Recognition Mechanism Research Articles

Research on separation mechanism of coal gangue photoelectric sorting recognition

Research on separation mechanism of coal gangue photoelectric sorting recognition

Enhanced Enantioselective Discrimination Regulated by Achiral Ligands in Chiral Metal-Organic Frameworks.

Enantioselective recognition is a fundamental property of chiral linkers in chiral metal-organic frameworks (CMOFs). However, clarifying the efficient enantioselective discrimination tailored by achiral linkers remains challenging to explain the chiral recognition mechanism and efficiency. Here, two CMOFs ([Zn2(l-Phe)2(bpa)2]n and [Zn2(l-Phe)2(bpe)2]n) with the completely different enantioselective recognition are synthesized from different nonchiral ligands and the same chiral ligands. The enantioselective recognition of CMOF is undoubtedly related to l-Phe, which differs in the hydrogen bonding to the Trp enantiomer. However, the electrochemical signals are weak and undifferentiated. [Zn2(l-Phe)2(bpe)2]n produces a flattened coplanar conformation with the -C═C- tether in the achiral ligand. The flattened achiral bpee ligand and its surrounding chiral phenylalanine molecules interact through multiple π-π stacking and hydrogen bonding, which together create a chiral sensor that facilitates the recognition of l-Trp. However, [Zn2(l-Phe)2(bpa)2]n produces a stepped conformation due to the -C-C- tether in the achiral ligand; despite the recognition effect of bpea, the recognition is unsatisfactory. Therefore, the chiral recognition of the two CMOFs stems from the synergistic effect between chiral and achiral ligands. This work shows that nonchiral ligands are also crucial in determining enantiomeric discrimination and opens up a new avenue for designing chiral materials.

A negatively charged cluster in the disordered acidic domain of GPIHBP1 provides selectivity in the interaction with lipoprotein lipase

GPIHBP1 is a membrane protein of endothelial cells that transports lipoprotein lipase (LPL), the key enzyme in plasma triglyceride metabolism, from the interstitial space to its site of action on the capillary lumen. An intrinsically disordered highly negatively charged N-terminal domain of GPIHBP1 contributes to the interaction with LPL. In this work, we investigated whether the plethora of heparin-binding proteins with positively charged regions found in human plasma affect this interaction. We also wanted to know whether the role of the N-terminal domain is purely non-specific and supportive for the interaction between LPL and full-length GPIHBP1, or whether it participates in the specific recognition mechanism. Using surface plasmon resonance, affinity chromatography, and FRET, we were unable to identify any plasma component, besides LPL, that bound the N-terminus with detectable affinity or affected its interaction with LPL. By examining different synthetic peptides, we show that the high affinity of the LPL/N-terminal domain interaction is ensured by at least ten negatively charged residues, among which at least six must sequentially arranged. We conclude that the association of LPL with the N-terminal domain of GPIHBP1 is highly specific and human plasma does not contain components that significantly affect this complex.

Help-Seeking Situations Related to Visual Interactions on Mobile Platforms and Recommended Designs for Blind and Visually Impaired Users.

While it is common for blind and visually impaired (BVI) users to use mobile devices to search for information, little research has explored the accessibility issues they encounter in their interactions with information retrieval systems, in particular digital libraries (DLs). This study represents one of the most comprehensive research projects, investigating accessibility issues, especially help-seeking situations BVI users face in their DL search processes. One hundred and twenty BVI users were recruited to search for information in six DLs on four types of mobile devices (iPhone, iPad, Android phone, and Android tablet), and multiple data collection methods were employed: questionnaires, think-aloud protocols, transaction logs, and interviews. This paper reports part of a large-scale study, including the categories of help-seeking situations BVI users face in their interactions with DLs, focusing on seven types of help-seeking situations related to visual interactions on mobile platforms: difficulty finding a toggle-based search feature, difficulty understanding a video feature, difficulty navigating items on paginated sections, difficulty distinguishing collection labels from thumbnails, difficulty recognizing the content of images, difficulty recognizing the content of graphs, and difficulty interacting with multilayered windows. Moreover, corresponding design recommendations are also proposed: placing meaningful labels for icon-based features in an easy-to-access location, offering intuitive and informative video descriptions for video players, providing structure information about a paginated section, separating collection/item titles from thumbnail descriptions, incorporating artificial intelligence image/graph recognition mechanisms, and limiting screen reader interactions to active windows. Additionally, the limitations of the study and future research are discussed.

