Analogous Fragments Research Articles

Intramolecular Cyclization and a Retro-Ene Reaction Enable the Rapid Fragmentation of a Vitamin B1-Derived Breslow Intermediate.

In solution, analogues of the Breslow intermediate formed during catalysis by benzoylformate decarboxylase (BFDC) undergo rapid, irreversible fragmentation. The ability of BFDC to prevent this reaction and preserve its cofactor is a striking example of an enzyme 'steering' a reactive intermediate towards a productive pathway. To understand how BFDC suppresses the off-pathway reactivity of this Breslow intermediate, a clear mechanistic understanding of the fragmentation reaction is required. Here, DFT calculations reveal an unexpected mechanism for the solution-phase fragmentation that involves an intramolecular cyclization and a subsequent retro-ene reaction to release the final products. Free energy profiles demonstrate that this pathway is significantly more facile than the previously proposed mechanism that invoked Breslow intermediate enolates as intermediates. Additional computations have been performed to understand why related Breslow intermediates do not undergo analogous fragmentation reactions. Calculations performed with two closely related Breslow intermediates suggest that subtle differences in the relative values of ΔG≠ for protonation and fragmentation dictate whether a given intermediate will fragment or not. These differences and the fragmentation mechanism unveiled in this work may have ramifications for the mechanism of BFDC and other thiamin-dependent enzymes and could provide general lessons related to the control of reactive intermediates by enzymes.

9-chloro-5,9-dienoic and other fatty acids from marine sponge <i>Penares</i> sp.

The fatty acids and their ethyl esters from an extract of a sponge Penares sp. (South China Sea) were fractionated by high-performance liquid chromatography and analyzed by gas chromatography-mass spectrometry using pyrrolidine, 4,4-dimethyloxazoline, dimethyl disulfide, and hydrogenated derivatives. In some cases, 1Н and 13С NMR spectroscopy was applied for the structural analysis of fatty acids. 71 С12–С28 acids, including 12 new compounds, were found. The new compounds were shown to be (5Z,9Z)-9-chloro-24-methy-5,9-pentacosadienoic, (5Z,9Z)-9-chloro-25-methyl-5,9-hexacosadienoic, (5Z,9Z)-9-chloro-24-methyl-5,9-hexacosadienoic, (5Z,9Z)-9-chloro-25-methyl-5,9-heptacosadienoic, 6-chloro-20-methyl-4-heneicosenoic, 6-chloro-19-methyl-4-heneicosenoic, 6-chloro-20-methyl-4-docosenoic, cis-17,18-methylene-tetracosanoic, 16,21-dimethyldocosanoic, 18,23-dimethyltetracosanoic, 16,18,22-trimethyltricosanoic, and 18,20,24-trimethylpentacosanoic acids. It was shown that the characteristic features of the fatty acid mixture were a high level of constituents with monomethylated chains (over 50%) and the nearly total substitution of common demospongic acids for their chloro-derivatives, previously unknown (5Z,9Z)-9-chloro-5,9-dienoic acids. The presence of analogous structural fragments in the fatty acids from Penares sp. and in some biologically active secondary metabolites from Penares sponges was discussed. The results of this work may be used for the structural, comparative and biosynthetic studies of marine lipids.

Study on the Mass Spectrometry Fragmentation Patterns for Rapid Screening and Structure Identification of Ketamine Analogues in Illicit Powders.

Ketamine analogues have been emerging in recent years and are causing severe health and social problems worldwide. Ketamine analogues use 2-phenyl-2-aminocyclohexanone as the basic structure and achieve physiological reactions similar to or even more robust than the prototype of ketamine by changing the substituents on the benzene ring (R1 and R2) and amine group (RN1). Therefore, the mass spectrometry (MS) fragmentation pathways and fragments of ketamine analogues have certain regularity. Eight ketamine analogues are systematically investigated by GC-QTOF/MS and LC-Q-Orbitrap MS/MS with the positive mode of electrospray ionization. The MS fragmentation patterns of ketamine analogues are summarized according to high-resolution MS data. The α-cleavage of carbon bond C1-C2 in the cyclohexanone moiety and further losses of CO, methyl radical, ethyl radical and propyl radical are the characteristic fragmentation pathways of ketamine analogues in EI-MS mode. The loss of H2O or the sequential loss of RN1NH2, CO and C4H6 are the distinctive fragmentation pathways of ketamine analogues in ESI-MS/MS mode. Moreover, these MS fragmentation patterns are first introduced for the rapid screening of ketamine analogues in suspicious powder. Furthermore, the structure of the ketamine analogue in suspicious powder is 2-(Methylamino)-2-(o-tolyl)cyclohexan-1-one, which is further confirmed by NMR. This study contributes to the identification of the chemical structure of ketamine analogues, which can be used for the rapid screening of ketamine analogues in seized chemicals.

