Afleveringen
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Hello and welcome to the NanoLSI podcast. Thank you for joining us today. In this episode we feature the latest research by Romain Amyot, Noriyuki Kodera, and Holger Flechsig at the Kanazawa University NanoLSI.
The research described in this podcast was published in Frontiers in Molecular Biosciences in November 2023
Kanazawa University NanoLSI website
https://nanolsi.kanazawa-u.ac.jp/en/
Researchers predict protein placement on AFM substrates
Researchers at Kanazawa University report in Frontiers in Molecular Biosciences a computational method to predict the placement of proteins on AFM substrates based on electrostatic interactions.
The observation of biomolecular structures using atomic force microscopy (AFM) and the direct visualization of functional conformational dynamics in high-speed AFM (HS-AFM) experiments have significantly advanced the understanding of biological processes at the nanoscale. In experiments, a biological sample is deposited on a supporting surface (AFM substrate) and is scanned by a probing tip to detect the molecular shape and its dynamical changes. The observation of protein dynamics under HS-AFM is a delicate balance between immobilizing the structure on the supporting surface while at the same time preventing too strong perturbations by immobilization.
The process of placing a biomolecular sample on the supporting surface and controlling its proper attachment is a challenge at the very start of every AFM observation. By the chemical composition of the buffer, interactions between the sample and substrate can be modified. Such surface modifications are often critical for successful AFM observations of protein structures and their functional motions. However, the molecular orientation of the sample is a priori unknown, and due to limitations in the spatial resolution of images, difficult to infer from a posteriori analysis.
Romain Amyot, Noriyuki Kodera, and Holger Flechsig from Kanazawa University have now developed a physical model to predict the placement of biomolecular structures on AFM substrates based on electrostatic interactions. The method considers the substrates commonly used in AFM experiments (mica, APTES-mica, lipid bilayers) and takes into account buffer conditions. In computer simulations, a large number of possible molecular arrangements on the AFM substrate are sampled, and from evaluating the corresponding interaction energies, the most favorable placement is determined. Furthermore, the analysis allows predictions of the imaging stability under tip scanning.
The authors provide several applications of the new method and obtain remarkable agreement of model predictions with previous experimental HS-AFM imaging of proteins. The findings can explain, for example, why HS-AFM observations of the Cas9 endonuclease, a protein playing a key role in genetic engineering applications, can reliably visualize functional relative motions of target DNA and Cas9 and capture DNA cleavage events at the single molecule level (see Fig. 1). Furthermore, as demonstrated for the ATP-powered chaperone machine ClpB, the model can explain how buffer conditions affect the stability of the sample-substrate complex and validate observations of previous HS-AFM experiments.
In summary, the new method allows to employ the enormous amount of available structural data for biomolecules to make predictions of the sample placement on AFM substrates even prior to an actual experiment, and it can also be applied for post-experimental analysis of AFM imaging data. The developed method is implemented within the freely available BioAFMviewer software package, providing a convenient platform for applications by the broad BioAFM community.
Reference
R. Amyot, K. Nakamoto, N. Kodera, H. Flechsi
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Sodium channel investigation
Hello and welcome to the NanoLSI podcast. Thank you for joining us today. In this episode we feature the latest research by Ayumi Sumino and Takashi Sumikama at the Kanazawa University NanoLSI.
The research described in this podcast was published in Nature Communications in December 2023
Kanazawa University NanoLSI website
https://nanolsi.kanazawa-u.ac.jp/en/
Sodium channel investigation
Researchers at Kanazawa University report in Nature Communications a high-speed atomic force microscopy study of the structural dynamics of sodium ion channels in cell membranes. The findings provide insights into the mechanism behind the generation of cell-membrane action potentials.
The transport of ions to and from a cell is controlled by pore-forming proteins embedded in the cell membrane. In particular, so-called voltage-gated sodium channels (VGSCs) govern the transfer of sodium (Na+) ions, and play an important role in the regulation of the membrane potential — the voltage difference between the cell’s exterior and interior. In electrically excitable cells such as neurons and muscle cells, VGSCs participate in the generation of action potentials; these are rapid changes in the membrane potential enabling the transmission of e.g. neural signals. The precise structural changes occurring in VGSCs are not completely understood, however. Now, Ayumi Sumino and Takashi Sumikama from Kanazawa University in collaboration with Katsumasa Irie from Wakayama Medical University and colleagues have succeeded in observing the structural dynamics of VGSC by means of high-speed atomic force microscopy (high speed-AFM), a method capable of imaging the nanostructure and subsecond dynamics of biomolecules.
