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1.
J Am Soc Mass Spectrom ; 35(4): 756-766, 2024 Apr 03.
Artigo em Inglês | MEDLINE | ID: mdl-38456425

RESUMO

G-quadruplex (G4) DNA can form highly stable secondary structures in the presence of metal cations, and research has shown its potential as a transcriptional regulator for oncogenes in the human genome. In order to explore the interactions of DNA with metal cations using mass spectrometry, employing complementary fragmentation methods can enhance structural information. This study explores the use of ion-ion reactions for sequential negative electron transfer collision-induced dissociation (nET-CID) as a complement to traditional ion-trap CID (IT-CID). The resulting nET-CID data for G4 anions with and without metal cations show an increase in fragment ion type diversity and yield of structurally informative ions relative to IT-CID. The nET-CID yields greater sequence coverage by virtue of fragmentation at the 3'-side of thymine residues, which is lacking with IT-CID. Potassium adductions to backbone fragments in IT-CID and nET-CID spectra were nearly identical. Of note is a prominent fragment resulting from a loss of a 149 Da anion seen in nET-CID of large, G-rich sequences, proposed to be radical anion guanine loss. Neutral loss of neutral guanine (151 Da) and deprotonated nucleobase loss (150 Da) have been previously reported, but this is the first report of radical anion guanine loss (149 Da). Confirmation of the identity of the 149 Da anion results from the examination of the homonucleobase sequence 5'-GGGGGGGG-3'. Loss of a charged adenine radical anion at much lower relative abundance was also noted for the sequence 5'-AAAAAAAA-3'. DFT modeling indicates that the loss of a nucleobase as a radical anion from odd-electron nucleic acid anions is a thermodynamically favorable fragmentation pathway for G.


Assuntos
Quadruplex G , Guanina , Humanos , Elétrons , Ânions/química , Cátions/química , Metais , DNA
2.
Nature ; 627(8004): 680-687, 2024 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-38448587

RESUMO

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.


Assuntos
Cátions , Ciclização , Indicadores e Reagentes , Proteínas , Triptofano , Cátions/química , Indicadores e Reagentes/química , Oxirredução , Proteoma/química , Triptofano/química , Peptídeos/química , Química Click , Proteínas/química
3.
Colloids Surf B Biointerfaces ; 237: 113839, 2024 May.
Artigo em Inglês | MEDLINE | ID: mdl-38492411

RESUMO

Herein, we have employed a supramolecular assembly of a cationic dye, LDS-698 and a common surfactant sodium dodecyl sulfate (SDS) as a turn-on fluorescent sensor for protamine (Pr) detection. Addition of cationic Pr to the solution of dye-surfactant complex brings negatively charged SDS molecules together through strong electrostatic interaction, assisting aggregation of SDS way before its critical micellar concentration (CMC). These aggregates encapsulate the dye molecules within their hydrophobic region, arresting non-radiative decay channels of the excited dye. Thus, the LDS-698•SDS assembly displays substantial enhancement in fluorescence intensity that follows a nice linear trend with Pr concentration, providing limit of detection (LOD) for Pr as low as 3.84(±0.11) nM in buffer, 124.4(±6.7) nM in 1% human serum and 28.3(±0.5) nM in 100% human urine. Furthermore, high selectivity, low background signal, large stokes shift, and emission in the biologically favorable deep-red region make the studied assembly a promising platform for Pr sensing. As of our knowledge it is the first ever Pr sensory platform, using a very common surfactant (SDS), which is economically affordable and very easily available in the market. This innovative approach can replace the expensive, exotic and specialized chemicals considered for the purpose and thus showcase its potential in practical applications.


