Influence of Nonspecific Interactions on Protein Associations: Implications for Biochemistry In Vivo.

The cellular interior is composed of a variety of microenvironments defined by distinct local compositions and composition-dependent intermolecular interactions. We review the various types of nonspecific interactions between proteins and between proteins and other macromolecules and supramolecular structures that influence the state of association and functional properties of a given protein existing within a particular microenvironment at a particular point in time. The present state of knowledge is summarized, and suggestions for fruitful directions of research are offered.

Bacterial spores respond to humidity similarly to hydrogels.

Bacterial spores have outstanding properties from the materials science perspective, which allow them to survive extreme environmental conditions. Recent work by [S. G. Harrellson et al., Nature 619, 500-505 (2023)] studied the mechanical properties of Bacillus subtilis spores and the evolution of these properties with the change of humidity. The experimental measurements were interpreted assuming that the spores behave as water-filled porous solids, subjected to hydration forces. Here, we revisit their experimental data using literature data on vapor sorption on spores and ideas from polymer physics. We demonstrate that upon the change of humidity, the spores behave like rubber with respect to their swelling, elasticity, and relaxation times. This picture is consistent with the knowledge of the materials comprising the bacterial cell walls-cross-linked peptidoglycan. Our results provide an interpretation of the mechanics of bacterial spores and can help in developing synthetic materials mimicking the mechanical properties of the spores.

Electrostatic coupling and water bridging in adsorption hierarchy of biomolecules at water-clay interfaces.

Clay minerals are implicated in the retention of biomolecules within organic matter in many soil environments. Spectroscopic studies have proposed several mechanisms for biomolecule adsorption on clays. Here, we employ molecular dynamics simulations to investigate these mechanisms in hydrated adsorbate conformations of montmorillonite, a smectite-type clay, with ten biomolecules of varying chemistry and structure, including sugars related to cellulose and hemicellulose, lignin-related phenolic acid, and amino acids with different functional groups. Our molecular modeling captures biomolecule-clay and biomolecule-biomolecule interactions that dictate selectivity and competition in adsorption retention and interlayer nanopore trapping, which we determine experimentally by NMR and X-ray diffraction, respectively. Specific adsorbate structures are important in facilitating the electrostatic attraction and Van der Waals energies underlying the hierarchy in biomolecule adsorption. Stabilized by a network of direct and water-bridged hydrogen bonds, favorable electrostatic interactions drive this hierarchy whereby amino acids with positively charged side chains are preferentially adsorbed on the negatively charged clay surface compared to the sugars and carboxylate-rich aromatics and amino acids. With divalent metal cations, our model adsorbate conformations illustrate hydrated metal cation bridging of carboxylate-containing biomolecules to the clay surface, thus explaining divalent cation-promoted adsorption from our experimental data. Adsorption experiments with a mixture of biomolecules reveal selective inhibition in biomolecule adsorption, which our molecular modeling attributes to electrostatic biomolecule-biomolecule pairing that is more energetically favorable than the biomolecule-clay complex. In sum, our findings highlight chemical and structural features that can inform hypotheses for predicting biomolecule adsorption at water-clay interfaces.

Unraveling the molecular mechanism for enhanced gas adsorption in mixed-metal MOFs via solid-state NMR spectroscopy.

The incorporation of multiple metal ions in metal-organic frameworks (MOFs) through one-pot synthesis can induce unique properties originating from specific atomic-scale spatial apportionment, but the extraction of this crucial information poses challenges. Herein, nondestructive solid-state NMR spectroscopy was used to discern the atomic-scale metal apportionment in a series of bulk Mg1-xCox-MOF-74 samples via identification and quantification of eight distinct arrangements of Mg/Co ions labeled with a 13C-carboxylate, relative to Co content. Due to the structural characteristics of metal-oxygen chains, the number of metal permutations is infinite for Mg1-xCox-MOF-74, making the resolution of atomic-scale metal apportionment particularly challenging. The results were then employed in density functional theory calculations to unravel the molecular mechanism underlying the macroscopic adsorption properties of several industrially significant gases. It is found that the incorporation of weak adsorption sites (Mg2+ for CO and Co2+ for CO2 adsorption) into the MOF structure counterintuitively boosts the gas adsorption energy on strong sites (Co2+ for CO and Mg2+ for CO2 adsorption). Such effect is significant even for Co2+ remote from Mg2+ in the metal-oxygen chain, resulting in a greater enhancement of CO adsorption across a broad composition range, while the enhancement of CO2 adsorption is restricted to Mg2+ with adjacent Co2+. Dynamic breakthrough measurements unambiguously verified the trend in gas adsorption as a function of metal composition. This research thus illuminates the interplay between atomic-scale structures and macroscopic gas adsorption properties in mixed-metal MOFs and derived materials, paving the way for developing superior functional materials.

