Bimetallic Ordered Large-Pore MesoMOFs for Simultaneous Enrichment and Dephosphorylation of Phosphopeptides

Immobilized metal ion affinity chromatography: waltz of metal ions and biomacromolecules

INTRODUCTION

Immobilized metal ion affinity chromatography (IMAC) is an effective method developed in the 1980s for the separation and purification of proteins. The system consists of a solid-phase matrix, a linking ligand, and a metal ion. The method is based on the ability of metal ions to bind specifically to certain specific amino acid residues of proteins, thereby selectively enriching and purifying proteins.

AREAS COVERED

This review aims to describe current knowledge of fundamental principle of IMAC and summarize the supports, chelating ligands, and metal ions of IMAC. In addition, how IMAC technology is used in proteomics and DNA research are highlighted.

EXPERT OPINION

Over the past decades, IMAC has been extensively utilized as a predominant technique for protein enrichment in a variety of biological and medical research, such as disease diagnosis, tumor biomarker identification, protein purification, and nucleic acid research. In the future, IMAC should be integrated with other proteomics technologies to promote the applications of metalloproteomes in disease diagnosis, metallodrug development and clinical translation.

From Nanozymes to Multi-Purpose Nanomaterials: The Potential of Metal-Organic Frameworks for Proteomics Applications

Metal-organic frameworks (MOFs) have the potential to revolutionize the biotechnological and medical landscapes due to their easily tunable crystalline porous structure. Herein, the study presents MOFs' potential impact on proteomics, unveiling the diverse roles MOFs can play to boost it. Although MOFs are excellent catalysts in other scientific disciplines, their role as catalysts in proteomics applications remains largely underexplored, despite protein cleavage being of crucial importance in proteomics protocols. Additionally, the study discusses evolving MOF materials that are tailored for proteomics, showcasing their structural diversity and functional advantages compared to other types of materials used for similar applications. MOFs can be developed to seamlessly integrate into proteomics workflows due to their tunable features, contributing to protein separation, peptide enrichment, and ionization for mass spectrometry. This review is meant as a guide to help bridge the gap between material scientists, engineers, and MOF chemists and on the other side researchers in biology or bioinformatics working in proteomics.

Bifunctional MNPs@UIO-66-Arg core-shell-satellite nanocomposites for enrichment of phosphopeptides

A facile and mild method based on self-assembled lysozyme (LYZ) to fabricate bifunctional MNPs@UIO-66-Arg core-shell-satellite nanocomposites (CSSNCs) is reported for the high-efficiency enrichment of phosphopeptides. Under physiological conditions, LYZ rapidly self-assembled into a robust coating on Fe3O4@SiO2 magnetic nanoparticles (MNPs) with abundant surface functional groups, which effectively mediate heterogeneous nucleation and growth of UIO-66 nanocrystals. Well-defined MNPs@UIO-66 CSSNCs with stacked pores, showing high specific surface area (333.65 m2 g- 1) and low mass transfer resistance, were successfully fabricated by fine-tuning of the reaction conditions including reaction time and acetic acid content. Furthermore, the UIO-66 shells were further modified with arginine to obtain bifunctional MNPs@UIO-66-Arg CSSNCs. Thanks to the unique morphology and synergistic effect of Zr-O clusters and guanidine groups, the bifunctional MNPs@UIO-66-Arg CSSNCs exhibited outstanding enrichment performance for phosphopeptides, delivering a low limit of detection (0.1 fmol), high selectivity (β-casein/BSA, mass ratio 1:2000), and good capture capacity (120 mg g- 1). The mechanism for phosphopeptides capture may attribute to the hydrogen bonds, electrostatic interactions, and Zr-O-P bonds between phosphate groups in peptides and guanidyl/Zr-O clusters on bifunctional MNPs@UIO-66-Arg CSSNCs. In addition, the small stacking pores on the core-shell-satellite architecture may selectively capture phosphopeptides with low molecular weight, eliminating interference of other large molecular proteins in complex biological samples.

