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.

High-efficient depletion and separation of histidine-rich proteins via Cu2+-chelated porous polymer microspheres

Depletion and separation of histidine-rich proteins from complicated biosamples are crucial for various downstream applications in proteome research and clinical diagnosis. Herein, porous polymer microspheres coated with polyacrylic acid (SPSDVB-PAA) were fabricated through double emulsion interfacial polymerization technique and followed by immobilization of Cu2+ ions on the surface of SPSDVB-PAA. The as-prepared SPSDVB-PAA-Cu with uniform size and nanoscale pore structure enabled coordination interaction of Cu2+ with histidine residues in his-rich proteins, resulting in high-performance adsorption. As metal affinity adsorbent, the SPSDVB-PAA-Cu exhibited favorable selectivity for adsorbing hemoglobin (Hb) and human serum albumin (HSA) with the maximum adsorption capacities of 152.2 and 100.7 mg g-1. Furthermore, the polymer microspheres were used to isolate histidine-rich proteins from human whole blood and plasma, underscoring their effectiveness. The liquid chromatography tandem mass spectrometry (LC-MS/MS) results indicated that the content of 14 most abundant proteins in human plasma was depleted from 81.6 % to 30.7 % and low-abundance proteins were enriched from 18.4 % to 69.3 % after treatment with SPSDVB-PAA-Cu, illustrating potential application of SPSDVB-PAA-Cu in proteomic research.

Selective Removal of Denatured Proteins Using MOF Nanopores

Here we present, for the first time, the selective adsorption of denatured proteins using a metal-organic framework (MOF), demonstrating promising potential for protein purification. Typical proteins, such as lysozyme and carbonic anhydrase B, enter the pores of MIL-101 through their narrow apertures when they are denatured to an unfolded state. Selective adsorption is achieved by finely tuning two key features: the sizes of the aperture and cage of the MOF nanopores, which are responsible for sorting unfolded polypeptide chains and inhibiting the translocation of the native form into the pores, respectively. By leveraging this selective adsorption, we successfully purified a mixture of native and denatured proteins by adding MOF to the mixture, achieving a native purity of over 99%.

Magnetic Dendritic Polymer Nanospheres for High-Performance Separation of Histidine-Rich Proteins

Magnetic nanospheres are becoming a promising platform for a wide range of applications in pharmacy, life science, and immunodiagnostics due to their high surface area, ease of synthesis and manipulation, fast separation, good biocompatibility, and recyclable performance. In this work, an innovative and efficient method is developed by in situ reducing and growing Ni(OH)₂ for the preparation of dendritic mesoporous nanocomposites of silica@Fe₃O₄/tannic acid@nickel hydroxide (dSiO₂@Fe₃O₄/TA@Ni(OH)₂). The flower-like nanospheres have good magnetic response, large surface area, and high histidine-rich protein (His-protein) purification performance. The dSiO₂@Fe₃O₄/TA@Ni(OH)₂ nanospheres were synthesized on the basis of a φ(NaSal/CTAB) of 1/1 and a mass of ferrous chloride tetrahydrate of 0.3 g, resulting in a saturation magnetization value of 48.21 emu/g, which means it can be collected within ∼1 min using a magnetic stand. Also, the BET test showed that the surface area is 92.47 m²/g and the pore size is ∼3.9 nm for dSiO₂@Fe₃O₄/TA@Ni(OH)₂ nanocomposites. Notably, the nickel hydroxide with unique flower-like structural features enables the combination of a large number of Ni²⁺ ions and His-proteins for high performance. The isolation and purification experiments of the synthesized dSiO₂@Fe₃O₄/TA@Ni(OH)₂ were performed by separating His-proteins from a matrix composed of bovine hemoglobin (BHb), bovine serum albumin (BSA), and lysozyme (LYZ). The result showed that the nanospheres have a high combination capacity of ∼1880 mg/g in a rapid equilibrium time of 20 min, which was selective for the adsorption of BHb. In addition, the stability and recyclability of BHb are 80% after seven cycles. Furthermore, the nanospheres were also used to isolate His-proteins from fetal bovine serum, proving its utility. Therefore, the strategy of separating and purifying His-proteins using dSiO₂@Fe₃O₄/TA@Ni(OH)₂ nanospheres is promising for practical applications.