Assuntos
Surfactantes Pulmonares , Tensoativos , Humanos , Tensoativos/química , Antídotos , Heparina , Dodecilsulfato de Sódio/química , Cátions/química
4.
Bioorg Med Chem ; 100: 117635, 2024 Feb 15.
Artigo em Inglês | MEDLINE | ID: mdl-38340641

RESUMO

Although many types of cationic lipids have been developed as efficient gene vectors, the construction of lipid molecules with simple procedures remains challenging. Passerini reaction, as a classic multicomponent reaction, could directly give the α-acyloxycarboxamide products with biodegradable ester and amide bonds. Herein, two series of novel cationic lipids with heterocyclic pyrrolidine and piperidine as headgroups were synthesized through Passerini reaction (P-series) and amide condensation (A-series), and relevant structure-activity relationships on their gene delivery capability was studied. It was found that although both of the two series of lipids could form lipid nanoparticles (LNPs) which could effectively condense DNA, the LNP derived from P-series lipids showed higher transfection efficiency, serum tolerance, cellular uptake, and lower cytotoxicity. Unlike the A-series LNPs, the P-series LNPs showed quite different structure-activity relationship, in which the relative site of the secondary amine had significant effect on the transfection performance. The othro-isomers of the P-series lipids had lower cytotoxicity, but poor transfection efficiency, which was probably due to their unstable nature. Taken together, this study not only validated the feasibility of Passerini reaction for the construction of cationic lipids for gene delivery, but also afforded some clues for the rational design of effective non-viral lipidic gene vectors.


Assuntos
Técnicas de Transferência de Genes , Lipídeos , Humanos , Lipídeos/farmacologia , Lipídeos/química , Relação Estrutura-Atividade , Transfecção , Cátions/química , Amidas
5.
J Phys Chem A ; 128(6): 1109-1123, 2024 Feb 15.
Artigo em Inglês | MEDLINE | ID: mdl-38316031

RESUMO

We report a combined experimental and computational study of adenosine cation radicals that were protonated at adenine and furnished with a radical handle in the form of an acetoxyl radical, •CH2COO, that was attached to ribose 5'-O. Radicals were generated by collision-induced dissociation (CID) and characterized by tandem mass spectrometry and UV-vis photodissociation action spectroscopy. The acetoxyl radical was used to probe the kinetics of intramolecular hydrogen transfer from the ribose ring positions that were specifically labeled with deuterium at C1', C2', C3', C4', C5', and in the exchangeable hydroxyl groups. Hydrogen transfer was found to chiefly involve 3'-H with minor contributions by 5'-H and 2'-H, while 4'-H was nonreactive. The hydrogen transfer rates were affected by deuterium isotope effects. Hydrogen transfer triggered ribose ring cleavage by consecutive dissociations of the C4'-O and C1'-C2' bonds, resulting in expulsion of a C6H9O4 radical and forming a 9-formyladenine ion. Rice-Ramsperger-Kassel-Marcus (RRKM) and transition-state theory (TST) calculations of unimolecular constants were carried out using the effective CCSD(T)/6-311++G(3d,2p) and M06-2X/aug-cc-pVTZ potential energy surfaces for major isomerizations and dissociations. The kinetic analysis showed that hydrogen transfer to the acetoxyl radical was the rate-determining step, whereas the following ring-opening reactions in ribose radicals were fast. Using DFT-computed energies, a comparison was made between the thermochemistry of radical reactions in adenosine and 2'-deoxyadenosine cation radicals. The 2'-deoxyribose ring showed lower TS energies for both the rate-determining 3'-H transfer and ring cleavage reactions.


Assuntos
Adenosina , Desoxiadenosinas , Ribose , Cinética , Deutério , Desoxirribose/química , Hidrogênio , Cátions/química , Radicais Livres/química
6.
ACS Appl Bio Mater ; 7(3): 1558-1568, 2024 Mar 18.
Artigo em Inglês | MEDLINE | ID: mdl-38373341

