Inactive Pair Research Articles

Irreversible light-activated SpyLigation mediates split-protein assembly in 4D.

The conditional assembly of split-protein pairs to modulate biological activity is commonly achieved by fusing split-protein fragments to dimerizing components that bring inactive pairs into close proximity in response to an exogenous trigger. However, current methods lack full spatial and temporal control over reconstitution, require sustained activation and lack specificity. Here light-activated SpyLigation (LASL), based on the photoregulation of the covalent SpyTag (ST)/SpyCatcher (SC) peptide-protein reaction, assembles nonfunctional split fragment pairs rapidly and irreversibly in solution, in engineered biomaterials and intracellularly. LASL introduces an ortho-nitrobenzyl(oNB)-caged lysine into SC's reactive site to generate a photoactivatable SC (pSC). Split-protein pairs of interest fused to pSC and ST are conditionally assembled via near-ultraviolet or pulsed near-infrared irradiation, as the uncaged SC can react with ST to ligate appended fragments. We describe procedures for the efficient synthesis of the photocaged amino acid that is incorporated within pSC (<5 days) as well as the design and cloning of LASL plasmids (1-4 days) for recombinant protein expression in either Escherichia coli (5-6 days) or mammalian cells (4-6 days), which require some prior expertise in protein engineering. We provide a chemoenzymatic scheme for appending bioorthogonal reactive handles onto E. coli-purified pSC protein (<4 days) that permits LASL component incorporation and patterned protein activation within many common biomaterial platforms. Given that LASL is irreversible, the photolithographic patterning procedures are fast and do not require sustained light exposure. Overall, LASL can be used to interrogate and modulate cell signaling in various settings.

Exploring kinase family inhibitors and their moiety preferences using deep SHapley additive exPlanations

BackgroundWhile it has been known that human protein kinases mediate most signal transductions in cells and their dysfunction can result in inflammatory diseases and cancers, it remains a challenge to find effective kinase inhibitor as drugs for these diseases. One major challenge is the compensatory upregulation of related kinases following some critical kinase inhibition. To circumvent the compensatory effect, it is desirable to have inhibitors that inhibit all the kinases belonging to the same family, instead of targeting only a few kinases. However, finding inhibitors that target a whole kinase family is laborious and time consuming in wet lab.ResultsIn this paper, we present a computational approach taking advantage of interpretable deep learning models to address this challenge. Specifically, we firstly collected 9,037 inhibitor bioassay results (with 3991 active and 5046 inactive pairs) for eight kinase families (including EGFR, Jak, GSK, CLK, PIM, PKD, Akt and PKG) from the ChEMBL25 Database and the Metz Kinase Profiling Data. We generated 238 binary moiety features for each inhibitor, and used the features as input to train eight deep neural networks (DNN) models to predict whether an inhibitor is active for each kinase family. We then employed the SHapley Additive exPlanations (SHAP) to analyze the importance of each moiety feature in each classification model, identifying moieties that are in the common kinase hinge sites across the eight kinase families, as well as moieties that are specific to some kinase families. We finally validated these identified moieties using experimental crystal structures to reveal their functional importance in kinase inhibition.ConclusionWith the SHAP methodology, we identified two common moieties for eight kinase families, 9 EGFR-specific moieties, and 6 Akt-specific moieties, that bear functional importance in kinase inhibition. Our result suggests that SHAP has the potential to help finding effective pan-kinase family inhibitors.

Set-Theoretic Formalism for Treating Ligand-Target Datasets.

Data on ligand–target (LT) interactions has played a growing role in drug research for several decades. Even though the amount of data has grown significantly in size and coverage during this period, most datasets remain difficult to analyze because of their extreme sparsity, as there is no activity data whatsoever for many LT pairs. Even within clusters of data there tends to be a lack of data completeness, making the analysis of LT datasets problematic. The current effort extends earlier works on the development of set-theoretic formalisms for treating thresholded LT datasets. Unlike many approaches that do not address pairs of unknown interaction, the current work specifically takes account of their presence in addition to that of active and inactive pairs. Because a given LT pair can be in any one of three states, the binary logic of classical set-theoretic methods does not strictly apply. The current work develops a formalism, based on ternary set-theoretic relations, for treating thresholded LT datasets. It also describes an extension of the concept of data completeness, which is typically applied to sets of ligands and targets, to the local data completeness of individual ligands and targets. The set-theoretic formalism is applied to the analysis of simple and joint polypharmacologies based on LT activity profiles, and it is shown that null pairs provide a means for determining bounds to these values. The methodology is applied to a dataset of protein kinase inhibitors as an illustration of the method. Although not dealt with here, work is currently underway on a more refined treatment of activity values that is based on increasing the number of activity classes.

