Pb2+ Uptake by Magnesite: The Competition between Thermodynamic Driving Force and Reaction Kinetics

When they are in put in contact with carbonate minerals dangerous environmental pollutants such as Pb2+ and Cd2+ are taken up by the solid phase assemblage and can be removed from aqueous solutions.*

As carbonates can be found almost everywhere and are easily exploitable this makes them interesting materials for environmental remediation.*

However, magnesite ( MGS ) is well-known for the slow dissolution and growth kinetics at room temperature conditions in the so-called dolomite problem.*

In their article “Pb2+ Uptake by Magnesite: The Competition between Thermodynamic Driving Force and Reaction Kinetics” Fulvio Di Lorenzo, Tobias Arnold and Sergey V. Churakov use in situ atomic force microscopy (AFM) to investigate the growth of {10.4} magnesite surfaces in the absence and in the presence of Pb2+ as well as the effect of solution ageing.*

In their study the authors attempt to answer the question if and under which circumstances magnesium carbonate could be used in removing Pb from wastewater.*

The experimental results presented in above mentioned article have the object to discuss and evaluate the theoretical possibilities and the practical limitations that must be taken into account for the development of environmental remediation technologies based on magnesite.*

The experiments conducted in this study by  Fulvio Di Lorenzo et al. demonstrate that, although the thermodynamic conditions are encouraging, the transformation reaction between magnesite and cerrusite makes it improbably that it will play a crucial role in the development of remediation processes for PbII pollution.*

The authors of the study conclude that, although the thermodynamic conditions are encouraging, an environmental remediation process based on MGS as the substrate for a solvent-mediated transformation reaction is unlikely to play a crucial part in industrial applications due to the slow kinetics of MGS dissolution. However, the sluggish kinetics of MGS precipitation is favourable for Pb entrapment by the precipitation of carbonate from Mg2+ and Pb2+-bearing solutions, leading to a strong PbII enrichment in the solid phase even in far-from-equilibirum conditions.*

The in situ flow-through Atomic Force Microscopy was performed using Arrow-UHFAuD AFM probes in tapping mode.

Figure 8 from “Pb2+ Uptake by Magnesite: The Competition between Thermodynamic Driving Force and Reaction Kinetics” by Fulvio Di Lorenzo et al:
 In situ observation of {10.4} surfaces of MGS in contact with acidic solution, pH 4 (HNO3). The images were acquired in tapping mode. The first row corresponds to height channels, while the second row reports the respective amplitude channels. (A) The dissolution at 25 °C is sluggish and it is not possible to detect any dissolution feature. (B) In the same conditions but at higher temperature (60 °C), dissolution features are observed on the {10.4} surfaces of MGS, despite the retrograde solubility. Yellow and blue lines of constant size are used to highlight the evolution of etch pits and step edges, respectively. This evidence demonstrates that the existence of kinetic barriers controls the dissolution of MGS at room temperature conditions. NanoWorld Arrow-UHFAuD AFM probes were used.
Figure 8 from “Pb2+ Uptake by Magnesite: The Competition between Thermodynamic Driving Force and Reaction Kinetics” by Fulvio Di Lorenzo et al:
 In situ observation of {10.4} surfaces of MGS in contact with acidic solution, pH 4 (HNO3). The images were acquired in tapping mode. The first row corresponds to height channels, while the second row reports the respective amplitude channels. (A) The dissolution at 25 °C is sluggish and it is not possible to detect any dissolution feature. (B) In the same conditions but at higher temperature (60 °C), dissolution features are observed on the {10.4} surfaces of MGS, despite the retrograde solubility. Yellow and blue lines of constant size are used to highlight the evolution of etch pits and step edges, respectively. This evidence demonstrates that the existence of kinetic barriers controls the dissolution of MGS at room temperature conditions.

