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.
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http://dx.doi.org/10.1073/pnas.2316569121 | DOI Listing |
Nat Commun
January 2025
Stockbridge School of Agriculture, University of Massachusetts, Amherst, MA, 01003, USA.
The extensive application of graphene nanosheets (GNSs) has raised concerns over risks to sensitive species in the aquatic environment. The humic acid (HA) corona is traditionally considered to reduce GNSs toxicity. Here, we evaluate the effect of sorbed HA (GNSs-HA) on the toxicity of GNSs to Gram positive Bacillus tropicus.
View Article and Find Full Text PDFAnal Chem
December 2024
Analytical & Testing Center, Sichuan University, Chengdu, Sichuan 610064, China.
Spherical nucleic acids (SNAs) usually suffer from an undesired protein corona and disrupt the function of nucleic acids (e.g., aptamer), thereby compromising recognition and response to proteins in the biological environment.
View Article and Find Full Text PDFACS Appl Mater Interfaces
December 2024
Air Force Research Laboratory, 711th Human Performance Wing, Wright-Patterson Air Force Base, Wright-Patterson AFB, Ohio 45433, United States.
Peptides, due to their diverse and controllable properties, are used as both liquid and gas phase recognition elements for both biological and chemical targets. While it is well understood how binding of a peptide to a biomolecule can be converted into a sensing event, there is not the same mechanistic level of understanding with regard to how peptides modulate the selectivity of semiconductor/conductor-based gas sensors. Notably, a rational, mechanistic study has not yet been performed to correlate peptide properties to the sensor response for volatile organic compounds (VOCs) as a function of chemical properties.
View Article and Find Full Text PDFbioRxiv
December 2024
Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, NY 10032.
Time-resolved cryo-EM (TRCEM) makes it possible to provide structural and kinetic information on a reaction of biomolecules before the equilibrium is reached. Several TRCEM methods have been developed in the past to obtain key insights into the mechanism of action of molecules and molecular machines on the time scale of tens to hundreds of milliseconds, which is unattainable by the normal blotting method. Here we present our TRCEM setup utilizing a polydimethylsiloxane (PDMS)-based microfluidics chip assembly, comprising three components: a PDMS-based, internally SiO-coated micromixer, a glass-capillary microreactor, and a PDMS-based microsprayer for depositing the reaction product onto the EM grid.
View Article and Find Full Text PDFSensors (Basel)
December 2024
Department of Medical Diagnostics, Centre for Advanced Materials and Technologies CEZAMAT, Warsaw University of Technology, 02822 Warsaw, Poland.
Microvolume ELISA platforms have become vital in diagnostics for their high-throughput capabilities and minimal sample requirements. High-quality substrates with advanced surface properties are essential for these applications. They enable both efficient biomolecule immobilization and antifouling properties, which are critical for assay sensitivity and specificity.
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