Search

Abstract: Most proteins function in cells where protein concentrations can reach 400g/l. However, most quantitative studies of protein properties are performed in idealized, dilute conditions. Recently developed in-cell NMR techniques can provide protein structure and other biophysical properties inside living cells at atomic resolution. Here we review how protein dynamics, including global and internal motions have been characterized by in-cell NMR, and then discuss the remaining challenges and future directions. [Copyright &y& Elsevier]

Methods for measuring longitudinal relaxation times of protons in heavily overlapped [sup 1]H NMR spectra are introduced and exemplified using a solution of cholesteryl acetate. The methods are based on 1-dimensional and 2-dimensional maximum quantum NMR spectroscopy (MAXY), which makes possible the selective detection of CH, CH[sub 2] and CH[sub 3] [sup 1]H NMR resonances. A modification of the BIRD pulse sequence to achieve selective inversion of protons bonded to either [sup 12]C or [sup 13]C is given. The approach should find application in studies of molecular dynamics where isotopic enrichment is not possible and the level of available sample dictates the use of [sup 1]H NMR spectroscopy. [ABSTRACT FROM AUTHOR]

The WRKY transcription factors play essential roles in a variety of plant signaling pathways associated with biotic and abiotic stress response. The transcriptional activity of many WRKY members are regulated by a class of intrinsically disordered VQ proteins. While it is known that VQ proteins interact with the WRKY DNA-binding domains (DBDs), also termed as the WRKY domains, structural information regarding VQ-WRKY interaction is lacking and the regulation mechanism remains unknown. Herein we report a solution NMR study of the interaction between Arabidopsis WRKY33 and its regulatory VQ protein partner SIB1. We uncover a SIB1 minimal sequence neccessary for forming a stable complex with WRKY33 DBD, which comprises not only the consensus "FxxhVQxhTG" VQ motif but also its preceding region. We demonstrate that the βN-strand and the extended βN-β1 loop of WRKY33 DBD form the SIB1 docking site, and build a structural model of the complex based on the NMR paramagnetic relaxation enhancement and mutagenesis data. Based on this model, we further identify a cluster of positively-charged residues in the N-terminal region of SIB1 to be essential for the formation of a SIB1-WRKY33-DNA ternary complex. These results provide a framework for the mechanism of SIB1-enhanced WRKY33 transcriptional activity. An NMR study on the SIB1-WRKY33 interaction identifies the minimal sequence in SIB1 that is essential for complex formation and provides a structural model for understanding how SIB1 regulates the DNA binding activity of WRKY33. [ABSTRACT FROM AUTHOR]

NMR spectroscopy can be used to measure molecular self-diffusion coefficients using a modified spin-echo pulse sequence known as the longitudinal eddy current delay (LED) method which incorporates pulsed magnetic field gradients. The effect of such gradients on multiple quantum coherences is investigated and shown to be of benefit for the measurement of diffusion coefficients using modest gradient strengths. The multiple quantum coherences involved in the spin operator 8Ix Iy Iy Sy of a weakly coupled SI spin system (13CH at natural abundance, in alanine in this case) were studied. The multiple quantum coherences included the quadruple-quantum (QQ) order of (3 I + S ), double-quantum (DQ) order of (3 I - S ) and (3 I + S ), and zero-quantum (ZQ) order of ( I - S ) with effective magnetogyric ratios of (3gammaH + gammaC), (3gammaH-gammaC), (gammaH + gammaC) and (gammaH-gammaC) respectively. The results show that the use of higher level quantum coherences for diffusion coefficient measurement can have the practical effect of significantly enhancing the gradient strength and this is important for slowly diffusing species. [ABSTRACT FROM AUTHOR]

Demonstrate the use of two-dimensional diffusion-edited total-correlation nuclear magnetic resonance spectroscopy in measuring diffusion coefficients of molecules in biofluids. Diffusion coefficients for the small endogenous species; Interpretation of the derived diffusion coefficients; Measurement of diffusion coefficient of various lipoprotein resonances.

Discusses an approach to the characterization of biomolecules in whole biological fluids based on simplification of 1H nuclear magnetic resonance (NMR) spectra. Differences in molecular diffusion coefficients alone and combinations of relaxation and diffusion parameters; Incorporation of both spectral editing features and solvent water resonance elimination.

Metabolism is a fundamental process that underlies human health and diseases. Nuclear magnetic resonance (NMR) techniques offer a powerful approach to identify metabolic processes and track the flux of metabolites at the molecular level in living systems. An in vitro study through in-cell NMR tracks metabolites in real time and investigates protein structures and dynamics in a state close to their most natural environment. This technique characterizes metabolites and proteins involved in metabolic pathways in prokaryotic and eukaryotic cells. In vivo magnetic resonance spectroscopy (MRS) enables whole-organism metabolic monitoring by visualizing the spatial distribution of metabolites and targeted proteins. One limitation of these NMR techniques is the sensitivity, for which a possible improved approach is through isotopic enrichment or hyperpolarization methods, including dynamic nuclear polarization (DNP) and parahydrogen-induced polarization (PHIP). DNP involves the transfer of high polarization from electronic spins of radicals to surrounding nuclear spins for signal enhancements, allowing the detection of low-abundance metabolites and real-time monitoring of metabolic activities. PHIP enables the transfer of nuclear spin polarization from parahydrogen to other nuclei for signal enhancements, particularly in proton NMR, and has been applied in studies of enzymatic reactions and cell signaling. This review provides an overview of in-cell NMR, in vivo MRS, and hyperpolarization techniques, highlighting their applications in metabolic studies and discussing challenges and future perspectives. [ABSTRACT FROM AUTHOR]

ATP (adenosine triphosphate) is a vital energy source for living organisms, and its biosynthesis and precise concentration regulation often depend on macromolecular machinery composed of protein complexes or complicated multidomain proteins. We have identified a single‐domain protein HK853CA derived from bacterial histidine kinases (HK) that can catalyze ATP synthesis efficiently. Here, we explored the reaction mechanism and multiple factors that influence this catalysis through a combination of experimental techniques and molecular simulations. Moreover, we optimized its enzymatic activity and applied it as an ATP replenishment machinery to other ATP‐dependent systems. Our results broaden the understanding of ATP biosynthesis and show that the single CA domain can be applied as a new biomolecular catalyst used for ATP supply. [ABSTRACT FROM AUTHOR]