Sustainable lithium extraction enabled by responsive metal-organic frameworks with ion-sieving adsorption effects.

Metal-organic frameworks (MOFs) are superior ion adsorbents for selectively capturing toxic ions from water. Nevertheless, they have rarely been reported to have lithium selectivity over divalent cations due to the well-known flexibility of MOF framework and the similar physiochemical properties of Li+ and Mg2+. Herein, we report an ion-sieving adsorption approach to design sunlight-regenerable lithium adsorbents by subnanoporous MOFs for efficient lithium extraction. By integrating the ion-sieving agent of MOFs with light-responsive adsorption sites of polyspiropyran (PSP), the ion-sieving adsorption behaviors of PSP-MOFs with 6.0, 8.5, and 10.0 Å windows are inversely proportional to their pore size. The synthesized PSP-UiO-66 with a narrowest window size of 6.0 Å shows high LiCl adsorption capacity up to 10.17 mmol g-1 and good Li+/Mg2+ selectivity of 5.8 to 29 in synthetic brines with Mg/Li ratio of 1 to 0.1. It could be quickly regenerated by sunlight irradiation in 6 min with excellent cycling performance of 99% after five cycles. This work sheds light on designing selective adsorbents using responsive subnanoporous materials for environmentally friendly and energy-efficient ion separation and purification.

Theoretical isotherm equation for adsorption-induced structural transition on flexible metal-organic frameworks.

Flexible metal-organic frameworks (MOFs) exhibit an adsorption-induced structural transition known as "gate opening" or "breathing," resulting in an S-shaped adsorption isotherm. This unique feature of flexible MOFs offers significant advantages, such as a large working capacity, high selectivity, and intrinsic thermal management capability, positioning them as crucial candidates for revolutionizing adsorption separation processes. Therefore, the interest in the industrial applications of flexible MOFs is increasing, and the adsorption engineering for flexible MOFs is becoming important. However, despite the establishment of the theoretical background for adsorption-induced structural transitions, no theoretical equation is available to describe S-shaped adsorption isotherms of flexible MOFs. Researchers rely on various empirical equations for process simulations that can lead to unreliable outcomes or may overlook insights into improving material performance owing to parameters without physical meaning. In this study, we derive a theoretical equation based on statistical mechanics that could be a standard for the structural transition type adsorption isotherms, as the Langmuir equation represents type I isotherms. The versatility of the derived equation is shown through four examples of flexible MOFs that exhibit gate opening and breathing. The consistency of the formula with existing theories, including the osmotic free energy analysis and intrinsic thermal management capabilities, is also discussed. The developed theoretical equation may lead to more reliable and insightful outcomes in adsorption separation processes, further advancing the direction of industrial applications of flexible MOFs.

Ultra-high-efficiency capture of lead ions over acetylenic bond-rich graphdiyne adsorbent in aqueous solution.

A satisfactory material with high adsorption capacity is urgently needed to solve the serious problem of environment and human health caused by lead pollution. Herein, hydrogen-substituted graphdiyne (HsGDY) was successfully fabricated and employed to remove lead ions from sewage and lead-containing blood. The as-prepared HsGDY exhibits the highest adsorption capacity of lead among the reported materials with a maximum adsorption capacity of 2,390 mg/g, i.e., ~five times larger than that of graphdiyne (GDY). The distinguished hexagonal hole and stack mode of HsGDY allows the adsorption of more lead via its inner side adsorption mode in one single unit space. In addition, the Pb 6s and H 1s hybridization promotes the strong bonding of lead atom adsorbed at the acetylenic bond of HsGDY, contributing to the high adsorption capacity. HsGDY can be easily regenerated by acid treatment and showed excellent regeneration ability and reliability after six adsorption-regeneration cycles. Langmuir isotherm model, pseudo second order, and density functional theory (DFT) demonstrated that the lead adsorption process in HsGDY is monolayer chemisorption. Furthermore, the HsGDY-based portable filter can handle 1,000 µg/L lead-containing aqueous solution up to 1,000 mL, which is nearly 6.67 times that of commercial activated carbon particles. And, the HsGDY shows good biocompatibility and excellent removal efficiency to 100 µg/L blood lead, which is 1.7 times higher than that of GDY. These findings suggest that HsGDY could be a promising adsorbent for practical lead and other heavy metal removal.

