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1.
Nature ; 629(8010): 98-104, 2024 May.
Article in English | MEDLINE | ID: mdl-38693411

ABSTRACT

Photobiocatalysis-where light is used to expand the reactivity of an enzyme-has recently emerged as a powerful strategy to develop chemistries that are new to nature. These systems have shown potential in asymmetric radical reactions that have long eluded small-molecule catalysts1. So far, unnatural photobiocatalytic reactions are limited to overall reductive and redox-neutral processes2-9. Here we report photobiocatalytic asymmetric sp3-sp3 oxidative cross-coupling between organoboron reagents and amino acids. This reaction requires the cooperative use of engineered pyridoxal biocatalysts, photoredox catalysts and an oxidizing agent. We repurpose a family of pyridoxal-5'-phosphate-dependent enzymes, threonine aldolases10-12, for the α-C-H functionalization of glycine and α-branched amino acid substrates by a radical mechanism, giving rise to a range of α-tri- and tetrasubstituted non-canonical amino acids 13-15 possessing up to two contiguous stereocentres. Directed evolution of pyridoxal radical enzymes allowed primary and secondary radical precursors, including benzyl, allyl and alkylboron reagents, to be coupled in an enantio- and diastereocontrolled fashion. Cooperative photoredox-pyridoxal biocatalysis provides a platform for sp3-sp3 oxidative coupling16, permitting the stereoselective, intermolecular free-radical transformations that are unknown to chemistry or biology.


Subject(s)
Amino Acids , Biocatalysis , Oxidative Coupling , Photochemical Processes , Amino Acids/biosynthesis , Amino Acids/chemistry , Amino Acids/metabolism , Biocatalysis/radiation effects , Directed Molecular Evolution , Free Radicals/chemistry , Free Radicals/metabolism , Glycine/chemistry , Glycine/metabolism , Glycine Hydroxymethyltransferase/metabolism , Glycine Hydroxymethyltransferase/chemistry , Indicators and Reagents , Light , Oxidative Coupling/radiation effects , Pyridoxal Phosphate/metabolism , Stereoisomerism , Amino Acids, Branched-Chain/chemistry , Amino Acids, Branched-Chain/metabolism
2.
Top Curr Chem (Cham) ; 382(2): 15, 2024 May 04.
Article in English | MEDLINE | ID: mdl-38703255

ABSTRACT

Aligned with the increasing importance of bioorthogonal chemistry has been an increasing demand for more potent, affordable, multifunctional, and programmable bioorthogonal reagents. More advanced synthetic chemistry techniques, including transition-metal-catalyzed cross-coupling reactions, C-H activation, photoinduced chemistry, and continuous flow chemistry, have been employed in synthesizing novel bioorthogonal reagents for universal purposes. We discuss herein recent developments regarding the synthesis of popular bioorthogonal reagents, with a focus on s-tetrazines, 1,2,4-triazines, trans-cyclooctenes, cyclooctynes, hetero-cycloheptynes, and -trans-cycloheptenes. This review aims to summarize and discuss the most representative synthetic approaches of these reagents and their derivatives that are useful in bioorthogonal chemistry. The preparation of these molecules and their derivatives utilizes both classical approaches as well as the latest organic chemistry methodologies.


Subject(s)
Cyclooctanes , Triazines , Triazines/chemistry , Triazines/chemical synthesis , Cyclooctanes/chemistry , Cyclooctanes/chemical synthesis , Alkynes/chemistry , Alkynes/chemical synthesis , Catalysis , Indicators and Reagents/chemistry , Molecular Structure
4.
ACS Sens ; 9(4): 2075-2082, 2024 Apr 26.
Article in English | MEDLINE | ID: mdl-38557006

ABSTRACT

Wearable sweat sensors have achieved rapid development since they hold great potential in personalized health monitoring. However, a typical difficulty in practical processes is the control of working conditions for biorecognition elements, e.g., pH level and ionic strength in sweat may decrease the affinity between analytes and recognition elements. Here, we developed a wearable sensing device for cortisol detection in sweat using an aptamer as the recognition element. The device integrated functions of sweat collection, reagent prestorage, and signal conversion. Especially, the components of prestored reagents were optimized according to the inherent characteristics of sweat samples and electrodes, which allowed us to keep optimal conditions for aptamers. The sweat samples were transferred from the inlet of the device to the reagent prestored chamber, and the dry preserved reagents were rehydrated with sweat and then arrived at the aptamer-modified electrodes. Sweat samples of volunteers were analyzed by the wearable sensing device, and the results showed a good correlation with those of the ELISA kit. We believe that this convenient and reliable wearable sensing device has significant potential in self-health monitoring.


