Exploring the persistence and spreading of antibiotic resistance from manure to biocompost, soils and vegetables.

The main avenue in which antibiotic resistance enters soils is through the application of livestock manure. However, whether antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) persist and spread to vegetables with the application of manure and manure products is still unclear. This study assessed seven kinds of cultured ARB, 221 ARGs subtypes and three transposon genes in the vegetable production chain (from manure to biocompost, soils and vegetables). Results showed that at least 80% of ARB, ARGs and transposon genes were removed after aerobic composting. However, aerobic composting did not reduce the diversity of ARGs in pig and chicken manure. A total of 19 ARGs subtypes still persisted during aerobic composting. Compared to the temperature-thermophilic stage, the number of bacteria resistant to erythromycin, the relative abundance of ARGs and IS613 increased 1.7-4.9 times at the temperature-decreasing stage. Direct application of biocompost introduced 11 ARGs subtypes to pakchoi, but these ARGs did not present in biocompost-amended soil. A transposon gene tnpA was also detected in the biocompost-amended soil, but surprisingly was found in the control vegetable. This demonstrated that the transposon gene is intrinsic in pakchoi. Bacterial community analysis and network analysis revealed that a specific genus Terrisporobacter carrying tetO, tetW ermB and tnpA persisted in the vegetable production chain, which may generate a potential risk in the following production. Our study illuminates the persistence and spreading of antibiotic resistance in the vegetable production chain which could help manage the ecological risks arising from antibiotic resistance in manure sources.

Protein Surface Structural Recognition in Inactive Areas: A New Immobilization Strategy for Acetylcholinesterase.

This work reported a new method of design for the immobilization of acetylcholinesterase (AChE) based on its molecular structure to improve its sensitivity and stability. The immobilization binding site on the surface of AChE was determined using MOLCAD's multi-channel functionality. Then, 11 molecules ((+)-catechin, (-)-epicatechin, (-)-gallocatechin, hesperetin, naringenin, quercetin, taxifolin, (-)-epicatechin gallate, flupirtine, atropine, and hyoscyamine) were selected from the ZINC database (about 50 000 molecules) as candidate affinity ligands for AChE. The fluorescence results showed that the binding constant Kb between AChE and the ligands ranged from 0.01344 × 104 to 4.689 × 104 M-1 and there was one independent class of binding site for the ligands on AChE. The AChE-ligand binding free energy ranged from -12.14 to -26.65 kJ mol-1. Naringenin, hesperetin, and quercetin were the three most potent immobilized affinity ligands. In addition, it was confirmed that the binding between the immobilized ligands only occurred at a single site, located in an inactive area on the surface of AChE, and did not affect the enzymatic activity as shown through a competition experiment and enzyme assay. This method based on protein surface structural recognition with high sensitivity and stability can be used as a generic approach for design of the enzyme immobilization and biosensor development.

A Continuum Poisson-Boltzmann Model for Membrane Channel Proteins.

Membrane proteins constitute a large portion of the human proteome and perform a variety of important functions as membrane receptors, transport proteins, enzymes, signaling proteins, and more. Computational studies of membrane proteins are usually much more complicated than those of globular proteins. Here, we propose a new continuum model for Poisson-Boltzmann calculations of membrane channel proteins. Major improvements over the existing continuum slab model are as follows: (1) The location and thickness of the slab model are fine-tuned based on explicit-solvent MD simulations. (2) The highly different accessibilities in the membrane and water regions are addressed with a two-step, two-probe grid-labeling procedure. (3) The water pores/channels are automatically identified. The new continuum membrane model is optimized (by adjusting the membrane probe, as well as the slab thickness and center) to best reproduce the distributions of buried water molecules in the membrane region as sampled in explicit water simulations. Our optimization also shows that the widely adopted water probe of 1.4 Å for globular proteins is a very reasonable default value for membrane protein simulations. It gives the best compromise in reproducing the explicit water distributions in membrane channel proteins, at least in the water accessible pore/channel regions. Finally, we validate the new membrane model by carrying out binding affinity calculations for a potassium channel, and we observe good agreement with the experimental results.

Characteristics and essences upon conjugation of imidacloprid with two model proteins.