Confined water-encapsulated activated carbon for capturing short-chain perfluoroalkyl and polyfluoroalkyl substances from drinking water.

The global ecological crisis of perfluoroalkyl and polyfluoroalkyl substances (PFASs) in drinking water has gradually shifted from long-chain to short-chain PFASs; however, the widespread established PFAS adsorption technology cannot cope with the impact of such hydrophilic pollutants given the inherent defects of solid-liquid mass transfer. Herein, we describe a reagent-free and low-cost strategy to reduce the energy state of short-chain PFASs in hydrophobic nanopores by employing an in situ constructed confined water structure in activated carbon (AC). Through direct (driving force) and indirect (assisted slip) effects, the confined water introduced a dual-drive mode in the confined water-encapsulated activated carbon (CW-AC) and completely eliminated the mass transfer barrier (3.27 to 5.66 kcal/mol), which caused the CW-AC to exhibit the highest adsorption capacity for various short-chain PFASs (C-F number: 3-6) among parent AC and other adsorbents reported. Meanwhile, benefiting from the chain length- and functional group-dependent confined water-binding pattern, the affinity of the CW-AC surpassed the traditional hydrophobicity dominance and shifted toward hydrophilic short-chain PFASs that easily escaped treatment. Importantly, the ability of CW-AC functionality to directly transfer to existing adsorption devices was verified, which could treat 21,000 bed volumes of environment-related high-load (~350 ng/L short-chain PFAS each) real drinking water to below the World Health Organization's standard. Overall, our results provide a green and cost-effective in situ upgrade scheme for existing adsorption devices to address the short-chain PFAS crisis.

Insertion of CO2 in metal ion-doped two-dimensional covalent organic frameworks.

Carbon capture is one of the essential low-carbon technologies required to achieve societal climate goals at the lowest cost. Covalent organic frameworks (COFs) are promising adsorbents for CO2 capture because of their well-defined porosity, large surface area, and high stability. Current COF-based CO2 capture is mainly based on a physisorption mechanism, exhibiting smooth and reversible sorption isotherms. In the present study, we report unusual CO2 sorption isotherms featuring one or more tunable hysteresis steps with metal ion (Fe3+, Cr3+, or In3+)-doped Schiff-base two-dimensional (2D) COFs (Py-1P, Py-TT, and Py-Py) as adsorbents. Synchrotron X-ray diffraction, spectroscopic and computational studies indicate that the sharp adsorption steps in the isotherm originate from the insertion of CO2 between the metal ion and the N atom of the imine bond on the inner pore surface of the COFs as the CO2 pressure reaches threshold values. As a result, the CO2 adsorption capacity of the ion-doped Py-1P COF is increased by 89.5% compared with that of the undoped Py-1P COF. This CO2 sorption mechanism provides an efficient and straightforward approach to enhancing the CO2 capture capacity of COF-based adsorbents, yielding insights into developing chemistry for CO2 capture and conversion.

Elastic heterogeneity governs asymmetric adsorption-desorption in a soft porous crystal.

