Random coil structures in bacterial proteins. Relationships of their amino acid compositions to flanking structures and corresponding genic base compositions

An in-silico receptor-pharmacophore based multistep molecular docking and simulation study to evaluate the inhibitory potentials against NS1 of DENV-2

DENV-2 strain is the most fatal and infectious of the five dengue virus serotypes. The non-structural protein NS1 encoded by its genome is the most significant protein required for viral pathogenesis and replication inside the host body. Thus, targeting the NS1 protein and designing an inhibitor to limit its stability and secretion is a propitious attempt in our fight against dengue. Four novel inhibitors are designed to target the conserved cysteine residues (C55, C313, C316, and C329) and glycosylation sites (N130 and N207) of the NS1 protein in an attempt to halt the spread of the dengue infection in the host body altogether. Numerous computer-aided drug designing techniques including molecular docking, molecular dynamics simulation, virtual screening, principal component analysis, and dynamic cross-correlation matrix were employed to determine the structural and functional activity of the NS1-inhibitor complexes. From our analysis, it was evident that the extent of structural and atomic level fluctuations of the ligand-bound protein exhibited a declining trend in contrast to unbound protein which was prominently noticeable through the RMSD, RMSF, Rg, and SASA graphs. The ADMET analysis of the four ligands revealed a promising pharmacokinetics and pharmacodynamic profile, along with good bioavailability and toxicity properties. The proposed drugs when bound to the targeted cavities resulted in stable conformations in comparison to their unbound state, implying they have good affinity promising effective drug action. Thus, they can be tested in vitro and used as potential anti-dengue drugs.Communicated by Ramaswamy H. Sarma.

Application of spectrochemical analysis with chemometrics to profile biochemical alterations in nanoplastic-exposed HepG2 cells

Humans are routinely exposed to nanoplastics (NPs) in various ways, and this exposure presents a significant health risk. Nevertheless, there remain gaps in our knowledge, particularly in the mechanisms of toxicity of NPs with different surface charges at very low environmental concentrations. Herein, a spectrochemical approach was used to profile the cytotoxicity of NPs with different surface charges in HepG2 cells. It was found that all three NPs can cause some biomolecular alterations in cells, affecting cellular lipids, proteins, amino acids, and genetic material. Of these, PS and PS-COOH led to a non-linear dose-response, which may be related to a biphasic dose-response, whereas PS-NH2 led to a linear dose-response with a gradual increase in toxicity with increasing exposure concentration. In addition, the spectroscopic results showed that surface modifications led to cellular biochemical changes and caused adverse biological effects, with PS-NH2 exhibiting higher toxicity compared to PS or PS-COOH along with an inhibition of cell proliferation. Surprisingly PS-COOH, although considered the least toxic NP, appears to cause DNA damage. Overall, the toxic effects of different surface-modified NPs in cells were detected for the first time by applying spectrochemical techniques, and these findings provide important data towards understanding the emerging widespread environmental pollution of NPs and their effects on humans.

Peroxide/Zero-valent iron (Fe0) pretreatment for promoting dewaterability of anaerobically digested sludge: A mechanistic study

Peroxide/Zero-valent iron (Fe⁰) was reported to promote dewaterability of anaerobically digested sludge (ADS), but the mechanism of how Peroxide/Fe⁰ facilitates ADS dewatering is unknown. This study therefore aims to uncover the details of how Peroxide/Fe° elevates ADS dewaterability. Experimental results showed that with 0.6 g Fe⁰/g TSS and 0.08 g peroxide/g TSS, capillary suction time, specific resistance to filtration, and time to filtration of ADS was 50.7 %, 41.4 %, and 54.4 % of that in the control, respectively. In this condition, water content of sludge cake decreased from 91.2 % ± 0.5 % (the control) to 68.6 % ± 1.3 %. The mechanism explorations revealed that the elevated dewaterability was mainly caused by role of OH and Fe(II)/Fe(III) species during Peroxide/Fe° pretreatment. OH decreased the polysaccharides and proteins in extracellular polymeric substance (EPS), then injured the cytoderm & cytomembrane through the releases of lactate dehydrogenase and N-acetylglucosamine, and further facilitated the decrease of intracellular substances, which disengaged the water trapped in ADS. In addition, the cell lysis caused by OH facilitated forming macro-pores. Moreover, OH converted the conformational structure of extracellular proteins, which may strengthen the ADS hydrophobicity, promoting the discharge of unbound water and ADS flocculation. Meanwhile, Fe(II)/Fe(III) benefited aggregating the denatured ADS particulates.