The Pol III transcriptome: Basic features, recurrent patterns, and emerging roles in cancer.

The RNA polymerase III (Pol III) transcriptome is universally comprised of short, highly structured noncoding RNA (ncRNA). Through RNA-protein interactions, the Pol III transcriptome actuates functional activities ranging from nuclear gene regulation (7SK), splicing (U6, U6atac), and RNA maturation and stability (RMRP, RPPH1, Y RNA), to cytoplasmic protein targeting (7SL) and translation (tRNA, 5S rRNA). In higher eukaryotes, the Pol III transcriptome has expanded to include additional, recently evolved ncRNA species that effectively broaden the footprint of Pol III transcription to additional cellular activities. Newly evolved ncRNAs function as riboregulators of autophagy (vault), immune signaling cascades (nc886), and translation (Alu, BC200, snaR). Notably, upregulation of Pol III transcription is frequently observed in cancer, and multiple ncRNA species are linked to both cancer progression and poor survival outcomes among cancer patients. In this review, we outline the basic features and functions of the Pol III transcriptome, and the evidence for dysregulation and dysfunction for each ncRNA in cancer. When taken together, recurrent patterns emerge, ranging from shared functional motifs that include molecular scaffolding and protein sequestration, overlapping protein interactions, and immunostimulatory activities, to the biogenesis of analogous small RNA fragments and noncanonical miRNAs, augmenting the function of the Pol III transcriptome and further broadening its role in cancer. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Processing > Processing of Small RNAs RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.

Using Digestion by IdeS Protease to Improve Quantification of Degradants in Monoclonal Antibodies by Non-Reducing Capillary Gel Electrophoresis.

Monoclonal antibodies (mAbs) have become predominant therapeutics by providing highly specific mechanisms of action enabling treatment of complex diseases. However, mAbs themselves are highly complex and require thorough testing and characterization to ensure efficacy and patient safety. In this regard, fragmentation is a degradation product of concern. The biotechnology industry uses capillary gel electrophoresis (CGE) to quantify fragmentation by electrophoretically resolving size variants, such as products resulting from partial reduction of interchain disulfides. However, standard CGE methods may not adequately separate less typical fragments, particularly when there is minimal size difference to the parent molecule. For mAb-1, a degradant only ∼11 kDa smaller than the intact mAb (∼149 kDa) was unable to be resolved under typical non-reducing conditions, preventing an accurate purity assessment and precluding tracking of product purity within stability studies. To address these deficiencies, a subunit-based non-reducing CGE method was developed to employ IdeS protease to produce F(ab')2 and Fc fragments, which resulted in baseline resolution of the clipped subunit species from its parent species. This enabled more accurate trending of purity throughout stability studies. Method characterization ensured that this subunit method monitored expected impurities observed by intact non-reducing CGE and thus could suitably replace non-reducing CGE in the release and stability testing panel. It also has the potential to replace reducing CGE based on its tracking of the deglycosylated Fc species. We believe this approach of utilizing proteases to develop subunit CGE methods for release and stability can be applied to other molecules when in need of resolving analogous fragments.

Cu(II) and Zn(II) complexes incorporated with active analogue fragments molecule of the aristolochic acid: Crystal structure and biological activity

Two complexes, [Cu(MDPAc)2(Phen)(H2O)·H2O] (MDPAc = 3,4-(methylenedioxy)phenylacetic-carboxylate, Phen = 1,10-Phenanthroline) and [Zn(MDPAc)2(2,2′-bipy)] (2,2′-bipy = 2,2′-bipyridine), were synthesized and successfully obtained as single crystals. The single-crystal structures of two complexes and the weak intermolecular force in the crystal were analyzed by Hirshfeld surface analysis. The competitive capacity of the complexes about calf thymus DNA (ct-DNA) was analyzed by fluorescence spectroscopy, and their antibacterial activity was determined by paper diffusion method. The cytotoxicity experiments of the complexes were carried out on two kinds of cancer cell lines (HepG, SKOV-3). The results show that the complexes had anti-tumor activity and cytotoxicity. Finally, molecular docking studies of the complexes with PI3K enzyme indicate that the complexes had beneficial biological activity.