Subject(s)
Aptamers, Nucleotide , Biosensing Techniques , Hydrocortisone , Sweat , Wearable Electronic Devices , Sweat/chemistry , Hydrocortisone/analysis , Humans , Aptamers, Nucleotide/chemistry , Biosensing Techniques/methods , Biosensing Techniques/instrumentation , Electrodes , Electrochemical Techniques/instrumentation , Electrochemical Techniques/methods , Indicators and Reagents/chemistry
5.
Forensic Sci Int ; 358: 112018, 2024 May.
Article in English | MEDLINE | ID: mdl-38581824

ABSTRACT

A number of solvents, (Solstice PF, Opteon SF33 and Amolea AS-300), are compared to the recommended carrier solvent of HFE7100 for the ninhydrin and 1,2-indandione formulations. As the supply of HFE7100 will cease by the end of 2025, suitable alternatives are required in the short-term to ensure the detection of latent fingermarks on porous surfaces is still effective. Although these solvents, with the exception of Amolea AS-300, are classified as per- and polyfluoroalkyl substances (PFAS); they are not classed as hazardous. The alternatives in this study have a low global warming potential and atmospheric lifetime and are volatile, non-flammable and non-ozone depleting, in addition to other desirable properties such as a high wetting-index. During Phase 2 trials with deposited fingermarks, HFE7100 provided the best performing results followed by Opteon SF33, Solstice PF and Amolea AS-300. A significant difference with a negligible effect size was observed for ninhydrin formulations (p-value 0.00179; ε2 0.00418) while a significant difference with a weak effect size was observed for 1,2-indanedione formulations (p-value 2.095 ×10-10; ε2 0.0167). Furthermore, HFE7100 provided the least ink diffusion and the brightest 1,2-indanedione luminosity (significant difference with a moderate effect size p-value 1.772 ×10-13; ε2 0.0434) but the HFE formulation turned cloudy more quickly and needed regular replacements. Phase 3 pseudo-operational trials of 100 porous items followed a similar trend whereby HFE7100 formulations detected the highest number of marks followed by Opteon SF33 and Solstice PF. Although HFE7100 is still the best performing carrier solvent, this study demonstrates that, in the short-term, Opteon SF33 and Solstice PF may have potential as non-flammable replacement carrier solvents while developing the long-term goal of solvent-less methods.


Subject(s)
Dermatoglyphics , Indans , Indicators and Reagents , Ninhydrin , Solvents , Humans , Solvents/chemistry , Indans/chemistry
6.
Anal Chem ; 96(15): 5815-5823, 2024 Apr 16.
Article in English | MEDLINE | ID: mdl-38575144

ABSTRACT

Microfluidic techniques are widely applied in biomolecular analysis and disease diagnostic assays. While the volume of the sample that is directly used in such assays is often only femto-to microliters, the "dead volume" of solutions supplied in syringes and tubing can be much larger, even up to milliliters, increasing overall reagent use and making analysis significantly more expensive. To reduce the difficulty and cost, we designed a new chip using a low volume solution for analysis and applied it to obtain real-time data for protein-protein interaction measurements. The chip takes advantage of air/aqueous two-phase droplet flow, on-chip rapid mixing within milliseconds, and a droplet capture method, that ultimately requires only 2 µL of reagent solution. The interaction is analyzed by particle diffusometry, a nonintrusive and precise optical detection method to analyze the properties of microparticle diffusion in solution. Herein, we demonstrate on-chip characterization of human immunodeficiency virus p24 antibody-antigen protein binding kinetics imaged via fluorescence microscopy and analyzed by PD. The measured kon and koff are 1 × 106 M-1 s-1 and 3.3 × 10-4 s-1, respectively, and agree with independent measurement via biolayer interferometry and previously calculated p24-antibody binding kinetics. This new microfluidic chip and the protein-protein interaction analysis method can also be applied in other fields that require low-volume solutions to perform accurate measurement, analysis, and detection.