Fe(II) catalyzing sodium percarbonate facilitates the dewaterability of waste activated sludge: Performance, mechanism, and implication

In this work, Fe(II) catalyzing sodium percarbonate (Fe(II)/SPC) was managed to facilitate waste activated sludge (WAS) dewatering for the first time. The results showed that after WAS was treated by 20 mg/g total suspended solids (TSS) Fe(II) and 50 mg/g TSS SPC, the water content of sludge cake (WC_SC) by press filtration and capillary suction time (CST) dropped from 90.8% ± 1.6% and 96.1 ± 4.0 s (the control) to 55.6% ± 1.4% and 30.1 ± 2.5 s, respectively. The mechanism investigations indicated that four intermediates or products (i.e., •OH, H₂O₂, Fe(II), and Fe(III)) generated in the Fe(II)/SPC process were responsible for the improved WAS dewaterability, and •OH and Fe(III) were the two major contributors. It was found that •OH collapsed and fragmented extracellular polymeric substances, damaged cell wall and permeabilized cytoplasmic membrane, and transformed conformation of the extracellular proteins secondary structure via both affecting the hydrogen bond maintaining α-helix and cracking disulfide bond in cysteine residues while Fe(III), the oxidization product of Fe(II), decreased the surface electronegativity and water-affinity surface areas of WAS flocs. As a result, the bound water release, flocculability, surface hydrophobicity, drain capability, and flowability of WAS flocs were strengthened whereas the compact surface structure, colloidal forces, network strength, gel-like structure, and apparent viscosity of WAS flocs were weakened. In addition, Fe(II)/SPC process also reduced the recalcitrant organics and fecal coliforms in sludge, which facilitated land application of dewatered sludge. The findings acquired in this work not only deepens our understanding of Fe(II)/SPC-involved WAS treatment process but also may guide engineers to develop both effective and promising strategies to better condition WAS for dewatering in the future.

Enhanced dewaterability of anaerobically digested sludge by in-situ free nitrous acid treatment

As the protonated form of nitrite, free nitrous acid (FNA) is a renewable chemical that can be produced on site from the anaerobic digestion liquor by nitritation, and has been widely employed to improve the fermentation of waste activated sludge (WAS). However, it is not clear whether and how FNA improves the dewaterability of anaerobically digested sludge (ADS). This work therefore aims to provide such supports through comparing the dewaterability of ADS treated by nitrite at different concentrations (0-250 mg/L) under three pH values (5.5, 6.3, or 7.2). Environmental results showed that nitrite was completely denitrified within 12 h, and its addition improved the dewaterability of ADS in all the cases. The optimal normalized capillary suction time of 18.0 ± 0.4 s L/g VSS was obtained at nitrite 50 mg/L and pH 5.5 (equivalent of 0.35 mg/L FNA) in comparison with corresponding value of 23.2 ± 0.4 s L/g·VSS at pH 5.5 (equivalent of 0 mg/L FNA). Under this scenario, 80.5% ± 2.0% of water content was obtained in the FNA-treated sample after press filtration while the corresponding value was 88.5% ± 1.7% in the control. The mechanism investigations showed that FNA treatment reduced surface negative charge of ADS flocs and caused disruption of extracellular polymeric substances and release of intracellular substances, which enhanced the flocculability, hydrophobicity, and flowability, but decreased the bound water content, fractal dimension, and viscosity of ADS. Additionally, FNA treatment altered the secondary structure of proteins through destroying the hydrogen bond, which led to a loose structure of protein, benefiting the exposure of hydrophobic sites or groups in EPS proteins. The findings obtained deepen our understanding of FNA affecting sludge dewatering and provide strong supports to sustainable operation of wastewater treatment plants.

How does zero valent iron activating peroxydisulfate improve the dewatering of anaerobically digested sludge?

Zero valent iron (ZVI) activating peroxydisulfate (PDS) was demonstrated to be effective in improving the dewaterability of anaerobically digested sludge (ADS). However, details of how ZVI/PDS enhances the dewaterability remain largely unknown. This work therefore aims to reveal the facts of what happen in ZVI/PDS involved ADS systems. Experimental results showed that ZVI/PDS treatment remarkably improved the dewaterability of ADS, with the minimal normalized capillary suction time of 8.6 ± 0.5 s L/g·VSS being obtained at the dosages of 2 g/g TSS ZVI and 0.5 g/g TSS PDS, which was 42.5% of that in the control. In this case, 71.2% ± 1.8% of water content (press filtration) was measured, which was 16.9% lower than that determined in the control. The mechanism investigations showed that ZVI activating PDS produced substantially reactive species, i.e., SO₄^•- and •OH, and these strong oxidative radicals decreased surface negative charges of ADS flocs, caused disruption of extracellular polymeric substances (EPS) and release of intracellular substances, and changed the secondary structure of proteins. Additionally, the products of ZVI oxidation, i.e., Fe²⁺ and Fe³⁺, were effective flocculants, thus their generation benefited the coagulation of ADS flocs through compressing double electric layers and neutralizing negative charges of sludge colloidal particles. As a result, the flocculability, hydrophobicity, and flowability of ADS were enhanced, but the bound water content, fractal dimension, and viscosity of ADS were decreased, which were responsible for the improvement of dewaterability. Further analyses exhibited that the contributions of these major contributors were different, and their contributions to the dewaterability improvement were in the order of SO₄^·- > ·OH > Fe²⁺/Fe³⁺. It was also found that ZVI/PDS treatment enhanced the degradation of recalcitrant organics, inactivation of the fecal coliforms, and mitigation of the toxicity of heavy metals in the dewatered sludge, which were beneficial to its land application.