Defective SO3H-MIL-101(Cr) for capturing different cationic metal ions: Performances and mechanisms

For broad-spectrum adsorption and capture toward cationic metal ions, a facile strategy was adopted to fabricate defective SO₃H-MIL-101(Cr) (SS-SO₃H-MIL-101(Cr)-X, X = 2, 3, 4) with enhanced vacancies using seignette salt (SS) as the modulating agent. The boosted adsorption performances of SS-SO₃H-MIL-101(Cr)-X toward eight different ions, including Ag⁺, Cs⁺, Pb²⁺, Cd²⁺, Ba²⁺, Sr²⁺, Eu³⁺ and La³⁺ in both individual component and mixed component systems, could be ascribed to the effective mass transfer resulting from the exposure of defective sites. Especially, the optimal SS-SO₃H-MIL-101(Cr)-3 could remove all the selected metal cations to below the permissible limits required by the World Health Organization (WHO) in the continuous-flow water treatment system. Furthermore, SS-SO₃H-MIL-101(Cr)-3 exhibited good adsorption capacity (189.6 mg·g^-1) toward Pb²⁺ under neutral condition and excellent desorption recirculation performance (removal efficiency > 95% after 5 cycles). Moreover, the adsorption mechanism involved the electrostatic adsorption and coordinative interactions resulting from complexation between the adsorption active sites and targeted cations (like Cr-O-M and S-O-M), which were explored systematically via both X-ray photoelectron spectroscopy (XPS) determination and density functional theory (DFT) calculations. Overall, this work provided guidance for modulating SS-SO₃H-MIL-101(Cr)-X to promote its potential application in widespread metal cations removal from wastewater.

Mass tag-encoded nanointerfaces for multiplexed mass spectrometric analysis and imaging of biomolecules

Revealing multiple biomolecules in the physiopathological environment simultaneously is crucial in biological and biomedical research. Mass spectrometry (MS) features unique technical advantages in multiplexed and label-free analyses. However, owing to comparably low abundance and poor ionization efficiency of target biomolecules, direct MS profiling of these biological species in vitro or in situ remains a challenge. An emerging route to solve this issue is to devise mass tag (MT)-encoded nanointerfaces which specifically convert the abundance or activity of biomolecules into amplified ion signals of mass tags, offering an ideal strategy for synchronous MS assaying and mapping of multiple targets in biofluids, cells and tissues. This review provides a thorough and organized overview of recent advances in MT-encoded nanointerfaces elaborately tailored for several practical applications in multiplexed MS bioanalysis and biomedical research. First, we start with elucidation of the structural characteristics and working principle of MT-encoded nanointerfaces in specific labeling and sensing of multiple biological targets. In addition, we further discuss the application scenarios of MT-encoded nanointerfaces particularly in multiplexed biomarker assays, cell analysis, and tissue imaging. Finally, the current challenges are pointed out and future prospects of these nanointerfaces in MS analysis are forecast.

Dual-Functional Coordination Polymer with High Proton Conductivity and a Low-Detection-Limit Fluorescent Probe

A coordination polymer with dual functions of high proton conductivity and highly sensitive fluorescent sensors demonstrates a great application potential. In this work, a cadmium-based coordination polymer (denoted as CP 1) with hydrothermal stability was synthesized. The abundant coordination water, lattice water, and amino groups make an extended hydrogen-bonding pathway for efficient proton migration, which endows CP 1 with the highest proton conductivity of 2.41 × 10^-3 S·cm^-1 at 353 K and 98% RH. Especially, the proton conductivity of the chitosan (CS) hybrid membrane containing CP 1 reaches a maximum value of 2.62 × 10^-2 S·cm^-1 under 343 K and 98% RH, which increases almost 7 times higher than that of the pure CS membrane due to the host-guest collaboration. Furthermore, luminescence studies revealed that CP 1 is a high-sensitivity and good-selectivity fluorescent probe for the detection of trace amounts of l-histidine with a lowest detection limit of 1.0 × 10^-8 M.

Engineering of nanomaterials for mass spectrometry analysis of biomolecules

Mass spectrometry (MS) based analysis has received intense attention in diverse biological fields. However, direct MS interrogation of target biomolecules in complex biological samples is still challenging, due to the extremely low abundance and poor ionization potency of target biological species. Innovations in nanomaterials create new auxiliary tools for deep and comprehensive MS characterization of biomolecules. More recently, growing research interest has been directed to the compositional and structural engineering of nanomaterials for enriching target biomolecules prior to MS analysis, enhancing the ionization efficiency in MS detection and designing biosensing nanoprobes in sensitive MS readout. In this review, we mainly focus on the recent advances in the engineering of nanomaterials towards their applications in sample pre-treatment, desorption/ionization matrices and ion signal amplification for MS profiling of biomolecules. This review will provide a toolbox of nanomaterials for researchers devoted to developing analytical methods and practical applications in the biological MS field.