Subject(s)
Microfluidic Analytical Techniques , Microfluidics , Humans , Kinetics , Diffusion , Indicators and Reagents , Microfluidic Analytical Techniques/methods
7.
Top Curr Chem (Cham) ; 382(2): 12, 2024 Apr 08.
Article in English | MEDLINE | ID: mdl-38589598

ABSTRACT

Organoselenium compounds have been the subject of extensive research since the discovery of the biologically active compound ebselen. Ebselen has recently been found to show activity against the main protease of the virus responsible for COVID-19. Other organoselenium compounds are also well-known for their diverse biological activities, with such compounds exhibiting interesting physical properties relevant to the fields of electronics, materials, and polymer chemistry. In addition, the incorporation of selenium into various organic molecules has garnered significant attention due to the potential of selenium to enhance the biological activity of these molecules, particularly in conjunction with bioactive heterocycles. Iodine and iodine-based reagents play a prominent role in the synthesis of organoselenium compounds, being valued for their cost-effectiveness, non-toxicity, and ease of handling. These reagents efficiently selenylate a broad range of organic substrates, encompassing alkenes, alkynes, and cyclic, aromatic, and heterocyclic molecules. They serve as catalysts, additives, inducers, and oxidizing agents, facilitating the introduction of different functional groups at alternate positions in the molecules, thereby allowing for regioselective and stereoselective approaches. Specific iodine reagents and their combinations can be tailored to follow the desired reaction pathways. Here, we present a comprehensive review of the progress in the selenylation of organic molecules using iodine reagents over the past decade, with a focus on reaction patterns, solvent effects, heating, microwave, and ultrasonic conditions. Detailed discussions on mechanistic aspects, such as electrophilic, nucleophilic, radical, electrochemical, and ring expansion reactions via selenylation, multiselenylation, and difunctionalization, are included. The review also highlights the formation of various cyclic, heterocyclic, and heteroarenes resulting from the in situ generation of selenium intermediates, encompassing cyclic ketones, cyclic ethers, cyclic lactones, selenophenes, chromones, pyrazolines, pyrrolidines, piperidines, indolines, oxazolines, isooxazolines, lactones, dihydrofurans, and isoxazolidines. To enhance the reader's interest, the review is structured into different sections covering the selenylation of aliphatic sp2/sp carbon and cyclic sp2 carbon, and then is further subdivided into various heterocyclic molecules.


Subject(s)
Iodine , Isoindoles , Organoselenium Compounds , Selenium , Iodine/chemistry , Indicators and Reagents , Organoselenium Compounds/chemistry , Lactones/chemistry , Carbon
8.
Curr Protoc ; 4(3): e1016, 2024 Mar.
Article in English | MEDLINE | ID: mdl-38511507

ABSTRACT

Investigating the function of target proteins for functional prospection or therapeutic applications typically requires the production and purification of recombinant proteins. The fusion of these proteins with tag peptides and fluorescently derived proteins allows the monitoring of candidate proteins using SDS-PAGE coupled with western blotting and fluorescent microscopy, respectively. However, protein engineering poses a significant challenge for many researchers. In this protocol, we describe step-by-step the engineering of a recombinant protein with various tags: TAT-HA (trans-activator of transduction-hemagglutinin), 6×His and EGFP (enhanced green fluorescent protein) or mCherry. Fusion proteins are produced in E. coli BL21(DE3) cells and purified by immobilized metal affinity chromatography (IMAC) using a Ni-nitrilotriacetic acid (NTA) column. Then, tagged recombinant proteins are introduced into cultured animal cells by using the penetrating peptide TAT-HA. Here, we present a thorough protocol providing a detailed guide encompassing every critical step from plasmid DNA molecular assembly to protein expression and subsequent purification and outlines the conditions necessary for protein transduction technology into animal cells in a comprehensive manner. We believe that this protocol will be a valuable resource for researchers seeking an exhaustive, step-by-step guide for the successful production and purification of recombinant proteins and their entry by transduction within living cells. © 2024 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: DNA cloning, molecular assembly strategies, and protein production Basic Protocol 2: Protein purification Basic Protocol 3: Protein transduction in mammalian cells.