Metal-organic frameworks (MOFs), which possess a high degree of crystallinity and a large surface area with tunable inorganic nodes and organic linkers, exhibit high stimuli-responsiveness and molecular adsorption selectivity that enable various applications. The adsorption in MOFs changes the crystalline structure and elastic moduli. Thus, the coexistence of adsorbed/desorbed sites makes the host matrices elastically heterogeneous. However, the role of elastic heterogeneity in the adsorption-desorption transition has been overlooked. Here, we show the asymmetric role of elastic heterogeneity in the adsorption-desorption transition. We construct a minimal model incorporating adsorption-induced lattice expansion/contraction and an increase/decrease in the elastic moduli. We find that the transition is hindered by the entropic and energetic effects which become asymmetric in the adsorption process and desorption process, leading to the strong hysteretic nature of the transition. Furthermore, the adsorbed/desorbed sites exhibit spatially heterogeneous domain formation, implying that the domain morphology and interfacial area between adsorbed/desorbed sites can be controlled by elastic heterogeneity. Our results provide a theoretical guideline for designing soft porous crystals with tunable adsorption hysteresis and the dispersion and domain morphology of adsorbates using elastic heterogeneity.

Single cobalt atoms anchored on Ti3C2Tx with dual reaction sites for efficient adsorption-degradation of antibiotic resistance genes.

The assimilation of antibiotic resistance genes (ARGs) by pathogenic bacteria poses a severe threat to public health. Here, we reported a dual-reaction-site-modified CoSA/Ti3C2Tx (single cobalt atoms immobilized on Ti3C2Tx MXene) for effectively deactivating extracellular ARGs via peroxymonosulfate (PMS) activation. The enhanced removal of ARGs was attributed to the synergistic effect of adsorption (Ti sites) and degradation (Co-O3 sites). The Ti sites on CoSA/Ti3C2Tx nanosheets bound with PO43- on the phosphate skeletons of ARGs via Ti-O-P coordination interactions, achieving excellent adsorption capacity (10.21 × 1010 copies mg-1) for tetA, and the Co-O3 sites activated PMS into surface-bond hydroxyl radicals (•OHsurface), which can quickly attack the backbones and bases of the adsorbed ARGs, resulting in the efficient in situ degradation of ARGs into inactive small molecular organics and NO3. This dual-reaction-site Fenton-like system exhibited ultrahigh extracellular ARG degradation rate (k > 0.9 min-1) and showed the potential for practical wastewater treatment in a membrane filtration process, which provided insights for extracellular ARG removal via catalysts design.

Direct imaging of micrometer-thick interfaces in salt-salt aqueous biphasic systems.

Unlike the interface between two immiscible electrolyte solutions (ITIES) formed between water and polar solvents, molecular understanding of the liquid-liquid interface formed for aqueous biphasic systems (ABSs) is relatively limited and mostly relies on surface tension measurements and thermodynamic models. Here, high-resolution Raman imaging is used to provide spatial and chemical resolution of the interface of lithium chloride - lithium bis(trifluoromethanesulfonyl)imide - water (LiCl-LiTFSI-water) and HCl-LiTFSI-water, prototypical salt-salt ABSs found in a range of electrochemical applications. The concentration profiles of both TFSI anions and water are found to be sigmoidal thus not showing any signs of a positive adsorption for both salts and solvent. More striking, however, is the length at which the concentration profiles extend, ranging from 11 to 2 µm with increasing concentrations, compared to a few nanometers for ITIES. We thus reveal that unlike ITIES, salt-salt ABSs do not have a molecularly sharp interface but rather form an interphase with a gradual change of environment from one phase to the other. This knowledge represents a major stepping-stone in the understanding of aqueous interfaces, key for mastering ion or electron transfer dynamics in a wide range of biological and technological settings including novel battery technologies such as membraneless redox flow and dual-ion batteries.

The 25-kDa linear polyethylenimine exerts specific antiviral activity against pseudorabies virus through interferencing its adsorption via electrostatic interaction.

