During replication, expression, and repair of the eukaryotic genome, cellular machinery must access the DNA wrapped around histone proteins forming nucleosomes. These octameric protein·DNA complexes are modular, dynamic, and flexible and unwrap or disassemble either spontaneously or by the action of molecular motors. Thus, the mechanism of formation and regulation of subnucleosomal intermediates has gained attention genome-wide because it controls DNA accessibility.*
In the article “Real-Time Multistep Asymmetrical Disassembly of Nucleosomes and Chromatosomes Visualized by High-Speed Atomic Force Microscopy” Bibiana Onoa, César Díaz-Celis, Cristhian Cañari-Chumpitaz, Antony Lee and Carlos Bustamante describe how they imaged nucleosomes and their more compacted structure with the linker histone H1 (chromatosomes) using high-speed atomic force microscopy to visualize simultaneously the changes in the DNA and the histone core during their disassembly when deposited on mica.*
Furthermore, Bibiana Onoa et al. trained a neural network and developed an automatic algorithm to track molecular structural changes in real time. *
The authors’ results show that nucleosome disassembly is a sequential process involving asymmetrical stepwise dimer ejection events. The presence of H1 restricts DNA unwrapping, significantly increases the nucleosomal lifetime, and affects the pathway in which heterodimer asymmetrical dissociation occurs. *
Bibiana Onoa et al. observe that tetrasomes are resilient to disassembly and that the tetramer core (H3·H4)2 can diffuse along the nucleosome positioning sequence. Tetrasome mobility might be critical to the proper assembly of nucleosomes and can be relevant during nucleosomal transcription, as tetrasomes survive RNA polymerase passage. These findings are relevant to understanding nucleosome intrinsic dynamics and their modification by DNA-processing enzymes. *
To characterize the nucleosomes dynamics in 2D, individual molecules were observed in buffer using an Ando-type high speed atomic force microscope together with NanoWorld Ultra-Short Cantilevers for HS-AFM of the USC-F1.2-K0.15 AFM probe type ( typical spring constant 0.15 N/m, typical resonance frequency in air 1200 kHz, resonance frequency 500–600 kHz in liquid). *
The AFM data presented in the article allow the authors to directly visualize the dynamics of DNA and histones during nucleosome and chromatosome disassembly, providing a simultaneous observation of DNA unwrapping and histone dissociation. *
The experimental and analytical strategy presented shows that real-time HS-AFM is a robust and powerful tool for studying single nucleosomes and chromatin dynamics. *
graphical abstract from Bibiana Onoa et al 2024 “Real-Time Multistep Asymmetrical Disassembly of Nucleosomes and Chromatosomes Visualized by High-Speed Atomic Force Microscopy”
*Bibiana Onoa, César Díaz-Celis, Cristhian Cañari-Chumpitaz, Antony Lee and Carlos Bustamante Real-Time Multistep Asymmetrical Disassembly of Nucleosomes and Chromatosomes Visualized by High-Speed Atomic Force Microscopy
ACS Central Science 2024, 10, 1, 122–137
DOI: https://doi.org/10.1021/acscentsci.3c00735
Open Access The article “Real-Time Multistep Asymmetrical Disassembly of Nucleosomes and Chromatosomes Visualized by High-Speed Atomic Force Microscopy” by Bibiana Onoa, César Díaz-Celis, Cristhian Cañari-Chumpitaz, Antony Lee and Carlos Bustamante 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 http://creativecommons.org/licenses/by/4.0/.