Subject(s)
Escherichia coli , Peptides , Animals , Escherichia coli/genetics , Recombinant Proteins/genetics , Recombinant Proteins/chemistry , Peptides/genetics , Peptides/metabolism , Indicators and Reagents/metabolism , Gene Products, tat/metabolism , Coloring Agents/metabolism , DNA/metabolism , Mammals/genetics , Mammals/metabolism
9.
Acc Chem Res ; 57(6): 855-869, 2024 Mar 19.
Article in English | MEDLINE | ID: mdl-38452397

ABSTRACT

ConspectusSince the pioneering work of Curtius and Fischer, chemical peptide synthesis has witnessed a century's development and evolved into a routine technology. However, it is far from perfect. In particular, it is challenged by sustainable development because the state-of-the-art of peptide synthesis heavily relies on legacy reagents and technologies developed before the establishment of green chemistry. Over the past three decades, a broad range of efforts have been made for greening peptide synthesis, among which peptide synthesis using unprotected amino acid represents an ideal and promising strategy because it does not require protection and deprotection steps. Unfortunately, C → N peptide synthesis employing unprotected amino acids has been plagued by undesired polymerization, while N → C inverse peptide synthesis with unprotected amino acids is retarded by severe racemization/epimerization owing to the iterative activation and aminolysis of high racemization/epimerization susceptible peptidyl acids. Consequently, there is an urgent need to develop innovative coupling reagents and strategies with novel mechanisms that can address the long-standing notorious racemization/epimerization issue of peptide synthesis.This Account will describe our efforts in discovery of ynamide coupling reagents and their application in greening peptide synthesis. Over an eight-year journey, ynamide coupling reagents have evolved into a class of general coupling reagents for both amide and ester bond formation. In particular, the superiority of ynamide coupling reagents in suppressing racemization/epimerization enabled them to be effective for peptide fragment condensation, and head-to-tail cyclization, as well as precise incorporation of thioamide substitutions into peptide backbones. The first practical inverse peptide synthesis using unprotected amino acids was successfully accomplished by harnessing such features and taking advantage of a transient protection strategy. Ynamide coupling reagent-mediated ester bond formation enabled efficient intermolecular esterification and macrolactonization with preservation of α-chirality and the configuration of the conjugated α,ß-C-C double bond. To make ynamide coupling reagents readily available with reasonable cost and convenience, we have developed a scalable one-step synthetic method from cheap starting materials. Furthermore, a water-removable ynamide coupling reagent was developed, offering a column-free purification of the target coupling product. In addition, the recycle of ynamide coupling reagent was accomplished, thereby paving the way for their sustainable industrial application.As such, this Account presents the whole story of the origin, mechanistic insights, preparation, synthetic applications, and recycle of ynamide coupling reagents with a perspective that highlights their future impact on peptide synthesis.


Subject(s)
Amides , Peptides , Indicators and Reagents , Peptides/chemistry , Amides/chemistry , Amino Acids/chemistry , Esters
10.
ACS Appl Mater Interfaces ; 16(12): 14561-14572, 2024 Mar 27.
Article in English | MEDLINE | ID: mdl-38500377