ATP (adenosine triphosphate) is a vital energy source for living organisms, and its biosynthesis and precise concentration regulation often depend on macromolecular machinery composed of protein complexes or complicated multidomain proteins. We have identified a single‐domain protein HK853CA derived from bacterial histidine kinases (HK) that can catalyze ATP synthesis efficiently. Here, we explored the reaction mechanism and multiple factors that influence this catalysis through a combination of experimental techniques and molecular simulations. Moreover, we optimized its enzymatic activity and applied it as an ATP replenishment machinery to other ATP‐dependent systems. Our results broaden the understanding of ATP biosynthesis and show that the single CA domain can be applied as a new biomolecular catalyst used for ATP supply. [ABSTRACT FROM AUTHOR]

Cross-linkers play a critical role in capturing protein dynamics in chemical cross-linking mass spectrometry techniques. Various types of cross-linkers with different backbone features are widely used in the study of proteins. However, it is still not clear how the cross-linkers' backbone affect their own structure and their interactions with proteins. In this study, we systematically characterized and compared methylene backbone and polyethylene glycol (PEG) backbone cross-linkers in terms of capturing protein structure and dynamics. The results indicate the cross-linker with PEG backbone have a better ability to capture the inter-domain dynamics of calmodulin, adenylate kinase, maltodextrin binding protein and dual-specificity protein phosphatase. We further conducted quantum chemical calculations and all-atom molecular dynamics simulations to analyze thermodynamic and kinetic properties of PEG backbone and methylene backbone cross-linkers. Solution nuclear magnetic resonance was employed to validate the interaction interface between proteins and cross-linkers. Our findings suggest that the polarity distribution of PEG backbone enhances the accessibility of the cross-linker to the protein surface, facilitating the capture of sites located in dynamic regions. By comprehensively benchmarking with disuccinimidyl suberate (DSS)/bis-sulfosuccinimidyl-suberate(BS3), bis-succinimidyl-(PEG)2 revealed superior advantages in protein dynamic conformation analysis in vitro and in vivo , enabling the capture of a greater number of cross-linking sites and better modeling of protein dynamics. Furthermore, our study provides valuable guidance for the development and application of PEG backbone cross-linkers. [ABSTRACT FROM AUTHOR]

To realize sensing and labeling biomarkers is quite challenging in terms of designing multimodal imaging probes. In this study, we developed a novel β‐galactosidase (β‐gal) activated bimodal imaging probe that combines near‐infrared (NIR) fluorescence and magnetic resonance imaging (MRI) to enable real‐time visualization of activity in living organisms. Upon β‐gal activation, Gal‐Cy‐Gd‐1 exhibits a remarkable 42‐fold increase in NIR fluorescence intensity at 717 nm, allowing covalent labeling of adjacent target enzymes or proteins and avoiding molecular escape to promote probe accumulation at the tumor site. This fluorescence reaction enhances the longitudinal relaxivity by approximately 1.9 times, facilitating high‐resolution MRI. The unique features of Gal‐Cy‐Gd‐1 enable real‐time and precise visualization of β‐gal activity in live tumor cells and mice. The probe's utilization aids in identifying in situ ovarian tumors, offering valuable assistance in the precise removal of tumor tissue during surgical procedures in mice. The fusion of NIR fluorescence and MRI activation through self‐immobilizing target enzymes or proteins provides a robust approach for visualizing β‐gal activity. Moreover, this approach sets the groundwork for developing other activatable bimodal probes, allowing real‐time in vivo imaging of enzyme activity and localization. [ABSTRACT FROM AUTHOR]

To realize sensing and labeling biomarkers is quite challenging in terms of designing multimodal imaging probes. In this study, we developed a novel β‐galactosidase (β‐gal) activated bimodal imaging probe that combines near‐infrared (NIR) fluorescence and magnetic resonance imaging (MRI) to enable real‐time visualization of activity in living organisms. Upon β‐gal activation, Gal‐Cy‐Gd‐1 exhibits a remarkable 42‐fold increase in NIR fluorescence intensity at 717 nm, allowing covalent labeling of adjacent target enzymes or proteins and avoiding molecular escape to promote probe accumulation at the tumor site. This fluorescence reaction enhances the longitudinal relaxivity by approximately 1.9 times, facilitating high‐resolution MRI. The unique features of Gal‐Cy‐Gd‐1 enable real‐time and precise visualization of β‐gal activity in live tumor cells and mice. The probe's utilization aids in identifying in situ ovarian tumors, offering valuable assistance in the precise removal of tumor tissue during surgical procedures in mice. The fusion of NIR fluorescence and MRI activation through self‐immobilizing target enzymes or proteins provides a robust approach for visualizing β‐gal activity. Moreover, this approach sets the groundwork for developing other activatable bimodal probes, allowing real‐time in vivo imaging of enzyme activity and localization. [ABSTRACT FROM AUTHOR]

Protein dynamics play a crucial role in their diverse functions. The intracellular environment significantly influences protein dynamics, particularly for intrinsically disordered proteins (IDPs). To comprehensively capture structural information from various proteins within cells and characterize protein dynamics, chemical cross‐linking mass spectrometry was employed. In this study, we introduce a hierarchical decoding strategy that enables the investigation of protein dynamics in vivo. Computational analysis based on distance restraints derived from cross‐links is used to infer protein dynamics in cells. To facilitate this analysis, we leverage the prior structure obtained from AlphaFold2. By employing this strategy, we can characterize the full‐length structure of multi‐domain proteins taking into account their distinct dynamic features. Furthermore, by combining restraint sampling with an unbiased sampling and evaluation approach, we can provide a comprehensive description of the intrinsic motion of IDPs. Consequently, the hierarchical strategy we propose holds significant potential in advancing our understanding of the molecular mechanisms that undelie protein functions in cells. [ABSTRACT FROM AUTHOR]

Protein dynamics play a crucial role in their diverse functions. The intracellular environment significantly influences protein dynamics, particularly for intrinsically disordered proteins (IDPs). To comprehensively capture structural information from various proteins within cells and characterize protein dynamics, chemical cross‐linking mass spectrometry was employed. In this study, we introduce a hierarchical decoding strategy that enables the investigation of protein dynamics in vivo. Computational analysis based on distance restraints derived from cross‐links is used to infer protein dynamics in cells. To facilitate this analysis, we leverage the prior structure obtained from AlphaFold2. By employing this strategy, we can characterize the full‐length structure of multi‐domain proteins taking into account their distinct dynamic features. Furthermore, by combining restraint sampling with an unbiased sampling and evaluation approach, we can provide a comprehensive description of the intrinsic motion of IDPs. Consequently, the hierarchical strategy we propose holds significant potential in advancing our understanding of the molecular mechanisms that undelie protein functions in cells. [ABSTRACT FROM AUTHOR]

