Tag: high-speed atomic force microscopy

Correlation of membrane protein conformational and functional dynamics

Membrane proteins (MPs) reside in the plasma membrane and perform various biological processes including ion transport, substrate transport, and signal transduction.*

Function-related conformational changes in membrane proteins occur in times scales ranging from nanoseconds to seconds.*

Obtaining time-resolved dynamic information of MPs in their membrane environment is still a major challenge.*

Although High Speed Atomic Force Microscopy (HS-AFM) images label-free samples such as DNA, soluble proteins, MPs, and intrinsically disordered proteins at ~1n~m lateral, ~0.1 nm vertical and ~100 ms temporal solution in aqueous environment and at ambient temperature and pressure, its temporal resolution is too slow to characterize many dynamic biological processes.*

In order to overcome this limitation Raghavendar Reddy Sanganna Gari, Joel José Montalvo-Acosta, George R. Heath, Yining Jiang, Xiaolong Gao, Crina M. Nimigean, Christophe Chipot and Simon Scheuring in their article Correlation of membrane protein conformational and functional dynamics use High Speed Atomic Force Microscopy Height Spectroscopy ( HS-AFM-HS) to characterize the microsecond timescale conformational changes of an integral-MP model system, i.e., the outer membrane protein G (OmpG) in a membrane environment.*

The positioning of the AFM tip is guided by HS-AFM imaging immediately before HS-AFM-HS-operation.*

NanoWorld Ultra-Short Cantilevers (USC) of the USC-F1.2-k0.15 type were used for the HS-AFM and HS-AFM-HS presented in the article.*