Laminin Isoforms in Human Dental Pulp: Lymphatic Vessels Express Laminin-332, and Schwann Cell-Associated Laminin-211 Modulates CD163 Expression of M2-like Macrophages.

Laminin, a basement membrane heterotrimeric glycoprotein composed of α/β/γ subunits, has important tissue-specific functions in the control of cellular behavior. Our recent study showed the colocalization of CD163+ M2-like macrophages with Schwann cells in human dental pulp, leading us to hypothesize that the laminin isoform of Schwann cells is associated with CD163 expression. The present study investigated the distribution of laminin isoforms in human dental pulp and the underlying mechanisms that affect macrophage phenotypes. Immunofluorescence analysis indicated that blood vessels were exclusively positive for laminin α4 and α5, whereas laminin α2 was associated with Schwann cells. Unexpectedly, laminin α3/laminin-332 (α3β3γ2) was detected on lymphatic vessels. In intact and carious teeth, CD163+ cells were associated with laminin α2, whereas CD206 single-positive cells were present inside, outside, and along blood vessels. In vitro incubation of THP-1 macrophages in plates coated with laminin-211/511 or its functionally analogous E8 fragments of α-chain (E8-α) indicated that cell shapes differed between macrophages grown on laminin-211/E8-α2 and macrophages grown on laminin-511/E8-α5. Laminin-211/E8-α2-coated plates upregulated CD163 expression, compared with laminin-511/E8-α5-coated plates. Integrin α3- and integrin α6-neutralizing Abs altered the shape of THP-1 macrophages and upregulated mRNA levels of CD206 and CD163 in macrophages grown on laminin-511; the neutralizing Abs did not affect macrophages grown on laminin-211. These findings suggest that laminin isoforms differentially regulate macrophage behavior via distinct integrin-laminin affinities. Of note, laminin-332 is expressed by pulpal lymphatic vessels, the existence of which has been debated; laminin-211 might have a role in maintaining CD163 expression on macrophages.

β-Ketophosphonates with Pentalenofuran Scaffolds Linked to the Ketone Group for the Synthesis of Prostaglandin Analogs.

β-Ketophosphonates with pentalenofurane fragments linked to the keto group were synthesized. The bulky pentalenofurane skeleton is expected to introduce more hindrance in the prostaglandin analogues of type III, greater than that obtained with the bicyclo[3.3.0]oct(a)ene fragments of prostaglandin analogues I and II, to slow down (retard) the inactivation of the prostaglandin analogues by oxidation of 15α-OH to the 15-keto group via the 15-PGDH pathway. Their synthesis was performed by a sequence of three high yield reactions, starting from the pentalenofurane alcohols 2, oxidation of alcohols to acids 3, esterification of acids 3 to methyl esters 4 and reaction of the esters 4 with lithium salt of dimethyl methanephosphonate at low temperature. The secondary compounds 6b and 6c were formed in small amounts in the oxidation reactions of 2b and 2c, and the NMR spectroscopy showed that their structure is that of an ester of the acid with the starting alcohol. Their molecular structures were confirmed by single crystal X-ray determination method for 6c and XRPD powder method for 6b.

Identification of good and bad fragments of tricyclic triazinone analogues as potential PKC-θ inhibitors through SMILES–based QSAR and molecular docking