Pseudorabies virus (PRV) is the causative agent of Aujeszky's disease, which is responsible for enormous economic losses to the global pig industry. Although vaccination has been used to prevent PRV infection, the effectiveness of vaccines has been greatly diminished with the emergence of PRV variants. Therefore, there is an urgent need to develop anti-PRV drugs. Polyethylenimine (PEI) is a cationic polymer and has a wide range of antibacterial and antiviral activities. This study found that a low dose of 1 µg/mL of the 25-kDa linear PEI had significantly specific anti-PRV activity, which became more intense with increasing concentrations. Mechanistic studies revealed that the viral adsorption stage was the major target of PEI without affecting viral entry, replication stages, and direct inactivation effects. Subsequently, we found that cationic polymers PEI and Polybrene interfered with the interaction between viral proteins and cell surface receptors through electrostatic interaction to exert the antiviral function. In conclusion, cationic polymers such as PEI can be a category of options for defense against PRV. Understanding the anti-PRV mechanism also deepens host-virus interactions and reveals new drug targets for anti-PRV.IMPORTANCEPolyethylenimine (PEI) is a cationic polymer that plays an essential role in the host immune response against microbial infections. However, the specific mechanisms of PEI in interfering with pseudorabies virus (PRV) infection remain unclear. Here, we found that 25-kDa linear PEI exerted mechanisms of antiviral activity and the target of its antiviral activity was mainly in the viral adsorption stage. Correspondingly, the study demonstrated that PEI interfered with the virus adsorption stage by electrostatic adsorption. In addition, we found that cationic polymers are a promising novel agent for controlling PRV, and its antiviral mechanism may provide a strategy for the development of antiviral drugs.

Bioinertization of NanoLC/MS/MS Systems by Depleting Metal Ions From the Mobile Phases for Phosphoproteomics.

We have successfully developed a bioinertized nanoflow LC/MS/MS (nanoLC/MS/MS) system for the highly sensitive analysis of phosphopeptides by depleting metal ions from the mobile phase. We found that not only direct contact of phosphopeptides with metal components, but also indirect contact with nanoLC pumps through the mobile phase causes significant losses during the recovery of phosphopeptides. Moreover, electrospray ionization was adversely affected by the mobile phase containing multiple metal ions as well as by the sample solvents contaminated with metal ions used in immobilized metal ion affinity chromatography for phosphopeptide enrichment. To solve these problems, metal ions were depleted by inserting an online metal ion removal device containing metal-chelating membranes between the gradient mixer and the autosampler. As a result, the peak areas of the identified phosphopeptides increased an average of 9.9-fold overall and 77-fold for multiply phosphorylated peptides with the insertion of the online metal ion removal system. This strategy would be applicable to the highly sensitive analysis of other phosphorylated biomolecules by microscale-LC/MS/MS.

Nanoalum adjuvanted vaccines: small details make a big difference.

Purified vaccine antigens offer important safety and reactogenicity advantages compared with live attenuated or whole killed virus and bacterial vaccines. However, they require the addition of adjuvants to induce the magnitude, duration and quality of immune response required to achieve protective immunity. Aluminium salts have been used as adjuvants in vaccines for almost a century. In the literature, they are often referred to as aluminium-based adjuvants (ABAs), or aluminium salt-containing adjuvants or more simply "alum". All these terms are used to group aluminium suspensions that are very different in terms of atomic composition, size, and shape. They differ also in stability, antigen-adsorption, and antigen-release kinetics. Critically, these parameters also have a profound effect on the character and magnitude of the immune response elicited. Recent findings suggest that, by reducing the size of aluminium from micro to nanometers, a more effective adjuvant is obtained, together with the ability to sterile filter the vaccine product. However, the behaviour of aluminium nanoparticles in vaccine formulations is different from microparticles, requiring specific formulation strategies, as well as a more detailed understanding of how formulation influences the immune response generated. Here we review the current state of art of aluminium nanoparticles as adjuvants, with a focus on their immunobiology, preparation methods, formulation optimisation and stabilisation.

How chemical defects influence the charging of nanoporous carbon supercapacitors.

SignificanceNanoporous carbon texture makes fundamental understanding of the electrochemical processes challenging. Based on density functional theory (DFT) results, the proposed atomistic approach takes into account topological and chemical defects of the electrodes and attributes to them a partial charge that depends on the applied voltage. Using a realistic carbon nanotexture, a model is developed to simulate the ionic charge both at the surface and in the subnanometric pores of the electrodes of a supercapacitor. Before entering the smallest pores, ions dehydrate at the external surface of the electrodes, leading to asymmetric adsorption behavior. Ions in subnanometric pores are mostly fully dehydrated. The simulated capacitance is in qualitative agreement with experiments. Part of these ions remain irreversibly trapped upon discharge.

On the mechanisms of ion adsorption to aqueous interfaces: air-water vs. oil-water.