Hofmeister Effect Promoted the Introduction of Tunable Large Mesopores in MOFs at Low Temperature for Femtomolar ALP Detection

In addressing the demand for hierarchically mesoporous metal-organic frameworks (HMMOFs) with adjustable large mesopores, a method based on the synergistic effects of low-temperature microemulsions and Hofmeister ions is developed. Low temperature dramatically enhanced the solubility of hydrophobic solvent in the microemulsion core, enlarging the mesopores in HMMOFs replica. Meanwhile, Hofmeister salt-in ions continuously controlled mesopore expansion by modulating the permeability of swelling agent into the microemulsion core. The large mesopores up to 33 nm provided sufficient space for the alkaline phosphatase (ALP) enrichment, and retained the remaining channel to facilitate the free mass diffusion. Leveraging these advantages, a colorimetric sensor is successfully developed using large-mesopore HMMOFs for femtomolar ALP detection based on the enrichment and cycling amplification principles. The sensor exhibited a linear detection range of 100 to 7500 fm and a limit of detection of 42 fm, presenting over 4000 times higher sensitivity than classic para-nitrophenyl phosphate colorimetric methods. Such high sensitivity highlights the importance of adjustable mesoporous structures of HMMOFs in advanced sensing applications, and prefigures their potential for detecting large biomolecules in diagnostics and biomedical research.

Hydrolytic nanozymes: Preparation, properties, and applications

Hydrolytic nanozymes, as promising alternatives to hydrolytic enzymes, can efficiently catalyze the hydrolysis reactions and overcome the operating window limitations of natural enzymes. Moreover, they exhibit several merits such as relatively low cost, easier recovery and reuse, improved operating stability, and adjustable catalytic properties. Consequently, they have found relevance in practical applications such as organic synthesis, chemical weapon degradation, and biosensing. In this review, we highlight recent works addressing the broad topic of the development of hydrolytic nanozymes. We review the preparation, properties, and applications of six types of hydrolytic nanozymes, including AuNP-based nanozymes, polymeric nanozymes, surfactant assemblies, peptide assemblies, metal and metal oxide nanoparticles, and MOFs. Last, we discuss the remaining challenges and future directions. This review will stimulate the development and application of hydrolytic nanozymes.

Cerium ions immobilized magnetic graphite nitride decorated with L-Alanyl-L-Glutamine as new chelator for enrichment of phosphopeptides

Cerium ions immobilized magnetic graphite nitride material have been prepared using L-Alanyl-L-Glutamine as the new chelator. The resulting Fe3O4/g-C3N4-L-Ala-L-Gln-Ce4+, as an immobilized metal ion affinity chromatography (IMAC) sorbent, was reusable. This is due to the strong coordination interaction between L-Alanyl-L-Glutamine and cerium ions. After a series of characterizations, the magnetic nanocomposite showed high surface area, good hydrophilicity, positive electricity, and magnetic response. Fe3O4/g-C3N4-L-Ala-L-Gln-Ce4+ had high sensitivity (0.1 fmol), selectivity (α-/β-casein/bovine serum albumin, 1:1:5000), and good recyclability (10 cycles). A total of 647 unique phosphopeptides mapped to 491 phosphoproteins were identified from A549 cell lysate by nano LC-MS analysis.

Ce-based solid-phase catalysts for phosphate hydrolysis as new tools for next-generation nanoarchitectonics

This review comprehensively covers synthetic catalysts for the hydrolysis of biorelevant phosphates and pyrophosphates, which bridge between nanoarchitectonics and biology to construct their interdisciplinary hybrids. In the early 1980s, remarkable catalytic activity of Ce4+ ion for phosphate hydrolysis was found. More recently, this finding has been extended to Ce-based solid catalysts (CeO2 and Ce-based metal-organic frameworks (MOFs)), which are directly compatible with nanoarchitectonics. Monoesters and triesters of phosphates, as well as pyrophosphates, were effectively cleaved by these catalysts. With the use of either CeO2 nanoparticles or elegantly designed Ce-based MOF, highly stable phosphodiester linkages were also hydrolyzed. On the surfaces of all these solid catalysts, Ce4+ and Ce3+ coexist and cooperate for the catalysis. The Ce4+ activates phosphate substrates as a strong acid, whereas the Ce3+ provides metal-bound hydroxide as an eminent nucleophile. Applications of these Ce-based catalysts to practical purposes are also discussed.