The aggregation of amyloidogenic proteins is often related to the occurrence of neurodegenerative diseases, including fused in sarcoma protein (FUS) in frontotemporal lobar degeneration and amyotrophic lateral sclerosis diseases. Recently, the SERF protein family has been reported to have a significant regulatory effect on amyloid formation, but it is still unclear about the detailed mechanisms of SERF acting on different amyloidogenic proteins. Herein, nuclear magnetic resonance (NMR) spectroscopy and fluorescence spectroscopy were used to explore interactions of ScSERF with three amyloidogenic proteins FUS‐LC, FUS‐Core, and α‐Synuclein. NMR chemical shift perturbations reveal them sharing similar interaction sites on the N‐terminal region of ScSERF. However, the amyloid formation of α‐Synuclein protein is accelerated by ScSERF, while ScSERF inhibits fibrosis of FUS‐Core and FUS‐LC proteins. Both the primary nucleation and the total amount of fibrils produced are detained. Our results suggest a diverse role of ScSERF in regulating the fibril growth of amyloidogenic proteins. [ABSTRACT FROM AUTHOR]

In‐cell NMR spectroscopy is an effective tool for observing proteins at atomic resolution in their native cellular environment. However, its utility is limited by its low sensitivity and the extensive line broadening caused by nonspecific interactions in the cells, which is even more pronounced in human cells due to the difficulty of overexpressing or delivering high concentrations of isotopically labeled proteins. Here, we present a high‐sensitivity tag (wPSP‐6F) containing two trifluoromethyl groups that can efficiently label globular proteins with molecular weights in the 6–40 kDa range under mild conditions. This tag allowed us to detect globular proteins in human cells at concentrations as low as 1.0 μM, which would not have been achievable with 15N or 3‐fluorotyrosine labeling. Moreover, we detected conformational changes and interactions of proteins in the cellular environment. The new sensitive 19F NMR tag may significantly expand the scope of protein NMR in human cells. [ABSTRACT FROM AUTHOR]

In‐cell NMR spectroscopy is an effective tool for observing proteins at atomic resolution in their native cellular environment. However, its utility is limited by its low sensitivity and the extensive line broadening caused by nonspecific interactions in the cells, which is even more pronounced in human cells due to the difficulty of overexpressing or delivering high concentrations of isotopically labeled proteins. Here, we present a high‐sensitivity tag (wPSP‐6F) containing two trifluoromethyl groups that can efficiently label globular proteins with molecular weights in the 6–40 kDa range under mild conditions. This tag allowed us to detect globular proteins in human cells at concentrations as low as 1.0 μM, which would not have been achievable with 15N or 3‐fluorotyrosine labeling. Moreover, we detected conformational changes and interactions of proteins in the cellular environment. The new sensitive 19F NMR tag may significantly expand the scope of protein NMR in human cells. [ABSTRACT FROM AUTHOR]

The Arabidopsis WRKY11 (AtWRKY11) protein is an important transcription factor involved in plant response to biotic and abiotic stresses. Its DNA-binding domain specifically binds to gene promoter regions harboring the W-box consensus motif. Herein we report the high-resolution structure of the AtWRKY11 DNA-binding domain (DBD) determined by solution NMR spectroscopy. The results show that AtWRKY11-DBD adopts an all-β fold comprising five β-strands packed in an antiparallel topology, stabilized by a zinc-finger motif. Structural comparison reveals that the long β 1 -β 2 loop shows the highest structural variation from other available WRKY domain structures. Moreover, this loop was further found to contribute to the binding between AtWRKY11-DBD and W-box DNA. Our current study provides atomic-level structural basis for further understanding the structure-function relationship of plant WRKY proteins. • This is the first structure reported for the IId subgroup of the WRKY superfamily. • The β1-β2 loop region of AtWRKY11-DBD shows high variation among other WRKY proteins. • The DNA-binding site on AtWRKY11 involves not only the consensus WRKY motif, but also the aforementioned β1-β2 loop region. • Our model of the AtWRKY11-DNA complex suggests the possible roles of the β1-β2 loop in binding DNA. [ABSTRACT FROM AUTHOR]

Nuclear magnetic resonance (NMR) has been used in a variety of fields due to its powerful analytical capability. To facilitate biochemical NMR (bioNMR) analysis for samples with a limited mass, a number of integrated systems have been developed by coupling microfluidics and NMR. However, there are few review papers that summarize the recent advances in the development of microfluidics-based NMR (μNMR) systems. Herein, we review the advancements in μNMR systems built on high-field commercial instruments and low-field compact platforms. Specifically, μNMR platforms with three types of typical microcoils settled in the high-field NMR instruments will be discussed, followed by summarizing compact NMR systems and their applications in biomedical point-of-care testing. Finally, a conclusion and future prospects in the field of μNMR were given. [ABSTRACT FROM AUTHOR]

Many cellular reactions involving proteins, including their biosynthesis, misfolding, and transport, occur in confined compartments. Despite its importance, a structural basis of understanding of how confined environments alter protein function is still lacking. Herein, we explore structure-function correlations of calmodulin (CaM), a multidomain protein involved in many calcium-mediated signaling pathways, in reverse micelles. Confinement dramatically alters CaM structure and function. The protein forms an extended structure in bulk water, but becomes compacted in reverse micelles. In addition, confinement changes the function of CaM. Specifically, the protein binds the MLCK, AcN19, and somatostatin peptides in dilute buffer, but binds only the MLCK and AcN19 peptides in reverse micelles. In summary, we determined a new CaM structure in reverse micelles and demonstrate that confinement can modulate both protein structure and function. [ABSTRACT FROM AUTHOR]