A Cooperative Jamming Based Joint Transceiver Design for Secure Communications in MIMO Interference Channels

In this paper, we investigate the problem of secure communications in multiple-input-multiple-output interference networks from the perspective of physical layer security. Specifically, the legitimate transmitter-receiver pairs are divided into different categories of active and inactive. To enhance the security performances of active pairs, inactive pairs serve as cooperative jammers and broadcast artificial noises to interfere with the eavesdropper. Besides, active pairs improve their own security by using joint transceivers. The encoding of active pairs and inactive pairs are designed by maximizing the difference of mean-squared errors between active pairs and the eavesdropper. In detail, the transmit precoder matrices of active pairs and inactive pairs are solved according to game theory and linear programming respectively. Experimental results show that the proposed algorithm has fast convergence speed, and the security performances in different scenarios are effectively improved.

Toward an electrophysiological "sweet spot" for deep brain stimulation in the subthalamic nucleus.

Enhanced beta-band activity recorded in patients suffering from Parkinson's Disease (PD) has been described as a potential physiomarker for disease severity. Beta power is suppressed by Levodopa intake and STN deep brain stimulation (DBS) and correlates with disease severity across patients. The aim of the present study was to explore the promising signature of the physiomarker in the spatial domain. Based on local field potential data acquired from 54 patients undergoing STN-DBS, power values within alpha, beta, low beta, and high beta bands were calculated. Values were projected into common stereotactic space after DBS lead localization. Recorded beta power values were significantly higher at posterior and dorsal lead positions, as well as in active compared with inactive pairs. The peak of activity in the beta band was situated within the sensorimotor functional zone of the nucleus. In contrast, higher alpha activity was found in a more ventromedial region, potentially corresponding to associative or premotor functional zones of the STN. Beta- and alpha-power peaks were then used as seeds in a fiber tracking experiment. Here, the beta-site received more input from primary motor cortex whereas the alpha-site was more strongly connected to premotor and prefrontal areas. The results summarize predominant spatial locations of frequency signatures recorded in STN-DBS patients in a probabilistic fashion. The site of predominant beta-activity may serve as an electrophysiologically determined target for optimal outcome in STN-DBS for PD in the future. Hum Brain Mapp 38:3377-3390, 2017. © 2017 Wiley Periodicals, Inc.

SparseMaps--A systematic infrastructure for reduced-scaling electronic structure methods. III. Linear-scaling multireference domain-based pair natural orbital N-electron valence perturbation theory.

Multi-reference (MR) electronic structure methods, such as MR configuration interaction or MR perturbation theory, can provide reliable energies and properties for many molecular phenomena like bond breaking, excited states, transition states or magnetic properties of transition metal complexes and clusters. However, owing to their inherent complexity, most MR methods are still too computationally expensive for large systems. Therefore the development of more computationally attractive MR approaches is necessary to enable routine application for large-scale chemical systems. Among the state-of-the-art MR methods, second-order N-electron valence state perturbation theory (NEVPT2) is an efficient, size-consistent, and intruder-state-free method. However, there are still two important bottlenecks in practical applications of NEVPT2 to large systems: (a) the high computational cost of NEVPT2 for large molecules, even with moderate active spaces and (b) the prohibitive cost for treating large active spaces. In this work, we address problem (a) by developing a linear scaling "partially contracted" NEVPT2 method. This development uses the idea of domain-based local pair natural orbitals (DLPNOs) to form a highly efficient algorithm. As shown previously in the framework of single-reference methods, the DLPNO concept leads to an enormous reduction in computational effort while at the same time providing high accuracy (approaching 99.9% of the correlation energy), robustness, and black-box character. In the DLPNO approach, the virtual space is spanned by pair natural orbitals that are expanded in terms of projected atomic orbitals in large orbital domains, while the inactive space is spanned by localized orbitals. The active orbitals are left untouched. Our implementation features a highly efficient "electron pair prescreening" that skips the negligible inactive pairs. The surviving pairs are treated using the partially contracted NEVPT2 formalism. A detailed comparison between the partial and strong contraction schemes is made, with conclusions that discourage the strong contraction scheme as a basis for local correlation methods due to its non-invariance with respect to rotations in the inactive and external subspaces. A minimal set of conservatively chosen truncation thresholds controls the accuracy of the method. With the default thresholds, about 99.9% of the canonical partially contracted NEVPT2 correlation energy is recovered while the crossover of the computational cost with the already very efficient canonical method occurs reasonably early; in linear chain type compounds at a chain length of around 80 atoms. Calculations are reported for systems with more than 300 atoms and 5400 basis functions.

