Recognition mechanism and sequence optimization of organophosphorus pesticides aptamers for better monitoring contaminations in food

Aptamers as a kind of biological recognition element have shown great potential in monitoring and the rapid quantification of organophosphorus pesticides(OPPs). However, molecules of OPPs are structurally similar and original aptamers selected by systematic evolution of ligands by exponential enrichment are usually long-chain bases, which hamper the further application under OPPs-aptamer recognition. The aim of the research was to develop a new strategy to design oligonucleotide sequences for binding OPPs by combination of experimental and molecular modeling methods. 3D models of aptamers binding OPPs were constructed, and binding energy and the most probable binding site for the OPPs were then determined by molecular docking, and the binding sites were further confirmed by the results of 2-AP replaced experiments. Based on the docking results, a new aptamer for detection 4 representative OPPs with only 29 bases was designed by reasonable truncation and mutation of the reported aptamer(named S4-29). The interaction between this new aptamer and OPPs were analyzed by molecular docking, microscale thermophoresis, circular dichroism and fluorometric analysis. The results revealed that the new aptamer exhibit more superior recognition performance to OPPs, which can be promote the monitoring ability of OPPs contaminations in food.

Egg rejection and egg recognition mechanisms in Oriental Reed Warblers

Background:Nest parasitism by cuckoos(Cuculus spp.)results in enormous reproductive failure and forces hosts to evolve antiparasitic strategies,i.e.,recognition of own eggs and rejection of cuckoo eggs.There are often sexual conflicts between male and female individuals in the expression of antiparasitic behavior due to the differences in reproductive inputs and division of labor.Methods:By adding a foreign egg made of blue soft clay to the host nest during early incubation period in the field,and by removing several host eggs and adding experimental eggs to control the proportion of two egg types in the nest,we examined egg rejection ability,egg recognition mechanism and sexual difference in egg rejection of the Oriental Reed Warbler(Acrocephalus orientalis),one of the major hosts of Common Cuckoos(Cuculus canorus).Results:Our results indicated that Oriental Reed Warblers can recognize and reject nearly 100%(73/75)of the nonmimetic eggs made of blue soft clay,and they could reject foreign eggs with 100%accuracy,regardless of the ratio of experimental eggs and its own eggs in the nest.Furthermore,all cases of egg rejections recorded by videos were only carried out by females.Conclusions:Oriental Reed Warblers have a high egg recognition ability and show a true recognition mechanism.Only female warblers perform egg rejection,suggesting that the sex for host egg incubation seems to play an important role in the evolution of egg recognition mechanisms.

Molecular dynamics simulation reveals DNA-specific recognition mechanism via c-Myb in pseudo-palindromic consensus of mim-1 promoter

This study aims to gain insight into the DNA-specific recognition mechanism of c-Myb transcription factor during the regulation of cell early differentiation and proliferation.Therefore,we chose the chicken myeloid gene,mitochondrial import protein 1(mim-1),as a target to study the binding specificity between potential dual-Myb-binding sites.The c-Myb-binding site in mim-1 is a pseudo-palindromic sequence AACGGTT,which contains two AACNG consensuses.Simulation studies in different biological scenarios revealed that c-Myb binding with mim-1 in the forward strand(complex F)is more stable than that in the reverse strand(complex R).The principal component analysis(PCA)dynamics trajectory analyses suggested an opening motion of the recognition helices of R2 and R3(R2R3),resulting in the dissociation of DNA from c-Myb in complex R at 330 K,triggered by the reduced electrostatic potential on the surface of R2R3.Furthermore,the DNA confirmation and hydrogen-bond interaction analyses indicated that the major groove width of DNA increased in complex R,which affected on the hydrogenbond formation ability between R2R3 and DNA,and directly resulted in the dissociation of DNA from R2R3.The steered molecular dynamics(SMD)simulation studies also suggested that the electrostatic potential,major groove width,and hydrogen bonds made major contribution to the DNA-specific recognition.In vitro trials confirmed the simulation results that c-Myb specifically bound to mim-1 in the forward strand.This study indicates that the three-dimensional(3D)structure features play an important role in the DNA-specific recognition mechanism by c-Myb besides the AACNG consensuses,which is beneficial to understanding the cell early differentiation and proliferation regulated by c-Myb,as well as the prediction of novel c-Myb-binding motifs in tumorigenesis.

Preparation and interaction mechanism analysis of single‑chain fragment variables against phenylethanolamine A

This is the first report on the screening,expression,and recognition mechanism analysis of single-chain fragment variable(scFv)against phenylethanolamine A(PEAA),a newly emergedβ-adrenergic agonist illegally used as a feed additive for growth promotion.The PEAA-specific scFv scFv,called scFv-32,was screened from hybridoma cell lines by phage display and was found to be optimally expressed in the E.coli system.The ic-ELISA results revealed an IC_(50)value of 10.34μg/L for scFv-32 and no cross-reactivity with otherβ-adrenergic agonists.Homology modeling and molecular docking revealed the key binding sites VAL178,TYP228,and ASP229.One hydrogen bond,two pisigma bonds,and one pi-pi bond maintain the formation of the antibody‒drug complex.Alanine scanning mutagenesis of the three predicted key binding sites showed that the mutants completely lost their recognition activity,which confirmed the accuracy of the theoretical analysis.These results are valuable for the preparation of scFvs and the analysis of the molecular recognition mechanism of antigen-antibodies.