Elucidating Chiral Resolution of Aromatic Amino Acids Using Glycopeptide Selectors: A Combined Molecular Docking and Chromatographic Study.

An asymmetric synthesis is a favorable approach for obtaining enantiomerically pure substances, but racemic resolution remains an efficient strategy. This study aims to elucidate the chiral resolution of aromatic amino acids and their elution order using glycopeptides as chiral selectors through molecular docking analysis. Chiral separation experiments were conducted using Vancomycin as a chiral additive in the mobile phase (CMPA) at various concentrations, coupled with an achiral amino column as the stationary phase. The Autodock Vina 1.1.2 software was employed to perform molecular docking simulations between each enantiomer (ligand) and Vancomycin (receptor) to evaluate binding affinities, demonstrate enantiomeric resolution feasibility, and elucidate chiral recognition mechanisms. Utilizing Vancomycin as CMPA at a concentration of 1.5 mM enabled the separation of tryptophan enantiomers with a resolution of 3.98 and tyrosine enantiomers with a resolution of 2.97. However, a poor chiral resolution was observed for phenylalanine and phenylglycine. Molecular docking analysis was employed to elucidate the lack of separation and elution order for tryptophan and tyrosine enantiomers. By calculating the binding energy, docking results were found to be in good agreement with experimental findings, providing insights into the underlying mechanisms governing chiral recognition in this system and the interaction sites. This comprehensive approach clarifies the complex relationship between chiral discrimination and molecular architecture, offering valuable information for creating and improving chiral separation protocols.

Mechanistic Insight Into the Conformational Changes of Cas8 Upon Binding to Different PAM Sequences in the Transposon-Encoded Type I-F CRISPR-Cas System.

The INTEGRATE system is a gene-editing approach that offers advantages over the widely used CRISPR-Cas9 system. It does not introduce double strand breaks in the target DNA but rather integrates the desired DNA sequence directly into it. The first step in the integration process is PAM recognition, which is critical to understanding and optimizing the system. Experimental testing revealed varying integration efficiencies of different PAM mutants, and computational simulations were carried out to gain mechanistic insight into the conformational changes of Cas8 during PAM recognition. Our results showed that the interaction between Arg246 and guanine at position (-1) of the target strand is critical for PAM recognition. We found that unfavorable interactions in the 5'-AC-3' PAM mutant disrupted this interaction and may be responsible for its 0% integration efficiency. Additionally, we discovered that PAM sequences not only initiate the integration process but also regulate it through an allosteric mechanism that connects the N-terminal domain and the helical bundle of Cas8. This allosteric regulation was present in all PAMs tested, even those with lower integration efficiencies, such as 5'-TC-3' and 5'-AC-3'. We identified the Cas8 residues that are involved in this regulation. Our findings provide valuable insights into PAM recognition mechanisms in the INTEGRATE system and can help improve the gene-editing technology.

The structural landscape of Microprocessor mediated pri-let-7 miRNA processing.

miRNA biogenesis is initiated upon cleavage of a primary miRNA (pri-miRNA) hairpin by the Microprocessor (MP), composed of the Drosha RNase III enzyme and its partner DGCR8. Multiple pri-miRNA sequence motifs affect MP recognition, fidelity, and efficiency. Here, we performed cryo-EM and biochemical studies of several let-7 family pri-miRNAs in complex with human MP. We show that MP has the structural plasticity to accommodate a range of pri-miRNAs. These structures revealed key features of the 5' UG sequence motif, more comprehensively represented as the "fUN" motif. Our analysis explains how cleavage of class-II pri-let-7 members harboring a bulged nucleotide generates a noncanonical precursor with a 1-nt 3' overhang. Finally, the MP-SRSF3-pri-let-7f1 structure reveals how SRSF3 contributes to MP fidelity by interacting with the CNNC-motif and Drosha's PAZ-like domain. Overall, this study sheds light on the mechanisms for flexible recognition, accurate cleavage, and regulated processing of different pri-miRNAs by MP.