Social interactions and their connection to aggression and ovarian development in orphaned worker bumblebees (Bombus impatiens)

This study examines the social dynamics of reproductive conflict. Orphaned worker bumblebees (Bombus impatiens) with comparatively high or low levels of social activity were paired to determine whether aggression and reproduction could be traced to earlier social interactions. The workers were paired according to their levels of social activity (a socially active+another socially active worker, socially active+socially inactive, and two socially inactive workers). The presence or absence of brood was also manipulated. The absence of brood increased both aggression and ovarian development, suggesting that aggression and reproduction are associated or that there is a third variable that affects both. Socially active pairs were significantly more aggressive: here, social activity can be taken as an early indicator of aggression. No such effect, however, was obtained on ovarian development as the socially active pairs did not differ on their degree of ovarian development compared to the others. Within the socially active+socially inactive pairs, the socially active worker did not have more developed ovaries and was not more aggressive than her socially inactive partner. Results highlight that environmental conditions (the absence of brood) can predict ovarian development and although social activity can be observed prior to aggression, differences in aggression do not translate into differences in ovarian development under these conditions.

Aminoquinoline Melanin-Concentrating Hormone 1-Receptor (MCH1-R) Antagonists

Structure-activity relationships of a 4-aminoquinoline MCH-1R antagonist lead series were explored by synthesis of analogs with modifications at the 2-, 4- and 6-positions of the original HTS hit. Improvements to the original screening lead were made by addition of lipophilic groups at the 2-position and biphenyl, cyclohexyl phenyl and hydrocinnamyl carboxamides at the 6-position. Viable modifications of the 4-amino group were limited and did not allow further optimization of the physical-chemical properties of this class of compounds. Transposition of the 4-amino group to the 2-position of the quinoline core structure provided the 2-aminoquinoline lead class with similar MCH1R binding affinity. A series of 2-aminoquinoline compounds was prepared and evaluated in MCH-1R binding and functional antagonist assays. Small dialkyl, methylalkyl, methylcycloalkyl and cyclic amines along with 3-substituted pyrrolidines were tolerated at the quinoline 2-position. The in vivo efficacy of compound A was explored and compared to that of a related inactive compound B to determine their effects on food intake and body weight in rodents. The biological activities of this matched active -inactive pair provide in vivo proof of concept in rodents that antagonism of MCH1R by a 2-aminoquinoline MCH1R antagonist which led to a reduction of food intake in an acute feeding assay paradigm.

A practical valence bond method: a configuration interaction method approach with perturbation theoretic facility.

The previously developed valence bond configuration interaction (VBCI) method (Wu, W.; Song, L.; Cao, Z.; Zhang, Q.; Shaik, S., J. Phys. Chem. A, 2002, 105, 2721) that borrows the general CI philosophy of the MO theory, is further extended in this article, and its methodological features are improved, resulting in three accurate and cost-effective procedures: (a) the effect of quadruplet excitation is incorporated using the Davidson correction, such that the new procedure reduces size consistency problems, with due improvement in the quality of the computational results. (b) A cost-effective procedure, named VBCI(D, S), is introduced. It includes doubly excited structures for active electrons and singly excited structures for inactive pairs. The computational results of VBCI(D, S) match those of VBCISD with much less computational effort than VBCISD. (c) Finally, a second-order perturbation theory is utilized as a means of configuration selection, and lead to considerable reduction of the computational cost, with little or no loss in accuracy. Applications of the new procedures to bond energies and barriers of chemical reactions are presented and discussed.

