activity

Missense p53 mutants often accumulate in tumors and drive progression through gain of function. MDM2 efficiently degrades wild-type p53 but fails to degrade mutant p53 in tumor cells. Previous studies revealed that mutant p53 inhibits MDM2 autoubiquitination, suggesting that the interaction inhibits MDM2 E3 activity. Recent work showed that MDM2 E3 activity is stimulated by intramolecular interaction between the RING and acidic domains. Here, we show that in the mutant p53-MDM2 complex, the mutant p53 core domain binds to the MDM2 acidic domain with significantly higher avidity than wild-type p53. The mutant p53-MDM2 complex is deficient in catalyzing ubiquitin release from the activated E2 conjugating enzyme. An MDM2 construct with extra copies of the acidic domain is resistant to inhibition by mutant p53 and efficiently promotes mutant p53 ubiquitination and degradation. The results suggest that mutant p53 interferes with the intramolecular autoactivation mechanism of MDM2, contributing to reduced ubiquitination and increased accumulation in tumor cells.

Conformational Details of Quantum Dot-DNA Resolved by Förster Resonance Energy Transfer Lifetime Nanoruler

DNA-nanoparticle conjugates are important tools in nanobiotechnology. Knowing the orientation, function, and length of DNA on nanoparticle surfaces at low nanomolar concentrations under physiological conditions is therefore of great interest. Here, we investigate the conformation of a 31 nucleotides (nt) long DNA attached to a semiconductor quantum dot (QD) via Förster resonance energy transfer (FRET) from Tb-DNA probes hybridized to different positions on the QD-DNA. Precise Tb-to-QD distance determination from 7 to 14 nm along 26 nt of the peptide-appended QD-DNA was realized by time-resolved FRET spectroscopy. The FRET nanoruler measured linear single-stranded (ssDNA) and double-stranded (dsDNA) extensions of ∼0.15 and ∼0.31 nm per base, reflecting the different conformations. Comparison with biomolecular modeling confirmed the denser conformation of ssDNA and a possibly more flexible orientation on the QD surface, whereas the dsDNA was fully extended with radial orientation. The temporally distinct photoluminescence decays of the different DNA-FRET configurations were used for prototypical DNA hybridization assays that demonstrated the large potential for extended temporal multiplexing. The extensive experimental and theoretical analysis of 11 different distances/configurations of the same QD-DNA conjugate provided important information on DNA conformation on nanoparticle surfaces and will be an important benchmark for the development and optimization of DNA-nanobiosensors.

Conformational Differences between Functional Human Immunodeficiency Virus Envelope Glycoprotein Trimers and Stabilized Soluble Trimers

Binding to the receptor CD4 triggers entry-related conformational changes in the human immunodeficiency virus type 1 (HIV-1) envelope glycoprotein (Env) trimer, (gp120/gp41)₃ Soluble versions of HIV-1 Env trimers (sgp140 SOSIP.664) stabilized by a gp120-gp41 disulfide bond and a change (I559P) in gp41 have been structurally characterized. Here, we use cross-linking/mass spectrometry to evaluate the conformations of functional membrane Env and sgp140 SOSIP.664. Differences were detected in the gp120 trimer association domain and C terminus and in the gp41 heptad repeat 1 (HR1) region. Whereas the membrane Env trimer exposes the gp41 HR1 coiled coil only after CD4 binding, the sgp140 SOSIP.664 HR1 coiled coil was accessible to the gp41 HR2 peptide even in the absence of CD4. Our results delineate differences in both gp120 and gp41 subunits between functional membrane Env and the sgp140 SOSIP.664 trimer and provide distance constraints that can assist validation of candidate structural models of the native HIV-1 Env trimer.IMPORTANCE HIV-1 envelope glycoprotein spikes mediate the entry of the virus into host cells and are a major target for vaccine-induced antibodies. Soluble forms of the envelope glycoproteins that are stable and easily produced have been characterized extensively and are being considered as vaccines. Here, we present evidence that these stabilized soluble envelope glycoproteins differ in multiple respects from the natural HIV-1 envelope glycoproteins. By pinpointing these differences, our results can guide the improvement of envelope glycoprotein preparations to achieve greater similarity to the viral envelope glycoprotein spike, potentially increasing their effectiveness as a vaccine.

