Prediction of the 3D conformation of a small peptide vaccine targeting Aß42 oligomers.

The original etiology of Alzheimer's disease (AD) is the deposition of amyloid-beta (Aß) proteins, which starts from the aggregation of the Aß oligomers. The optimal therapeutic strategy targeting Aß oligomer aggregation is the development of AD vaccines. Despite the fact that positive progress has been made for experimental attempts at AD vaccines, the physicochemical and even structural properties of these AD vaccines remain unclear. In this study, through immunoinformatic and molecular dynamics (MD) simulations, we first designed and simulated an alternative of vaccine TAPAS and found that the structure of the alternative can reproduce the 3D conformation of TAPAS determined experimentally. Meanwhile, immunoinformatic methods were used to analyze the physicochemical properties of TAPAS, including immunogenicity, antigenicity, thermal stability, and solubility, which confirm well the efficacy and safety of the vaccine, and validate the scheme reliability of immunoinformatic and MD simulations in designing and simulating the TAPAS vaccine. Using the same scheme, we predicted the 3D conformation of the optimized ACI-24 peptide vaccine, an Aß peptide with the first 15 residues of Aß42 (Aß1-15). The vaccine was verified once to be effective against both full-length Aß1-42 and truncated Aß4-42 aggregates, but an experimental 3D structure was absent. We have also explored the immune mechanism of the vaccine at the molecular level and found that the optimized ACI-24 and its analogues can block the growth of either full-length Aß1-42 or truncated Aß4-42 pentamer by contacting the hydrophobic residues within the N-terminus and ß1 region on the contact surface of either pentamer. Additionally, residues (D1, D7, S8, H13, and Q15) were identified as the key residues of the vaccine to contact either of the two Aß oligomers. This work provides a feasible implementation scheme of immunoinformatic and MD simulations for the development of AD small peptide vaccines, validating the power of the scheme as a parallel tool to the experimental approaches and injecting molecular-level information into the understanding and design of anti-AD vaccines.

Origin of stronger binding of ionic pair (IP) inhibitor to Aß42 than the equimolar neutral counterparts: synergy mechanism of IP in disrupting Aß42 protofibril and inhibiting Aß42 aggregation under two pH conditions.

Fibrous aggregates of beta-amyloid (Aß) is a hallmark of Alzheimer's disease (AD). Several major strategies of drugs or inhibitors, including neutral molecules, positive or negative ions, and dual-inhibitor, are used to inhibit the misfolding or aggregation of Aß42, among which a kind of dual-inhibitor composed of a pair of positive and negative ions is emerging as the most powerful candidate. This knowledge lacks the origin of the strong inhibitory effect and synergy mechanisms blocking the development and application of such inhibitors. To this end, we employed 1 : 1 ionic pairs (IP) of oppositely charged benzothiazole molecules (+)BAM1-EG6 (Pos) and (-)BAM1-EG6 (Neg) as well as equimolar neutral BAM1-EG6 (Neu) counterpart at two pH conditions (5.5 and 7.0) to bind Aß42 targets, Aß42 monomer (AßM), soluble pentamer (AßP), and pentameric protofibril (AßF) models, respectively, corresponding to the products of three toxic Aß42 development pathways, lag, exponential and fibrillation phases. Simulated results illustrated the details of the inhibitory mechanisms of IP and Neu for the AßY (Y = M, P, or F) in the three different phases, characterizing the roles of Pos and Neg of IP as well as their charged, hydrophobic groups and linker playing in the synergistic interaction, and elucidated a previously unknown molecular mechanism governing the IP-Aß42 interaction. Most importantly, we first revealed the origin of the stronger binding of IP inhibitors to Aß42 than that of the equimolar neutral counterparts, observing a perplexing phenomenon that the physiological condition (pH = 7.0) than the acidic one (pH = 5.5) is more favorable to the enhancement of IP binding, and finally disclosed that solvation is responsible to the enhancement because at pH 7.0, AßP and AßF act as anionic membranes, where solvation plays a critical role in the chemoelectromechanics. The result not only provides a new dimension in dual-inhibitor/drug design and development but also a new perspective for uncovering charged protein disaggregation under IP-like inhibitors.

Identification and characterization of the conformation and size of amyloid-ß (42) oligomers targeting the receptor LilrB2.