ABSTRACT

Uridine diphosphate (UDP)-glucosyltransferases (UGTs) have received increasing attention in the field of ginsenoside Rh2 conversion. By harnessing the metal chelation between transition metal ions and imidazole groups present on His-tagged enzymes, a specific immobilization of the enzyme within metal-organic frameworks (MOFs) is achieved. This innovative approach not only enhances the stability and reusability of the enzyme but also enables one-step purification and immobilization. Consequently, the need for purifying crude enzyme solutions is effectively circumvented, resulting in significant cost savings during experimentation. The use of immobilized enzymes in catalytic reactions has shown great potential for achieving higher conversion rates of ginsenoside Rh2. In this study, highly stable mesoporous Zn-Ni MOF materials were synthesized at 150 °C by a solvothermal method. The UGT immobilized on the Zn-Ni MOF (referred to as UGT@Zn-Ni MOF) exhibited superior pH adaptability and thermal stability, retaining approximately 76% of its initial activity even after undergoing 7 cycles. Furthermore, the relative activity of the immobilized enzyme remained at an impressive 80.22% even after 45 days of storage. The strong specific adsorption property of Zn-Ni MOF on His-tagged UGT was confirmed through analysis using polyacrylamide gel electrophoresis. UGT@Zn-Ni MOF was used to catalyze the conversion reaction, and the concentration of rare ginsenoside Rh2 was generated at 3.15 µg/mL. The results showed that Zn-Ni MOF is a material that can efficiently purify and immobilize His-tagged enzyme in one step and has great potential for industrial applications in enzyme purification and ginsenoside synthesis.


Subject(s)
Ginsenosides , Glycosyltransferases , Enzymes, Immobilized/chemistry , Indicators and Reagents , Zinc
11.
PLoS One ; 19(3): e0299364, 2024.
Article in English | MEDLINE | ID: mdl-38551992

ABSTRACT

The purpose of this study is to examine the possibility of GO to be used as an adsorbent for five novel potentially hazardous azo-dyes for their removal from aqueous solution. Adsorption characteristics of GO for azo-dyes removal were investigated by means of experimental and computational DFT as well as Monte Carlo approaches. Experimental studies include the effect of adsorbent dose, contact time, and initial concentration, while computational investigation involves DFT and Monte Carlo (MC) simulations. Through DFT studies geometric, electronic, and thermodynamic parameters were explored and possible mechanism of interactions and adsorption energies by predicted through MC by searching lowest possible adsorption complexes. Experimental data were evaluated by Langmuir models in order to describe the equilibrium isotherms. Equilibrium data fitted well to the Langmuir model. Thermodynamic parameters i.e., free energy change, enthalpy change, and entropy change revealed that the removal of azo-dyes by adsorption on the surface of GO molecular sieves was spontaneous. Nature of the process was found to be physiosorption involving non-covalent interaction. The study unveiled that GO can be used as an efficient adsorbent material for the adsorption of azo-dyes from aqueous solution.


Subject(s)
Azo Compounds , Water Pollutants, Chemical , Adsorption , Kinetics , Thermodynamics , Indicators and Reagents , Water , Coloring Agents , Hydrogen-Ion Concentration
12.
Anal Methods ; 16(13): 1948-1956, 2024 Mar 28.
Article in English | MEDLINE | ID: mdl-38445900

ABSTRACT

Nucleic acids, which have been employed in medicines for various diseases, are attracting attention as a new pharmaceutical model. Depending on the target substances, nucleic acid medicines with various nucleic acid chain lengths (several tens of nucleotides [nt] to several thousands of nt) exist. The purification of synthesized nucleic acids is crucial as various impurities remain in the crude product after synthesis. Presently, reversed-phase high-performance liquid chromatography (RP-HPLC) represents an effective purification method for nucleic acids. However, the information regarding the HPLC conditions for separating and purifying nucleic acids of various chain lengths is insufficient. Thus, this technical note describes the separation and purification of short-, medium-, and long-stranded nucleic acids (several tens of nt to thousands of nt) by RP-HPLC with various mobile phases and octadecyl-based columns with various pore sizes, such as normal (9-12 nm), wide (30 nm), and super wide (>30 nm) pores.


Subject(s)
Nucleic Acids , RNA , Chromatography, High Pressure Liquid/methods , Indicators and Reagents , Nucleotides
13.
J Chromatogr A ; 1720: 464771, 2024 Apr 12.
Article in English | MEDLINE | ID: mdl-38447433