Study of chiral recognition mechanism of O,O-diethyl (p-methylbenzenesulfonamindo)-aryl(alkyl)-methylphosphonates by HPLC with a series of CSPs

Five chiral stationary phases (CSPs) were used to separate the enantiomers of a series of O,O-diethyl (p-methyl-benzenesulfonamindo)-aryl(alkyl)-methylphosphonates. A chiral recognition mechanism was presented to explain the resolution of these compounds. Results show that CSP with strong π-acceptor 3,5-dinitrobenzoyl group and high steric hindrance has the best resolution ability in chiral separation of O,O-diethyl (p-methylbenzenesulfonamindo)-aryl(alkyl)-methylphosphonates. When a CSP has just a strong π-acceptor 3,5-dinitrobenzoyl or high steric hindrance it does not have good chiral resolution ability. The chiral recognition is more difficult when the CSP has more than one asymmetric center.

Recognition of an additional mechanism leading to myocardial abnormalities

A growing body of evidence explicitly suggests the significant role of inflammatory processes in the development and progressive deterioration of vascular diseases and cardiomyopathies.1-3 In recent years, a large variety of infections have been reported to be associated with the development of cardiomyopathy; the pathogenic factors include rickets, bacteria, protozoa and other parasites,and also, at least 17 viruses.2。

Development of a competitive array for discriminative determination of amphenicols in egg based on ribosomal protein L16

Objective:Amphenicols(chloramphenicol,thiamphenicol and forfenicol)can cause aplastic anaemia and other severe side effects to consumers;therefore,it is necessary to inspect their residues in foods of animal origin.However,there has been no report on the use of amphenicols receptor for the determination of their residues,and none of the previously reported immunoassays for amphenicols can differentiate the specifc species.Materials and Methods:In this study,the ribosomal protein L16 of Escherichia coli was frst expressed,and its intermolecular interaction mechanisms with the three amphenicols was studied using the molecular docking technique.The protein was then combined with three enzymelabelled conjugates to develop a direct competitive array on microplate for determination of the three drugs in egg.Results:Due to the use of principal component analysis to analyse the data,this method could discriminate the three drugs in the range 0.1–10 ng/mL,and the limits of detection for the three drugs were in the range of 0.0002–0.0009 ng/mL.The analysis results for the unknown egg samples were consistent with a liquid chromatography–tandem mass spectrometry method,and the method performances were superior to the previous immunoassays for amphenicols.Conclusion:This is the frst paper reporting the use of ribosomal protein L16 to develop a competitive array for discriminative determination of amphenicols in food samples.

哺乳动物TRIM71蛋白RNA结合特性的分子机制研究

TRIM71 is an RNA-binding protein with ubiquitin ligase activity.Numerous functions of mammalian TRIM71,including cell cycle regulation,embryonic stem cell(ESC)self-renewal,and reprogramming of pluripotent stem cells,are related to its RNA-binding property.We previously reported that a long noncoding RNA(lnc RNA)Trincr1 interacts with mouse TRIM71(m TRIM71)to repress FGF/ERK pathway in mouse ESCs(m ESCs).Herein,we identify an RNA motif specifically recognized by m TRIM71 from Trincr1 RNA,and solve the crystal structure of the NHL domain of m TRIM71 complexed with the RNA motif.Similar to the zebrafish TRIM71,m TRIM71 binds to a stem-loop structured RNA fragment of Trincr1,and an adenosine base at the loop region is crucial for the m TRIM71 interaction.We map similar hairpin RNAs preferably bound by TRIM71 in the m RNA UTRs of the cell-cycle related genes regulated by TRIM71.Furthermore,we identify key residues of m TRIM71,conserved among mammalian TRIM71 proteins,required for the RNA-binding property.Single-site mutations of these residues significantly impair the binding of TRIM71 to hairpin RNAs in vitro and to m RNAs of Cdkn1a/p21 and Rbl2/p130 in m ESCs.Furthermore,congenital hydrocephalus(CH)specific mutation of m TRIM71 impair its binding to the RNA targets as well.These results reveal molecular mechanism behind the recognition of RNA by mammalian TRIM71 and provide insights into TRIM71 related diseases.