Dim and small target detection in complex background is considered a difficult and challenging problem. Conventional algorithms using the local difference/mutation possibly produce high missed or mistaken detection rates. In this paper, we propose an effective algorithm for detecting dim and small infrared targets. In order to synchronously enhance targets and suppress complex background clutters, we adopt an adaptive entropy-based window selection technique to construct a novel local difference measure (LDM) map of an input image, which measures the dissimilarity between the current region and its neighboring ones. In this way, the window size can be adaptively regulated according to local statistical properties. Compared with the original image, the LDM map has less background clutters and noise residual. This guarantees the lower false alarm rates under the same probability of detection. Subsequently, a simple threshold is used to segment the target. More than 600 dim and small infrared target images against different complex and noisy backgrounds were utilized to validate the detection performance of the proposed approach. Extensive experimental results demonstrate that the proposed method not only works more stably for different target movements and signal-to-clutter ratio values, but also has a better performance compared with classical baseline methods. The evaluation results suggest that the proposed method is simple and effective with regard to detection accuracy. [ABSTRACT FROM AUTHOR]

Enhancement of images with weak edges faces great challenges in imaging applications. In this study, the authors propose a novel image enhancement approach based on intuitionistic fuzzy sets. The proposed method first divides an image into sub‐object and sub‐background areas, and then successively implements new fuzzification, hyperbolisation, and defuzzification operations on each area. In this way, an enhanced image is obtained, where the visual quality of region of interest (ROI) is significantly improved. Several types of images are utilised to validate the proposed method with respect to the enhancement performance. Experimental results demonstrate that the proposed algorithm not only works more stably for different types of images, but also has better enhancement performance, in comparison to conventional methods. This is a great merit of such design for discerning specific ROIs. [ABSTRACT FROM AUTHOR]

Retinoid X receptor (RXRα) is a nuclear receptor (NR) for retinoic acid (RA) and regulates various NR signaling pathways. Ligand-binding domain (LBD) of RXRα can bind with its ligand 9-cis-RA and cofactors, and mediate the forming of homodimer and homotetramer of RXRα and its heterodimer with other NRs, conferring RXRα the ability to play complicated roles in development and diseases. Due to the coexistence of monomer, dimer and tetramer, there are difficulties to study the structure and interaction of RXRα-LBD with its ligands and cofactors in solution and to distinguish the roles of different forms of RXRα in cell. Here, through analyzing available structures of RXRα-LBD, we selected two residues, D379 and L420, in the homodimer interface to design three mutants of RXRα-LBD. Recombinant proteins of the three mutants showed decreased proportions of dimer and tetramer but unchanged overall structure and binding affinities to 9-cis-RA, corepressor SMRT, and coactivator SRC2. Especially, the double-site mutant RXRα-LBDD379A−L420G existed as a uniform monomer. Furthermore, L420 was found to play a similar role in forming RXRα-LBD homodimer and its heterodimer with various NRs, while the role of D379 varies a lot, as it shows almost no interaction with RARα/β, LXRα/β, and THRα/β. This study provides a new insight into the mechanism for forming RXRα-LBD homodimer and its heterodimer with other NRs, and will facilitate the studies on the structure and interaction of RXRα-LBD with ligands, cofactors and drugs in solution, and the broad physiological functions of RXRα cooperating with various NRs in cell. • Mutation of D379 or L420 can destabilize the homodimer of RXRα-LBD. • Double-site mutant of D379 and L420 exists as a uniform monomer. • Mutation of D379 and L420 does not change the binding to RA and cofactors. • Mutation of L420 impairs the interaction of RXRα-LBD with RARα-LBD. • D379 plays little role in the interaction of RXRα-LBD with RARα-LBD. [ABSTRACT FROM AUTHOR]

Single cell analysis has drawn increasing interest from the research community due to its capability to interrogate cellular heterogeneity, allowing refined tissue classification and facilitating novel biomarker discovery. With the advancement of relevant instruments and techniques, it is now possible to perform multiple omics including genomics, transcriptomics, metabolomics or even proteomics at single cell level. In comparison with other omics studies, single‐cell metabolomics (SCM) represents a significant challenge since it involves many types of dynamically changing compounds with a wide range of concentrations. In addition, metabolites cannot be amplified. Although difficult, considerable progress has been made over the past decade in mass spectrometry (MS)‐based SCM in terms of processing technologies and biochemical applications. In this review, we will summarize recent progress in the development of promising MS platforms, sample preparation methods and SCM analysis of various cell types (including plant cell, cancer cell, neuron, embryo cell, and yeast cell). Current limitations and future research directions in the field of SCM will also be discussed. [ABSTRACT FROM AUTHOR]

Nitroreductase (NTR) is an important biomarker widely used to evaluate the degree of tumor hypoxia. Although a few optical methods have been reported for detecting nitroreductase at low concentration ranges, an effective strategy for nitroreductase monitoring in vivo without limits to the imaging depth is still lacking. Herein, a novel dual‐mode NIR fluorescence and 19F MRI agent, FCy7‐NO2, is proposed for imaging tumor hypoxia. We show that FCy7‐NO2 serves as not only a rapid NIR fluorescence enhanced probe for monitoring and bioimaging of nitroreductase in tumors, but also a novel 19F MR chemical shift‐sensitive contrast agent for selectively detecting nitroreductase catalyzed reduction. Notably, integrating two complementary imaging technologies into FCy7‐NO2 enables sensitive detection of nitroreductase in a broad concentration range without tissue‐depth limit. In general, this agent has a remarkable response to nitroreductase, which provides a promising method for understanding tumor evolution and its physiological role in the hypoxic microenvironment. [ABSTRACT FROM AUTHOR]

Nitroreductase (NTR) is an important biomarker widely used to evaluate the degree of tumor hypoxia. Although a few optical methods have been reported for detecting nitroreductase at low concentration ranges, an effective strategy for nitroreductase monitoring in vivo without limits to the imaging depth is still lacking. Herein, a novel dual‐mode NIR fluorescence and 19F MRI agent, FCy7‐NO2, is proposed for imaging tumor hypoxia. We show that FCy7‐NO2 serves as not only a rapid NIR fluorescence enhanced probe for monitoring and bioimaging of nitroreductase in tumors, but also a novel 19F MR chemical shift‐sensitive contrast agent for selectively detecting nitroreductase catalyzed reduction. Notably, integrating two complementary imaging technologies into FCy7‐NO2 enables sensitive detection of nitroreductase in a broad concentration range without tissue‐depth limit. In general, this agent has a remarkable response to nitroreductase, which provides a promising method for understanding tumor evolution and its physiological role in the hypoxic microenvironment. [ABSTRACT FROM AUTHOR]