ABSTRACT

During collagen biosynthesis, proline is post-translationally converted to hydroxyproline by specific enzymes. This amino acid, unique to collagen, plays a crucial role in stabilizing the collagen triple helix structure and could serve as an important biomarker for collagen content and quality analysis. Hydroxyproline has four isomers, depending on whether proline is hydroxylated at position 4 or 3 and on whether the cis- or trans- conformation is formed. Moreover, as extensive hydrolysis of collagen is required for its amino acid analysis, epimerization may also occur, although to a lesser extent, giving a total of eight possible isomers. The aim of the present study was to develop a reversed-phase high-performance liquid chromatography-UV-mass spectrometry (RPLC-UV-MS) method for the separation and quantification of all eight hydroxyproline isomers. After the chiral derivatization of the hydroxyproline isomers with Nα-(2,4-dinitro-5-fluorophenyl)-L-valinamide (L-FDVA), to enable their UV detection, the derivatized diastereoisomers were separated by testing different C18 column technologies and morphologies and optimizing operative conditions such as the mobile phase composition (solvent, additives), elution mode, flow rate and temperature. Baseline resolution of all eight isomers was achieved on a HALO® ES-C18 reversed-phase column (150×1.5 mm, 2.7 µm, 160 Å) using isocratic elution and MS-compatible mobile phase. The optimized method was validated for the quantification of hydroxyproline isomers and then applied to different collagen hydrolysates to gain insight and a deeper understanding of hydroxyproline abundances in different species (human, chicken) and sources (native, recombinant).


Subject(s)
Collagen , Proline , Humans , Hydroxyproline/analysis , Chromatography, High Pressure Liquid/methods , Collagen/analysis , Collagen/chemistry , Indicators and Reagents
14.
J Histochem Cytochem ; 72(4): 233-243, 2024 Apr.
Article in English | MEDLINE | ID: mdl-38553997

ABSTRACT

Xylene is the commonest clearing agent even though it is hazardous and costly. This study evaluated the clearing properties of coconut oil as an alternative cost-effective clearing agent for histological processes. Ten (10) prostate samples fixed in formalin were taken and each one was cut into 4 before randomly separating them into four groups (A, B, C and D). Tissues were subjected to ascending grades of alcohol for dehydration. Group A was cleared in xylene and Groups B, C, and D were cleared at varying times of 1hr 30mins, 3hrs, and 4hrs in coconut oil respectively before embedding, sectioning, and staining were carried out. Gross and histological features were compared. Results indicated a significant shrinkage in coconut oil-treated specimen compared with the xylene-treated specimen and only the tissues cleared in coconut oil for 4hrs were as rigid as the tissues cleared in xylene (p > 0.05). No significant difference was found in either of the sections when checked for cellular details and staining quality (p > 0.999). Coconut oil is an efficient substitute for xylene in prostate tissues with a minimum clearing time of 4hrs, as it is environmentally friendly and less expensive, but causes significant shrinkage to prostate tissue.


Subject(s)
Formaldehyde , Xylenes , Coconut Oil , Xylenes/chemistry , Staining and Labeling , Indicators and Reagents
15.
Bioconjug Chem ; 35(3): 286-299, 2024 Mar 20.
Article in English | MEDLINE | ID: mdl-38451202

ABSTRACT

Chemoselective protein modification plays extremely important roles in various biological, medical, and pharmaceutical investigations. Mimicking the mechanism of the chemoselective reaction between natural azaphilones and primary amines, this work successfully simplified the azaphilone scaffold into much simpler 3-acyl-4-pyranones. Examinations confirmed that these slim-size mimics perfectly kept the unique reactivity for selective conjugation with the primary amines including lysine residues of peptides and proteins. The newly developed pyranone tool presents remarkably increased aqueous solubility and compatible second-order rate constant by comparison with the original azaphilone. Additional advantages also include the ease of biorthogonal combinative use with a copper-catalyzed azide-alkyne Click reaction, which was conveniently applied to decorate lysozyme with neutral-, positive- and negative-charged functionalities in parallel. Moderate-degree modification of lysozyme with positively charged quaternary ammoniums was revealed to increase the enzymatic activities.