Based on the mechanism of action of PKC-θ, the inhibition of this enzyme is considered a potential target for the treatment of autoimmune diseases such as rheumatoid arthritis (RA), inflammatory bowel disease (IBD), and psoriasis. In the present study, 57 structurally diverse tricyclic triazinone analogues as potential PKC-θ inhibitors has been taken into consideration for QSAR analysis through Monte Carlo optimization. QSAR models are developed using the balance of correlation method in the CORAL software with two target functions (TF1 and TF2). The models constructed with IIC are found more robust and authentic. The established QSAR model with best $$ {R}_{\mathrm{calibration}}^2 $$ = 0.9653 for split 3 is considered the topmost model. The predictabilities of the recommended QSAR model are assessed through various statistical parameters. The outlier of each model is also identified using the applicability domain (AD). The common mechanistic interpretation of the increasing and decreasing attributes has been extracted by evaluating the correlation weights of diverse structural attributes obtained in three Monte Carlo optimization runs from two splits, i.e., split 3 and 4. In the last, the result of mechanistic interpretation is validated by performing the docking studies of compounds PKC03, PKC07, PKC16, PKC25, and PKC56 in the experimental structure of protein kinase C-θ (PDB ID: 4Q9Z). The numerical value of the correlation coefficient between calculated activity and binding affinity is found 0.9597. Hence, the developed QSAR models are descriptive and predictive in nature and the results are in sound agreement with the experimental observations.

Complexity assessments for decidable fragments of set theory. II: A taxonomy for ‘small’ languages involving membership

We carry on a long-standing investigation aimed at identifying fragments of set theory that are potentially useful in automated verification with proof-checkers, such as ÆtnaNova, based on the set-theoretic formalism. This note provides a complete taxonomy of the polynomial and the NP-complete fragments consisting of all conjunctions that involve, besides variables intended to range over the von Neumann set-universe, a collection of constructs drawn from the Boolean set operators ∪,∩,∖ and the membership relators ∈ and ∉. This is done in sight of combining the aforementioned taxonomy with one recently put together for analogous fragments involving, in place of the relators ∈ and ∉, the Boolean relators ⊆,= and the predicates ‘⋅=∅’ and ‘Disj(⋅,⋅)’ (respectively meaning ‘the argument set is empty’ and ‘the arguments are disjoint sets’), along with their opposites ‘⊈,≠,⋅≠∅’ and ‘¬Disj(⋅,⋅)’.

Synthesis and Biological Evaluation of 5-benzyl-3-pyridyl-1H-1,2,4-triazole Derivatives as Xanthine Oxidase Inhibitors.

Topiroxostat is an excellent xanthine oxidase (XO) inhibitor, possessing a specific 3,5-diaryl-1,2,4-triazole framework. The present work was aimed to investigate the preliminary structure-activity relationship (SAR) of 2-cyanopyridine-4-yl-like fragments of topiroxostat analogues. A series of 5-benzyl-3-pyridyl-1H-1,2,4-triazole derivatives (1a-j and 2a-j) were designed and synthesized by replacement of the 2-cyanopyridine-4-yl moiety with substituted benzyl groups. XO inhibitory activity in vitro was evaluated. Furthermore, molecular modeling simulations were performed to predict the possible interactions between the synthesized compounds and XO binding pocket. The SARs analysis demonstrated that 3,5-diaryl-1,2,4-triazole framework is not essential; in spite of its lower potency, 5-benzyl-3-pyridyl-1H-1,2,4-triazole is an acceptable scaffold for XO inhibitory activity to some extent. A 3'-nitro and a 4'-sec-butoxy group link to the benzyl moiety will be welcome. Furthermore, the most promising compound, 1h, was identified with an IC50 value of 0.16 μM, and the basis of XO inhibition by 1h was rationalized through the aid of molecular modelling studies. Compound 1h could be a lead compound for further investigation and the present work may provide some insight into the search for more structurally diverse XO inhibitors with topiroxostat as a prototype.

Improving the mass efficiency of a composite launch vehicle head fairing with a sandwich structure

Analysis of practical experience in the construction and operation of the main fairings of launch vehicles has revealed the currently widely used sandwich structures with composite load-bearing sheathing combined with a cellular filler. The considered structures are characterized by a rather large number of parameters whose variation significantly changes the mass of an article.An approach to optimizing such structures as the main fairing of a launch vehicle in terms of mass has been further developed. The approach includes the essentially improved components of fragments of known analogs, previously developed by a team of authors, as well as the new fragments, which were not taken into consideration before. In contrast to known works, the approach has made it possible to solve the complex multi-parametric task on the optimal design of the considered class of equipment, almost without loss of accuracy. To this end, the optimization process was divided into several stages based on the reasonable levels of parameters’ significance that are included in the objective function ‒ a minimal mass. An analysis of effectiveness of the reinforcement structure for bearing sheaths has been performed, as well as the preliminary optimization of a cellular filler’s properties, which significantly simplified the selection of their optimal parameters. It has been shown that at a minimum gain in mass due to the optimal reinforcement scheme, which is approximately 5 % compared to a quasi-homogeneous sheath, there is an actual risk of a two-fold increase in the mass of a sheath when choosing a substantially non-optimal structure of the sheath.The result of this study is the established rational parameters for a scheme of reinforcement of bearing sheaths and a cellular filler, as well as their geometric parameters, which ensured a reduction in the mass of the main fairing in comparison with the basic variant, by 51 % or 118.2 kg. The results obtained allow further development and improvement, with almost no changes in its concept and structure in the direction of integration of auxiliary structural elements of the head fairing into optimization