RESUMO

Ionic liquid (IL) cationic species have recently captivated the attention of pharmacists, biochemists, and biomedical scientists as promising antibacterial agents to deal with the multidrug resistance bacteria crisis. The structure and functional groups of ILs influence their physiochemical properties and biological activities. However, a comprehensive study is required to fully understand the details of the antibacterial activity of ILs carrying various functional groups. Herein, dicationic ILs (DCILs) are reported based on imidazolium rings as efficient antibacterial agents. The DCILs carried various functionalities such as 2-hydroxybutyl (DCIL-1), 2-hydroxy-3-isopropoxypropyl (DCIL-2), 2-hydroxy-3-(methacryloyloxy)propyl (DCIL-3), 2-hydroxy-2-phenylethyl (DCIL-4), and 2-hydroxy-3-phenoxypropyl (DCIL-5). The structure-antibacterial activity relationships of the DCILs against Gram-positive (Staphylococcus aureus) and Gram-negative bacteria (Escherichia coli and Pseudomonas aeruginosa) were comprehensively studied through antibacterial tests, morphology analysis, and adhesion tests. The experimental assays revealed an antibacterial efficacy order of DCIL-5 > DCIL-1 > DCIL-4 > DCIL-2 > DCIL-3. The all-atom molecular dynamics (MD) simulation showed a deep permeation of the hydrophobic -OPh functional group of DCIL-5 through the E. coli membrane model in agreement with the experimental observations. Current findings assist scientists in designing new task-specific DCILs for effective interactions with biological membranes for different applications.


Assuntos
Líquidos Iônicos , Líquidos Iônicos/farmacologia , Líquidos Iônicos/química , Escherichia coli , Antibacterianos/farmacologia , Antibacterianos/química , Relação Estrutura-Atividade , Cátions/química
7.
Langmuir ; 40(10): 5314-5325, 2024 Mar 12.
Artigo em Inglês | MEDLINE | ID: mdl-38408899

RESUMO

Zwitterionic polymers are an emerging family of effective, low-fouling materials that can withstand unintended interactions with biological systems while exhibiting enhanced activity in bacterial matrix deterioration and biofilm eradication. Herein, we modularly synthesized an amphiphilic block copolymer, ZABCP, featuring potential bacteriostatic properties composed of a charge-switchable polyzwitterionic segment and a redox-sensitive pendant disulfide-labeled polymethacrylate block. The leucine-appended polyzwitterionic segment with alternatively positioned cationic amine and anionic carboxylate functionalities undergoes charge alterations (+ve → 0 → -ve) on pH variation. By introducing appropriate amphiphilicity, ZABCP forms distinct vesicles with redox-sensitive bilayer membranes and zwitterionic shielding coronas, enabling switching of surface charge. ZABCP vesicles exhibit 180 ± 20 nm hydrodynamic diameter, and its charge switching behavior in response to pH was confirmed by the change of zeta potential value from -23 to +36 mV. The binding interaction between ZABCP vesicles with lysozyme and pepsin proteins strengthens when the surface charge shifts from neutral (pH 7.4) to either anionic or cationic. This surface-charge-switchable phenomenon paves the way for implementing cationic ZABCP vesicles for bacterial cell growth inhibition, which is shown by the pronounced transition of cellular morphology, including clustering, aggregation, or elongation as well as membrane disruption for both Bacillus subtilis (Gram-positive) and Escherichia coli (Gram-negative). Such enhanced bacteriostatic activity could be ascribed to a strong electrostatic interaction between cationic vesicles and negatively charged bacterial membranes, leading to cell membrane disruption. Overall, this study provides a tailor-made approach to adopt low-fouling properties and potential bacteriostatic activity using zwitterionic polymers through precise control of pH.


Assuntos
Incrustação Biológica , Incrustação Biológica/prevenção & controle , Proteínas/metabolismo , Cátions/química , Membrana Celular/metabolismo , Polímeros/química , Propriedades de Superfície
8.
Sci Total Environ ; 922: 171062, 2024 Apr 20.
Artigo em Inglês | MEDLINE | ID: mdl-38401717