Subject(s)
Lysine , Muramidase , Lysine/chemistry , Indicators and Reagents , Peptides/chemistry , Amines , Azides/chemistry , Click Chemistry , Alkynes/chemistry
16.
Bioelectrochemistry ; 157: 108672, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38428185

ABSTRACT

Modern biosensing technology plays a crucial role in combating the spread of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). However, the associated assays remain costly, considering their extensive daily use. In response, we developed a simplified one-step SARS-CoV-2 protease assay that reduces both time and financial expenses. This approach eliminates the need for extra reagents, enzymes, or antibodies. The simplification involves a photo-sensitive Bengal red-tagged substrate peptide, allowing specific cross-linking upon protease-substrate recognition. This process forms a di-tyrosine product with a distinctive fluorescence signal readout, enabling the detection of SARS-CoV-2 in patient serum samples. This method anticipates a major reduction in assay costs in the near future.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , COVID-19/diagnosis , Indicators and Reagents , Antibodies, Viral , Proteins , Peptides , Peptide Hydrolases
17.
Nat Comput Sci ; 4(3): 224-236, 2024 Mar.
Article in English | MEDLINE | ID: mdl-38532137

ABSTRACT

Here we used machine learning to engineer genetically encoded fluorescent indicators, protein-based sensors critical for real-time monitoring of biological activity. We used machine learning to predict the outcomes of sensor mutagenesis by analyzing established libraries that link sensor sequences to functions. Using the GCaMP calcium indicator as a scaffold, we developed an ensemble of three regression models trained on experimentally derived GCaMP mutation libraries. The trained ensemble performed an in silico functional screen on 1,423 novel, uncharacterized GCaMP variants. As a result, we identified the ensemble-derived GCaMP (eGCaMP) variants, eGCaMP and eGCaMP+, which achieve both faster kinetics and larger ∆F/F0 responses upon stimulation than previously published fast variants. Furthermore, we identified a combinatorial mutation with extraordinary dynamic range, eGCaMP2+, which outperforms the tested sixth-, seventh- and eighth-generation GCaMPs. These findings demonstrate the value of machine learning as a tool to facilitate the efficient engineering of proteins for desired biophysical characteristics.


Subject(s)
Calcium Signaling , Calcium , Calcium/metabolism , Coloring Agents , Indicators and Reagents , Machine Learning
18.
J Colloid Interface Sci ; 664: 650-666, 2024 Jun 15.
Article in English | MEDLINE | ID: mdl-38490040

ABSTRACT

Functionalized single-walled carbon nanotubes (SWCNTs) hold immense potential for diverse biomedical applications due to their biocompatibility and optical properties, including near-infrared fluorescence. Specifically, SWCNTs have been utilized to target cells as a vehicle for drug delivery and gene therapy, and as sensors for various intracellular biomarkers. While the main internalization route of SWCNTs into cells is endocytosis, methods for enhancing the cellular uptake of SWCNTs are of great importance. In this research, we demonstrate the use of a transfecting reagent for promoting cell internalization of functionalized SWCNTs. We explore different types of SWCNT functionalization, namely single-stranded DNA (ssDNA) or polyethylene glycol (PEG)-lipids, and two different cell types, embryonic kidney cells and adenocarcinoma cells. We show that internalizing PEGylated functionalized SWCNTs is enhanced in the presence of the transfecting reagent, where the effect is more pronounced for negatively charged PEG-lipid. However, ssDNA-SWCNTs tend to form aggregates in the presence of the transfecting reagent, rendering it unsuitable for promoting internalization. For all cases, cellular uptake is visualized by near-infrared fluorescence microscopy, showing that the SWCNTs are typically localized within the lysosome. Generally, cellular internalization was higher in the adenocarcinoma cells, thereby paving new avenues for drug delivery and sensing in malignant cells.


Subject(s)
Adenocarcinoma , Nanotubes, Carbon , Humans , Indicators and Reagents , Microscopy, Fluorescence , Polyethylene Glycols
19.
Nature ; 627(8004): 680-687, 2024 Mar.
Article in English | MEDLINE | ID: mdl-38448587

ABSTRACT

Methods for selective covalent modification of amino acids on proteins can enable a diverse array of applications, spanning probes and modulators of protein function to proteomics1-3. Owing to their high nucleophilicity, cysteine and lysine residues are the most common points of attachment for protein bioconjugation chemistry through acid-base reactivity3,4. Here we report a redox-based strategy for bioconjugation of tryptophan, the rarest amino acid, using oxaziridine reagents that mimic oxidative cyclization reactions in indole-based alkaloid biosynthetic pathways to achieve highly efficient and specific tryptophan labelling. We establish the broad use of this method, termed tryptophan chemical ligation by cyclization (Trp-CLiC), for selectively appending payloads to tryptophan residues on peptides and proteins with reaction rates that rival traditional click reactions and enabling global profiling of hyper-reactive tryptophan sites across whole proteomes. Notably, these reagents reveal a systematic map of tryptophan residues that participate in cation-π interactions, including functional sites that can regulate protein-mediated phase-separation processes.