Figure 1 from “Correlation of membrane protein conformational and functional dynamics” by R.R. Sanganna Gari et al: HS-AFM imaging of OmpG in lipid bilayers at pH 7.6 and pH 5.0. a OmpG at pH 7.6 (Supplementary movie 1, left; frame rate: 200 ms per frame). A OmpG dimer is highlighted with dashed outline in all frames. Arrowheads in t = 11.6 s: Loop-6 fluctuating over the lumen. Arrowhead in t = 12.0 s: Fully open state. b Correlation average (n = 2752) of the HS-AFM movie frames (344 frames recorded over 68.8 s, full color scale: 0.0 nm < height < 1.25 nm, where the membrane level was set to 0.0 nm). c Correlation average of OmpG dimers. The topography outline (based on the molecular structure in 1e), serves as a visual guide to locate loop-6 and loop-2 in the topography and is highlighted by the dashed outline (the position of loop-6 is indicated by the asterisk based on its location in the structure (e)). Inner dashed outline show barrel lumen. d Standard deviation (std) map (n = 2752) from the averaging process in (b) (full color scale from blue to red: 0.05 nm < std < 0.19 nm) and topography outlines as in (c). e X-ray structure (PDB 2iwv) of the open OmpG conformation. Loop-6 (arrowhead L6) stands out of the image plane towards the viewer. Loop-2 (L2) forms a beta strand pointing away from the β-barrel, well detected by HS-AFM in the open state (b). f OmpG at pH 5.0 (Supplementary movie 1, right; frame rate: 200 ms per frame). A OmpG dimer is highlighted with dashed outline in all frames. g Correlation average (n = 2472) of the HS-AFM movie frames (309 frames recorded over 61.8 s, full color scale: 0.0 nm < height < 0.7 nm, where the membrane level was set to 0.0 nm). h Correlation average of OmpG dimers. For comparison, the topography outline of the open state (e) is shown (the position of loop-6 is indicated by the asterisk). i Standard deviation (std) map (n = 2472) from the averaging process in (g) (full color scale from blue to red: 0.04 nm < std < 0.07 nm) and topography outlines as in (h). j X-ray structure (PDB 2iww) of the closed OmpG conformation shown in the same orientation as in (e). Loop-6 (L6) folds over the β-barrel lumen in a lid-like manner. Loop-2 (L2) does not form a β-strand in the closed state, in agreement with absence of topography in this region in (h). Black dashed line: outline based on (e) for comparison. NanoWorld USC-F1.2-k0.15 AFM probes were used for the HS-AFM.
Figure 1 from “Correlation of membrane protein conformational and functional dynamics” by R.R. Sanganna Gari et al:
HS-AFM imaging of OmpG in lipid bilayers at pH 7.6 and pH 5.0.
a OmpG at pH 7.6 (Supplementary movie 1, left; frame rate: 200 ms per frame). A OmpG dimer is highlighted with dashed outline in all frames. Arrowheads in t = 11.6 s: Loop-6 fluctuating over the lumen. Arrowhead in t = 12.0 s: Fully open state. b Correlation average (n = 2752) of the HS-AFM movie frames (344 frames recorded over 68.8 s, full color scale: 0.0 nm < height < 1.25 nm, where the membrane level was set to 0.0 nm). c Correlation average of OmpG dimers. The topography outline (based on the molecular structure in 1e), serves as a visual guide to locate loop-6 and loop-2 in the topography and is highlighted by the dashed outline (the position of loop-6 is indicated by the asterisk based on its location in the structure (e)). Inner dashed outline show barrel lumen. d Standard deviation (std) map (n = 2752) from the averaging process in (b) (full color scale from blue to red: 0.05 nm < std < 0.19 nm) and topography outlines as in (c). e X-ray structure (PDB 2iwv) of the open OmpG conformation. Loop-6 (arrowhead L6) stands out of the image plane towards the viewer. Loop-2 (L2) forms a beta strand pointing away from the β-barrel, well detected by HS-AFM in the open state (b). f OmpG at pH 5.0 (Supplementary movie 1, right; frame rate: 200 ms per frame). A OmpG dimer is highlighted with dashed outline in all frames. g Correlation average (n = 2472) of the HS-AFM movie frames (309 frames recorded over 61.8 s, full color scale: 0.0 nm < height < 0.7 nm, where the membrane level was set to 0.0 nm). h Correlation average of OmpG dimers. For comparison, the topography outline of the open state (e) is shown (the position of loop-6 is indicated by the asterisk). i Standard deviation (std) map (n = 2472) from the averaging process in (g) (full color scale from blue to red: 0.04 nm < std < 0.07 nm) and topography outlines as in (h). j X-ray structure (PDB 2iww) of the closed OmpG conformation shown in the same orientation as in (e). Loop-6 (L6) folds over the β-barrel lumen in a lid-like manner. Loop-2 (L2) does not form a β-strand in the closed state, in agreement with absence of topography in this region in (h). Black dashed line: outline based on (e) for comparison.
Figure 2 from “Correlation of membrane protein conformational and functional dynamics” by R.R. Sanganna Gari et al: Single channel electrophysiology and HS-AFM height spectroscopy recordings of OmpG in lipid bilayers. Representative 60-ms segments of OmpG single channel recordings at pH 7.6 (a) and pH 5.0 (b) at +40 mV membrane potential (longer traces in Supplementary Figs. 2 and 3). Cartoon representation of single channel recording experimental setup is shown in inset of (a). OmpG (yellow) in open state (PDB:2IWV) is placed in a lipid bilayer (green) surrounded by buffer (light blue shade) and potassium and chloride ions are shown as red and blue spheres. Red arrow indicates ion flow through OmpG in response to voltage application. Dwell time histograms of open and closed states at pH 7.6 (c) and pH 5.0 (d) from single-channel recordings (see Supplementary Table 1). Representative 60-ms segments of OmpG HS-AFM-HS recordings at pH 7.6 (e) and pH 5.0 (f) (longer traces in Supplementary Fig. 4). Cartoon representation of HS-AFM height spectroscopy experimental setup is shown in inset of (e). An oscillating AFM tip (orange) detects conformational changes of loop motion. Dwell time histograms of open and closed states at pH 7.6 (g) and pH 5.0 (h) from HS-AFM-HS recordings (Supplementary Table 2). In HS-AFM-HS the low state represents the open state, where the HS-AFM tip can descend into the β-barrel, and the high state represents the closed state, where loop-6 covers the beta barrel barring access of the HS-AFM tip to the cavity. All current-time and height-time traces were filtered at 20 kHz during analysis. The state dwell-time histograms are shown using log binning for better visualization of the components49. Red traces in (a) and (b) represent idealized current-time traces using clampfit software. Red traces in (e) and (f) represent idealized height-time traces using the STaSI algorithm (see Methods). NanoWorld USC-F1.2-k0.15 AFM probes were used for the HS-AFM-HS.
Figure 2 from “Correlation of membrane protein conformational and functional dynamics” by R.R. Sanganna Gari et al:
Single channel electrophysiology and HS-AFM height spectroscopy recordings of OmpG in lipid bilayers.
Representative 60-ms segments of OmpG single channel recordings at pH 7.6 (a) and pH 5.0 (b) at +40 mV membrane potential (longer traces in Supplementary Figs. 2 and 3). Cartoon representation of single channel recording experimental setup is shown in inset of (a). OmpG (yellow) in open state (PDB:2IWV) is placed in a lipid bilayer (green) surrounded by buffer (light blue shade) and potassium and chloride ions are shown as red and blue spheres. Red arrow indicates ion flow through OmpG in response to voltage application. Dwell time histograms of open and closed states at pH 7.6 (c) and pH 5.0 (d) from single-channel recordings (see Supplementary Table 1). Representative 60-ms segments of OmpG HS-AFM-HS recordings at pH 7.6 (e) and pH 5.0 (f) (longer traces in Supplementary Fig. 4). Cartoon representation of HS-AFM height spectroscopy experimental setup is shown in inset of (e). An oscillating AFM tip (orange) detects conformational changes of loop motion. Dwell time histograms of open and closed states at pH 7.6 (g) and pH 5.0 (h) from HS-AFM-HS recordings (Supplementary Table 2). In HS-AFM-HS the low state represents the open state, where the HS-AFM tip can descend into the β-barrel, and the high state represents the closed state, where loop-6 covers the beta barrel barring access of the HS-AFM tip to the cavity. All current-time and height-time traces were filtered at 20 kHz during analysis. The state dwell-time histograms are shown using log binning for better visualization of the components49. Red traces in (a) and (b) represent idealized current-time traces using clampfit software. Red traces in (e) and (f) represent idealized height-time traces using the STaSI algorithm (see Methods).

*Raghavendar Reddy Sanganna Gari, Joel José Montalvo-Acosta, George R. Heath, Yining Jiang, Xiaolong Gao, Crina M. Nimigean, Christophe Chipot and Simon Scheuring
Correlation of membrane protein conformational and functional dynamics
Nature Communications volume 12, Article number: 4363 (2021)
DOI: https://doi.org/10.1038/s41467-021-24660-1

Please follow this external link to read the full article: https://rdcu.be/cAE2S

Open Access : The article “Correlation of membrane protein conformational and functional dynamics” by Raghavendar Reddy Sanganna Gari, Joel José Montalvo-Acosta, George R. Heath, Yining Jiang, Xiaolong Gao, Crina M. Nimigean, Christophe Chipot 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/.

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/.