Serum species identification using mid-infrared and far-infrared spectroscopy combined with neural network algorithms

Serum is a widely used biological fluid containing rich biological information, commonly employed in clinical diagnosis and medical treatment. However, since human serum contains genetic information of races and involves national information security, accurate identification of species serum is required for customs import and export trade. In this study, we propose a species serum identification method combining mid-infrared and far-infrared spectroscopy with neural network algorithms. By collecting spectra of 147 serum samples from 8 species and conducting preliminary analysis on specific spectral ranges, differences between spectra of certain species were identified. Subsequently, a Convolutional Neural Network (CNN) model was constructed for species identification and classification, achieving recognition accuracy of 95.00 % for human and non-human serums (binary classification) and 8 species of serums (octal classification). Through correlation analysis, the corresponding relationships between species serums and their spectral characteristic regions, as well as relevant molecular groups and chemical bonds, were clarified. This reveals the underlying mechanism for species recognition based on serum spectra. Furthermore, by nesting multiple segmented progressive sub-models and optimizing the weight ratios of spectral features, the accuracy of species recognition was improved to 98.95 % while the computational complexity was greatly reduced. These results provide a reliable and efficient method for rapid differentiation of species serums, with important implications for the identification of other biological fluids.

Cowpea lipid transfer protein 1 regulates plant defense by inhibiting the cysteine protease of cowpea mosaic virus

Many virus genomes encode proteases that facilitate infection. The molecular mechanism of plant recognition of viral proteases is largely unexplored. Using the system of Vigna unguiculata and cowpea mosaic virus (CPMV), we identified a cowpea lipid transfer protein (LTP1) which interacts with CPMV-encoded 24KPro, a cysteine protease, but not with the enzymatically inactive mutant 24KPro(C166A). Biochemical assays showed that LTP1 inhibited 24KPro proteolytic cleavage of the coat protein precursor large coat protein-small coat protein. Transient overexpression of LTP1 in cowpea reduced CPMV infection, whereas RNA interference-mediated LTP1 silencing increased CPMV accumulation in cowpea. LTP1 is mainly localized in the apoplast of uninfected plant cells, and after CPMV infection, most of the LTP1 is relocated to intracellular compartments, including chloroplast. Moreover, in stable LTP1-transgenic Nicotiana benthamiana plants, LTP1 repressed soybean mosaic virus (SMV) nuclear inclusion a protease activity, and accumulation of SMV was significantly reduced. We propose that cowpea LTP1 suppresses CPMV and SMV accumulation by directly inhibiting viral cysteine protease activity.

Deciphering Bacterial Chemorepulsion: The Complex Response of Microbes to Environmental Stimuli.

Bacterial motility relying on flagella is characterized by several modes, including swimming, swarming, twitching, and gliding. This motility allows bacteria to adapt remarkably well to hostile environments. More than 50% of bacteria naturally contain flagella, which are crucial for bacterial chemotaxis motility. Chemotaxis can be either positive, where bacteria move towards a chemical source, or negative, known as chemorepulsion, where bacteria move away from the source. Although much is known about the mechanisms driving chemotaxis towards attractants, the molecular mechanisms underlying chemorepulsion remain elusive. Chemotaxis plays an important role in the colonization of the rhizosphere by rhizobacteria. Recently, researchers have systematically studied the identification and recognition mechanisms of chemoattractants. However, the mechanisms underlying chemorepellents remain unclear. Systematically sorting and analyzing research on chemorepellents could significantly enhance our understanding of how these compounds help probiotics evade harmful environments or drive away pathogens.