RESUMO

The following research provides novel and relevant insights into potential environmental consequences of combination of various organic cations with commercial systemic herbicide (dicamba), in accordance with a 'herbicidal ionic liquids' (HILs) strategy. Toxicity assays of five dicamba-based HILs comprising different hydrophobic and hydrophilic cations, namely choline [CHOL][DIC], ethyl betainate [BETC2][DIC], decyl betainate [BETC10][DIC], hexadecyl betainate [BETC16][DIC] and didecyldimethylammonium [DDA][DIC]), have been tested towards bacteria (Pseudomonas putida, Escherichia coli, Bacillus subtilis), algae (Chlorella vulgaris), fresh and marine water crustaceans (Daphnia magna, Artemia franciscana). The structure of respective substituents in the cation emerged as a decisive determinant of toxicity in the case of tested species. In consequence, small ions of natural origin ([CHOL] and [BETC2]) demonstrated toxicity numerous orders of magnitude lower compared to fully synthetic [DDA]. These results emphasize the role of cations' hydrophobicity, as well as origin, in the observed acute toxic effect. Time-dependent toxicity assays also indicated that betaine-type cations comprising an ester bond can rapidly transform into less harmful substances, which can generally result in a reduction in toxicity by even several orders of magnitude. Nonetheless, these findings challenge the concept of ionic liquids with herbicidal activity and give apparent parallels to adjuvant-dependent toxicity issues recently noted in typical herbicidal formulations.


Assuntos
Chlorella vulgaris , Herbicidas , Líquidos Iônicos , Pseudomonas putida , Herbicidas/toxicidade , Herbicidas/química , Dicamba/química , Líquidos Iônicos/toxicidade , Líquidos Iônicos/química , Cátions/química
9.
Colloids Surf B Biointerfaces ; 236: 113807, 2024 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-38417348

RESUMO

The stability of membranes formed by ionizable cationic lipids, which constitute the primary components in lipid nanoparticles capable of endosomal escape, is explored using coarse-grained dissipative particle dynamics. Three types of ionizable model lipids with different tail structures are considered. Endosome acidification causes the ionization of lipids, leading to an increased repulsive range between their headgroups. When electrostatic repulsion is modeled as a conservative force with a long-range cutoff distance (rc,HH), the membrane and vesicle experience a loss of structural integrity and develop holes as rc,HH is beyond a critical value, which varies with the tail structure. When Coulombic repulsion is explicitly incorporated and intensified, a fully ionized lipid membrane undergoes a loss of structural integrity, displaying a qualitative similarity to the effect observed with the increase in rc,HH on the membrane stability. Qualitatively similar results are obtained for partially ionized membranes as the fraction of charged lipids increases. The stability of a mixed lipid membrane containing both ionizable and conventional lipids is also investigated. The disruption of the bilayer structure occurs for a sufficiently high charged fraction. The membrane instability can be attributed to the decrease in the packing parameter, which significantly deviates from unity as the interaction range increases.


Assuntos
Nanopartículas , Cátions/química , Fenômenos Químicos , Nanopartículas/química , Lipídeos/química , Bicamadas Lipídicas/química
10.
J Mol Graph Model ; 128: 108717, 2024 05.
Artigo em Inglês | MEDLINE | ID: mdl-38281418

RESUMO

The effect of the increase in the alkyl chain length of cation on the properties of deep eutectic solvents based on ethylene glycol has been investigated employing classical molecular dynamics simulations. The change in the structural and dynamic properties in both the bulk and liquid-vapor interface is explored through various analyses. The interaction between the anion and the ethylene glycol increases with an increase in the alkyl chain length of the cation, as observed in the increase of the lifetime of the hydrogen bond formed between the two. The terminal carbon atoms are found to be closer to each other when the cation changes from tetraethylammonium to tetrabutylammonium. The cations are located closer to the interface, and the association of the alkyl chains becomes more significant with increased alkyl chain length, decreasing the surface tension values.