Collagen is the most abundant structural protein in mammals. *
Type I collagen in its fibril form has a characteristic pattern structure that alternates two regions called gap and overlap. The structure and properties of collagens are highly dependent on the water and mineral content of the environment. *
In the article “Interfacial water on collagen nanoribbons by 3D AFM” Diana M. Arvelo, Clara Garcia-Sacristan, Enrique Chacón, Pedro Tarazona and Ricardo Garcia describe how they apply three dimensional atomic force microscopy (3D AFM) to characterize at angstrom-scale resolution the interfacial water structure of collagen nanoribbons.*
Three-dimensional AFM (3D AFM) is an AFM method developed for imaging at high-spatial resolution solid–liquid interfaces in the three spatial coordinates.*
This method has provided atomic-scale images of hydration and solvation layers on a variety of rigid and atomically flat surfaces, such as mica, gibbsite, boehmite, graphite, or 2D materials.*
However, imaging hydration layers on soft materials such as collagen is more challenging than on atomically flat crystalline surfaces.*
On the one hand, the force applied by the AFM tip might deform the protein. On the other hand, the height variations across gap and overlap regions might complicate the imaging of interfacial water.*
In recent years, 3D AFM has expanded its capabilities to image interfacial water on soft materials such as proteins, biopolymers, DNA, lipids, membrane proteins, and cells.*
Those experiments were performed with hydrophilic SiOx AFM tips which are negatively charged under neutral pH conditions.*
The imaging contrast mechanisms and the role of the AFM tip’s composition on the observed solvation structure are under discussion.*
More generally, both theory and experiments performed with very high salt concentrations indicated that the contrast observed in 3D AFM reflects an interplay between water particle and surface charge density distributions.*
For their article the authors apply 3D AFM to study at molecular-scale spatial resolution the structure of interfacial water on collagen nanoribbons.*
Diana M. Arvelo et al. study the influence of the AFM tip’s charge and the salt concentration on the interfacial solvent structure. They report that the interfacial structure depends on the water particle and ion charge density distributions. A non-charged AFM tip reveals the formation of hydration layers on both gap and overlap regions. A negatively charged AFM tip shows that on a gap region, the solvation structure might depart from that of the hydration layers. This effect is attributed to the adsorption of ions from the solution. Those ions occupy the voids existing between collagen molecules in the gap region. *
A home-made three-dimensional AFM was implemented on a commercially available AFM. 3D AFM was performed in the amplitude modulation mode by exciting the AFM cantilever at its first eigenmode.
At the same time when the AFM cantilever oscillates with respect to its equilibrium position, a sinusoidal signal is applied to the z-piezo to modify the relative z-distance between the sample and the AFM tip. *
Diana M. Arvelo et al. have used z-piezo displacements with amplitudes of 2.0 nm and a period (frequency) of 10 ms (100 Hz). The z-piezo signal is synchronized with the xy-displacements in such a way that for each xy-position on the surface of the material, the AFM tip performs a single and complete z-cycle. The z-data are read out every 10.24 µs and stored in 512 pixels (256 pixels per half cycle). Each xy-plane of the 3D map contains 80 × 64 pixels. Hence, the total time to acquire such a 3D-AFM image is 52 s.*
The 3D AFM experiments were performed with two types of AFM probes with different surface chemistries which have different chemical properties in aqueous solutions.*
The high-density carbon/diamond-like AFM tips grown on quartz-like AFM cantilevers that Diana M. Arvelo et al. et al used ( NanoWorld Ultra-Short CantileversUSC-F1.2-k7.3 for high-speed AFM) remain uncharged at pH 7.4 and are called “neutral” AFM tips in the article.
The silicon AFM cantilevers with silicon AFM tips (NanoWorld Arrow-UHFAuD ultra-high frequency AFM probes) are negatively charged at neutral pH (silicon tips for short in the text) and were used to observe the formation of collagen nanoribbons.
All silicon AFM tips are readily oxidized and are usually covered by a thin native oxide layer which is hydrophilic.
The hydroxyl groups on the surface of the silicon AFM tip become negatively charged while the carbon AFM tips remain neutral (unchanged).
To image at angstrom-scale resolution, the interfacial water structure on the collagen requires reducing the lateral and vertical imaging sizes, respectively, to 5 and 1.5 nm.*
First, the authors introduce the results obtained with carbon-based tips (uncharged, NanoWorld Ultra-Short CantileversUSC-F1.2-k7.3 for high-speed AFM). Figure 2 (of the cited article) shows some representative 2D force xz panels obtained on gap and overlap regions of a collagen nanoribbon in a concentration of 300 mM KCl. The panels are extracted from a 3D AFM image. The interlayer distances in a gap region are d1 = 0.28 nm and d2 = 0.33 nm (average values) [Fig. 2(a)], while those in an overlap region are d1 = 0.29 and d2 = 0.32 nm (average values) [Fig. 2(b)]. Those values coincide within the experimental error with the values expected for hydration layers on hydrophilic surfaces.