VGSCs can be in three different states: resting, inactive and active. In the latter state, Na+ ions can pass through the channel; in the resting and inactive states, which are structurally different, ions cannot pass. The basic structure of a VGSC consists of two modules: voltage sensor domains and pore domains. These domains form a square arrangement, with the ion pore at its center. An important open question is whether the voltage sensor domains dissociate from the pore domains when the channel closes.
So how did they go about determining this?
Sumino and colleagues performed experiments on three VGSCs. One is the sodium channel of a particular bacterium (Arcobacter butzleri), the other two are mutants of it. These three VGSCs have different voltage dependencies, with activation voltages starting at -120 mV, -50 mV and 0 mV, so that at the experimental conditions (0 mV), the VGSCs are in different states.
In order to provide insights into the structural dynamics of these three VGSCs, the researchers applied high speed-AFM, a powerful technique for producing image sequences of biochemical compounds. A single AFM image is generated by laterally moving a tip just above the sample’s surface; during this xy-scanning motion, the tip’s position in the direction perpendicular to the xy-plane (the z-coordinate) will follow the sample’s height profile. The variation of the z-coordinate of the tip then produces a height map — the image of the sample. The generation of such AFM images in rapid succession then produces a video recording of the sample.
The HS-AFM results revealed that for the mutant VGSC in the resting state, the voltage sensor domains are indeed dissociated from the pore domains. Furthermore, the researchers found that the dissociated voltage sensor domains of neighboring channels connect to form pairs — this is referred to as dimerization.
The observation of the dissociation of voltage sensor domains, as well as the dimerization between pore channels,
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Zijn er afleveringen die ontbreken?
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Researchers fix the chirality of helical proteins
Hello and welcome to the NanoLSI podcast. Thank you for joining us today. In this episode we feature the latest research by Naoki Ousaka, Mark J. MacLachlan and Shigehisa Akine at the Kanazawa University NanoLSI.
The research described in this podcast was published in Nature Communications in October 2023
Kanazawa University NanoLSI website
https://nanolsi.kanazawa-u.ac.jp/en/
Researchers fix the chirality of helical proteins
Researchers at Kanazawa University report in Nature Communications how they can control chirality inversion in α helical peptides.
The function of a protein is determined by its structure – prompting great interest in how to manipulate these structures. The structure is defined not just by the sequence of amino acids that make it, but the shape these acids make – the secondary structure – as well as how that shape is then folded. The most common secondary protein structure is the α-helix, which can coil to the right or left. This coiling direction in turn determines how it engages with other chiral structures, which may be the form of a light beam or another molecule. Although molecular components and environmental factors can favor a particular coiling direction over the other, helical molecules tend to flip between the two coil directions. Now Naoki Ousaka, Mark J. MacLachlan and Shigehisa Akine at Kanazawa University in Japan have shown how they can control and fix the coil direction.
Helical proteins are chiral molecules, which means that the molecule’s shape cannot be fitted into its mirror image. In nature helical proteins often have other chiral components, such as sugars or amino acids, and these will determine which way the protein coils. However, there is a lot of interest in synthesizing artificial helical proteins that have different chemical components and hence functions not found in nature, and these may not have other chiral components. Nonetheless having both types or “enantiomers” of the chiral molecule can be hazardous because of the significant differences in behavior between the two chiral forms, one of which may be benign or even therapeutic while the other is toxic. Hence, there is demand for other ways of selecting and fixing the chirality.
So how did they go about this?
Ousaka, MacLachlan and Akine synthesized α helical molecules solely from achiral components. They included bulky segments so that the molecule tended towards the larger rings of the α helical structure, as well as side chains of piperidine – molecular components that are common in pharmaceuticals. These side chains can be cross linked to “staple” the molecule into either the righthanded or lefthanded coil, inhibiting flipping between the two – chiral inversion. Finally they added another molecular component, known as an ester – the L-Val-OH residue. This would switch the direction of the coil in response to acidic or basic environments due to preferences in the interaction between oxygen atoms in the ester and the amino acid backbone.
The researchers used a range of chiral characterization methods including circular dichroism, nuclear magnetic resonance and liquid chromatography. They found that with the molecule stapled just once, it would slow down the flipping between enantiomers by a factor of 106, although this still occurred over minutes. Changing the solution to acid or alkali also successfully determined which enantiomer was favoured. However, stapling the molecule twice slowed down the chirality inversion by a factor of 1012, so that the molecular chirality was stable for years. This increased energy barrier to chirality inversion could then be overcome by heating the sample to very high temperatures to switch bet
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Genetic switches in tumor development
Hello and welcome to the NanoLSI podcast. Thank you for joining us today. In this episode we feature the latest research by Masanobu Oshima at the Kanazawa University NanoLSI.