[Computational prediction of human immunodeficiency resistance to reverse transcriptase inhibitors]

Human immunodeficiency virus (HIV) causes acquired immunodeficiency syndrome (AIDS) and leads to over one million of deaths annually. Highly active antiretroviral treatment (HAART) is a gold standard in the HIV/AIDS therapy. Nucleoside and non-nucleoside inhibitors of HIV reverse transcriptase (RT) are important component of HAART, but their effect depends on the HIV susceptibility/resistance. HIV resistance mainly occurs due to mutations leading to conformational changes in the three-dimensional structure of HIV RT. The aim of our work was to develop and test a computational method for prediction of HIV resistance associated with the mutations in HIV RT. Earlier we have developed a method for prediction of HIV type 1 (HIV-1) resistance; it is based on the usage of position-specific descriptors. These descriptors are generated using the particular amino acid residue and its position; the position of certain residue is determined in a multiple alignment. The training set consisted of more than 1900 sequences of HIV RT from the Stanford HIV Drug Resistance database; for these HIV RT variants experimental data on their resistance to ten inhibitors are presented. Balanced accuracy of prediction varies from 80% to 99% depending on the method of classification (support vector machine, Naive Bayes, random forest, convolutional neural networks) and the drug, resistance to which is obtained. Maximal balanced accuracy was obtained for prediction of resistance to zidovudine, stavudine, didanosine and efavirenz by the random forest classifier. Average accuracy of prediction is 89%.

Cobalt(ii) cation binding by proteins

Herein, a set of non-homologous proteins (238) that could bind the cobalt(ii) cations was selected from all the available Protein Data Bank structures with Co²⁺ cations.

The influence of flanking secondary structures on amino Acid content and typical lengths of 3/10 helices

We used 3D structures of a highly redundant set of bacterial proteins encoded by genes of high, average, and low GC-content. Four types of connecting bridges—regions situated between any of two major elements of secondary structure (alpha helices and beta strands)—containing a pure random coil were compared with connecting bridges containing 3/10 helices. We included discovered trends in the original “VVTAK Connecting Bridges” algorithm, which is able to predict more probable conformation for a given connecting bridge. The highest number of significant differences in amino acid usage was found between 3/10 helices containing bridges connecting two beta strands (they have increased Phe, Tyr, Met, Ile, Leu, Val, and His usages but decreased usages of Asp, Asn, Gly, and Pro) and those without 3/10 helices. The typical (most common) length of 3/10 helices situated between two beta strands and between beta strand and alpha helix is equal to 5 amino acid residues. The preferred length of 3/10 helices situated between alpha helix and beta strand is equal to 3 residues. For 3/10 helices situated between two alpha helices, both lengths (3 and 5 amino acid residues) are typical.

Structural and antigenic features of the synthetic SF23 peptide corresponding to the receptor binding fragment of diphtheria toxin

The SF23 peptide corresponding to the receptor binding fragment of diphtheria toxin (residues 508-530) has been synthesized. This fragment forming a protruding beta hairpin has been chosen because it is the less mutable B-cell epitope. Affine chromatography and ELISA show that antibodies from the sera of persons infected by toxigenic Corynebacterium diphtheriae and those immunized by diphtheria toxoid are able to bind the synthetic SF23 peptide. There are antibodies recognizing the SF23 peptide in the serum of horses hyperimmunized with diphtheria toxoid. Analysis of circular dichroism spectra show formation of beta hairpin by the peptide. Taken together, the results showed that the structure of the less mutable epitope of C. diphtheriae toxin was reproduced by the short SF23 peptide. Since antibodies against that epitope should block its interactions with cellular receptor (heparin-binding epidermal growth factor), the SF23 peptide can be considered as a promising candidate for synthetic vaccine development. Fluorescence quenching studies showed the existence of chloride and phosphate binding sites on the SF23 molecule. Phosphate containing adjuvants (aluminum hydroxyphosphate or aluminum hydroxyphosphate sulfate) are recommended to increase the SF23 immunogenic properties.

Secondary structure preferences of mn (2+) binding sites in bacterial proteins

3D structures of proteins with coordinated Mn²⁺ ions from bacteria with low, average, and high genomic GC-content have been analyzed (149 PDB files were used). Major Mn²⁺ binders are aspartic acid (6.82% of Asp residues), histidine (14.76% of His residues), and glutamic acid (3.51% of Glu residues). We found out that the motif of secondary structure “beta strand-major binder-random coil” is overrepresented around all the three major Mn²⁺ binders. That motif may be followed by either alpha helix or beta strand. Beta strands near Mn²⁺ binding residues should be stable because they are enriched by such beta formers as valine and isoleucine, as well as by specific combinations of hydrophobic and hydrophilic amino acid residues characteristic to beta sheet. In the group of proteins from GC-rich bacteria glutamic acid residues situated in alpha helices frequently coordinate Mn²⁺ ions, probably, because of the decrease of Lys usage under the influence of mutational GC-pressure. On the other hand, the percentage of Mn²⁺ sites with at least one amino acid in the “beta strand-major binder-random coil” motif of secondary structure (77.88%) does not depend on genomic GC-content.