Assuntos
Solventes Eutéticos Profundos , Simulação de Dinâmica Molecular , Ânions/química , Cátions/química , Etilenoglicóis , Solventes/química
11.
Chembiochem ; 25(6): e202300834, 2024 03 15.
Artigo em Inglês | MEDLINE | ID: mdl-38284327

RESUMO

Leveraging liposomes for drug and nucleic acid delivery, though promising due to reduced toxicity and ease of preparation, faces challenges in stability and efficiency. To address this, we synthesized cationic amphiphiles from amino acids (arginine, lysine, and histidine). Histidine emerged as the superior candidate, leading to the development of three histidine-rich cationic amphiphiles for liposomes. Using the hydration method, we have prepared the liposomes and determined the optimal N/P ratios for lipoplex formation via gel electrophoresis. In vitro transfection assays compared the efficacy of our lipids to Fugene, while MTT assays gauged biocompatibility across cancer cell lines (MDA-MB 231 and MCF-7). The histidine-based lipid demonstrated marked potential in enhancing drug and nucleic acid delivery. This improvement stemmed from increased zeta potential, enhancing electrostatic interactions with nucleic acids and cellular uptake. Our findings underscore histidine's crucial role over lysine and arginine for effective delivery, revealing a significant correlation between histidine abundance and optimal performance. This study paves the way for histidine-enriched lipids as promising candidates for efficient drug and nucleic acid delivery, addressing key challenges in the field.


Assuntos
Lipossomos , Ácidos Nucleicos , Lipossomos/química , Aminoácidos , Histidina/química , Lisina/química , Transfecção , Arginina/química , Lipídeos/química , Cátions/química
12.
J Am Chem Soc ; 146(5): 3086-3093, 2024 Feb 07.
Artigo em Inglês | MEDLINE | ID: mdl-38266163

RESUMO

In the last 40 years, cation-π interactions have become part of the lexicon of noncovalent forces that drive protein binding. Indeed, tetraalkylammoniums are universally bound by aromatic cages in proteins, suggesting that cation-π interactions are a privileged mechanism for binding these ligands. A prominent example is the recognition of histone trimethyllysine (Kme3) by the conserved aromatic cage of reader proteins, dictating gene expression. However, two proteins have recently been suggested as possible exceptions to the conventional understanding of tetraalkylammonium recognition. To broadly interrogate the role of cation-π interactions in protein binding interactions, we report the first large-scale comparative evaluation of reader proteins for a neutral Kme3 isostere, experimental and computational mechanistic studies, and structural analysis. We find unexpected widespread binding of readers to a neutral isostere with the first examples of readers that bind the neutral isostere more tightly than Kme3. We find that no single factor dictates the charge selectivity, demonstrating the challenge of predicting such interactions. Further, readers that bind both cationic and neutral ligands differ in mechanism: binding Kme3 via cation-π interactions and the neutral isostere through the hydrophobic effect in the same aromatic cage. This discovery explains apparently contradictory results in previous studies, challenges traditional understanding of molecular recognition of tetraalkylammoniums by aromatic cages in myriad protein-ligand interactions, and establishes a new framework for selective inhibitor design by exploiting differences in charge dependence.


Assuntos
Histonas , Lisina/análogos & derivados , Ligantes , Modelos Moleculares , Histonas/química , Cátions/química
13.
Food Chem Toxicol ; 183: 114202, 2024 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-38007213

RESUMO

Ionic liquids (ILs) are a class of low melting point salts with physicochemical properties that make them suitable for a range of industrial applications. Accumulating evidence suggests that certain ILs are cytotoxic and potential environmental pollutants, thus understanding the structural features that promote IL cytotoxicity is important. Amphiphilic ionic liquids (AmILs), a class of ILs with lipophilic N-alkyl chains, containing aromatic head groups are generally more cytotoxic than their aliphatic counterparts, however the impact of other head group properties are less clear. This study therefore sought to provide new structure activity relationship (SAR) insights regarding the role of the cationic head group on AmIL cytotoxicity. A series of AmILs bearing a range of structurally diverse aromatic cations varying in size, charge, and lipophilicity was synthesised and screened against human MDA-MB-231 breast cancer cells. It was found that larger and more lipophilic head groups increased cytotoxicity, although the magnitude of the changes were modest. The mitochondrial effects of representative ILs were assessed. The AmILs induced mitochondrial dysfunction in MDA-MB-231 cells at cytotoxic concentrations, suggesting that they target mitochondria. The new SAR information from this study may assist in the design of AmILs with controlled cytotoxicity.