SHIP2 is a multi-domain inositol 5-phosphatase binding to a variety of phosphotyrosine (pY)-containing proteins through its SH2 domain, so as to regulate various cell signaling pathways by modulating the phosphatidylinositol level in the plasma membrane. Unfavorably, Helicobacter pylori can hijack SHIP2 through the CagA protein to induce gastric cell carcinogenesis. To date, the interaction between SHIP2 and CagA was not analyzed from a structural point of view. Here, the binding of SHIP2-SH2 with Tyr-phosphorylated peptides from four EPIYA motifs (A/B/C/D) in CagA was studied using NMR spectroscopy. The results showed that EPIYA-C and -D bind to a similar interface of SHIP2-SH2, including a pY-binding pocket and a hydrophobic pocket, to achieve high affinity, while EPIYA-A and -B bind to a smaller interface of SHIP2-SH2 with weak affinity. By summarizing the interface and affinity of SHIP2-SH2 for CagA EPIYA-A/B/C/D, c-MET and FcgR2B ITIM, it was proposed that, potentially, SHIP2-SH2 has a selective preference for L > I > V for the aliphatic residues at the pY+3 position in its ligand. This study reveals the rule of the ligand sequence bound by SHIP2-SH2 and the mechanism by which CagA protein hijacks SHIP2, which will help design a peptide inhibitor against SHIP2-SH2. [ABSTRACT FROM AUTHOR]

α-Synuclein (α-syn) is the main protein component of Lewy bodies, the major pathological hallmarks of Parkinson's disease (PD). C-terminally truncated α-syn is found in the brain of PD patients, reduces cell viability and tends to form fibrils. Nevertheless, little is known about the mechanisms underlying the role of C-terminal truncation on the cytotoxicity and aggregation of α-syn. Here, we use nuclear magnetic resonance spectroscopy to show that the truncation alters α-syn conformation, resulting in an attractive interaction of the N-terminus with membranes and molecular chaperone, protein disulfide isomerase (PDI). The truncated protein is more toxic to mitochondria than full-length protein and diminishes the effect of PDI on α-syn fibrillation. Our findings reveal a modulatory role for the C-terminus in the cytotoxicity and aggregation of α-syn by interfering with the N-terminus binding to membranes and chaperone, and provide a molecular basis for the pathological role of C-terminal truncation in PD pathogenesis. C-terminal truncation of a-syn results in a more extended and exposed conformation, providing further insight into the pathological role of this truncation event in the progression of Parkinson's disease. [ABSTRACT FROM AUTHOR]

Few reports are found working on the features and functions of the human telomere G-triplex (ht-G3) though the telomere G-quadruplex has been intensely studied and widely implemented to develop various biosensors. We herein report that ht-G3 lights up Thioflavin T (ThT) and establish a sensitive biosensing platform for RNA detection by introducing a target recycling strategy. An optimal condition was selected out for ht-G3 to promote ThT to generate a strong fluorescence. Accordingly, an ht-G3-based molecular beacon was successfully designed against the corresponding RNA sequence of the SARS-CoV-2 N-gene. The sensitivity for the non-amplified RNA target achieves 0.01 nM, improved 100 times over the conventional ThT–based method. We believe this ht-G3/ThT–based label-free strategy could be widely applied for RNA detection. [ABSTRACT FROM AUTHOR]

Against an intricate infrared cloudy-sky background, jamming objects such as the edges of clouds in the scene have a similar thermal intensity measure with respect to the background as small targets. This may cause high false alarm rates and low probabilities of detection according to conventional small target detection methods. In this paper, we propose a weighted local difference measure (WLDM)-based scheme for the detection of small targets against various complex cloudy-sky backgrounds. Initially, a WLDM map is achieved to simultaneously enhance targets and suppress background clutters and noise. In this way, the true targets can be easily separated from jamming objects. After that, a simple adaptive threshold is used to segment the targets. More than 460 infrared small target images against diverse intricate cloudy-sky backgrounds were utilized to validate the detection capability of the WLDM-based method. Experimental results demonstrate that the proposed algorithm not only works more robustly for different cloudy-sky backgrounds, target movements, and signal-to-clutter ratio (SCR) values but also has a better performance with regard to the detection accuracy, in comparison to traditional baseline methods. In particular, the proposed method is able to significantly improve SCR values of the images. [ABSTRACT FROM AUTHOR]

We propose an effective small-target detection approach based on weighted image entropy. The approach weights the local entropy measure by the multiscale grayscale difference followed by an adaptive threshold operation, which aims to improve the signal-to-noise ratio for cases in which jamming objects in the scene have similar thermal intensity measure with respect to the background as small target. The detection capability of the proposed approach has been validated on six real sequences, and the results demonstrate its significance and improvement. [ABSTRACT FROM AUTHOR]

We report the conformation of a newly discovered specific lanthanide ion (Ln3+) binding protein, lanmodulin (LanM), and its interaction with Ln3+ in Escherichia coli cells using the in-cell NMR technique. We found that LanM remains unfolded and fails to bind Ln3+ in Escherichia coli cells due to the abundance of phosphate groups. [ABSTRACT FROM AUTHOR]

Lactate, primarily produced by the gut microbiota, performs as a necessary "information transmission carrier" between the gut and the microbiota. To investigate the role of lactate in the gut epithelium cell–microbiota interactions as a metabolic signal, we performed a combinatory, global, and unbiased analysis of metabolomic and transcriptional profiling in human colon epithelial cells (Caco-2), using a lactate treatment at the physiological concentration (8 mM). The data demonstrated that most of the genes in oxidative phosphorylation were significantly downregulated in the Caco-2 cells due to lactate treatment. Consistently, the levels of fumarate, adenosine triphosphate (ATP), and creatine significantly decreased, and these are the metabolic markers of OXPHOS inhibition by mitochondria dysfunction. The one-carbon metabolism was affected and the polyol pathway was activated at the levels of gene expression and metabolic alternation. In addition, lactate significantly upregulated the expressions of genes related to self-protection against apoptosis. In conclusion, lactate participates in gut–gut microbiota communications by remodeling the metabolomic and transcriptional signatures, especially for the regulation of mitochondrial function. This work contributes comprehensive information to disclose the molecular mechanisms of lactate-mediated functions in human colon epithelial cells that can help us understand how the microbiota communicates with the intestines through the signaling molecule, lactate. [ABSTRACT FROM AUTHOR]