A metal–organic framework composite loaded with coumarin guests as a turn-on luminescent sensor for detection of cysteine in aqueous solution

In this work, a composite material (ACE@UiO-66-NH2) has been synthesized conveniently by loading a cysteine-responsive molecular probe Acrylic acid 3-acetyl-2-oxo-2H-chromen-7-yl ester (ACE) on a UiO-type zirconium-based metal–organic framework (UiO-66-NH2). Furthermore, the resulting ACE@UiO-66-NH2 demonstrated to be a fluorescent turn-on probe for selective recognition of Cys from other amino acids in aqueous HEPES buffer systems. Additionally, the proposed recognition mechanism has been confirmed by 1H NMR and TLC. The study provided a promising approach to rationally design MOF-based fluorescent sensor for Cys in aqueous system.

Structural basis for the ligand recognition and G protein subtype selectivity of kisspeptin receptor.

Kisspeptin receptor (KISS1R), belonging to the class A peptide-GPCR family, plays a key role in the regulation of reproductive physiology after stimulation by kisspeptin and is regarded as an attractive drug target for reproductive diseases. Here, we demonstrated that KISS1R can couple to the Gi/o pathway besides the well-known Gq/11 pathway. We further resolved the cryo-electron microscopy (cryo-EM) structure of KISS1R-Gq and KISS1R-Gi complexes bound to the synthetic agonist TAK448 and structure of KISS1R-Gq complex bound to the endogenous agonist KP54. The high-resolution structures provided clear insights into mechanism of KISS1R recognition by its ligand and can facilitate the design of targeted drugs with high affinity to improve treatment effects. Moreover, the structural and functional analyses indicated that conformational differences in the extracellular loops (ECLs), intracellular loops (ICLs) of the receptor, and the "wavy hook" of the Gα subunit may account for the specificity of G protein coupling for KISS1R signaling.

Understanding and manipulating the recognition of necrosis-inducing secreted protein 1 (NIS1) by BRI1-associated receptor kinase 1 (BAK1)

Necrosis-inducing secreted protein 1 (NIS1) is a core effector of Ascomycota and Basidiomycota fungi. They inhibit the immune responses of host plants mainly through interaction with the multi-functional coreceptor BRI1-associated receptor kinase 1 (BAK1). However, the structural mechanism of the NIS1 family and how they are recognized by BAK1 are unknown. Herein, we report the first crystal structure of the NIS1 family protein, the Magnaporthe oryzae NIS1 (MoNIS1), analyze the recognition mechanism of NIS1s by BAK1, and explore regulation of the NIS1-BAK1 interaction by a chemical compound. MoNIS1 exists as a β barrel formed by eight β strands, a folding mode that has not been reported. Hydrogen/deuterium exchange mass spectrometry (HDX-MS) assay suggested that β4-β5 loop and β5 strand of MoNIS1 participate in OsBAK1 interaction, which was supported by further single-point mutational assays. For OsBAK1, HDX-MS assay suggested four regions involved in MoNIS1 interaction. Additionally, we identified a compound that blocks MoNIS1-OsBAK1 interaction in vitro and inhibits the virulence of M. oryzae on rice. Collectively, we determined the first structure of NIS1 family effectors, presented the recognition mechanism of NIS1 by BAK1, and showed that blocking NIS1-BAK1 interaction could be a new target for fungicide development.

Nonequilibrium Antigen Recognition during Infections and Vaccinations

The initial immune response to an acute primary infection is a coupled process of antigen proliferation, molecular recognition by naive B cells, and their subsequent clonal expansion. This process contains a fundamental problem: the recognition of an exponentially time-dependent antigen signal. Here, we show that an efficient immune response must be stringently constrained to B-cell lineages with high antigen binding affinity. We propose a tuned proofreading mechanism for primary recognition of new antigens, where the molecular recognition machinery is adapted to the complexity of the immune repertoire. We show that this process produces potent, specific, and fast recognition of antigens, maintaining a spectrum of genetically distinct B-cell lineages as input for affinity maturation. Our analysis maps the proliferation-recognition dynamics of a primary infection to a generalized Luria-Delbrück process, akin to the dynamics of the classic fluctuation experiment. This map establishes a link between signal recognition dynamics and evolution. We derive the resulting statistics of the activated immune repertoire: Antigen binding affinity, expected size, and frequency of active B-cell clones are related by power laws, which define the class of generalized Luria-Delbrück processes. Their exponents depend on the antigen and B-cell proliferation rate, the number of proofreading steps, and the lineage density of the naive repertoire. We extend the model to include spatiotemporal processes, including the diffusion-recognition dynamics of a vaccination. Empirical data of activated mouse immune repertoires are found to be consistent with activation involving about three proofreading steps. The model predicts key clinical characteristics of acute infections and vaccinations, including the emergence of elite neutralizers and the effects of immune aging. More broadly, our results establish infections and vaccinations as a new probe into the global architecture and functional principles of immune repertoires. Published by the American Physical Society 2024