Next, the authors repeated the experiment using other salt concentrations. Figure 2(c) shows that the interlayers distances (within the experimental error) do not depend on the salt concentration or the collagen region. Diana M. Arvelo et al. remark that entropic effects make the second layer more disordered than the first; therefore, d2 ≥ d1.
The structure and properties of collagens are highly dependent on the water and mineral content of the environment.
For a neutral AFM tip (USC-F1.2-k7.3), the interfacial water structure is characterized by the oscillation of the water particle density distribution with a value of 0.3 nm (hydration layers). The interfacial structure does not depend on the collagen region.
Hydration layers are observed in overlap regions, while in gap regions, the interfacial solvent structure is dominated by electrostatic interactions. These interactions generate interlayer distances of 0.2 nm.
The achieved results still need to be explained by the theory of 3D AFM. More detailed theoretical simulations, which are beyond the scope of the cited study, will be required to quantitatively explain the interlayer distances observed over gap regions.
However, the results presented by the authors highlight the potential of 3D AFM to identify the solvent structures on proteins and the complexity of those interfaces.*
Figure 2 from Diana M. Arvelo et al. 2024 “Interfacial water on collagen nanoribbons by 3D AFM” Interfacial liquid water structure on collagen provided by an uncharged tip. (a) 2D force maps (x, y) of the interfacial water structure in the gap region. The map is obtained in a 300 mM KCl solution. The force–distance curves in the bottom of the image are obtained from the top panel. (b) 2D force maps (x, y) of the interfacial water structure in the overlap region. The force–distance curves in the bottom of the image are obtained from the top panel. (c) Statistics of d1 and d2 distances measured from several collagen–water interfaces. The individual force–distance curves from the bottom panels of (a) and (b) are plotted in gray. The average force–distance curve is highlighted by a thick continuous line. The experiments are performed with USC-F1.2-k7.3 cantilevers. Experimental parameters: f = 745 kHz; k = 6.7 N m−1; Q = 8.3; A0 = 150 pm; Asp = 100 pm.
Figure 3 from Diana M. Arvelo et al. 2024 “Interfacial water on collagen nanoribbons by 3D AFM” Interfacial liquid water structure on collagen provided by a negatively charged tip. (a) 2D force maps (x, y) of the interfacial water structure in the gap region. The map is obtained in a 300 mM KCl solution. The force–distance curves in the bottom of the image are obtained from the top panel. (b) 2D force maps (x, y) of the interfacial water structure in the overlap region. The force–distance curves in the bottom of the image are obtained from the top panel. (c) Statistics of d1 and d2 distances measured from several collagen–water interfaces. In the bottom panels of (a) and (b), the individual force–distance curves from the bottom panels of (a) and (b) are plotted in gray. The average force–distance curve is highlighted by a thick continuous line. The images were captured using ArrowUHF AuD cantilevers. Experimental parameters: f = 745 kHz; k = 8.3 N m−1; Q = 4.5; A0 = 170 pm; Asp = 100 pm.
*Diana M. Arvelo, Clara Garcia-Sacristan, Enrique Chacón, Pedro Tarazona and Ricardo Garcia Interfacial water on collagen nanoribbons by 3D AFM
Journal of Chemical Physics 160, 164714 (2024)
DOI: https://doi.org/10.1063/5.0205611
The article “Interfacial water on collagen nanoribbons by 3D AFM” by Diana M. Arvelo, Clara Garcia-Sacristan, Enrique Chacón, Pedro Tarazona and Ricardo Garcia 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/.