Assuntos
Líquidos Iônicos , Humanos , Líquidos Iônicos/toxicidade , Líquidos Iônicos/química , Estrutura de Grupo , Relação Estrutura-Atividade , Cátions/química
14.
Int J Phytoremediation ; 26(2): 178-192, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-37409646

RESUMO

In the present study, we report the chemical modification of the dried and fallen pine needles (PNs) via a simple protocol using KMnO4 oxidation. The oxidized PNs (OPNs) were evaluated as adsorbents using some cationic and anionic dyes. The successful synthesis of OPNs adsorbent was characterized by various techniques to ascertain its structural attributes. The adsorbent showed selectivity for the cationic dyes with 96.11% removal (Pr) for malachite green (MG) and 89.68% Pr for methylene blue (MB) in 120 min. Kinetic models namely, pseudo-first order, pseudo-second order, and Elovich were applied to have insight into adsorption. Additionally, three adsorption isotherms, i.e., Langmuir, Freundlich, and Temkin were also applied. The dye adsorption followed a pseudo-second-order kinetic model with R2 > 0.99912 for MG and R2 > 0.9998 for MB. The adsorbent followed the Langmuir model with a maximum adsorption capacity (qm) of 223.2 mg/g and 156.9 mg/g for MG and MB, respectively. Furthermore, the OPNs showed remarkable regeneration and recyclability up to nine adsorption-desorption cycles with appreciable adsorption for both the dyes. The use of OPNs as an adsorbent for the removal of dyes from wastewater, therefore, provides an ecologically benign, low-cost, and sustainable solution.


We have carried out the chemical modification of the dried and fallen pine needles (PNs) via a simple protocol using KMnO4 oxidation. The oxidized PNs (OPNs) were evaluated as adsorbents using some cationic and anionic dyes and the adsorbent showed selectivity for the cationic dyes. As far as the authors are aware, no such report has been documented in the literature wherein an adsorbent based on oxidized PNs with a simple protocol has been used for dye removal.


Assuntos
Corantes , Poluentes Químicos da Água , Corantes/química , Biodegradação Ambiental , Águas Residuárias , Corantes de Rosanilina , Cátions/química , Adsorção , Cinética , Azul de Metileno/química , Poluentes Químicos da Água/química
15.
Nature ; 625(7995): 508-515, 2024 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-37967579

RESUMO

Recent years have seen revived interest in computer-assisted organic synthesis1,2. The use of reaction- and neural-network algorithms that can plan multistep synthetic pathways have revolutionized this field1,3-7, including examples leading to advanced natural products6,7. Such methods typically operate on full, literature-derived 'substrate(s)-to-product' reaction rules and cannot be easily extended to the analysis of reaction mechanisms. Here we show that computers equipped with a comprehensive knowledge-base of mechanistic steps augmented by physical-organic chemistry rules, as well as quantum mechanical and kinetic calculations, can use a reaction-network approach to analyse the mechanisms of some of the most complex organic transformations: namely, cationic rearrangements. Such rearrangements are a cornerstone of organic chemistry textbooks and entail notable changes in the molecule's carbon skeleton8-12. The algorithm we describe and deploy at https://HopCat.allchemy.net/ generates, within minutes, networks of possible mechanistic steps, traces plausible step sequences and calculates expected product distributions. We validate this algorithm by three sets of experiments whose analysis would probably prove challenging even to highly trained chemists: (1) predicting the outcomes of tail-to-head terpene (THT) cyclizations in which substantially different outcomes are encoded in modular precursors differing in minute structural details; (2) comparing the outcome of THT cyclizations in solution or in a supramolecular capsule; and (3) analysing complex reaction mixtures. Our results support a vision in which computers no longer just manipulate known reaction types1-7 but will help rationalize and discover new, mechanistically complex transformations.