Experimental observations revealed that the amyloid-ß 42 oligomer (AßO) can directly bind to the LilrB2 D1D2(LDD) receptor with nanomolar-affinity, leading to changes in synaptic plasticity and cognitive deficits. However, the dependence of neurotoxicity on the morphology, size, and aggregation stage (SP1, SP2) of AßO, as well as the specific molecular mechanism of AßO-LDD interaction, remain uncertain. To address these uncertainties, we investigated the interaction between the LDD neuroreceptor and AßO with different Aß42 species (nontoxic species, toxic species, and protofibril) and sizes. Our results showed that the LDD selectively binds AßO species rather than the Aß42 monomer, accommodating various Aß42 dimers and trimers as well as SP2 AßO, in a specific pose in the pocket of the LDD receptor (region I). Additionally, protofibrils with exposed ß1/ß2 regions can also bind to region I of the LDD receptor, as observed experimentally (Cao, et al., Nat. Chem., 2018, 10, 1213; and Aim et al., Nat. Commun., 2021, 12, 3451). More extensively, we identified two additional regions of the LDD receptor, regions II and III, suitable for binding to larger AßO species at the SP1 with different molecular weights and conformations, accounting for the stronger binding strength obtained experimentally. We suggest that the two regions are more competitive than region I in causing toxicity by AßO binding. The detailed and systematic characterization for the complexes generated between the LDD receptor and various AßO species, including the protofibril, offers deep insight into the dependence of neurotoxicity on the AßO size and conformation at the molecular level, and provides novel and specific targets for drug design of Alzheimer's disease.

Two novel phosphorus/potassium-degradation bacteria: Bacillus aerophilus SD-1/Bacillus altitudinis SD-3 and their application in two-stage composting of corncob residue.

For effective utilization of corncob residue to realize green circular production, using composting to obtain a high-quality and low-cost biomass fertilizer has become a very important transformation avenue. In this paper, two novel phosphorus/potassium-degradation bacterial strains were isolated from tobacco straw and identified as Bacillus aerophilus SD-1/Bacillus altitudinis SD-3 (abbreviated as SD-1/SD-3). These identified two novel bacteria SD-1/SD-3 show that the soluble phosphorus content of SD-1/SD-3 reached 360.89 mg L-1/403.56 mg L-1 in the shake flask test, and the mass concentration of soluble potassium is 136.56 mg L-1/139.89 mg L-1. In addition, the Laccase (Lac), Lignin peroxidase (LiP), and Manganese peroxidase (MnP) activities of SD-1 and SD-3 are 54.45 U L-1/394.84 U L-1/222.79 U L-1 and 46.27 U L-1/395.26 U L-1/203.98 U L-1 respectively, with the carboxy-methyl cellulase (CMCase) of 72.07 U mL-1 and 52.69 U mL-1. Meanwhile, the effects of three different combinations of cultures, i.e., no inoculation (K1), inoculation of SD-1/SD-3 on day 21 (K2) and on day 0 (G) are investigated to understand the influence on the degradation degree of corncob residue compost. The results of K2 compost treatment showed that the effective P/K content increased nearly 3.1/2.4 times, the degradation of cellulose/lignin was 49.1/68.0%, and the germination rate was 110.23%, which were higher than other experiment groups K1/G. In conclusion, knowledge of this paper will be very useful for the industrial sector for the treatment of complex corncob residue.

Identification of the probable structure of the sAPPα-GABABR1a complex and theoretical solutions for such cases.

Amyloid precursor protein (APP) is the core of the pathogenesis of Alzheimer's disease (AD). Existing studies have shown that the soluble secreted APP (sAPPα) fragment obtained from the hydrolysis of APP by α-secretase has a synaptic function. Thereinto, a nine-residue fragment (APP9mer) of the extension domain region of sAPPα can bind directly and selectively to the N-terminal sushi1 domain (SD1) of the γ-aminobutyric acid type B receptor subunit 1a (GABABR1a) protein, which can influence synaptic transmission and plasticity by changing the GABABR1a conformation. APP9mer is a highly flexible, disordered region, and as such it is difficult to experimentally determine the optimal APPmer-SD1 binding complex. In this study we constructed two types of APP9mer-SD1 complexes through molecular docking and molecular dynamics simulation, aiming to explore the recognition function and mechanism of the specific binding of APP9mer with SD1, from which the most probable APPmer-SD1 model conformation is predicted. All the data from the analyses of RMSD, RMSF, PCA, DCCM and MM/PBSA binding energy as well as comparison with the experimental dissociation constant Kd suggest that 2NC is the most likely conformation to restore the crystal structure of the experimental APP9mer-SD1 complex. Of note, the key recognition residues of APP9mer are D24, D25, D27, W29 and W30, which mainly act on the 9-45 residue domain of SD1 (consisting of two loops and three short ß-chains at the N-terminus of SD1). The mini-model with key residues identified establishes the molecular basis with deep insight into the interaction between APP and GABABR1a and provides a target for the development of therapeutic strategies for modulating GABABR1a-specific signaling in neurological and psychiatric disorders. More importantly, the study offers a theoretical solution for how to determine a biomolecular structure with a highly flexible, disordered fragment embedded within. The flexible fragment involved in a protein structure has to be deserted usually during the structural determination with experimental methods (e.g. X-ray crystallography, etc.).