[Display omitted] • Over 40 metabolites were detected in G. lucidum extracts. Notably, we identified previously unreported metabolites. • Most metabolite contents increased rapidly from period I to II. Following this, they decreased until reaching period VII. • The optimal time to harvest G. lucidum is during period IV. • Cytochrome P450 genes GlCYP1 , GlCYP3 , GlCYP5 , GlCYP6 and GlCYP13 may have critical roles in the biosynthesis of GAs. Ganoderma lucidum (G. lucidum) is a rare medicinal fungus with various beneficial properties. One of its main components, ganoderic acids (GAs), are important triterpenoids known for their sedative and analgesic, hepatoprotective, and anti-tumor activities. Understanding the growth and development of the G. lucidum fruiting body is crucial for determining the optimal time to harvest them. In this study, we used nuclear magnetic resonance (NMR) spectroscopy to systematically characterize the metabolites of G. lucidum at seven distinct developmental stages. We also measured the contents of seven kinds of GAs using LC-MS/MS. A total of 49 metabolites were detected in G. lucidum , including amino acids, sugars, organic acids and GAs. During the transition from the bud development period (I) to the budding period (II), we observed a rapid accumulation of glucose, tyrosine, nicotinamide ribotide, inosine and GAs. After the budding period, the contents of most metabolites decreased until the mature period (VII). In addition, the contents of GAs showed an initial raising, followed by a decline during the elongation period, except for GAF, which exhibited a rapid raise during the mature stage. We also detected the expression of several genes involved in GA synthesis, finding that most genes including 16 cytochrome P450 monooxygenase were all down-regulated during periods IV and VII compared to period I. These findings provide valuable insights into the dynamic metabolic profiles of G. lucidum throughout its growth stage, and it is recommended to harvest G. lucidum at period IV. [ABSTRACT FROM AUTHOR]

Aflatoxin B 1 (AFB 1) is a well-known carcinogen for human health, and requires sensitive and rapid methods for monitoring. Here, we developed an Avi-tagged nanobody (AviTag-Nb) and incorporated it into the biotin-streptavidin-amplified ELISA (BA-ELISA) and magnetic bead-based ELISA (MB-ELISA) to detect AFB 1. After optimization, BA-ELISA and MB-ELISA achieved 50% inhibitory concentrations (IC 50) of 0.28 and 0.53 ng/mL, respectively, and provided results within 50 and 26 min, making them more sensitive and time-saving compared to the classic ELISA. The detection limits (LODs) of BA-ELISA and MB-ELISA were down to 0.07 and 0.12 ng/mL, respectively, ensuring their practical application in AFB 1 analysis. Additionally, both assays provided satisfactory recoveries (90.0%–97.2%) and favorable relative standard deviation (4.00%–10.5%) when tested with spiked cereal samples, aligning well with the results obtained from HPLC. Therefore, the AviTag-Nb shows promise as a valuable reagent in immunoassays, and the proposed BA-ELISA and MB-ELISA methods can serve as practical analytical tools for determining AFB 1 in real samples. • A bifunctional and clonable AviTag-nanobody fusion protein for AFB 1 was constructed. • In vivo biotinylated AviTag-nanobody was used to test AFB 1 by BA-ELISA and MB-ELISA. • The developed methods are more sensitive and less time-consuming than classic ELISA. • AviTag-nanobody fusion can be used as a great probe for immunoassay of food toxins. [ABSTRACT FROM AUTHOR]

Protein methylation is crucial in epigenetics, and targeting the involved methyltransferases shows great potential for therapeutic intervention with several inhibitors in clinical trials for oncology indications. Therefore, characterization of protein methylation is essential for understanding the methyltransferase function and discovering chemical inhibitors and antagonists. While NMR has been used to measure methylation rates, isotopic labeling of protein or methyl donors can be costly and cannot characterize demethylation of proteins extracted from natural sources. Our method employs a four-quantum filter 1H-13C experiment that selectively detects methyl groups, providing a simple way to characterize methylation and demethylation features of methyltransferases and demethylases, respectively, without requiring isotopic labeling. In our experiments, we successfully observed the methylation of H3 under lysate from various cells and tissues of mice with cancerous growth. The results revealed that H3 undergoes both mono- and dimethylation in all the tested lysates, but at varying rates and degrees. Significantly lower H3 methylation rates and levels were observed in both cervical tumor and breast tumor lysates compared with the corresponding cancerous cells and healthy cells lysates. These findings highlight the variability of histone H3 methylation patterns among healthy cells, cancerous cells, tumor tissues, and different tumor types, and suggest that this method has great potential in facilitating the development of effective interventions against these diseases. By characterizing the methylation features of suspected tumors or areas of concern, it provides valuable insights into the underlying mechanisms of cancer development and aids in identifying potential targets for therapeutic interventions. [Display omitted] • A novel NMR method to monitor protein methylation and demethylation without isotopic labeling. • The method can be used to monitor methylation kinetics of H3 under lysates from various cells and tissues. • The method provides different metabolism pathways of SAM, and offers potential help for drug development and treatment. [ABSTRACT FROM AUTHOR]

SH2 domain-containing inositol 5-phosphatase 2 (SHIP2) plays an essential role in regulating phosphatidylinositol level in human cell, and is recruited to many phosphotyrosine (pY)-dependent signal transduction pathways by the SH2 domain. In immunity signaling, immunoreceptor FcγRIIB binds to SHIP2-SH2 via its Y292-phosphorylated immunoreceptor tyrosine-based inhibitory motif (ITIM) and transmits inhibitory signal, which regulates B cell and neuronal cell activity and is associated with immune diseases and Alzheimer's disease. To date, the interaction between SHIP2 and FcγRIIB has not been analyzed from a structural point of view. Here, the binding of SHIP2-SH2 with Y292-phosphorylated FcγRIIB-ITIM was analyzed using NMR spectroscopy. The results demonstrated that SHIP2-SH2 mainly utilizes two regions including a pY-binding pocket and a specificity pocket formed by βD, βE, and EF-loop, to bind with FcγRIIB-ITIM in high affinity. In addition to the two regions, the BG-loop of SHIP2-SH2 functions as an auxiliary interface enhancing affinity. By comparing the binding of SHIP2-SH2 with ligands from FcγRIIB and c-MET, a hepatocyte growth factor receptor associated with tumorigenesis, significant differences in interface and affinity were found, suggesting that SHIP2-SH2 applies diverse patterns for binding to different ligand proteins. Moreover, S49, S51, and R70 of SHIP2 were identified to mediate the binding of both FcγRIIB and c-MET, while R28 and Q107 were found to only participate in the binding of c-MET and FcγRIIB respectively. Taken together, this study reveals the diverse mechanisms of SHIP2-SH2 for recognizing different ligands, and provides important clues for selectively manipulating various signaling pathways and specific drug design. [ABSTRACT FROM AUTHOR]