Fluorescent probes for recognition of ATP

Adenosine 5＇-triphosphate（ATP） not only participates in various physiological activities as the universal energy currency but also implicates in various pathological processes in living cells. Consequently,sensitive and selective detection ATP in live cells, tissues, as well as environmental samples, are urgently demanded. Due to the simple and convenient operation, economy cost, high selectivity for analyte, well biocompatibility and low cytotoxicity, fluorescent sensors for monitoring ATP have aroused great attention of researchers. In recent years, a large number of fluorescent sensors for detecting ATP have developed. This manuscript summarized most of these sensors and the interaction-mechanism between ATP and sensors, mainly including electrostatic interaction, p-p interaction, covalent bonding or hydrogen bond, or combinations of them, and the advantages of each strategy were also generalized.Here, a viewpoint of classification was shown where the sensors were divided into five typed ones according to the structure of probes used.

Structural insight into chitin perception by chitin elicitor receptor kinase 1 of Oryza sativa

Plants have developed innate immune systems to fight against pathogenic fungi by monitoring pathogenic signals known as pathogen-associated molecular patterns(PAMP)and have established endo symbiosis with arbuscular mycorrhizal(AM)fungi through recognition of mycorrhizal(Myc)factors.Chitin elicitor receptor kinase 1 of Oryza sativa subsp.Japonica(OsC ERK1)plays a bifunctional role in mediating both chitin-triggered immunity and symbiotic relationships with AM fungi.However,it remains unclear whether OsC ERK1 can directly recognize chitin molecules.In this study,we show that OsC ERK1 binds to the chitin hexamer((NAG)6)and tetramer((NAG)4)directly and determine the crystal structure of the OsC ERK1-(NAG)6complex at 2?.The structure shows that one OsC ERK1 is associated with one(NAG)6.Upon recognition,chitin hexamer binds OsC ERK1 by interacting with the shallow groove on the surface of LysM 2.These structural findings,complemented by mutational analyses,demonstrate that LysM 2 is crucial for recognition of both(NAG)6and(NAG)4.Altogether,these findings provide structural insights into the ability of OsC ERK1 in chitin perception,which will lead to a better understanding of the role of OsCERK1 in mediating both immunity and symbiosis in rice.

Stereoselective interactions of chiral dipeptides on amylose based chiral stationary phases

Dipeptides are stereo-specifically involved in several biological functions that are challenging to separate enantiomerically. Elution order of enantiomers is an important issue in chiral chromatography. Amylose tris-(3,5-dimethylphenylcarbamate) chiral stationary phase(CSP) is the best and most-widely-used CSP in chiral separations, but experimental data of enantiomeric separation of dipeptides on this CSP is lacking. Simulation studies were conducted to determine the order of elution and the chiral recognition mechanism of didpetides on this CSP. Results indicated that the docking energy of SR-enantiomers were higher than SS-antipodes. The range of docking energies for SR-enantiomers was -7.44 to -5.92 kcal/mol with CSP, but -7.15 to -5.87 kcal/mol for SS-stereoisomers. Therefore it is predicted that SS-enantiomer will elute first, followed by SR-antipode. Furthermore, hydrogen bondings, van der Waal's interactions and electrostatic interactions were observed among SR- and SSenantiomers and chiral grooves of CSP. The number of hydrogen bonds was one in each enantiomer binding except S-Ala-R-Tyr, which contained two hydrogen bonds. No hydrogen bond was found in S-Ala-R-Trp, S-Leu-S-Trp, and S-Leu-S-Tyr dipeptides bindings. The chiral recognition mechanisms dictate different strengths of stereoselective bindings of the enantiomers on CSP.

A New Biselector Chiral Stationary Phase Derived from Tartaric Acid and Its Enantioseparation Evaluation

Two chiral selectors were synthesized from tartaric acid. The selectors were simultaneously immobilized on 3-aminopropyl silica gel to obtain a new biselector chiral stationary phase （CSP） in order to determine the influence of selector structure of biselector CSPs on the chiral recognition capability. For comparison, the single-selector CSP was also prepared. The biselector CSP shows an improved overall chiral recognition capability in comparison with the single-selector CSP. During the enantioseparation, temporary diastereoisomers are likely formed by complexation between a chiral analyte and the two selectors on the biselector CSP. The functional groups in the two selectors are complementary in electronic effect and/or in steric hindrance for the chiral recognition.

Preparation and characterization of phenyl carbamate derivative P-cyclodextrin bonded phase for chiral HPLC

A partially substituted β-cyclodextrin chiral stationary phase was prepared by the reaction of phenyl isocyanate. The enantiomers of a series of O,O-diethyl(p-methylbenzenesulfonamido)-aryl(or alkyl)-methylphos-. phonates were studied on the prepared phenyl carbamate derivative β-cyclodextrin bonded phase and a commercial ( S)-(.+ )-l-(l-naphthyl)ethylcarbamate derivative β-cyclodextrin bonded phase on normal phase chromato-graphic condition. Results show that the prepared phenyl carbamate derivative β-cyclodextrin bonded phase has better enantiomeric selectivity to the series of compounds. A chiral recognition mechanism was suggested for the separation of these novel organic phosphorus enantiomers.