Subject(s)
Cations , Cyclization , Indicators and Reagents , Proteins , Tryptophan , Cations/chemistry , Indicators and Reagents/chemistry , Oxidation-Reduction , Proteome/chemistry , Tryptophan/chemistry , Peptides/chemistry , Click Chemistry , Proteins/chemistry
20.
Zhonghua Yi Xue Za Zhi ; 104(11): 857-864, 2024 Mar 19.
Article in Chinese | MEDLINE | ID: mdl-38462362

ABSTRACT

Objective: To establish the threshold value of human leukocyte antigen (HLA) mixed antigen reagent screening test results, and to verify it by HLA single antigen reagent confirmation test results. Methods: The results of 2 255 serum samples tested for HLA antibodies by HLA mixed antigen reagent in the department of HLA Laboratory, the First Affiliated Hospital of Soochow University from October 2017 to December 2021 were retrospectively analyzed. Among them, 1 139 samples were also tested by single antigen HLA Class-Ⅰ reagent and 1 116 samples were also tested by single antigen HLA Class-Ⅱ reagent. Based on the same antigens coated with both reagents, the Mean Fluorescence Intensity (MFI) and Nomalized Background ratio (NBG ratio) of 12 HLA Class-Ⅰ beads and 5 HLA Class-Ⅱ beads in the HLA mixed antigen reagent and the MFI of 77 anti-HLA class-Ⅰ antibodies and 35 anti-HLA class-Ⅱ antibodies detected by HLA single antigen reagent were recorded. The MFI and NBG ratio of HLA mixed antigen reagent beads in 1 139 or 1 116 samples were segmented according to the positive rate of antibodyies detected by the single antigen reagent corresponding to the antigens coated with each HLA mixed antigen reagent bead, and the results of the HLA mixed antigen screening test were verified by the HLA single antigen reagent confirmation test. Results: The threshold values of MFI and NBG ratio of HLA mixed antigen reagent's 17 beads were established. The MFI of No. 1 to No. 17 beads of HLA mixed antigen reagent ranged from 26.86 to 21 925.58, and the NBG ratio ranged from 0 to 434.65. According to the positive detection rate of HLA single antigen reagent corresponding to the coated antigens, the MFI and NBG ratio of the beads of HLA mixed antigen reagent were divided into positive interval, suspicious positive interval, suspicious negative interval and negative interval. The positive rates of anti-HLA class-Ⅰ antibodies by HLA mixed antigen reagent and single antigen HLA Class-Ⅰ reagent were 87.5% (997/1 139) and 66.3% (755/1 139). The positive rates of anti-HLA class-Ⅱ antibodies were 63.4% (707/1 116) and 44.9% (501/1 116). In the samples with suspicious negative, suspicious positive and positive results of HLA class-Ⅰ、Ⅱ antibodies detected by HLA mixed antigen reagent, the positive detection rates of single antigen HLA Class-Ⅰ reagent were 14.9% (17/114), 41.3% (145/351) and 91.3% (590/646), respectively. The positive detection rates of single antigen HLA Class-Ⅱ reagent were 15.5% (58/375), 26.5% (81/306) and 88.8% (356/401), respectively. Conclusions: In this study, the threshold values of MFI and NBG ratio of HLA mixed antigen reagent screening test are established, and the threshold values are verified by the results of HLA single antigen reagent confirmation test. HLA mixed reagent screening test can be used for screening of HLA antibodies, and if necessary, it should be combined with HLA single antigen confirmatory test for clinical detection of HLA antibodies.


Subject(s)
HLA Antigens , Histocompatibility Antigens Class II , Humans , Indicators and Reagents , Retrospective Studies , Histocompatibility Testing/methods , Histocompatibility Antigens Class I , Isoantibodies , Graft Rejection
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