RUNX1-ETO: Attacking the Epigenome for Genomic Instable Leukemia

Oncogenic fusion protein RUNX1-ETO is the product of the t(8;21) translocation, responsible for the most common cytogenetic subtype of acute myeloid leukemia. RUNX1, a critical transcription factor in hematopoietic development, is fused with almost the entire ETO sequence with the ability to recruit a wide range of repressors. Past efforts in providing a comprehensive picture of the genome-wide localization and the target genes of RUNX1-ETO have been inconclusive in understanding the underlying mechanism by which it deregulates native RUNX1. In this review; we dissect the current data on the epigenetic impact of RUNX1 and RUNX1-ETO. Both share similarities however, in recent years, research focused on epigenetic factors to explain their differences. RUNX1-ETO impairs DNA repair mechanisms which compromises genomic stability and favors a mutator phenotype. Among an increasing pool of mutated factors, regulators of DNA methylation are frequently found in t(8;21) AML. Together with the alteration of both, histone markers and distal enhancer regulation, RUNX1-ETO might specifically disrupt normal chromatin structure. Epigenetic studies on the fusion protein uncovered new mechanisms contributing to leukemogenesis and hopefully will translate into clinical applications.

Novel Endotype Xanthanase from Xanthan-Degrading Microbacterium sp. Strain XT11

Under general aqueous conditions, xanthan appears in an ordered conformation, which makes its backbone largely resistant to degradation by known cellulases. Therefore, the xanthan degradation mechanism is still unclear because of the lack of an efficient hydrolase. Here, we report the catalytic properties of MiXen, a xanthan-degrading enzyme identified from the genus Microbacterium MiXen is a 952-amino-acid protein that is unique to strain XT11. Both the sequence and structural features suggested that MiXen belongs to a new branch of the GH9 family and has a multimodular structure in which a catalytic (α/α)₆ barrel is flanked by an N-terminal Ig-like domain and by a C-terminal domain that has very few homologues in sequence databases and functions as a carbohydrate-binding module (CBM). Based on circular dichroism, shear-dependent viscosity, and reducing sugar and gel permeation chromatography analysis, we demonstrated that recombinant MiXen efficiently and randomly cleaved glucosidic bonds within the highly ordered xanthan substrate. A MiXen mutant free of the C-terminal CBM domain partially lost its xanthan-hydrolyzing ability because of decreased affinity toward xanthan, indicating the CBM domain assisted MiXen in hydrolyzing highly ordered xanthan via recognizing and binding to the substrate. Furthermore, side chain substituents and the terminal mannosyl residue significantly influenced the activity of MiXen via the formation of barriers to enzymolysis. Overall, the results of this study provide insight into the hydrolysis mechanism and enzymatic properties of a novel endotype xanthanase that will benefit future applications.IMPORTANCE This work characterized a novel endotype xanthanase, MiXen, and elucidated that the C-terminal carbohydrate-binding module of MiXen could drastically enhance the hydrolysis activity of the enzyme toward highly ordered xanthan. Both the sequence and structural analysis demonstrated that the catalytic domain and carbohydrate-binding module of MiXen belong to the novel branch of the GH9 family and CBMs, respectively. This xanthan cleaver can help further reveal the enzymolysis mechanism of xanthan and provide an efficient tool for the production of molecular modified xanthan with new physicochemical and physiological functions.

Interfacial Conformation of Hydrophilic Polyphosphoesters Affects Blood Protein Adsorption

Synthetic polymers are commonly used as protein repelling materials for a variety of biomedical applications. Despite their widespread use, the fundamental mechanism underlying protein repellence is often elusive. Such insights are essential for improving existing and developing new materials. Here, we investigate how subtle differences in the chemistry of hydrophilic polyphosphoesters influence the adsorption of the human blood proteins serum albumin and fibrinogen. Using thermodynamic measurements, surface-specific vibrational spectroscopy, and Brewster angle microscopy, we investigate protein adsorption, hydration, and steric repulsion properties of the polyphosphoester polymers. Whereas both surface hydration and polymer conformation of the polymers vary substantially as a consequence of the chemical differences in the polymer structure, the protein repellency ability of these hydrophilic materials appears to be dominated by steric repulsion.