*Fulvio Di Lorenzo, Tobias Arnold, and Sergey V. Churakov
Pb2+ Uptake by Magnesite: The Competition between Thermodynamic Driving Force and Reaction Kinetics
Minerals 2021, 11(4), 415
DOI: https://doi.org/10.3390/min11040415

Please follow this external link to read the full article: https://www.mdpi.com/2075-163X/11/4/415

Open Access : The article “Pb2+ Uptake by Magnesite: The Competition between Thermodynamic Driving Force and Reaction Kinetics” by Fulvio Di Lorenzo, Tobias Arnold, and Sergey V. Churakov is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit https://creativecommons.org/licenses/by/4.0/.

High-speed atomic force microscopy highlights new molecular mechanism of daptomycin action

The current pandemic is not the only health threat worldwide. Another worry is the increasing antibiotic resistance which increases the fear to run out of effective antibiotics.

This is one of the reasons why antimicrobial peptides (AMPs) are gaining more and more interest.

The lipopeptide Daptomycin ( DAP ) has been therapeutically used as a last resort antibiotic against multidrug-resistant enterococci and staphylococci in the past. Unfortunately, some strains have become resistant to Dap in recent years. There still is a knowledge-gap on the details of Dap activity. It is therefore important to understand the structure-activity relationships of AMPs on membranes in order to develop more antibiotics of this type as a countermeasure to the spread of resistance.*

High Speed Atomic Force Microscopy ( HS-AFM ) makes it possible to observe dynamic biological processes on a molecular level.

In the article “High-speed atomic force microscopy highlights new molecular mechanism of daptomycin action” Francesca Zuttion, Adai Colom, Stefan Matile, Denes Farago, Frédérique Pompeo, Janos Kokavecz, Anne Galinier, James Sturgis and Ignacio Casuso describe how, by using the possibilities offered by high speed atomic force microscopy, they were able to confirm some up until now hypothetical models and additionally detected some previously unknown molecular mechanisms. *

The HS-AFM imaging made it possible for the authors to observe the development of the dynamics of interaction at the molecular-level over several hours. *

They investigated the lipopeptide Daptomycin under infection-like conditions and could confirm Dap oligomerization and the existence of half pores. *

They also mimicked bacterial resistance conditions by increasing the CL-content in the membrane. *

By correlating the results of other research techniques such as FRET, SANS, NMR, CD or electrophysiology techniques with the results they achieved with high speed atomic force microscopy F. Zuttion et al. were able to confirm several, previously, hypothetical models, and detect several unknown molecular mechanisms. *

It is to be hoped that the possibilities offered by HS-AFM imaging will stimulate new models and insight on the structure-activity relationship of membrane-interacting molecules and also open up the possiblity to increase the throughput of screening of molecular candidates considerably. *

NanoWorld USC ( Ultra-Short AFM Cantilevers) of the USC-F1.2-k0.15 type, which are specially designed for the use in high speed atomic force microscopy, were used for the HS-AFM imaging described in the article cited below. These AFM probes have a typical resonance frequency of 1200 kHz and have a wear resistant AFM tip made from high density carbon.

Figure 4 Sub-MIC Dap on POPG at 37 °C. Tens of minutes from “High-speed atomic force microscopy highlights new molecular mechanism of daptomycin action” by Francesca Zuttion et al. NanoWorld Ultra-Short AFM Cantilevers USC-F1.2-k0.15 AFM probes for HS-AFM imaging were used.
Figure 4 Sub-MIC Dap on POPG at 37 °C. Tens of minutes from “High-speed atomic force microscopy highlights new molecular mechanism of daptomycin action” by Francesca Zuttion et al.
Intermediate stages a A new structure appeared: dimples, zones of thinner membrane thickness, whose diameter was in the range 7 ± 2 nm. Most dimples diffuse, but some remained static (colour scale: 3 nm). Movie details: frame rate 97 ms; zoom of a full image of 150 nm × 90 nm and 256 × 160 pixels. b The dimple diffusion consisted of swinging trajectories, implying membrane-mediated dimple-dimple attraction (colour scale: 3 nm). b, right, Energy profile of the interaction of the dimples obtained derived from 120 centre-to-centre distance measurements that contains as the oligomers two energy minima. Movie details: frame rate 83 ms; full image of 150 nm × 150 nm and 256 × 256 pixels. c In some membrane zones, clusters of dimples, reminiscent of cubic phases, developed (colour scale: 4 nm). Movie details: frame rate 74 ms; full image of 90 nm × 60 nm and 256 × 160 pixels. d The clusters of dimples were moderately dynamical in time, with moderate internal rearrangements (colour scale: 4 nm). Movie details: frame rate 74 ms; full image of 25 nm × 16 nm and 256 × 160 pixels. e The other deformation found was elongated-humps on top of the POPG membrane. e, left, An elongated-hump in the proximity of a cluster of dimples (colour scale: 4 nm). e, right, A close-up and a profile of an elongated-hump. Additional images of elongated-humps on Supplementary Fig. 1. Movie details: frame rate 479 ms; zoom of full image of 250 nm × 200 nm and 300 × 256 pixels. f It was observed that the dimples and the elongated-humps fused and gave yield to pores of toroidal structure where a protruding ring surrounds the pore (colour scale: 4 nm). Movie details: frame rate 74 ms; full image of 40 nm × 40 nm and 256 × 160 pixels.