Substrate binding and inhibition mechanism of norepinephrine transporter.

Norepinephrine transporter (NET; encoded by SLC6A2) reuptakes the majority of the released noradrenaline back to the presynaptic terminals, thereby affecting the synaptic noradrenaline level1. Genetic mutations and dysregulation of NET are associated with a spectrum of neurological conditions in humans, making NET an important therapeutic target1. However, the structure and mechanism of NET remain unclear. Here we provide cryogenic electron microscopy structures of the human NET (hNET) in three functional states-the apo state, and in states bound to the substrate meta-iodobenzylguanidine (MIBG) or the orthosteric inhibitor radafaxine. These structures were captured in an inward-facing conformation, with a tightly sealed extracellular gate and an open intracellular gate. The substrate MIBG binds at the centre of hNET. Radafaxine also occupies the substrate-binding site and might block the structural transition of hNET for inhibition. These structures provide insights into the mechanism of substrate recognition and orthosteric inhibition of hNET.

A novel chemical probe based on the salamo-Co(II) complex for the highly selective fluorescence detection of tyrosine

A new and rare Salamo-Co(II) complex probe L-Co2+ was designed and synthesised. The structure of the [Co3(L)2(μ-OAc)2(MeOH)2]⋅2H2O complex was obtained by X-ray diffraction experiments. Three Co(II) atoms are in a line in the complex, and all Co(II) atoms form a 6-coordinated octahedral configuration. The probe L-Co2+ selectively recognises tyrosine in DMF/H2O (8:2, v/v). Upon addition of tyrosine, the fluorescence intensity of L-Co2+ was enhanced in a short time. The probe showed high selectivity and sensitivity for tyrosine, detection limit is 4.27 × 10−8 M. The recognition mechanism of probe L-Co2+ for Tyr was inferred by FT-IR spectra, UV spectroscopy, ESI mass spectra and DFT calculations. Finally, due to the simplicity and specificity of the identification process, the probe was also subjected to a test paper experiment and a milk assay.

A Bispecific Chimeric Aptamer Design Platform Based on c-MET Aptamer with a Replaceable Redundant Region.

Molecular engineering enables the creation of aptamers with novel functions, but the prerequisite is a deep understanding of their structure and recognition mechanism. The cellular-mesenchymal epithelial transition factor (c-MET) is garnering significant attention due to the critical role of the c-MET/HGF signaling pathway in tumor development and invasion. This study reports a strategy for constructing novel chimeric aptamers that bind to both c-MET and other specific proteins. c-MET was identified to be the molecular target of a DNA aptamer, HF3-58, selected through cell-SELEX. The binding structure and mechanism of HF3-58 with c-MET were systematically studied, revealing the scaffold, recognition, and redundancy regions. Through molecular engineering design, the redundancy region was replaced with other aptamers possessing stem-loop structures, yielding novel chimeric aptamers with bispecificity for binding to c-MET and specific proteins. A chimeric bispecific aptamer HF-3b showed the ability to mediate the adhesion of T-cells to tumor cells, suggesting the prospective utility in tumor immunotherapy. These findings suggest that aptamer HF3-58 can serve as a molecular engineering platform for the development of diverse multifunctional ligands targeting c-MET. Moreover, comprehensive understanding of the binding mechanisms of aptamers will provide guidance for the design of functional aptamers, significantly expanding their potential applications.