Electron Ionization of Imidazole and Its Derivative 2-Nitroimidazole

Imidazole (IMI) is a basic building block of many biologically important compounds. Thus, its electron ionization properties are of major interest and essential for the comparison with other molecular targets containing its elemental structure. 2-Nitroimidazole (2NI) contains the imidazole ring together with nitrogen dioxide bound to the C2 position, making it a radiosensitizing compound in hypoxic tumors. In the present study, we investigated electron ionization of IMI and 2NI and determined the mass spectra, the ionization energies, and appearance energies of the most abundant fragment cations. The experiments were complemented by quantum chemical calculations on the thermodynamic thresholds and potential energy surfaces, with particular attention to the calculated transition states for the most important dissociation reactions. In the case of IMI, substantially lower threshold values (up to ~ 1.5 eV) were obtained in the present work compared to the only available previous electron ionization study. Closer agreement was found with recent photon ionization values, albeit the general trend of slightly higher values for the case of electron ionization. The only exception for imidazole was found in the molecular cation at m/z 40 which is tentatively assigned to the quasi-linear HCCNH+/ HCNCH+. Electron ionization of 2NI leads to analogous fragment cations as in imidazole, yet different dissociation pathways must be operative due to the presence of the NO2 group. Regarding the potential radiosensitization properties of 2NI, electron ionization is characterized by dominant parent cation formation and release of the neutral NO radical.

First Report of Cotton leafroll dwarf virus Associated with Cotton Blue Disease Symptoms in Alabama

During 2017, virus-like symptoms were observed in cotton fields in six counties in coastal Alabama infested by the whitefly Bemisia tabaci (Genn.) and cotton aphid Aphis gossypii (Glover). Symptoms consisted of foliar distortion, curling, rolling, bluish-green discoloration, vein-clearing, shortened internodes that resulted in dwarfing of plants, and reduced boll set. Disease incidence ranged from 3 to 30% per field, resulting in approximately 560 kg/ha loss, and affecting 25% of the 50,585-ha cotton crop in Alabama, with a loss of approximately 50,000 bales valued at $19 million dollars. Leaves were collected from symptomatic cotton plants, Gossypium hirsutum L., in Barbour County, AL, during late August and mid-September 2017. Total DNA and RNA were purified and subjected to DNA and RNAseq Illumina Hi-Seq 2500 (paired-end reads, 150-bp) shotgun sequencing. The de novo-assembled DNA contigs yielded no match to viral sequences available in the GenBank database. However, one RNA de novo assembled contig (103 reads) of 1,143 bp (accession no. MK015625), located at nucleotide coordinates 3,830 to 4,972, was annotated as Cotton leafroll dwarf virus (CLRDV) “atypical isolate” from Argentina (KF359947), based on 97.1% similarity and 98% coverage (BLASTn, GenBank). The CLRDV belongs to the genus Polerovirus (family Luteoviridae), which are aphid-transmitted, positive-sense single-stranded RNA viruses with a genome size of approximately 5.8 kb (Distefano et al. 2010). To verify the Illumina results, the polymerase chain reaction (PCR) primer pair AL674F-5′-CCGTAGCGGTCATCGTCTTT/AL1407R-5′-TAACCCTGACACAGTGGGGA was designed based on a region conserved in all six available CLRDV genome sequences (GenBank accession nos. GU167940, HQ827780, KF359946, KF359947, KF906260, and KF906261) and was used in parallel with the primers CLRDV3675F and Pol3982R (Sharman et al. 2015) for reverse transcription PCR amplification of total RNA purified from symptomatic cotton plants (n = 3). An amplicon of the expected size was obtained using the primers, AL674F/1407R and CLRDV3675F/Pol3982R, at 733 bp (accession no. MH883237) and 310 bp (accession no. MH883236) in size, respectively. Bidirectional Sanger sequencing confirmed CLRDV presence, based on the BLASTn score of 94 and 99% similarity for the AL674F/1407R and CLRDV3675F/Pol3982R amplicon sequence, having a closest match to CLRDV from South America (GU167940 and KF906261, respectively). Pairwise distance analysis (Muhire et al. 2014) of the CLRDV fragments from Alabama cotton plants with the analogous genome fragment from the six available CLRDV isolates from South America indicated 91.5 to 99.3% nt sequence identity, suggesting the U.S. isolate is closely related, but not identical, to previously reported CLRDV isolates. The CLRDV, endemic to Africa and/or Asia-Pacific (Ray et al. 2016), was introduced into Brazil and Argentina during 2005 and 2010, respectively (Correa et al. 2005; Distefano et al. 2010). Although A. gossypii is the only known CLRDV vector, and it was prevalent in symptomatic cotton fields during 2017, aphid transmissibility of the Alabama isolate has not been verified. Whether the CLRDV becomes established and causes economic losses to the U.S. cotton crop remains to be determined. To our knowledge, this is the first detection of the exotic CLRDV in U.S. cotton plantings.