Battle of the Sexes in Best of Breed: Sex Influences Dogs' Success in the Show Ring

Simple Summary

When breeding dogs, the dam and the sire contribute equally to the genetics of each of their puppies, and so each parent should be equally important to show-ring success. The current study collated samples of dog show results to explore relationships between sex and the likelihood of success in the show ring. It focused on toy and giant breeds to explore any differences in equity, if it existed, at either end of the size spectrum. It revealed that the rate at which male and female dogs were exhibited were similar but that male dogs were a significant advantage of winning Best of Breed titles.

Abstract

Much of the research on pedigree dog breeding has been directed towards understanding the implications of reduced genetic diversity and the prevalence of inherited disorders. An example is the potential role of the popular sire effect in perpetuating genetic defects. If male dogs are more likely than bitches to be identified as examples of members of a breed that align with breed standard, they may be selected for breeding earlier. This may contribute to the influence of individual males and contribute to popular sire effect. Conversely, if breed standards are written in a sex-neutral fashion, and if dogs are entered, exhibited, and judged in a sex-neutral fashion, then we would expect the success of female dogs in the show ring to be equal to that of their male counterparts. With a focus on toy and giant breeds, the current pilot study collated samples of dog show results to explore relationships between sex and the likelihood of success in the show ring. It focused on toy and giant breeds to explore any differences in equity, if it existed, at either end of the size and concomitant age-at-maturation spectrum. For the purpose of this study, toy breeds were those that weigh < 10 kg at maturity while giant breed dogs were those that exceed 45 kg. Within these two clusters, the least (n = 3) and most popular (n = 3) breeds were then selected to explore any potential role of sex on success in the show ring. The popularity of breeds was determined using the numbers of dogs registered with the Australian National Kennel Council. Using results from dog shows (n = 18) from 2015 to 2016, data on 1,080 dogs were obtained. Within these 12 breeds for the 18 shows, there were 137 Best of Breed (BOB) titles awarded: Pug (n = 18), Toy Poodle (n = 18), Bullmastiff (n = 14), Rottweiler (n = 17), Fox Terrier (Smooth) (n = 18), Bloodhound (n = 3), Schnauzer (miniature) (n = 15), Great Dane (n = 17), Norfolk Terrier (n = 10), Norwich Terrier (n = 5), Central Asian Shepherd Dog (n = 2). Despite the near parity of male and female dogs being exhibited, of these 137 titles, 86 (62.8%) were awarded to male dogs (at least 41 individuals) and 51 (37.2%) to female dogs (at least 32 individuals) showing that male dogs are more likely to win BOB titles (χ² = 9.4455, df = 1, p-value = 0.002117). Among the toy subset of breeds, this effect was higher (χ² = 6.798, df = 1, p-value = 0.009126) than among the giant breed subset, for whom the advantage to male dogs did not reach statistical significance versus χ² = 3.0967, df = 1, p-value = 0.07845). This suggests that judges find the male dogs more appealing, presumably because they are more aligned with breed standards.

RA-XXV and RA-XXVI, Bicyclic Hexapeptides from Rubia cordifolia L.: Structure, Synthesis, and Conformation

Two RA-series bicyclic hexapeptides, RA-XXV (4) and RA-XXVI (5), which have no N-methyl group at Tyr-5, were isolated from the roots of Rubia cordifolia L. Their amino acid compositions and sequences were determined by interpretation of MS, and 1D and 2D NMR data and their relative structures were elucidated by XRD analysis of 4 and RA-XXVI acetate (6). The absolute stereochemistry of 4 was established by the total synthesis of 4, and that of 5, by the chemical correlation with 4. Peptides 4 and 5 exhibited cytotoxicity toward human promyelocytic leukemia HL-60 (IC₅₀ =0.062 and 0.066 μm, respectively) and human colonic carcinoma HCT-116 (IC₅₀ =0.028 and 0.051 μm, respectively) cell lines. Analysis of the conformational structures of 4 and 6 in the crystalline state and those of 4 and 5 in solution revealed that the N-methyl group at Tyr-5 functions to make this series of peptides preferentially adopt the active conformation.