Nanobodies (Nbs) have shown great potential in immunodetection of small-molecule contaminants in food and environmental monitoring. However, the limited knowledge of the mechanism of Nbs binding to small molecules has hampered the development of high-affinity Nbs and assay improvement. We previously reported two homologous nanobodies Nb26 and Nb28 specific to aflatoxin B 1 (AFB 1), with the former exhibiting higher sensitivity in ELISA. Herein, Nb26 was selected as the model antibody to resolve its solution nuclear magnetic resonance (NMR) structure, and investigate its AFB 1 recognition mechanism. The results revealed that Nb26 exhibits a typical immunoglobulin fold and its AFB 1 -binding interface is uniquely located in complementarity-determining region 3 (CDR3) and framework region 2 (FR2). This finding was applied to improve the binding activity of Nb28 against AFB 1 by constructing two Nb28-based mutants A50V and S102D, resulting in 2.3- and 3.3-fold sensitivity enhancement over the wild type, respectively. This study develops an NMR-based strategy to analyze the underlying mechanism of Nb against AFB 1 , and successfully generated two site-modified Nbs with improved detection sensitivity. It is believed that this work could greatly expand the applications of Nbs by providing a way to enhance the binding activity. [ABSTRACT FROM AUTHOR]

Abstract: It has been well accepted that the double quantum (DQ) correlated-spectroscopy revamped by asymmetric z-gradient echo detection (CRAZED) signal is enveloped in the profile function t 2 exp[−(t 2 +2t 1)/T 2], but this function is too simple to describe the spin echo characteristics of the CRAZED free induction decay signal. In this paper the DQ CRAZED experiment is analyzed by including the homogeneous and inhomogeneous broadening effects, and a formula for the time domain DQ CRAZED signal is obtained. This formula includes the chemical shift echo and the inhomogeneous echo, both appearing at t 2 =2t 1. Experiments have confirmed the theory. [Copyright &y& Elsevier]

Abstract: The Vogel–Fulcher–Tammann equation, which is widely applied in condensed matter physics, is for the first time applied to analysis of the hydrogen exchange rates of DNA as a function of temperature. The VFT equation, which for hydrogen exchange should read , contains a constant temperature . When we analyzed the hydrogen exchange rates for the thrombin binding DNA aptamer d(GGTTGGTGTGGTTGG) as a function of temperature using the VFT equation, we found that happens to be the melting temperature of the DNA. A quantitative relationship is established between the VFT equation and the Arrhenius equation. Under suitable conditions the VFT equation can be reduced to the Arrhenius equation. [Copyright &y& Elsevier]

The effect of acetonitrile (ACN) on the low-affinity interaction between human serum albumin (HSA) and ibuprofen (IBP) was studied using 1H-NMR techniques. Both chemical shift and relaxation measurements showed the addition of ACN to the solutions decreased the binding affinity of IBP to HSA and reduced the hydrophobic interaction between them. The self-diffusion coefficients of IBP were measured as a function of the drug concentration at different ACN concentrations. The association constant, Ka, for ligand–HSA complexes and the number of binding sites, n, are evaluated by the application of Langmuir isotherm. The results indicated that the value of n was about 38 without ACN, and about 26 with ACN concentration 12% (v/v%). The decreased binding capacity of IBP to HSA in the presence of ACN was mainly attributed to the competition of ACN with IBP to the low-affinity binding sites of HSA molecule. [Copyright &y& Elsevier]

The Ca2+-mediated conformational transition of the protein calmodulin (CaM) is essential to a variety of signal transduction pathways. Whether the transition in living cells is similar to that observed in buffer is not known. Here, we report the direct observation by 19F NMR spectroscopy of the transition of the Ca2+-free and -bound forms in Xenopus laevis oocytes at different Ca2+ levels. We find that the Ca2+-bound CaM population increased greatly upon binding the target protein myosin light-chain kinase (MLCK) at the same Ca2+ level. Paramagnetic NMR spectroscopy was also exploited for the first time to obtain long-range structural constraints in cells. Our study shows that 19F NMR spectroscopy can be used to obtain long-range structural constraints in living eukaryotic cells and paves the way for quantification of protein binding constants. [ABSTRACT FROM AUTHOR]

Diacylglycerol kinase (DgkA) is a small integral membrane protein, responsible for the ATP-dependent phosphorylation of diacylglycerol to phosphatidic acid. Its structures reported in previous studies, determined in detergent micelles by solution NMR and in monoolein cubic phase by X-ray crystallography, differ significantly. These differences point to the need to validate these detergent-based structures in phospholipid bilayers. Here, we present a well-defined homo-trimeric structure of DgkA in phospholipid bilayers determined by magic angle spinning solid-state NMR (ssNMR) spectroscopy, using an approach combining intra-, inter-molecular paramagnetic relaxation enhancement (PRE)-derived distance restraints and CS-Rosetta calculations. The DgkA structure determined in lipid bilayers is different from the solution NMR structure. In addition, although ssNMR structure of DgkA shows a global folding similar to that determined by X-ray, these two structures differ in monomeric symmetry and dynamics. A comparative analysis of DgkA structures determined in three different detergent/lipid environments provides a meaningful demonstration of the influence of membrane mimetic environments on the structure and dynamics of membrane proteins. Jianping Li et al. present the homo-trimeric structure of the small integral membrane protein diacylglycerol kinase (DgkA) in phospholipid bilayers determined by magic angle spinning solid-state NMR spectroscopy. They compare the structure with structures solved by solution NMR and X-ray crystallography and provide insights into the influence of membrane mimetic environments on membrane proteins. [ABSTRACT FROM AUTHOR]

We for the first time report that the activated CRISPR-Cas12a system trans-cleaves DNA G-quadruplexes (G4). The cleavage activity on human telomere G4 and TBA G4 was investigated and verified by FRET, CD, gel electrophoresis and NMR. We believe that this finding will pave a new avenue for advancing the applications of CRISPR-Cas12a and G4 in biosensing and biochemistry. [ABSTRACT FROM AUTHOR]