The research described in this podcast was published in Cancer Research in November 2023
Kanazawa University NanoLSI website
https://nanolsi.kanazawa-u.ac.jp/en/
Genetic switches in tumor development
Researchers at Kanazawa University report in Cancer Research how Kras and p53 mutations influence the tumor suppressor and promoter functions of a TGF- ß pathway. The findings may lead to a new approach for colorectal cancer therapy.
Both the progression and the suppression of tumors are governed by biomolecular processes. Often, a particular process is involved in either cancer progression or suppression. Cancer treatment in the form of drugs then typically focuses on the respective deactivation or activation of the relevant biomolecular process. However, it has been established that a process known as transforming growth factor ß (TGF-ß) signaling*1 plays a role in both tumor suppression and progression. Now, Masanobu Oshima from Kanazawa University and colleagues have studied the precise genetic conditions underlying the outcome of TGF-ß signaling. Their findings may help the development of new therapeutic strategies for particular cancers.
The suppressive effect of TGF-ß signaling happens through the stimulation of cell differentiation — the process through which dividing cells acquire their type or function. The malignant progression of cancers, on the other hand, comes from a process called epithelial-mesenchymal transition (EMT), in which an epithelial cell transforms into a mesenchymal cell type. The former is a ‘stationary’ type of cell, found in epithelial tissue, whereas the latter is a more ‘migratory’ type of cell found in development and cancer.
So how did they investigate these processes and what did they found out?
Oshima and colleagues performed experiments with tumor-derived organoids. They confirmed that TGF-ß family cytokine, activin plays a role in tumor suppression and progression dependent on the mutation types of driver genes. In certain cancer cells treated with activin, the researchers noted that the partial EMT is induced with tumor aggressiveness and development. On the other hand, certain mutated activin receptors were found to have cancer suppressor capabilities, which made the scientists conclude that genetic alterations underlie the dual function of activins.
One of the two relevant genes is Kras which relays signals that regulate cell growth, division and differentiation. Oshima and colleagues found that a mutation of Kras blocks TGF-ß/activin-induced growth suppression. The other gene is known as Trp53, which encodes tumor protein 53, playing an important role in cancer regulation. A combination of Kras and Trp53 mutations at hot spots, known as gain-of-function mutation, was found to not just block tumor suppression but promote partial EMT and tumor proliferation.
The experiments were done with mouse intestinal tumor-derived organoids with defined genetic backgrounds, which makes the results relevant for therapeutic strategies for human colorectal cancer. Quoting the scientists: “Based on these results, the control of TGF- ß/activin signaling appears to be an important preventive and therapeutic strategy against the malignant progression of colorectal cancer carrying […] mutations”.
Reference
Dong Wang, Mizuho Nakayama, Chang Pyo Hong, Hiroko Oshima, and Masanobu Oshima. Gain-of-function p53 mutation acts as a genetic switch for T
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Researchers tune the speed of chirality switching
Hello and welcome to the NanoLSI podcast. Thank you for joining us today. In this episode we feature the latest research by Shigehisa Akine at the Kanazawa University NanoLSI.
The research described in this podcast was published in Science Advances in November 2023
Kanazawa University NanoLSI website
https://nanolsi.kanazawa-u.ac.jp/en/
Researchers tune the speed of chirality switching
Researchers at Kanazawa University report in Science Advances how they can accelerate and decelerate chirality inversion in large cage molecules using alkali metal ion binding.
Chiral molecules can have dramatically different functional properties while sharing identical chemical formulae and almost identical structures. The molecular structure of two types of a chiral molecule – so-called enantiomers – are mirror images of each other where one cannot be superposed on the other any more than your right hand can fit front-to-back on the left. While a lot of chiral molecules are traditionally considered fixed as left- or right-handed, chiral molecules based on helices are known to be able to switch in response to changes in their environment. Now researchers led by Shigehisa Akine at Kanazawa University have demonstrated how environmental changes can also accelerate or decelerate this chiral inversion process, providing “a novel time-programmable switchable system”.
The researchers focused their study on “metallocryptand (R6)-LNi3”, an organic molecule featuring metal atoms in a cage-like molecular structure that can exist in one of two possible forms described as the P or M type (right- and left-handed, respectively). In its pure form (R6)-LNi3 has a preferred ratio of P type to M type of 12:88. Starting from a 50:50 ratio, the molecules will flip between one form and the other with a preference for flipping towards the M type to meet that ratio. The researchers measured this change in ratio using NMR and circular dichroic spectroscopy. However, add an alkali metal into the cage cavity and this preference can change.
By adding alkali metal ions to the solution of the (R6)-LNi3 the researchers could confirm that the metal ions readily bound to the metallocryptand from the changes in the spectroscopic signatures of the molecules. In addition, the bound ion also shifted the preferred ratio by a margin and with a speed that depended on which alkali metal was used.