Airflow limitation in obstructive airway disease is characterized by narrowing of the airway lumen from excessive contraction of airway smooth muscle (ASM) and remodeling of the airway wall which includes changes in the extracellular matrix (ECM) of the ASM layer.*
Previous studies on human airway smooth muscle cells ( hASMC ) have independently assessed the influence of extracellular matrix (ECM) proteins on substrates of supra-physiological stiffnesses, such as tissue culture plastic or glass.*
While the influence of discrete substrate stiffness on hASMC behavior has been examined, manipulation of both substrate stiffness and ECM proteins simultaneously (as expected in disease) has not been extensively modeled in vitro.*
In the article “Stiffness Mediated-Mechanosensation of Airway Smooth Muscle Cells on Linear Stiffness Gradient Hydrogels” Yong Hwee Tan, Kimberley C. W. Wang, Ian L. Chin, Rowan W. Sanderson, Jiayue Li, Brendan F. Kennedy, Peter B. Noble and Yu Suk Choi highlight the interplay and complexities between stiffness and ECM protein type on hASMC mechanosensation, relevant to airway remodelling in obstructive airway diseases.*
The authors first determined a physiological range of ASM layer stiffness using a porcine airway and used these empirical recordings to inform the fabrication of a linear stiffness gradient platform coated with different ECM proteins.*
Using this linear stiffness gradient platform, Yong Hwee Tan et al. profiled hASMC morphology, contractile function with alpha-smooth muscle actin (αSMA) and mechanisms of mechanosensation, specifically with nuclear translocalization of Yes-associated protein (YAP) and lamin-A expression.*
Yong Hwee Tan et al.’s assessment of hASMC mechanosensation utilized an innovative hydrogel platform delivering a linear stiffness gradient to understand stiffness-mediated cell behavior with an ECM substrate for cellular adhesion. *
The employment of a stiffness gradient that was designed after empirical measurements performed on ex vivo ASM tissue, enabled the presentation of physiologically relevant stiffnesses to study hASMC behavior.*
Using this platform, the authors of the article found that hASMC mechanosense underlying mechanical cues more than the types of proteins they are anchored to by screening hASMC morphology, contractile phenotype, and mechanomarker expression, with a few exceptions.*
While the authors acknowledge that the findings from their study were done using cells from only one donor they still think that their study provides a proof of concept for the relevance of hASMC mechanosensation to ECM stiffness, and is another step in the right direction for understanding the pathophysiological impact of airway remodeling in obstructive diseases and exploring potential avenues for improving therapy through greater fidelity of in vitro platforms that include key concepts of mechanosensation. *
Yong Hwee Tan et al. wanted to use the same method which is used to assess hydrogel stiffness, namely atomic force microscopy (AFM), to measure ASM stiffness.*
However, nanoscale measurements of ASM strips by AFM proved to be difficult due to an uneven tissue surface after de-epithelialization (Figure S1C, Supporting Information of the cited article), resulting in false force triggering.
To validate the translation of stiffness values measured from macroscale compression (ASM strips) to nanoscale indentation (AFM on hydrogels), Yong Hwee Tan et al. fabricated additional hydrogels of four different stiffnesses using well-characterized polyacrylamide and compared the stiffness of hydrogels measured by uniaxial compression tester and atomic force microscopy (Figure S2A, Supporting Information of the cited article).
The nanoscale stiffness of hydrogels was assessed using an atomic force microscope (AFM) with NanoWorld triangular Pyrex-NitridePNP-TR AFM probes (the longer AFM cantilever beam – CB 2 – with 200 µm length was used).
These AFM tips probed hydrogels immersed in 1 × PBS with 2 nN, an approach velocity of 2 µm s−1 and a retraction velocity of 10 µm s−1.
Young’s modulus was determined from linear portions of contact-generated force curves using a custom-written code in Igor Pro.
All probe indentations were made in triplicate and averaged for a stiffness measurement in kilopascals (kPa).
An example force curve is shown in Figure S2B, Supporting Information of the cited article. Validation of a linear stiffness gradient was achieved with eight indentations on the hydrogel, 2 mm away from both edges of the hydrogel and at 1 mm intervals along the stiffness gradient axis. Measurements were plotted against displacement from the hydrogel edge (soft to stiff) (Figure 2B of the cited article).