Optical and electrical properties of semi-insulating GaN:C grown by MBE

ABSTRACTSemi-insulating wurtzite GaN:C of high optical quality is obtained with CCl4or CS2 doping sources in plasma-assisted molecular-beam epitaxy in Ga-rich growth conditions. The highest resistivity (107Ω-cm) is found for [C] in the low 1018cm−3range. An increasing fraction of carbon appears to form electrically inactive pair defects for higher doping levels causing the concentration of uncompensated residual donors to be higher in films with [C] in the 1019cm−3range compared with [C] in the 1018cm−3range. Blue (2.9 eV) and yellow (2.2 eV) luminescence bands are associated with carbon-related defects, and additional support is provided for the association of the blue luminescence with the carbon-acceptor deactivating pair defect. Finally, the temperature dependence of the resistivity is described within the grain-boundary controlled transport model of Salzmanet al., Appl. Phys. Lett.76, 1431 (2000).

Behavioural risk factors in the reproduction of inbred and outbred oldfield mice

The present study investigated two rarely measured aspects of inbreeding depression: the relationship between inbreeding and behaviour, and the possibility that inbred individuals that survive infancy may still suffer from inbreeding depression by failing to breed or failing to show appropriate mating or parental behaviours. Specifically, the relationship between (1) behaviour at pairing and reproductive success, (2) inbreeding and reproductive success and (3) inbreeding and pairing behaviour, was examined in two subspecies of the oldfield mouse,Peromyscus polionotusEffects of parental and offspring inbreeding were separated through experimental design and analysis. Activity level during the first 25 days after pairing predicted future reproductive success: pairs that remained less active during the nocturnal (active) period were significantly less likely to breed than pairs that remained more active. Inbred females took significantly longer to produce their first litters and were less likely to produce litters than were outbred females, independently of whether females were related to their mates (i.e. whether their offspring would be inbred). Inactive pairs averaged fewer surviving pups than did active pairs. Inbreeding coefficient of female was a significant predictor of activity level in one of the two subspecies, suggesting that inbreeding may affect behaviour. Inbred adult females showed inbreeding depression in the form of lower conception rates and fewer surviving offspring, although the specific traits affected differed for the two subspecies. The implications for captive breeding programs, and likely causes of the subspecific differences, are discussed.

Raman study of an active and inactive pair of anticonvulsant compounds: 1-benzyl-5,5-diphenyl-2,4-dioxo-3-imidazolidineacetic acid and 3-(2,4-dichlorobenzyl)-5,5-diphenyl-2,4-dioxo-1-imidazolidineacetic acid

Raman study of an active and inactive pair of anticonvulsant compounds: 1-benzyl-5,5-diphenyl-2,4-dioxo-3-imidazolidineacetic acid and 3-(2,4-dichlorobenzyl)-5,5-diphenyl-2,4-dioxo-1-imidazolidineacetic acid

Pulsed magnetic fields improve osteoblast activity during the repair of an experimental osseous defect.

The influence of pulsed low-frequency electromagnetic fields (PEMFs) on bone formation was investigated in studies of the healing process of transcortical holes, bored at the diaphyseal region of metacarpal bones of six adult horses, exposed for 30 days to PEMFs (28 G peak amplitude, 1.3 ms rise time, and 75 Hz repetition rate). A pair of Helmholtz coils, continuously powered by a pulse generator, was applied for 30 days to the left metacarpal bone, through which two holes, of equal diameter and depth, had been bored at the diaphyseal region. Two equal holes, bored at the same level in the right metacarpal and surrounded by an inactive pair of Helmholtz coils, were used as controls. All horses were given an intravenous injection of 25-30 mg/kg of tetracycline chloride on the 15th and again on the 25th day after the operation and were killed 5 days later. The histomorphometric analysis indicated that both the amount of bone formed during 30 days and the mineral apposition rate during 10 days (deduced from the interval between the two tetracycline labels) were significantly greater (p < 0.01 and p < 0.0001, respectively) in the PEMF-treated holes than in the controls. As did a previous investigation, these preliminary findings indicate that PEMFs at low frequency not only stimulate bone repair but also seem to improve the osteogenic phase of the healing process, at least in our experimental conditions.