Aggregation Dynamics Characteristics of Seven Different Aß Oligomeric Isoforms-Dependence on the Interfacial Interaction.

The aggregation of ß-amyloid (Aß) peptides has been confirmed to be associated with the onset of Alzheimer's disease (AD). Among the three phases of Aß aggregation, the lag phase has been considered to be the best time for early Aß pathological deposition clinical intervention and prevention for potential patients with normal cognition. Aß peptide exists in various lengths in vivo, and Aß oligomer in the early lag phase is neurotoxic but polymorphous and metastable, depending on Aß length (isoform), molecular weight, and specific phase, and therefore hardly characterized experimentally. To cope with the problem, molecular dynamics simulation was used to investigate the aggregation process of five monomers for each of the seven common Aß isoforms during the lag phase. Results showed that Aß(1-40) and Aß(1-38) monomers aggregated faster than their truncated analogues Aß(4-40) and Aß(4-38), respectively. However, the aggregation rate of Aß(1-42) was slower than that of its truncated analogues Aß(4-42) rather than that of Aßpe(3-42). More importantly, Aß(1-38) is first predicted as more likely to form stable hexamer than the remaining five Aß isoforms, as Aß(1-42) does. It is hydrophobic interaction mainly (>50%) from the interfacial ß1 and ß2 regions of two reactants, pentamer and monomer, aggregated by Aß(1-38)/Aß(1-42) rather than by other Aß isoforms, that drives the hexamer stably as a result of the formation of the effective hydrophobic collapse. This paper provides new insights into the aggregation characteristics of Aß with different lengths and the conditions necessary for Aß to form oligomers with a high molecular weight in the early lag phase, revealing the dependence of Aß hexamer formation on the specific interfacial interaction.

Inverted loading strategy regulates the Mn-OV-Ce sites for efficient fenton-like catalysis.

Regulating interfacial active sites to improve peroxymonosulfate (PMS) activation efficiency is a hot topic in the heterogeneous catalysis field. In this study, we develop an inverted loading strategy to engineer asymmetric Mn-OV-Ce sites for PMS activation. Mn3O4@CeO2 prepared by loading CeO2 nanoparticles onto Mn3O4 nanorods exhibits the highest catalytic activity and stability, which is due to the formation of more oxygen vacancies (OV) at the Mn-OV-Ce sites, and the surface CeO2 layer effectively inhibits corrosion by preventing the loss of manganese ion active species into the solution. In situ characterizations and density functional theory (DFT) studies have revealed effective bimetallic redox cycles at asymmetric Mn-OV-Ce active sites, which promote surface charge transfer, enhance the adsorption reaction activity of active species toward pollutants, and favor PMS activation to generate (•OH, SO4•-, O2•- and 1O2) active species. This study provides a brand-new perspective for engineering the interfacial behavior of PMS activation.

Recognition of Aß oligomer by LilrB2 acceptor: a tetracoordinated zipper mechanism.

Leukocyte immunoglobulin-like receptor B2 (LilrB2) is one of discovered cell surface ß-amyloid (Aß) receptors and taken as a promising therapeutic target for the treatment of Alzheimer's disease (AD). Aß42 oligomer rather than monomer is toxic to neuronal cells and can directly bind to LilrB2, resulting in synaptic loss and cognitive impairment in the development of AD. Therefore, uncovering the mechanism of interaction between Aß42 oligomer and LilrB2 becomes the first step to obtain a clear drug target and specific binding sites. Herein, a tetracoordinated mechanism for the Aß oligomer-LilrB2 binding was first put forward by employing Aß42 dimer mimic-antiparallel copies of Aß42 core fragment 16KLVFFA21, to bind LilrB2 as models, in which four key residues (F5/F6/L12/F14) in the Aß42 mimic are bound strongly with LilrB2 residue(s) or accommodated by four hydrophobic cavities in LilrB2 to generate a stable complex. Bi-dentate binding, however, cannot keep the complex Aß42 mimic-LilrB2 stable. The inhibitor fluspirilene can disturb the binding of four key residues of Aß42 to LilrB2, justifying the tetracoordinated zipper mechanism on the other hand.

Toxicity Mechanism of Aß42 Oligomer in the Binding between the GABABR1a sushi1 Domain and Amyloid Precursor Protein 9mer: A Mechanism like Substitution Reaction.