Figure 2 from Yong Hwee Tan et al. 2024 “Stiffness Mediated-Mechanosensation of Airway Smooth Muscle Cells on Linear Stiffness Gradient Hydrogels”: Linear stiffness gradient hydrogel fabrication. A) A schematic of a two-step polymerization process. i) 120 µL of mixed polyacrylamide (PA) solution (% acrylamide + % bis-acrylamide) was added to the primary mold and left to polymerize under ii) a methacrylated coverslip for 20 min. iii) Wedge-shaped 1° gel was removed and flipped for placement of a iv) secondary mold before v) addition of a second 120 µL PA solution and polymerized under a vi) dichlorodimethylsilane-coated coverslip for 20 min. vii) Removal of coverslip and mold completes the fabrication of bi-layered stiffness gradient hydrogel. viii) the dotted arrow indicating the direction of gradient and atomic force microscopy (AFM) measurement. B) Young’s moduli gradient measured by AFM. Twelve hydrogels were selected (one gel per batch) and assessed for stiffness, yielding a gradient of 4.0 kPa mm−1, with a range of 1.7 ± 1.2 to 29.6 ± 4.3 kPa (R2 = 0.998, n = 8). Data are presented as mean ± SD.
Figure S2 from Yong Hwee Tan et al. 2024 “Stiffness Mediated-Mechanosensation of Airway Smooth Muscle Cells on Linear Stiffness Gradient Hydrogels”: (A) Correlation of Young’s modulus from macroscale stiffness (UCT) assessment with nanoindentation (AFM), was conducted using cylindrical PA hydrogels of different Acrylamide %/Bis-acrylamide % derived from Tse and Engler [47] 10 %/0.06 %, 10 %/0.1 %, 10 %/0.15 % and 10 %/0.3 % (Linear regression, P < 0.0001, R2 = 0.9288, n = 4). Data are presented as mean SEM. (B) An example force curve from atomic force microscopy with an approach velocity of 2 μm/s, until a 2 nN trigger force was registered, and retraction of indenter at 10 μm/s.*Yong Hwee Tan, Kimberley C. W. Wang, Ian L. Chin, Rowan W. Sanderson, Jiayue Li, Brendan F. Kennedy, Peter B. Noble and Yu Suk Choi Stiffness Mediated-Mechanosensation of Airway Smooth Muscle Cells on Linear Stiffness Gradient Hydrogels
Advanced Healthcare Materials 2024, 2304254
DOI: https://doi.org/10.1002/adhm.202304254
The article “Stiffness Mediated-Mechanosensation of Airway Smooth Muscle Cells on Linear Stiffness Gradient Hydrogels” by Yong Hwee Tan, Kimberley C. W. Wang, Ian L. Chin, Rowan W. Sanderson, Jiayue Li, Brendan F. Kennedy, Peter B. Noble and Yu Suk Choi 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/.
![Figure S2 from Yong Hwee Tan et al. 2024 “Stiffness Mediated-Mechanosensation of Airway Smooth Muscle Cells on Linear Stiffness Gradient Hydrogels”:(A) Correlation of Young’s modulus from macroscale stiffness (UCT) assessment with nanoindentation (AFM), was conducted using cylindrical PA hydrogels of different Acrylamide %/Bis-acrylamide % derived from Tse and Engler [47] 10 %/0.06 %, 10 %/0.1 %, 10 %/0.15 % and 10 %/0.3 % (Linear regression, P < 0.0001, R2 = 0.9288, n = 4). Data are presented as mean SEM. (B) An example force curve from atomic force microscopy with an approach velocity of 2 μm/s, until a 2 nN trigger force was registered, and retraction of indenter at 10 μm/s. NanoWorld triangular Pyrex-Nitride PNP-TR AFM probes were used to assess the stiffness of the hydrogels with atomic force microscopy.](https://www.nanoworld.com/blog/wp-content/uploads/2024/07/Fig-S2-from-Young-Hwee-Tan-2024-Stiffness-Mediated-Mechanosensation-of-Airway-Smooth-Muscle-Cells-on-Linear-Stiffness-Gradient-Hydrogels-NanoWorld-PNP-TR-AFM-probe.jpg)