Assuntos
Algoritmos , Técnicas de Química Sintética , Ciclização , Redes Neurais de Computação , Terpenos , Cátions/química , Bases de Conhecimento , Terpenos/química , Técnicas de Química Sintética/métodos , Produtos Biológicos/síntese química , Produtos Biológicos/química , Reprodutibilidade dos Testes , Soluções
16.
Proteins ; 92(2): 179-191, 2024 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-37789571

RESUMO

The cation-aromatic database (CAD) is a comprehensive repository of cation-aromatic motifs found in experimentally determined protein structures, first reported in 2007 [Proteins, 2007, 67, 1179]. The present article is an update of CAD that contains information of approximately 27.26 million cation-aromatic motifs. CAD uses three distance parameters (r, d1, and d2) to determine the position of the cation relative to the centroid of the aromatic residue and classifies the motifs as cation-π or cation-σ interactions. As of June 2023, about 193 936 protein structures were retrieved from Protein Data Bank, and this resulted in the identification of an impressive number of 27 255 817 cation-aromatic motifs. Among these motifs, spherical motifs constituted 94.09%, while cylindrical motifs made up the remaining 5.91%. When considering the interaction of metal ions with aromatic residues, 965 564 motifs are identified. Remarkably, 82.08% of these motifs involved the binding of metal ions to the amino acid HIS. Moreover, the analysis of binding preferences between cations and aromatic residues revealed that the HIS-HIS, PHE-ARG, and TRP-ARG pairs exhibited a preferential geometry. The motif pair HIS-HIS was the most prevalent, accounting for 19.87% of the total, closely followed by TYR-LYS at 10.17%. Conversely, the motif pair TRP-HIS had the lowest occurrence, representing only 4.20% of the total. The data generated help in revealing the characteristics and biological functions of cation-aromatic interactions in biological molecules. The updated version of CAD (Cation-Aromatic Database V2.0) can be accessed at https://acds.neist.res.in/cadv2.


Assuntos
Aminoácidos , Proteínas , Aminoácidos/química , Cátions/química , Metais
17.
Biotechnol Prog ; 40(1): e3395, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-37828820

RESUMO

Charge heterogeneity of monoclonal antibodies is considered a critical quality attribute and hence needs to be monitored and controlled by the manufacturer. Typically, this is accomplished via separation of charge variants on cation exchange chromatography (CEX) using a pH or conductivity based linear gradient elution. Although an effective approach, this is challenging particularly during continuous processing as creation of linear gradient during continuous processing adds to process complexity and can lead to deviations in product quality upon slightest changes in gradient formation. Moreover, the long length of elution gradient along with the required peak fractionation makes process integration difficult. In this study, we propose a novel approach for separation of charge variants during continuous CEX chromatography by utilizing a combination of displacement mode chromatography and salt-based step elution. It has been demonstrated that while the displacement mode of chromatography enables control of acidic variants ≤26% in the CEX eluate, salt-based step gradient elution manages basic charge variant ≤25% in the CEX eluate. The proposed approach has been successfully demonstrated using feed materials with varying compositions. On comparing the designed strategy with 2-column concurrent (CC) chromatography, the resin specific productivity increased by 95% and resin utilization increased by 183% with recovery of main species >99%. Further, in order to showcase the amenability of the designed CEX method in continuous operation, the method was examined in our in-house continuous mAb platform.


Assuntos
Anticorpos Monoclonais , Cloreto de Sódio , Anticorpos Monoclonais/química , Cromatografia por Troca Iônica/métodos , Cloreto de Sódio/química , Cátions/química
18.
J Colloid Interface Sci ; 656: 457-465, 2024 Feb 15.
Artigo em Inglês | MEDLINE | ID: mdl-38006868

RESUMO

Ion specific effects on the charging and aggregation features of zein nanoparticles (ZNP) were studied in aqueous suspensions by electrophoretic and time-resolved dynamic light scattering techniques. The influence of mono- and multivalent counterions on the colloidal stability was investigated for positively and negatively charged particles at pH values below and above the isoelectric point, respectively. The sequence of the destabilization power of monovalent salts followed the prediction of the indirect Hofmeister series for positively charged particles, while the direct Hofmeister series for negatively charged ones assumed a hydrophobic character for their surface. The multivalent ions destabilized the oppositely charged ZNPs more effectively and the aggregation process followed the Schulze-Hardy rule. For some multivalent ions, strong adsorption led to charge reversal resulting in restabilization of the suspensions. The experimental critical coagulation concentrations (CCCs) could be well-predicted with the theory developed by Derjaguin, Landau, Verwey and Overbeek indicating that the aggregation processes were mainly driven by electrical double layer repulsion and van der Waals attraction. The ion specific dependence of the CCCs is owing to the modification of the surface charge through ion adsorption at different extents. These results are crucial for drug delivery applications, where inorganic electrolytes are present in ZNP samples.