Amyloid-ß peptide (Aß), characterized by its abnormal folding into neurotoxic aggregates, impairs synaptic plasticity and causes synaptic loss associated with Alzheimer's disease (AD). The neurotoxicity of Aß oligomers via the binding to various cell-surface receptors was frequently observed experimentally; however, the toxic mechanism still remains unknown. In this paper, we study the intervention of Aß oligomers to the receptor-peptide binding in the GABABR1a sushi1-APP 9mer complex, a key node in increasing short-term synaptic facilitation in the mouse hippocampus and decreasing neuronal activity by inhibiting neurotransmitter release by molecular dynamics simulations. The residue types of Aß42 oligomers involved in the intervention and core contact areas of the receptor were first identified, by which an unprecedented toxicity mechanism of Aß42 oligomers is proposed. These involved residues of Aß42 oligomers are positively charged residues Asp and Glu, and the core area of GABABR1a sushi1 domain is the Coil one, sharing the rich negatively charged residues R19/R21/R25/R45 with the pocket, in which APP 9mer is locked. The presence of an Aß42 oligomer rather than of a monomer stretches these key residues in the core area and consequently "unlocks and releases" the APP 9mer from its initial pocket, unsteadying the sushi1 domain and taking into toxic effect. It looks like a chemical "substitution" reaction, Aß42 oligomer + GABABR1a sushi1-APP 9mer complex → Aß42 oligomer-GABABR1a sushi1 complex + APP 9mer. Further analysis reveals that the toxicity of Aß42 oligomer to GABABR1a sushi1 domain stability depends on the residue number of the contact area and the size of Aß42 oligomer, in which semi-extended trimeric Aß42 oligomer is identified as the most toxic one. This work provides a novel insight into the mechanism of Aß oligomeric toxicity to neuroreceptors and sets an important precedent for dealing with Aß oligomeric toxicity to other receptors at the molecular level.

Small-Molecule Targeted Aß42 Aggregate Degradation: Negatively Charged Small Molecules Are More Promising than the Neutral Ones.

Heavy evidence has confirmed that Aß42 oligomers are the most neurotoxic aggregates and play a critical role in the occurrence and development of Alzheimer's disease by causing functional neuron death, cognitive damage, and dementia. Disordered Aß42 oligomers are challenging therapeutic targets, and no drug is currently in clinical use that modifies the properties of their monomeric states. Here, a negatively charged molecule (ER), rather than the neutral TS1 one, is identified by a molecular dynamics simulation method to be more capable of binding and sequestering the intrinsically disordered amyloid-ß peptide Aß42 in its soluble pentameric state as well as its monomeric components. Results reveal that the ERs interact with Aß and inhibit the primary nucleation pathways in its aggregation process in entropic expansion mechanism for both Aß42 and Aß40 oligomers but with opposite characteristics of hydrophobic surface area (HSA). The interaction between Aß42 oligomer and either charged ER or neutral TS1/TS0 characterizes decreased HSA, and the decrease in ER-involved case is highly visible, consistent with the observations from in silico and in vitro studies. By contrast, the presence of these inhibitors causes the HSA of Aß40 oligomer to change undetectably and there is even a bit of increase in the histidine isomerized Aß40 oligomer. The HSA distinction between Aß42 and Aß40 oligomer is possibly derived from the different effects of M35-inhibitor interaction, which is analogous to the effect of M35 oxidation. In comparison with the neutral TS1/TS0 inhibitors, ER is more prone to bind the residues located in the central (ß1) and C-terminal (ß2) regions of Aß42 peptide, two key nucleation regions for Aß intramolecular folding, intermolecular aggregation, and assembly. Notably, ER can strongly bind the charged residues, such as K16, K28, D23, to greatly disturb the potential stabilizer (e.g., salt-bridge, etc.) in metastable Aß42 oligomers and protofibrils. These results illustrate the strategy of overcoming Alzheimer's disease from inhibiting its early stage Aß aggregation with two kinds of small molecules to alter their behavior for therapeutic purposes and strongly recommend paying more attention to the engineering and development of negatively charged inhibitors, the long-term underappreciated ones, targeting the early stage Aß aggregates.

A novel lignin degradation bacteria-Bacillus amyloliquefaciens SL-7 used to degrade straw lignin efficiently.

Using tobacco straw (Ts) and lignin as the sole carbon source, a strain was isolated from Ts and identified as Bacillus amyloliquefaciens SL-7 by 16S rDNA gene-sequencing technology.7-day incubation of Bacillus amyloliquefaciens SL-7 can reduce the chemical oxygen demand (COD) by 69.35% in lignin mineral salt medium. The activity of Manganese peroxidase (MnP) reached maximum level 258.57 U L-1, and Lignin peroxidase (Lip) was 422.68 U L-1 at 4th day. The highest Laccase (Lac) activity (55.95 U L-1) was observed at 3th day. After straw-liquid fermentation degradation of 15 days, the bacterial could degrade 28.55% lignin of the straw which was close to that of fungi. Compared with the control group and effective microorganisms (EM) group, the lignin degradation rate in Bacillus amyloliquefaciens SL-7 group increased by 22.26% and 11.70% at 41-day compost fermentation of tobacco straw. These show the strain has strong lignin degradation performance.