Contribution of Chemical Modifications and Conformational Epitopes to IgE Binding by Ara h 3

Roasting is known to change the allergenic properties of peanuts. To study these observations at a molecular level, the relationship of IgE binding to the structure of Ara h 3 from raw and roasted peanuts was assessed. Ara h 3 (A3) was purified from raw (R), light roast (LR) and dark roast (DR) peanuts, the purity was assessed using sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and the secondary structures were compared with circular dichroism (CD) spectroscopy. In order to understand the contribution of structure to IgE binding, the R A3 was partially denatured (PD) by heat treatment (65 °C for 2 h), subjected to CD spectroscopy and IgE spot blot analysis with sera from peanut- allergic individuals. While we observed that the secondary structure of purified A3 from R and LR peanut in solution was affected by the reduction of disulfide bonds and heat treatment when purified from the peanut following the roasting process, only small alterations were seen in the secondary structure. The purified LR A3 bound higher levels of IgE than the RA3. CD spectroscopy of PD A3 revealed a reduction in the percentage of alpha helices, and serum IgE binding. Therefore, while A3 purified from roasted peanuts did not show significant changes in secondary structure, it showed higher IgE binding than R A3. Therefore, the higher IgE binding to LR A3 was more likely to be due to chemical modifications than structural changes. However, a decrease in the IgE binding was seen if R A3 was deliberately unfolded, indicating that the structure played an important role in IgE binding to A3.

Aggregation and conformational changes of silver carp myosin as affected by the ultrasound-calcium combination system

BACKGROUND

Ultrasound and Ca²⁺ have been used separately to increase myosin properties in fish processing. However, little is know about how myosin changes are affected by Ca²⁺ and ultrasound in combination. The present study aimed to investigate the effects of the ultrasound-calcium combination system on aggregation and conformational changes of silver carp myosin.

RESULTS

Ultrasound facilitated a Ca²⁺ -induced increase in turbidity. As the Ca²⁺ concentration increased from 0 to 100 mmol L^-1 , there was an obvious increase in the turbidity, solubility and mean hydrated particle size of myosin after ultrasound treatment compared to without treatment. Moreover, changes of total and reactive SH contents depended on the ultrasound-calcium combination conditions. Under this combination system, myosin surface hydrophobicity significantly increased for the synergistic effect of ultrasound and Ca²⁺ . Furthermore, the ultrasound-calcium combination conditions could affect myosin gelation, with better gelation properties being observed for myosin treated with a combination of 60 mmol L^-1 Ca²⁺ and 9 min of ultrasound.

CONCLUSION

The combination system reported in the present study was beneficial for myosin unfolding, facilitating intermolecular interactions between Ca²⁺ and myosin. Ultrasound treatment promoted myosin aggregation via the induction of Ca²⁺ and reduced the critical concentration of Ca²⁺ required to aggregate myosin. In the fish processing industry, this combination system can enhance the gelation properties of surimi-based products. © 2018 Society of Chemical Industry.

Influence of thermal treatment on the characteristics of major oyster allergen Cra g 1 (tropomyosin)

BACKGROUND

Shellfish, including oysters, often cause allergic reactions in adults. Thermal treatment is one of the most common technologies for dealing with seafood, which may affect biological properties. The present study aimed to evaluate the impact of heating on the conformation and potential allergenicity of oyster-derived tropomyosin (Cra g 1).

RESULTS

Sodium dodecylsulphate-polyacrylamide gel electrophoresis showed that there was an apparent band at 35 kDa of raw tropomyosin after purification and more significant polymers appeared in the heated protein. Interestingly, obvious changes in the intensity of the circular dichroism signal and 1-anilino-8-naphthalene sulfonate-binding fluorescence were observed especially in the case of the roasted form, which was associated with an increase in antibody reactivity. The degree of immunoglobulin (Ig)E binding of this treatment was demonstrated in the order roasted > boiled > raw. Furthermore, sequence alignment and amino acid composition revealed that Cra g 1 shared relatively high homology to tropomyosins from other shellfish and was also abundant in lysine that was apt to be modified by reducing sugars during heating.

CONCLUSION

Heated Cra g 1 produces higher IgE reactivity than the raw form as a result of the denaturation and formation of polymers. These findings will benefit the diagnosis and management of potential allergenicity as a result of shellfish. © 2018 Society of Chemical Industry.