Assuntos
Nanopartículas , Zeína , Eletrólitos/química , Nanopartículas/química , Cátions/química , Suspensões
19.
J Mol Graph Model ; 126: 108645, 2024 01.
Artigo em Inglês | MEDLINE | ID: mdl-37812869

RESUMO

The local chemical reactivity of FOX-7 (1,1-diamino-2,2-nitroethylene, also known as DADNE from DiAminoDiNitroEthylene) was elucidated through a quantitative study of the electrostatic potential on the molecular surface, topological analysis based on Bader's theory, and the EDA-NOCV method. Unlike (O2N)2CC(NH2)H2N⋯Cp2MCH3+ complexes, which exhibit both σ-donor and π-acceptor features, the situation is different concerning the (H2N)2CC(NO2)(O)NO⋯Cp2MCH3+ complexes, where both charge transfers correspond to the σ-donation. The two charge transfers reinforce each other, resulting in increased stability for (H2N)2CC(NO2)(O)NO⋯Cp2MCH3+. This seems to strengthen the (H2N)2CC(NO2)(O)NO⋯M={Ti,Zr,Hf} bond, which may explain the high stability of (H2N)2CC(NO2)(O)NO⋯Cp2MCH3+ compared to (O2N)2CC(NH2)-H2N⋯Cp2MCH3+. Results from topological analysis revealed that the decreased sensitivity to decomposition of CNO2 bonds depends on the chemical nature of the interacting metal, and the best achievements are obtained for the Hf-based complex. Our results demonstrate that the interaction of M={Ti,Zr,Hf} with CNO2 is more favourable than that with CNH2, this specific action on the trigger bond may support the use of Metallocene Methyl Cations (MMC) as possible neutralisers.


Assuntos
Dióxido de Nitrogênio , Titânio , Cátions/química
20.
Int J Biol Macromol ; 257(Pt 2): 128747, 2024 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-38101668

RESUMO

In present study, eco-friendly sulfated cellulose-magnetic biocomposite was successfully synthesized with a simple method from hemp biomass. ATR-FTIR was used to determine chemical changes, while FE-SEM-EDS, STEM, XRD, TG/DTA, and BET techniques were employed to identify changes in morphology, elemental composition, crystal structure, and thermal degradation. Moreover, the saturation magnetization and pHpzc values of the MSHB were also determined. The effectiveness of magnetic sulfated hemp biomass (MSHB) was tested in the removal of cationic dyes from wastewater, including methylene blue (MB), crystal violet (CV), and malachite green oxalate (MGO). The adsorption all three dyes to MSHB, the pseudo-second-order kinetic model and the Langmuir model were determined to be more appropriate, and was endothermic and spontaneous from thermodynamic parameters, too. The maximum MSHB adsorption capacities were found to be 457.6, 509.3, and 1300 mg/g for MB, CV, and MGO at 298 K. With increasing temperature, it also drastically increased in capacity. The outstanding property of the MSHB is that it shows high removal performance wide pH range, even after ten cycles its high removal efficiency is still over 96 % for all three dyes and almost unaffected from dense matrix medium. These results demonstrate that MSHB is remarkable adsorbent for removing cationic dyes.


Assuntos
Cannabis , Corantes de Rosanilina , Poluentes Químicos da Água , Corantes/química , Celulose/química , Sulfatos , Biomassa , Óxido de Magnésio , Adsorção , Cátions/química , Cinética , Violeta Genciana/química , Fenômenos Magnéticos , Poluentes Químicos da Água/química , Concentração de Íons de Hidrogênio
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