Since the introduction of imidacloprid in the early 1990s, it has become one of the most widely applied insecticides, and currently represents about 20% of the global pesticide market (Tomizawa, M.; Casida, J. E. J. Agric. Food Chem 2011, 59, 2883-2886). In the context of this study, our major aim was to comprehensively scrutinize the nature of imidacloprid with two typical model proteins, lysozyme and albumin, by means of circular dichroism (CD), steady-state and time-resolved fluorescence, and molecular modeling at the molecular level. Far-UV CD verified that the spatial structure of both proteins was altered with a distinct reduction of α helix in the presence of imidacloprid suggesting unfolding of the protein (i.e., protein damage). The data of steady-state and time-resolved fluorescence showed that the conjugation of imidacloprid with lysozyme yielded quenching by a static mechanism (KSV = 3.841 × 10(4) M(-1)), while combined static and dynamic properties existed for albumin tryptophan (Trp)-214 fluorescence. Molecular modeling simulations displayed that the imidacloprid binding site was near to the Trp-62 and Trp-63 residues of lysozyme, and it was located at the subdomain IIA (warfarin-azapropazone site) of albumin. Furthermore, the primary forces between protein and imidacloprid are hydrogen bond, hydrophobic, and π-π interactions, but the affinity of lysozyme with imidacloprid is much lower than albumin, probably because the affinity distinctions stem from discrepancy in the three-dimensional structure of the two globular proteins. The results presented here will help to further understand the credible mechanism by which the toxicological implication of neonicotinoid insecticides is palliated by carrier protein.

Bioevaluation of human serum albumin-hesperidin bioconjugate: insight into protein vector function and conformation.

Hesperidin is a flavanone glycoside widely available for dietary intake in citrus fruits or citrus fruit derived products; however, exhaustive and reliable data are scarcely available for biological activity when it exerts protective health effects in humans. The principal intent of this work is to check binding domain and structural changes of human serum albumin (HSA), the primary carrier of flavonoids, in blood plasma association with hesperidin by employing molecular modeling, steady state and time-resolved fluorescence, and circular dichroism (CD) methods. From molecular modeling simulations, subdomains IIA and IIIA, which correspond to Sudlow's sites I and II, respectively, were earmarked to possess affinity for hesperidin, but the affinity of site I with flavanone is greater than that of site II. This corroborates the site-specific probe and hydrophobic 8-anilino-1-naphthalenesulfonic acid (ANS) displacement results placing the hesperidin at warfarin-azapropazone and indole-benzodiazepine sites. Steady state and time-resolved fluorescence manifested that static type, due to HSA-hesperidin complex formation (1.941 × 10(4) M(-1)), is the operative mechanism for the diminution in the tryptophan (Trp)-214 fluorescence. Moreover, via alterations in three-dimensional fluorescence and CD spectral properties, we can securely draw the conclusion that the polypeptide chain of HSA is partially destabilized after conjugation with hesperidin. We anticipate that this study can provide better knowledge of bioavailability such as absorption, biodistribution, and elimination, of hesperidin in vivo, to facilitate the comprehension of the biological responses to physiologically relevant flavanones.

Chiral recognition of metalaxyl enantiomers by human serum albumin: evidence from molecular modeling and photophysical approach.

Metalaxyl is an acylamine fungicide, belonging to the most widely known member of the amide group. This task is aimed to scrutinize binding region and spatial structural change of principal vector human serum albumin (HSA) complex with (R)-/(S)-metalaxyl by exploiting molecular modeling, steady-state and time-resolved fluorescence, and circular dichroism (CD) approaches. According to molecular modeling, (R)-metalaxyl is situated within subdomains IIA and IIIA and the affinity of site I with (R)-metalaxyl is greater than site II, whereas (S)-metalaxyl is only located at subdomain IIA and the affinity of (S)-metalaxyl with site I is superior compared with that with (R)-metalaxyl. This coincides with the competitive ligand binding, guanidine hydrochloride-induced unfolding of protein, and hydrophobic 8-anilino-1-naphthalenesulfonic acid experiments; the acting forces between (R)-/(S)-metalaxyl and HSA are hydrophobic, π-π interactions, and hydrogen bonds, as derived from molecular modeling. Fluorescence emission manifested that the complex of (R)-/(S)-metalaxyl to HSA is the formation of adduct with an affinity of 10(4) M(-1), which corroborates the time-resolved fluorescence that the static type was operated. Furthermore, the changes of far-UV CD spectra evidence the polypeptide chain of HSA partially unfolded after conjugation with (R)-/(S)-metalaxyl. Through this work, we envisage that it can offer central clues on the biodistribution, absorption, and bioaccumulation of (R)-/(S)-metalaxyl.

Human serum albumin stability and toxicity of anthraquinone dye alizarin complexone: an albumin-dye model.

The complexation between the primary vector of ligands in blood plasma, human serum albumin (HSA) and a toxic anthraquinone dye alizarin complexone, was unmasked by means of circular dichroism (CD), molecular modeling, steady state and time-resolved fluorescence, and UV/vis absorption measurements. The structural investigation of the complexed HSA through far-UV CD, three-dimensional and synchronous fluorescence shown the polypeptide chain of HSA partially destabilizing with a reduction of α-helix upon conjugation. From molecular modeling and competitive ligand binding results, Sudlow's site I, which was the same as that of warfarin-azapropazone site, was appointed to retain high-affinity for alizarin complexone. Moreover, steady state fluorescence displayed that static type and Förster energy transfer is the operational mechanism for the vanish in the tryptophan (Trp)-214 fluorescence, this corroborates time-resolved fluorescence that HSA-alizarin complexone adduct formation has an affinity of 10(5) M(-1), and the driving forces were found to be chiefly π-π, hydrophobic, and hydrogen bonds, associated with an exothermic free energy change. These data should be utilized to illustrate the mechanism by which the toxicological action of anthraquinone dyes is mitigated by transporter HSA.