New Insights into Development of Transglutaminase 2 Inhibitors as Pharmaceutical Lead Compounds

Transglutaminase 2 (EC 2.3.2.13; TG2 or TGase 2) plays important roles in the pathogenesis of many diseases, including cancers, neurodegeneration, and inflammatory disorders. Under normal conditions, however, mice lacking TGase 2 exhibit no obvious abnormal phenotype. TGase 2 expression is induced by chemical, physical, and viral stresses through tissue-protective signaling pathways. After stress dissipates, expression is normalized by feedback mechanisms. Dysregulation of TGase 2 expression under pathologic conditions, however, can potentiate pathogenesis and aggravate disease severity. Consistent with this, TGase 2 knockout mice exhibit reversal of disease phenotypes in neurodegenerative and chronic inflammatory disease models. Accordingly, TGase 2 is considered to be a potential therapeutic target. Based on structure–activity relationship assays performed over the past few decades, TGase 2 inhibitors have been developed that target the enzyme’s active site, but clinically applicable inhibitors are not yet available. The recently described the small molecule GK921, which lacks a group that can react with the active site of TGase 2, and efficiently inhibits the enzyme’s activity. Mechanistic studies revealed that GK921 binds at an allosteric binding site in the N-terminus of TGase 2 (amino acids (a.a.) 81–116), triggering a conformational change that inactivates the enzyme. Because the binding site of GK921 overlaps with the p53-binding site of TGase 2, the drug induces apoptosis in renal cell carcinoma by stabilizing p53. In this review, we discuss the possibility of developing TGase 2 inhibitors that target the allosteric binding site of TGase 2.

An Algorithm for Computing Side Chain Conformational Variations of a Protein Tunnel/Channel

In this paper, a novel method to compute side chain conformational variations for a protein molecule tunnel (or channel) is proposed. From the conformational variations, we compute the flexibly deformed shapes of the initial tunnel, and present a way to compute the maximum size of the ligand that can pass through the deformed tunnel. By using the two types of graphs corresponding to amino acids and their side chain rotamers, the suggested algorithm classifies amino acids and rotamers which possibly have collisions. Based on the divide and conquer technique, local side chain conformations are computed first, and then a global conformation is generated by combining them. With the exception of certain cases, experimental results show that the algorithm finds up to 327,680 valid side chain conformations from 12⁸~12³³ conformation candidates within three seconds.

Nucleoside macrocycles formed by intramolecular click reaction: efficient cyclization of pyrimidine nucleosides decorated with 5'-azido residues and 5-octadiynyl side chains

Copper(I)-promoted "click" cyclization in the presence of TBTA afforded nucleoside macrocycles in very high yields (≈70%) without using protecting groups. To this end, dU and dC derivatives functionalized at the 5-position of the nucleobase with octadiynyl side chains and with azido groups at the 5'-position of the sugar moieties were synthesized. The macrocycles display freely accessible Watson-Crick recognition sites. The conformation of the 16-membered macrocycle was deduced from X-ray analysis and ¹H,¹H-NMR coupling constants. The sugar conformation (N vs S) was different in solution as compared to the solid state.

The Chirality Chain in Valine: How the Configuration at the Cα Position through the O cis C'CαN Torsional System Leads to Distortion of the Planar Group CαC'(O cis )O trans to a Flat Tetrahedron

Solid-state structures, based on a Cambridge Structural Database (CSD) search, show that there is a CαN/C'O cis attraction in the torsional system O cis C'CαN of valine, causing a chirality chain. The Cα configuration controls the chirality of the rotation around the C'-Cα bond, which in turn induces a distortion of the planar unit CαC'(O)O to a flat asymmetric tetrahedron. Conformational "reactions" take place in an energy profile with respect to clockwise and counterclockwise rotation around the C'-Cα bond as well as stretching and flattening of the tetrahedron. The molecular property CαN/C'O cis attraction of valine is maintained in its di- and tripeptides.

Structure of the Fc fragment of the NIST reference antibody RM8671

As the link between antigen binding and immune activation, the antibody Fc region has received extensive structural study. In this report, the structure of the Fc fragment of the NIST IgG1 mAb (reference material 8671) is described at 2.1 Å resolution in space group P212121, with approximate unit-cell parameters a = 50, b = 80, c = 138 Å. Prior Fc structures with a wide variety of modifications are also surveyed, focusing on those in the same crystal form. To facilitate the analysis of conformations, a reference frame and a two-parameter metric are proposed, considering the CH2 domains as mobile with respect to a fixed dimeric CH3 core. Over several human Fc structures, a significant variation in Fc elbow conformations is observed, which may serve to facilitate the regulation of Fc effector signaling.