Semax as a Universal Drug for Therapy and Research

In this review, based on published experimental and clinical data (1980‒2016), a comparative analysis of the structures and effects of Semax (peptide drug) and its analogue fragments was carried out. The effect of these oligopeptides on various body systems is examined. The multiple effects of Semax for a number of diseases have been collected for a single scheme of corrective processes. The rationale for the long-term therapeutic effects of this peptide drug is presented. A comparative analysis of the temporal dynamics of the expression of certain genes is carried out.

Fragmentation of a Monoclonal Antibody by Peroxotungstate.

Tungsten and tungsten oxide leachates found in glass pre-filled syringes were identified to initiate protein precipitation and aggregation. Here, we tested the possibility of tungsten and tungsten oxide to induce the chemical degradation of proteins via reaction with hydrogen peroxide, a possible impurity present in protein formulations, to yield peroxotungstate. A monoclonal antibody (mAb) was incubated with various concentrations of peroxotungstate and the reaction mixtures analyzed by SDS-PAGE and mass spectrometry. Exposure of a mAb to 1.07-1070ppm peroxotungstate (based on tungsten content) at temperatures of 4°C and 22°C (pH5-7) induced protein fragmentation. The extent of fragmentation increased with higher temperatures, lower pH and higher peroxotungstate concentrations. The mAb fragments were identified to contain different combinations of heavy chains (H) and light chains (L). Analogous mAb fragments were generated when the protein was exposed to H2O2 and orthotungstate at levels as low as 5ppm. In addition, extracts from tungsten pins used to manufacture glass pre-filled syringes, in combination with H2O2 caused comparable fragmentation of the mAb. Mass spectrometric identification of the fragments suggests fragment generation by oxidativedisulfide bond cleavage between the heavy and light chains, confirmed by mass spectrometry data on product formation. The mechanism of oxidative fragmentation was separately confirmed with insulin. Fragmentation of the mAb by peroxotungstate is proposed to occur through inter-chain disulfide bond oxidation to form thiosulfinate (CyS(═O)SCy) and thiosulfonate [CyS(═O)2SCy], followed by hydrolysis.

The action of a negative allosteric modulator at the dopamine D2 receptor is dependent upon sodium ions

Sodium ions (Na+) allosterically modulate the binding of orthosteric agonists and antagonists to many class A G protein-coupled receptors, including the dopamine D2 receptor (D2R). Experimental and computational evidences have revealed that this effect is mediated by the binding of Na+ to a conserved site located beneath the orthosteric binding site (OBS). SB269652 acts as a negative allosteric modulator (NAM) of the D2R that adopts an extended bitopic pose, in which the tetrahydroisoquinoline moiety interacts with the OBS and the indole-2-carboxamide moiety occupies a secondary binding pocket (SBP). In this study, we find that the presence of a Na+ within the conserved Na+-binding pocket is required for the action of SB269652. Using fragments of SB269652 and novel full-length analogues, we show that Na+ is required for the high affinity binding of the tetrahydroisoquinoline moiety within the OBS, and that the interaction of the indole-2-carboxamide moiety with the SBP determines the degree of Na+-sensitivity. Thus, we extend our understanding of the mode of action of this novel class of NAM by showing it acts synergistically with Na+ to modulate the binding of orthosteric ligands at the D2R, providing opportunities for fine-tuning of modulatory effects in future allosteric drug design efforts.