CeO2-Based Porous Carbonaceous Frameworks as Antioxidant Nanozymes for Scavenging Reactive Oxygen Species and Adsorbing Benzo[a]pyrene

Barbecue smoke, car exhaust, cigarette smoke, and other waste gases contain toxic reactive oxygen species (ROS) and polycyclic aromatic hydrocarbons (PAHs). Herein, CeO2-based porous carbonaceous frameworks (CeO2 PCFs) were explored as antioxidant nanozymes to scavenge ROS and absorb benzo[a]pyrene (B[a]P). Using cerium-based frameworks as the precursors, CeO2 PCFs were constructed by high-temperature calcination. Due to excellent superoxide dismutase-like and catalase-like activity, CeO2 PCFs could effectively eliminate superoxide radical, hydroxyl radical, and hydrogen peroxide. The 2,2'-azino-bis (3-ethylbenzthiazoline-6-sulfonic acid) free radical scavenging assay had substantiated free radical scavenging ability of CeO2 PCFs. In addition, with a large surface area and porous structure, CeO2 PCFs could adsorb B[a]P efficiently. The designed CeO2 PCFs may provide a new opportunity as scavengers of ROS and absorbents of PAHs in some harmful gases.

Hierarchically Porous MOFs Synthesized by Soft-Template Strategies

The past few decades have been witnessing the rapid research boom of metal-organic frameworks (MOFs), which are assembled from metal nodes and multitopic organic linkers. In virtue of their modular assembly mode, they can be tailored according to desired functions to satisfy numerous potential applications. However, most initially reported MOFs were restricted to the microporous regime, limiting their practical applications with bulk molecules involved. Therefore, the research attention was immediately directed toward enlarging the intrinsic pore size of frameworks by extending the secondary building units or organic ligands. Unfortunately, the synthesis of more extended ligands is frequently tedious, and the most resultant MOFs are not sufficiently stable, restricting their popularization. The soft-template strategy is recognized as a promising avenue to produce hierarchically porous MOFs (HPMOFs), although early attempts generally failed due to the incompatibility between the surfactant self-assembly and guided crystallization process of MOF precursors in the organic phase. Therefore, developing a rational soft-template strategy to achieve the precise control of morphology and porosity of HPMOFs is of great significance.In this Account, we present our recent progress on the development and applications of HPMOFs prepared by soft-template strategies. We highlight the key issues upon using the soft-template strategy to synthesize HPMOFs. To enhance the interaction between the template and MOF precursor, a long-chain monocarboxylic acid strategy is introduced to synthesize HPMOFs with irregular mesopores in the organic phase. Then, to improve the order of mesopores, an aqueous-phase synthesis method using amphoteric surfactants as templates is developed to prepare ordered HPMOFs. To further enlarge the pore size and make the synthesis conditions of MOFs compatible with the self-assembly of surfactants, a salting-in species-induced self-assembly strategy is proposed and coupled with the structure-directing properties of copolymer templates to synthesize a series of HPMOFs with large mesopores and even macropores. This salting-in ion-mediated self-assembly (SIMS) strategy paves the way to modify the pore size, pore structure, morphology, and chemical composition of HPMOFs. The separated but intimately interconnected hierarchical pores in the resultant HPMOFs can not only realize rapid mass transport but also isolate different-size guest molecules so that they are competent for a broad range of applications including protein digestion, cascade catalysis, enzyme-assisted substrate sensing, and DNA cleavage. Finally, the limitations, challenges, and future developments of this rapidly evolving field are described. This Account with a highlight to the soft-template strategies not only provides interesting insights to understand the assembly process between templates and MOFs but also inspires an optimization of the properties of HPMOFs from diverse aspects for desired applications.