J(77 Se,1 H) and J(77 Se,13 C) couplings of seleno-carbohydrates obtained by 77 Se satellite 1D 13 C spectroscopy and 77 Se selective HR-HMBC spectroscopy

Seleno-carbohydrates are those in which the oxygen of the glycosidic bond or the hydroxyl group is artificially replaced with selenium. This substitution changes ¹ H and ¹³ C chemical shifts and produces spin coupling constants involving ⁷⁷ Se. Coupling constants, such as ^2-3 J(⁷⁷ Se, ¹ H), are likely to be useful for conformational analyses of glycans because such couplings are never observed in natural glycans. Several papers have discussed the relationship between ^2-3 J(⁷⁷ Se, ¹ H) and conformation; however, only few reports describe ^1-3 J(⁷⁷ Se, ¹³ C), which could also be useful. Here, we obtain ⁷⁷ Se coupling constants of seleno-carbohydrates from ⁷⁷ Se-selective HR-HMBC and ⁷⁷ Se satellites in 1D ¹³ C spectra and examine their conformations using the Newman projection scheme.

Osmolyte Induced Tumorigenesis and Metastasis: Interactions With Intrinsically Disordered Proteins

In spite of a great deal of work, the biochemical mechanisms underlying tumorigenesis and metastasis are not yet fully understood. Specifically regarding metastasis many authors consider that malignancy is caused by the accumulation of mutations. However, evidence is gathering to show that tumors are composed of heterogeneous cell populations subjected to selective pressures. In this micro evolutionary scenario, intra- and extra-cellular selective pressures will determine which subpopulations of tumor cells will thrive and be able to dissociate from the tumor as autonomous metastatic cells. We propose here that alteration of conformations of transcription factors confer novel non-canonical functions that may induce oncogenesis and metastasis in a mutation independent manner. We argue that the functional plasticity of transcription factors is due to intrinsically disordered domains (IDRs) of proteins. IDRs prevent spontaneous folding of proteins into well-defined three-dimensional structures. Because most transcription factors contain IDRs, each could potentially interact with many ligands. This high degree of functional pleiotropy would then be ultimately responsible for the metastatic phenotype. The conformations of proteins can be altered by chemical chaperones collectively known as osmolytes. Osmolytes are small organic molecules permeable through biological membranes that can accumulate in cells, increase the thermodynamic stability of proteins, modulate enzyme activity and prevent protein aggregation. Thus, by modifying IDRs, osmolytes could subvert the homeostatic regulatory network of cells. Untargeted metabolomic analysis of oral cancer cells showed that those with the greatest metastatic potential contained several osmolytes that were absent in the non-metastatic cells. We hypothesize that high concentrations of osmolytes might promote conformational alterations of transcription factors that favor metastatic behavior. This hypothesis is eminently testable by investigating whether: (a) the intracellular microenvironment of metastatic cells differs from non-metastatic cells and whether osmolytes are responsible for this change and (b) high intracellular concentrations of osmolytes are sufficient to induce structural modifications in regulatory protein so as to establish novel interactive networks that will constitute the metastatic phenotype. Synthetic cell penetrating peptides mimicking IDRs could act as sensitive probes. By exposing the peptides to the microenvironments of living tumor and metastatic tumor cells one should be able to compare the chemical shifts as revealed by spectra obtained by nuclear magnetic resonance (NMR).

Routes of phosphoryl group transfer during signal transmission and signal decay in the dimeric sensor histidine kinase ArcB

The Arc (anoxic redox control) two-component system of Escherichia coli, comprising ArcA as the response regulator and ArcB as the sensor histidine kinase, modulates the expression of numerous genes in response to respiratory growth conditions. Under reducing growth conditions, ArcB autophosphorylates at the expense of ATP, and transphosphorylates ArcA via a His292 → Asp576 → His717 → Asp54 phosphorelay, whereas under oxidizing growth conditions, ArcB catalyzes the dephosphorylation of ArcA-P by a reverse Asp54 → His717 → Asp576 → Pi phosphorelay. However, the exact phosphoryl group transfer routes and the molecular mechanisms determining their directions are unclear. Here, we show that, during signal propagation, the His292 → Asp576 and Asp576 → His717 phosphoryl group transfers within ArcB dimers occur intra- and intermolecularly, respectively. Moreover, we report that, during signal decay, the phosphoryl group transfer from His717 to Asp576 takes place intramolecularly. In conclusion, we present a mechanism that dictates the direction of the phosphoryl group transfer within ArcB dimers and that enables the discrimination of the kinase and phosphatase activities of ArcB.