Evolutionarily recent, insertional fission of mitochondrial cox2 into complementary genes in bilaterian Metazoa

BackgroundMitochondrial genomes (mtDNA) of multicellular animals (Metazoa) with bilateral symmetry (Bilateria) are compact and usually carry 13 protein-coding genes for subunits of three respiratory complexes and ATP synthase. However, occasionally reported exceptions to this typical mtDNA organization prompted speculation that, as in protists and plants, some bilaterian mitogenomes may continue to lose their canonical genes, or may even acquire new genes. To shed more light on this phenomenon, a PCR-based screen was conducted to assess fast-evolving mtDNAs of apocritan Hymenoptera (Arthropoda, Insecta) for genomic rearrangements that might be associated with the modification of mitochondrial gene content.ResultsSequencing of segmental inversions, identified in the screen, revealed that the cytochrome oxidase subunit II gene (cox2) of Campsomeris (Dielis) (Scoliidae) was split into two genes coding for COXIIA and COXIIB. The COXII-derived complementary polypeptides apparently form a heterodimer, have reduced hydrophobicity compared with the majority of mitogenome-encoded COX subunits, and one of them, COXIIB, features increased content of Cys residues. Analogous cox2 fragmentation is known only in two clades of protists (chlorophycean algae and alveolates), where it has been associated with piecewise relocation of this gene into the nucleus. In Campsomeris mtDNA, cox2a and cox2b loci are separated by a 3-kb large cluster of several antiparallel overlapping ORFs, one of which, qnu, seems to encode a nuclease that may have played a role in cox2 fission.ConclusionsAlthough discontinuous mitochondrial protein genes encoding fragmented, complementary polypeptides are known in protists and some plants, split cox2 of Campsomeris is the first case of such a gene arrangement found in animals. The reported data also indicate that bilaterian animal mitogenomes may be carrying lineage-specific genes more often than previously thought, and suggest a homing endonuclease-based mechanism for insertional mitochondrial gene fission.

Novel chemical degradation pathways of proteins mediated by tryptophan oxidation: tryptophan side chain fragmentation.

This minireview focuses on novel degradation pathways of proteins in solution via intermediary tryptophan (Trp) radical cations, which are generated via photo-induced electron transfer to suitable acceptors such as disulfide bonds. Gas-phase mass spectrometry studies had indicated the potential for Trp radical cations to fragment via release of 3-methylene-3H-indol-1-ium from the side chain. HPLC-MS/MS analysis demonstrates that analogous fragmentation reactions occur during the exposure of peptides and proteins to light or accelerated stability testing. The light exposure of selected peptides and monoclonal antibodies leads to the conversion of Trp to glycine (Gly) or glycine hydroperoxide (GlyOOH), where GlyOOH could be reduced to hydroxyglycine, which undergoes subsequent cleavage. Product formation is consistent with Cα -Cβ fragmentation of intermediary Trp radical cations. For the peptide octreotide and specific glycoforms of IgG1 Fc domains, Trp side chain cleavage in aqueous solution is indicated by the formation of 3-methyleneindolenine (3-MEI), which adds to nucleophilic side chains, for example to Lys residues adjacent to the original Trp residues. Trp side chain cleavage leads to novel reaction products on specific peptide and protein sequences, which may have consequences for potency and immunogenicity.

Answer to professor H. Werheit’s comment on the article “Is linear group X–Y–Z in boron carbide the weakest link in the structure?”

The author of the comment and the authors of the paper speak about different things. The paper considered the structure of a fragment of the boron carbide structure. The results of quantum-chemical calculations were compared with the structure of the analogous fragments of boron carbide single crystals and their derivatives. The author of the comment analyzed the structure of polycrystals only on the basis of their IR and Raman spectral studies.