The adsorption of ions to water-hydrophobe interfaces influences a wide range of phenomena, including chemical reaction rates, ion transport across biological membranes, and electrochemical and many catalytic processes; hence, developing a detailed understanding of the behavior of ions at water-hydrophobe interfaces is of central interest. Here, we characterize the adsorption of the chaotropic thiocyanate anion (SCN-) to two prototypical liquid hydrophobic surfaces, water-toluene and water-decane, by surface-sensitive nonlinear spectroscopy and compare the results against our previous studies of SCN- adsorption to the air-water interface. For these systems, we observe no spectral shift in the charge transfer to solvent spectrum of SCN-, and the Gibb's free energies of adsorption for these three different interfaces all agree within error. We employed molecular dynamics simulations to develop a molecular-level understanding of the adsorption mechanism and found that the adsorption for SCN- to both water-toluene and water-decane interfaces is driven by an increase in entropy, with very little enthalpic contribution. This is a qualitatively different mechanism than reported for SCN- adsorption to the air-water and graphene-water interfaces, wherein a favorable enthalpy change was the main driving force, against an unfavorable entropy change.

Adsorption free energy predicts amyloid protein nucleation rates.

Primary nucleation is the fundamental event that initiates the conversion of proteins from their normal physiological forms into pathological amyloid aggregates associated with the onset and development of disorders including systemic amyloidosis, as well as the neurodegenerative conditions Alzheimer's and Parkinson's diseases. It has become apparent that the presence of surfaces can dramatically modulate nucleation. However, the underlying physicochemical parameters governing this process have been challenging to elucidate, with interfaces in some cases having been found to accelerate aggregation, while in others they can inhibit the kinetics of this process. Here we show through kinetic analysis that for three different fibril-forming proteins, interfaces affect the aggregation reaction mainly through modulating the primary nucleation step. Moreover, we show through direct measurements of the Gibbs free energy of adsorption, combined with theory and coarse-grained computer simulations, that overall nucleation rates are suppressed at high and at low surface interaction strengths but significantly enhanced at intermediate strengths, and we verify these regimes experimentally. Taken together, these results provide a quantitative description of the fundamental process which triggers amyloid formation and shed light on the key factors that control this process.

Confinement effects facilitate low-concentration carbon dioxide capture with zeolites.

Engineered systems designed to remove CO2 from the atmosphere need better adsorbents. Here, we report on zeolite-based adsorbents for the capture of low-concentration CO2. Synthetic zeolites with the mordenite (MOR)-type framework topology physisorb CO2 from low concentrations with fast kinetics, low heat of adsorption, and high capacity. The MOR-type zeolites can have a CO2 capacity of up to 1.15 and 1.05 mmol/g for adsorption from 400 ppm CO2 at 30 °C, measured by volumetric and gravimetric methods, respectively. A structure-performance study demonstrates that Na+ cations in the O33 site located in the side-pocket of the MOR-type framework, that is accessed through a ring of eight tetrahedral atoms (either Si4+ or Al3+: eight-membered ring [8MR]), is the primary site for the CO2 uptake at low concentrations. The presence of N2 and O2 shows negligible impact on CO2 adsorption in MOR-type zeolites, and the capacity increases to ∼2.0 mmol/g at subambient temperatures. By using a series of zeolites with variable topologies, we found the size of the confining pore space to be important for the adsorption of trace CO2. The results obtained here show that the MOR-type zeolites have a number of desirable features for the capture of CO2 at low concentrations.

Disparate External Electric Field Effect on the Adsorption and Shear Behavior of Monovalent and Trivalent Ions in Electrolyte Solution.

Reducing friction is of great interest, and an external potential applied to the friction pair can regulate lubricity. Electrochemical atomic force microscopy (EC-AFM) is used to study the tribological and adsorption behavior of monovalent and trivalent ionic solutions between charged surfaces. An opposite trend of coefficient of friction (COF) and normal force that varies with the applied electric potential is witnessed. Direct force measurements and theoretical models have disclosed that, for the NaCl solution, the negative electric field reduces the COF by increasing cation adsorption. As for LaCl3 solution, the positive electric field promotes the primary adsorption of anions on HOPG, resulting in the disappearance of the attractive ion-ion correlation between the trivalent ions, thereby reducing the COF. The shear behavior of adsorbed ions in electrolyte solution is sensitive to their valence, because of their different surface force contribution. The study further provides a framework to optimize the design of hydration lubrication.