Combinatorial Synthesis of New Pyrimidine- and Purine-β-d-Ribonucleoside Nucleolipids: Their Distribution Between Aqueous and Organic Phases and Their In Vitro Activity Against Human- and Rat Glioblastoma Cells In Vitro

Two series of nucleolipids, O-2',3'-heptanylidene- as well as O-2',3'-undecanylidene ketals of six β-d-ribonucleosides (type A) and partly N-farnesyl derivatives thereof (type B) were prepared in a combinatorial manner. All novel compounds were characterized by elemental analysis and/or ESI mass spectrometry and by UV-, ¹ H-, and ¹³ C-NMR spectroscopy. Conformational parameters of the nucleosides and nucleolipids were calculated from various ³ J(H,H), ³ J(¹ H,¹³ C), and ⁵ J(F,H) coupling constants. For a drug profiling, the parent nucleosides and their lipophilic derivatives were studied with respect to their distribution (log P) between water and n-octanol as well as water and cyclohexane. From these data, qualitative conclusions were drawn concerning their possible blood-brain barrier passage efficiency. Moreover, nucleolipids were characterized by their molecular descriptor amphiphilic ratio (a.r.), which describes the balance between the hydrophilicity of the nucleoside headgroup and the lipophilicity of the lipid tail. All compounds were investigated in vitro with respect to their cytostatic/cytotoxic activity toward human glioblastoma (GOS 3) as well as rat malignant neuroectodermal BT4Ca cell lines in vitro. In order to differentiate between anticancer and side-effects of the novel nucleolipids, they were also studied on their activity on differentiated human THP-1 macrophages.

Implications of Metal Binding and Asparagine Deamidation for Amyloid Formation

Increasing evidence suggests that amyloid formation, i.e., self-assembly of proteins and the resulting conformational changes, is linked with the pathogenesis of various neurodegenerative disorders such as Alzheimer’s disease, prion diseases, and Lewy body diseases. Among the factors that accelerate or inhibit oligomerization, we focus here on two non-genetic and common characteristics of many amyloidogenic proteins: metal binding and asparagine deamidation. Both reflect the aging process and occur in most amyloidogenic proteins. All of the amyloidogenic proteins, such as Alzheimer’s β-amyloid protein, prion protein, and α-synuclein, are metal-binding proteins and are involved in the regulation of metal homeostasis. It is widely accepted that these proteins are susceptible to non-enzymatic posttranslational modifications, and many asparagine residues of these proteins are deamidated. Moreover, these two factors can combine because asparagine residues can bind metals. We review the current understanding of these two common properties and their implications in the pathogenesis of these neurodegenerative diseases.

Calix[6]arene-based atropoisomeric pseudo[2]rotaxanes

Some examples of atropoisomeric pseudorotaxanes in which the isomerism arises by the different conformations adopted by the wheel are reported here. Upon threading hexahexyloxycalix[6]arene 1 with ammonium axles 2⁺ or 3⁺, bearing biphenyl or trifluoromethylbenzyl moieties, respectively, two atropoisomeric pseudorotaxanes were formed in which the calix[6]-wheel 1 adopts the 1,2,3-alternate and cone conformations. The interconversion between them cannot be obtained by simple rotation around the ArCH₂Ar bonds of the calixarene wheel, which is blocked by the presence of the axle inside its cavity. Therefore, it can only be obtained through a mechanism of de-threading/re-threading of the axle. In all the examined cases, the 1,2,3-alternate and cone atropoisomers are, respectively, the kinetic and the thermodynamic ones.