*Francesca Zuttion, Adai Colom, Stefan Matile, Denes Farago, Frédérique Pompeo, Janos Kokavecz, Anne Galinier, James Sturgis and Ignacio Casuso
High-speed atomic force microscopy highlights new molecular mechanism of daptomycin action
Nature Communications volume 11, Article number: 6312 (2020)
DOI: https://doi.org/10.1038/s41467-020-19710-z

Please follow this external link to read the full article: https://rdcu.be/ciaW2

Open Access : The article “High-speed atomic force microscopy highlights new molecular mechanism of daptomycin action” by Francesca Zuttion, Adai Colom, Stefan Matile, Denes Farago, Frédérique Pompeo, Janos Kokavecz, Anne Galinier, James Sturgis and Ignacio Casuso is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit https://creativecommons.org/licenses/by/4.0/.

Millisecond dynamics of an unlabeled amino acid transporter

Excitatory amino acid transporters (EAATs) are important in many physiological processes and crucial for the removal of excitatory amino acids from the synaptic cleft.*

In the article “Millisecond dynamics of an unlabeled amino acid transporter “ Tina R. Matin, George R. Heath, Gerard H. M. Huysmans, Olga Boudker and Simon Scheuring develop and apply high-speed atomic force microscopy line-scanning (HS-AFM-LS) combined with automated state assignment and transition analysis for the determination of transport dynamics of unlabeled membrane-reconstituted GltPh, a prokaryotic EAAT homologue, with millisecond temporal resolution.*

Among the bulk and single-molecule techniques, high-speed atomic force microscopy ( HS-AFM ) stands out with its ability to provide real-time structural and dynamical information of single molecules. HS-AFM images label-free molecules under close-to-physiological conditions with ~0.1 nm vertical and ~1 nm lateral imaging resolution. Furthermore, HS-AFM has typically ~100 ms temporal resolution, giving access to structure–dynamics relationship of proteins, though the achievable imaging speed depends on sample characteristics like scan size and surface corrugation.

Recently in a quest to achieve higher temporal resolutions, the authors of the cited article used HS-AFM line scanning (HS-AFM-LS) for the analysis of single-protein dynamics. *

Line scanning, using a conventional AFM, has been used to study protein–protein interactions earlier. In HS-AFM-LS, the slow-scan axis (y-direction) is disabled. Therefore, instead of imaging an x/y-area, the scientists scan over one horizontal x-line several hundreds to thousands of times per second, thus reaching millisecond temporal resolution. The topographical readouts of this line are stacked one after another, resulting in kymographs of the dynamical behavior of the molecules. Therefore, HS-AFM-LS has between 2 and 3 orders of magnitude higher temporal resolution than HS-AFM imaging and should allow the detection of fast transporter dynamics and possible intermediate states that have so far escaped kinetic characterization. *

All AFM images presented in this study were taken using a HS-AFM operated in amplitude modulation mode (with typical free and setpoint amplitudes, Afree = 1.0 nm and Aset = 0.9 nm, respectively using optimized scan and feedback parameters. NanoWorld Ultra-Short Cantilevers ( NanoWorld’s AFM probe series especially dedicated for High Speed Scanning) of the USC-F1.2-k0.15 type were used. In the presented experiments, four different buffer conditions were used. *