Potential toxicity and affinity of triphenylmethane dye malachite green to lysozyme.

Malachite green is a triphenylmethane dye that is used extensively in many industrial and aquacultural processes, generating environmental concerns and health problems to human being. In this contribution, the complexation between lysozyme and malachite green was verified by means of computer-aided molecular modeling, steady state and time-resolved fluorescence, and circular dichroism (CD) approaches. The precise binding patch of malachite green in lysozyme has been identified from molecular modeling and ANS displacement, Trp-62, Trp-63, and Trp-108 residues of lysozyme were earmarked to possess high-affinity for this dye, the principal forces in the lysozyme-malachite green adduct are hydrophobic and π-π interactions. Steady state fluorescence proclaimed the complex of malachite green with lysozyme yields quenching through static type, which substantiates time-resolved fluorescence measurements that lysozyme-malachite green conjugation formation has an affinity of 10(3)M(-1). Moreover, via molecular modeling and also CD data, we can safely arrive at a conclusion that the polypeptide chain of lysozyme partially destabilized upon complexation with malachite green. The data emerged here will help to further understand the toxicological action of malachite green in human body.

Features of the complex of food additive hesperidin to hemoglobin.

The purpose of the current work was to examine the complexation of a mammalian protein, hemoglobin (Hb) with a food additive hesperidin at physiological conditions. Molecular modeling, fluorescence, and circular dichroism (CD) methods were exploited to analyze the binding domain, affinity, and the effects of hesperidin conjugation on Hb spatial structure. From molecular modeling, central cavity of Hb was assigned to retain high-affinity for hesperidin, this corroborates the steady state fluorescence and hydrophobic ANS probe results. The association of hesperidin with Hb emerges fluorescence quenching via static type, this phenomenon display that the ground state complex formation with an affinity of 10(4)M(-1), and hypsochromic effect transpires. Additionally, the alterations of synchronous fluorescence, CD, and three-dimensional fluorescence suggest that the polypeptide chain of Hb partially folding after conjugation with hesperidin. The above data suggest that Hb plays a significant role in the plasma distribution and transportation of hesperidin and related dietary flavonoids.

Characterization of Alizarin Red S binding sites and structural changes on human serum albumin: a biophysical study.

Alizarin Red S (ARS), is a water-soluble, widely used anthraquinone dye synthesized by sulfonation of alizarin. In this report, the binding of ARS to human serum albumin (HSA) was characterized by employing fluorescence, UV/vis absorption, circular dichroism (CD), and molecular modeling methods. The data of fluorescence spectra displayed that the binding of ARS to HSA is the formation of HSA-ARS complex at 1:1 stoichiometric proportion. Hydrophobic probe 8-anilino-1-naphthalenesulfonic acid (ANS) was employed and elucidated that the dye was located in subdomain IIIA. This phenomenon corroborates the result of site-specific probe displacement experiments, which demonstrate the dye is at indole-benzodiazepine site (Sudlow's site II); and it is also consistent with guanidine hydrochloride (GuHCl) induced HSA unfolding studies and molecular modeling simulations. The features of the dye, which led to structural perturbations of HSA, have also been studied in detail by methods of UV/vis, CD and three-dimensional fluorescence spectroscopy.

QSAR models for predicting toxicity of polychlorinated dibenzo-p-dioxins and dibenzofurans using quantum chemical descriptors.

By partial least square regression, simple quantitative structure-activity relationship (QSAR) models were developed for the toxicity of polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs). Quantum chemical descriptors computed by semi-empirical PM3 method were used as predictor variables. Three optimal QSAR models are developed for 25 PCDDs, 35 PCDFs, 25 PCDDs and 35 PCDFs together, respectively. The cross-validated Q (cum) (2) values for the three QSAR models of 25 PCDDs, 35 PCDFs, 25 PCDDs and 35 PCDFs together are 0.816, 0.629 and 0.603, respectively, indicating good predictive capabilities for the biological toxicity of these PCDD/Fs. The present study suggests that quantum chemical descriptors of POPs indeed govern the binding affinity of these chemicals for aryl hydrocarbon receptors. Moreover, different models contain different molecular descriptors to define respective equation, which suggests that the relationship between molecular structure and the binding affinity of these chemicals for aryl hydrocarbon receptors is complex.