Fast and sensitive detection of E.coli O157: H7 is significantly essential for clinical management as well as for transmission prevention during disease outbreaks. Though many types of detection strategies have been implemented for measuring E.coli O157: H7, most of them still rely on complex instruments or tedious/laborious setups, which restrict their applications in resource-limited scenarios. Herein, we introduce an eye-based microfluidic aptasensor (EA-Sensor) for fast detection of E.coli O157: H7 without the assist of any instruments. We demonstrate the perfect coupling of aptamer sensing, hybridization chain reaction (HCR)-amplification and a distance-based visualized readout to quantitatively determine the pathogen concentration. We first used gel-electrophoresis assay to evaluate the system and the results proved that E.coli O157: H7 was well recognized by the aptamer and HCR could increase the signal by about 100 folds. In addition, the Aptamer specificity and signal-amplification ability were verified on the EA-Sensor for sensing E.coli O157: H7 by naked eyes. Furthermore, we demonstrated that E.coli O157: H7 in milk could be accurately and conveniently measured with good performance. With the benefits of operation integration and strategy integration, our EA-Sensor shows advantages of high specificity, easy operation, efficient amplification and visualized readout, which offers a favorable point-of-care tool for E.coli O157: H7 or other pathogen detection in resource-constrained settings. Image 1 • An eye-based aptasensor (EA-Sensor) is developed for point-of-care detection of E.coli O157:H7. • Integration of aptamer recognition, HCR amplification and a visualized readout is firstly realized for pathogen detection. • On-chip measurement of E.coli O157:H7 in milk samples was successfully achieved. [ABSTRACT FROM AUTHOR]

Abstract: Ligand-based nuclear magnetic resonance (NMR) approaches have shown great promise in the study of ligand–protein interaction. But these approaches suffer from interference from the nonspecific binding. Here a saturation transfer difference (STD) NMR method to map the group epitope and to measure the dissociation constant (K D) of specific interaction between ligand and protein is presented. The interference from nonspecific binding was corrected by recording STD NMR spectra of ligand–protein solutions with and without inhibitor saturating the mutually specific binding site and subtracting one from the other. The method was examined with l-tryptophan (Trp), naproxen (Nap), and human serum albumin (HSA) as model ligand, inhibitor, and protein, respectively. Results agree well with other reports of Trp–HSA interaction. [Copyright &y& Elsevier]

A fast NMR experiment is proposed for measuring correlation spectroscopy (COSY) spectra with diagonal peaks completely removed or largely suppressed. This new pulse sequence is based on double quantum spectroscopy but with delayed detection, so that the double quantum coherence is effectively transferred to single quantum coherence. Therefore, the pulse sequence can be named “2-1” COSY. [ABSTRACT FROM AUTHOR]

To eliminate the effects of complex background signals and to enhance the accuracy of the diffusion coefficient measurement, derivative NMR spectroscopy with negligible loss of the spectral quality is introduced based on the customized Savitzky-Golay method and used to construct diffusion-ordered NMR spectroscopy (DOSY). The criterion of the method was established by simulations. The application of this method on mouse urine and serum showed that the accuracy and precision of diffusion coefficient measurements in a complex background were improved to enhance the identification of molecules. [ABSTRACT FROM AUTHOR]

Molecular chaperones are diverse families of proteins that play key roles in protein homeostasis. They assist the folding of client proteins or prevent them from irreversible aggregation under stress conditions. Diverse chaperone families contribute to different aspects of protein homeostasis by interacting with a wide range of client proteins. Despite the vital roles of chaperones in cell survival, the molecular mechanisms underlying chaperone functions remain elusive, due to the non‐specificity of chaperone‐client interactions and the intrinsic flexibility of the clients. Our understanding of the chaperone functional mechanisms, especially regarding chaperone‐client interactions, has greatly expanded in recent years, thanks to the significant contribution from various NMR studies. Solution NMR methods have unique advantages in characterizing disordered protein structures, detecting weak and non‐specific interactions, and probing conformational dynamics of proteins and protein complexes, etc., and therefore are especially powerful in the studies of chaperone structure‐function relationships. In this review, we summarize some of the current knowledge of molecular chaperones, with emphasis on common features of chaperone‐client interactions and examples on a number of specific systems in which solution NMR methods were used to provide essential insights into their functional mechanisms. [ABSTRACT FROM AUTHOR]

SP_0782 from Streptococcus pneumoniae is a dimeric PC4-like protein binding single-stranded DNA (ssDNA), and is potentially involved in maintenance of genome stability and natural transformation. SP_0782 binds with different lengths of ssDNA in various patterns through accommodating nucleotides differently in its two DNA-binding regions (DBRs). Here, we report the characterization of a novel site, leucine 20 (L20), which is not located in the DBRs but impairs the DNA binding when mutated to alanine (L20A). The L20A mutation markedly reduced the DNA-binding affinity of SP_0782 for ssDNA dT19G1, and affected the formation of high-order SP_0782:dT19G1 complexes. The side chain of L20 shows interactions with several residues at the backside of the DBRs in apo SP_0782 structure, and the L20A mutation led to a change of circular dichroism (CD) spectrum and broad chemical shift perturbations (CSPs) in NMR spectrum compared with the wild type. The most affected residues in NMR spectrum included F39 and R49 located in DBR2, as well as K60 in DBR1, which was suggested to be important for cooperative binding of ssDNA by the two subunits in SP_0782 dimer. Thus, the L20A mutation caused a local conformational change of SP_0782, which exerted an indirect effect on the DNA-binding interface and therefore impaired the affinity for ssDNA dT19G1. Interestingly, this L20 site is conserved in bacterial but not eukaryotic PC4-like proteins, suggesting an evolutionary divergence. This study provides an insight into the structure-function relationship of SP_0782, and an amino-acid site probably targeted for inhibiting bacteria selectively. • L20A mutation markedly impairs the binding affinity of SP_0782 for dT19G1. • L20A mutation changes the local conformation of SP_0782. • L20A mutation exerts an indirect effect on the DNA-binding interface of SP_0782. • The L20 site is conserved in bacterial but not eukaryotic PC4-like proteins. [ABSTRACT FROM AUTHOR]