As the authors state in their article they find that GltPh transporters can operate much faster than previously reported, with state dwell-times in the 50 ms range, and report the kinetics of an intermediate transport state with height between the outward- and inward-facing states. Transport domains stochastically probe transmembrane motion, and reversible unsuccessful excursions to the intermediate state occur. The presented approach and analysis methodology are generally applicable to study transporter kinetics at system-relevant temporal resolution.*

Figure 2 from “Millisecond dynamics of an unlabeled amino acid transporter” by Tina R. Matin et al.
HS-AFM line scanning (HS-AFM-LS): millisecond temporal resolution of unlabeled transporter dynamics.:
a HS-AFM image of a membrane packed with GltPh exposing the extracellular face before HS-AFM-LS (apo condition: 20 mM Tris-HCl, pH7.5, 150 mM KCl). Dashed lines indicate the position of the central scan line where subsequent HS-AFM-LS is performed. b Six seconds of a HS-AFM-LS kymograph with 3.3 ms line acquisition speed. Each transporter domain appears as a vertical line. c Projection (top) and height profile (bottom) of b. d HS-AFM image after HS-AFM-LS. The lateral position of recognizable features in a–d are indicated by arrowheads. e One second high-magnification views of dashed regions 1, 2, and 3 in b. Transport domain excursions to the inward-facing state appear as dark dwells along the vertical time axis. f Projection (top) and height profile (bottom) of e. Arrowheads indicate the position of the seven protomers in the kymograph (red: active protomer #5). g Height/time traces (gray) and state fits (red) of the active domain (protomer #5) in e. This figure is representative of the experimental sequence for the >50 replicates analyzed in this work.
NanoWorld Ultra-Short Cantilevers ( NanoWorld's AFM probe series especially dedicated for High Speed Scanning) of the USC-F1.2-k0.15 type (8 μm length, nominal spring constant of 0.15 N/m, nominal resonance frequency of ∼650 kHz and quality factor of ∼1.5 in buffer) were used.
Figure 2 from “Millisecond dynamics of an unlabeled amino acid transporter” by Tina R. Matin et al.
HS-AFM line scanning (HS-AFM-LS): millisecond temporal resolution of unlabeled transporter dynamics.:
a HS-AFM image of a membrane packed with GltPh exposing the extracellular face before HS-AFM-LS (apo condition: 20 mM Tris-HCl, pH7.5, 150 mM KCl). Dashed lines indicate the position of the central scan line where subsequent HS-AFM-LS is performed. b Six seconds of a HS-AFM-LS kymograph with 3.3 ms line acquisition speed. Each transporter domain appears as a vertical line. c Projection (top) and height profile (bottom) of b. d HS-AFM image after HS-AFM-LS. The lateral position of recognizable features in a–d are indicated by arrowheads. e One second high-magnification views of dashed regions 1, 2, and 3 in b. Transport domain excursions to the inward-facing state appear as dark dwells along the vertical time axis. f Projection (top) and height profile (bottom) of e. Arrowheads indicate the position of the seven protomers in the kymograph (red: active protomer #5). g Height/time traces (gray) and state fits (red) of the active domain (protomer #5) in e. This figure is representative of the experimental sequence for the >50 replicates analyzed in this work.

*Tina R. Matin, George R. Heath, Gerard H. M. Huysmans, Olga Boudker and Simon Scheuring
Millisecond dynamics of an unlabeled amino acid transporter
Nature Communications volume 11, Article number: 5016 (2020)
DOI: https://doi.org/10.1038/s41467-020-18811-z

Please follow this external link to read the full article: https://rdcu.be/cbuOU

Open Access : The article “Millisecond dynamics of an unlabeled amino acid transporter” by Tina R. Matin, George R. Heath, Gerard H. M. Huysmans, Olga Boudker and Simon Scheuring is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit https://creativecommons.org/licenses/by/4.0/.