FBSA-Net: A novel model based on attention mechanisms for emotion recognition in VR and 2D scenes

Recent studies have found that electroencephalographic (EEG) features from different frequency bands and different brain regions contribute differently to emotion recognition (ER) in virtual reality (VR) and two-dimensional (2D) scenes. Despite achievements in the task of ER in both VR and 2D environments, there has not been much prior effort to develop a unified ER model that can be applied to both VR and 2D environments. We propose a novel Frequency-Band-Spatial-based Attention Network, named FBSA-Net, for ER in VR and 2D scenes. Specifically, FBSA-Net adaptively captures the frequency-band-spatial relationship of EEG signals through cascade fusion of frequency-band attention (FBA) module and spatial attention (SA) module. The FBA module can automatically assign FBA weights to each band feature. The SA module then applies the ProbeParse attention mechanism to adaptively explore channel relationships both within and across brain regions, thus facilitating a comprehensive understanding of the global features of the EEG signals. The model's efficacy was validated through the VRSDEED dataset, created from emotion induction experiments using VR and 2D induction programs. Multiple comparative experiments have shown that FBSA-Net achieved state-of-the-art recognition results on VRSDEED datasets, achieving average recognition accuracies of 96.63% and 96.49% in VR and 2D scenes, respectively. The research results indicate that the significant contribution of FBSA-Net is not only reflected in the ability to provide ER using the same model in VR and 2D environments, but also in its excellent ability to distinguish between the emotional states in these two scenarios, providing a valuable reference for using the same model for ER.

The first ER-targeting flavone-based fluorescent probe for Cys: Applications in real-time tracking in an epilepsy model and food analysis

Epilepsy is one of the most commonly-seen neurological disorders, and both endoplasmic reticulum stress (ERS) and oxidative stress (OS) have been demonstrated to be associated with epileptic seizures. As one of the three endogenous thiol-containing amino acids, cysteine (Cys) is recognized not only as an important biomarker of various biological processes but also widely used as a significant additive in the food industry. However, the exact role that Cys plays in ERS has not been well answered up to now. In this paper, we reported the first flavone-based fluorescent probe (namely BFC) with nice endoplasmic reticulum (ER)-targeting ability, which was capable of monitoring Cys in a fast response (3.0 min), large stokes shift (130 nm) and low detection limit (10.4 nM). The recognition mechanism of Cys could be attributed to the addition-cyclization reaction involving a Cys residue and an acrylate group, resulting in the release of the strong excited-state intramolecular proton transfer (ESIPT) emission molecule of benzoflavonol (BF). The low cytotoxicity and good biocompatibility of the probe BFC allowed for monitoring the fluctuation of endogenous Cys levels under both ERS and OS processes, as well as in zebrafish models of epilepsy. Quantitative determination of Cys with the probe BFC was also achieved in three different food samples. Additionally, a probe-immersed test strips integrated with a smartphone device was successfully constructed for on-site colorimetric detection of Cys. Undoubtedly, our work provided a valuable tool for tracking Cys levels in both an epilepsy model and real food samples.

Structural insight into binding site access and ligand recognition by human ABCB1.

ABCB1 is a broad-spectrum efflux pump central to cellular drug handling and multidrug resistance in humans. However, its mechanisms of poly-specific substrate recognition and transport remain poorly resolved. Here we present cryo-EM structures of lipid embedded human ABCB1 in its apo, substrate-bound, inhibitor-bound, and nucleotide-trapped states at 3.4-3.9 Å resolution without using stabilizing antibodies or mutations and each revealing a distinct conformation. The substrate binding site is located within one half of the molecule and, in the apo state, is obstructed by transmembrane helix (TM) 4. Substrate and inhibitor binding are distinguished by major differences in TM arrangement and ligand binding chemistry, with TM4 playing a central role in all conformational transitions. Our data offer fundamental new insights into the role structural asymmetry, secondary structure breaks, and lipid interactions play in ABCB1 function and have far-reaching implications for ABCB1 inhibitor design and predicting its substrate binding profiles.