Strategies for Incorporating Catalytically Active Polyoxometalates in Metal-Organic Frameworks for Organic Transformations

Polyoxometalates (POMs) can benefit from immobilization on solid supports to overcome their difficulty in processability and stability. Among the reported solid supports, metal-organic frameworks (MOFs) offer a crystalline, versatile platform for depositing highly active POMs. The combination of these structures can at times benefit from the combined reactivity of both the POM and MOF, sometimes synergistically, to improve catalysis while balancing desirable properties like porosity, substrate diffusion, or stability. In this Review, we survey the strategies for immobilizing POMs within MOF structures, with an emphasis on how physical and catalytic properties of the parent materials are affected in the composite when employed in organic transformations.

Facile synthesis of metal-organic framework-derived SiW12@Co3O4 and its peroxidase-like activity in colorimetric assay

Over the past few years, artificial enzymes have attracted enormous attention due to their high stabilities and cost-effective productions. In this work, metal-organic framework-derived SiW₁₂@Co₃O₄ was synthesized in large quantities by stirring the mixture at ambient temperature and calcination. The obtained SiW₁₂@Co₃O₄ exhibited a highly inherent peroxidase-like activity and excellent stability. Kinetic studies demonstrated that the synthesized SiW₁₂@Co₃O₄ had a strong binding affinity to 3,3',5,5'-tetramethylbenzidine (TMB), stronger than HRP had. Specifically, the peroxidase-like activity of SiW₁₂@Co₃O₄ in an aqueous solution was well maintained after incubation at an elevated temperature, at an extreme pH and for a long time. A SiW₁₂@Co₃O₄-based method was further developed for H₂O₂ and one-pot glucose detection with good sensitivity and reliability. The facile synthesis approach is expected to facilitate the practical use of metal-organic frameworks and their derivatives as enzyme mimics in the future.

Boron-titanate monolayer nanosheets for highly selective adsorption of immunoglobulin G

Boron-titanate monolayer nanosheets were prepared through a scalable step by step intercalation approach for anchoring 3-mercaptopropyltriethoxysilane (MPTS) on the surface. MPTS provides clickable sites with 4-vinylphenylboronic acid (VPBA) via a thiol-ene (TE) click reaction to obtain monolayer titanate nanosheets with boronic acid ligands immobilized on the surface. The nanosheets obtained are denoted as VPBA-MPTS-TiNSs, with a lateral dimension of a few dozen nanometers and with a thickness of ca. 3.5 nm. The nanosheets exhibit a superior adsorption capacity of 1669.7 mg g-1 and favorable selectivity for the adsorption of glycoproteins by employing immunoglobulin G (IgG) as the protein model. The adsorbed IgG is thereafter readily collected by using 0.1% (m/v) cetane trimethyl ammonium bromide (CTAB) as the eluent. The practical applications of VPBA-MPTS-TiNSs are further demonstrated by the selective adsorption/purification of IgG from human serum.

A series of metal–organic loops templated by [SiMo12O40]4− and [β-Mo8O26]4− anions using double chelating ligands: amperometric sensing and selective photocatalytic properties

By changing the POM anions and TM ions, a series of compounds with multi-nuclear loops was formed.

Pyridine boronic acid-polyoxometalate based porous hybrid for efficient depletion of high abundant glycoproteins in plasma

A porous hybrid, namely PW₁₂@TiO₂-Si(Et)Si/Pba, is fabricated by the modification of PW₁₂@TiO₂-Si(Et)Si with pyridine boronic acid via a solvothermal method. The covalent interactions between the boronic acid group of the hybrid and the glycosylated site of proteins provide the as-prepared hybrid with favorable adsorption performance towards glycoproteins. The adsorption behaviors of glycoproteins onto the hybrid fit well with the Langmuir model, and the adsorption capacities for glycoprotein IgG and Trf are high, up to 348.5 mg g^-1 and 262.6 mg g^-1, respectively. Thus, a protocol for the depletion of high abundant glycoproteins from human plasma is proposed. The percentage contents of Trf, IgG, haptoglobinis and IgM are reduced from 7.38%, 5.5%, 3.01% and 1.02% to 0.951%, 4.7%, 0.126% and 0.76%, respectively. 85 low abundant proteins are identified from the raw plasma after the depletion of the high abundance proteins, demonstrating the potential of PW₁₂@TiO₂-Si(Et)Si/Pba hybrid in proteomic studies.