Inactivation, Aggregation and Conformational Changes of Polyphenol Oxidase from Quince (Cydonia oblonga Miller) Juice Subjected to Thermal and High-Pressure Carbon Dioxide Treatment

Polyphenol oxidase (PPO) causes the browning reaction in fruits and vegetables and deteriorates the quality. Thermal treatment for enzyme inactivation may result in defects as opposed to high pressure CO₂ (HPCD) processing. In this study, the changes in activity, dissociation, aggregation and conformation of purified PPO from thermal and HPCD treated juice were investigated. HPCD exhibited inactivation of PPO at 55–65 °C whereas thermal processing alone at the same temperature resulted in PPO still showing activity. Under thermal treatment at 25 and 65 °C, the browning degree was higher (0.39 and 0.24) than for HPCD-treated juice (0.23 and 0.12). Fluorescence and circular dichroism spectral results indicated that HPCD induced large decreases in intensities, revealing a rearrangement of the secondary structure and destruction of the native configuration of the PPO molecule. The particle size distribution (PSD) pattern revealed structural modification leading to initial dissociation and subsequent aggregation of PPO after HPCD treatment. Polyacrylamide gel electrophoresis (PAGE) analysis exhibited that molecular size of protein was 40 kDa. In conclusion, the HPCD method was found to be more effective than thermal treatment to inactivate PPO. Structural modifications provided better insights into the phenomena of activation and inactivation of PPO.

Inert and seed-competent tau monomers suggest structural origins of aggregation

Tauopathies feature progressive accumulation of tau amyloids. Pathology may begin when these amplify from a protein template, or seed, whose structure is unknown. We have purified and characterized distinct forms of tau monomer—inert (M_i) and seed-competent (M_s). Recombinant M_s triggered intracellular tau aggregation, induced tau fibrillization in vitro, and self-assembled. M_s from Alzheimer’s disease also seeded aggregation and self-assembled in vitro to form seed-competent multimers. We used crosslinking with mass spectrometry to probe structural differences in M_i vs. M_s. Crosslinks informed models of local peptide structure within the repeat domain which suggest relative inaccessibility of residues that drive aggregation (VQIINK/VQIVYK) in M_i, and exposure in M_s. Limited proteolysis supported this idea. Although tau monomer has been considered to be natively unstructured, our findings belie this assumption and suggest that initiation of pathological aggregation could begin with conversion of tau monomer from an inert to a seed-competent form.

When doctors perform autopsies to look at the brain tissue of people with Alzheimer’s disease, they find toxic buildups of certain proteins – in particular, a protein called tau – in structures called ‘aggregates’. People with more severe dementia have more tau aggregates in their brain. Aggregates form when individual proteins stick together in repetitive patterns, much like the way a single Lego block might attach to another identical one. Like all proteins, tau is built from a string of amino acids that folds into a specific shape. Normally folded tau proteins do not form aggregates. It was not clear that an individual tau protein had two distinct forms—structures associated with health (“good”) or disease (“bad”).

Mirbaha et al. have now studied the folding pattern of purified tau proteins with a sophisticated technology called mass spectrometry. This technique can measure changes in tiny amounts of protein. Some of the purified proteins had been extracted from human brains (from people with and without Alzheimer’s). To detect which of the proteins were toxic, Mirbaha et al. also grew simple human cells in a dish that were designed to react specifically to the bad forms of tau. This allowed the good and bad forms of tau to be isolated.

Mirbaha et al. discovered that in the good form of tau the parts of the protein that allow it to stick to itself are hidden, folded inside. By contrast, the bad form of tau exposes the parts that allow it to aggregate, enabling the protein to build upon itself to form a large, toxic assembly.

The shape-shifting concept established by Mirbaha et al. might apply to other proteins that form toxic aggregates. This could help us to better understand how many other neurodegenerative diseases develop and progress. Recognizing that the shapes that tau forms can be categorized as either ‘good’ or ‘bad’ may also help to develop new treatments for Alzheimer’s disease. Drugs could be designed to stabilize the good form of tau, or to help remove the bad form from the brain. Furthermore, if the shape-shift described by Mirbaha et al. can be measured early enough in patients, it may allow treatments for Alzheimer’s before people have developed any detectable symptoms.

Stereoselective nucleophilic addition reactions to cyclic N-acyliminium ions using the indirect cation pool method: Elucidation of stereoselectivity by spectroscopic conformational analysis and DFT calculations

In this study, six-membered N-acyliminium ions were generated by the “indirect cation pool” method and reacted with several nucleophiles. These reactions afforded disubstituted piperidine derivatives with high diastereoselectivities and good to excellent yields. The conformations of the obtained N-acyliminium ions were studied by low temperature NMR analyses and DFT calculations and were found to be consistent with the Steven’s hypothesis.