So what is causing this effect?
The researchers attribute the different rates and ratios to differences in binding constants not just between the metal ion and the two forms of the molecule but also a virtual binding constant for the molecule transitioning between the two. The binding between a caesium ion and the P type molecule was more than 20 times greater than that with the M type so the solution eventually switched to a higher proportion of the P type with a P:M ratio of 75:25 over the course of 21 hours. The final ratio with a rubidium ion was similarly bias to the P type reaching a slightly lower ratio of 72:28 but in just 100 minutes. With potassium ion the equilibrium ratio was lower again at 68:32 but reached within just a minute, three orders of magnitude faster than for the caesium ion. The researchers attribute this speed to the large virtual bonding constant with the transitioning molecule.
With smaller ions – lithium and sodium ions – the preferred molecular type did not actually change but the final ratio was reached much faster. It is the first time researchers have demonstrated that such chiral inversion can be sped up and slowed down by tuning the molecules environment.
“This research can provide a new insight into the development of an on-de
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Researchers identify the dynamic behavior of a key SARS-CoV-2 accessory protein
Hello and welcome to the NanoLSI podcast. Thank you for joining us today. In this episode we feature the latest research by Richard Wong at Kanazawa University alongside Noritaka Nishida at Chiba University.
The research described in this podcast was published in the Journal of Physical Chemistry Letters in September 2023
Kanazawa University NanoLSI website
https://nanolsi.kanazawa-u.ac.jp/en/
Researchers identify the dynamic behavior of a key SARS-CoV-2 accessory protein
Researchers at Kanazawa University report in the Journal of Physical Chemistry Letters high-speed atomic force microscopy studies that shed light on the possible role of the open reading frame 6 (or, ORF6) protein in COVID19 symptoms.
While many countries across the world are experiencing a reprieve from the intense spread of SARS-CoV-2 infections that led to tragic levels of sickness and multiple national lockdowns at the start of the decade, cases of infection persist. A better understanding of the mechanisms that sustain the virus in the body could help find more effective treatments against sickness caused by the disease, as well as arming against future outbreaks of similar infections. With this in mind there has been a lot of interest in the accessory proteins that the virus produces to help it thrive in the body.
“Similar to other viruses, SARS-CoV-2 expresses an array of accessory proteins to re-program the host environment to favor its replication and survival,” explain Richard Wong at Kanazawa University and Noritaka Nishida at Chiba University and their colleagues in this latest report. Among those accessory proteins is ORF6. Previous studies have suggested that ORF6 potently interferes with the function of interferon 1 (that is, IFN-I), a particular type of small protein used in the immune system, which may explain the instances of asymptomatic infection with SARS-CoV2. There is also evidence that ORF6 causes the retention of certain proteins in the cytoplasm while disrupting mRNA transport from the cell, which may be means for inhibiting IFN-I signalling. However, the mechanism for this protein retention and transport disruption was not clear.
So how did they figure it out?
Well, to shed light on these mechanisms the researchers first looked into what clues various software programs might give as to the structure of ORF6. These indicated the likely presence of several intrinsically disordered regions. Nuclear magnetic resonance measurements also confirmed the presence of a very flexible disordered segment. Although the machine learning algorithm AlphaFold2 has proved very useful for determining how proteins fold, the presence of these intrinsically disordered regions limits its use for establishing the structure of ORF6 so the researchers used high-speed atomic force microscopy (or AFM), which is able to identify structures by “feeling” the topography of samples like a record player needle feels the grooves in vinyl.
Using high speed AFM the researchers established that ORF 6 is primarily in the form of ellipsoidal filaments of oligomers – strings of repeating molecular units but shorter than polymers. The length and circumference of these filaments was greatest at 37 °C and least at 4 °C, so the presence of fever could be beneficial for producing larger filaments. Substrates made of lipids – fatty compounds – also encouraged the formation of larger oligomers. Because high speed AFM captures images so quickly it was possible to grasp not just the structures but also some of the dynamics of the ORF6 behavior, including circular motion, protein assembly and flipping. In addition, further computer anal
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Researchers define a nanopipette fabrication protocol for high resolution cell imaging
Hello and welcome to the NanoLSI podcast. Thank you for joining us today. In this episode we feature the latest research by Yasufumi Takahashi at the Kanazawa University NanoLSI.
The research described in this podcast was published in Analytical Chemistry in August 2023
Kanazawa University NanoLSI website
https://nanolsi.kanazawa-u.ac.jp/en/
Researchers define a nanopipette fabrication protocol for high resolution cell imaging
Researchers at Kanazawa University report in Analytical Chemistry how to produce nanopipettes that reliably provide nanoscale resolution scanning ion conductance microscopy images of living cells.
A nanoscale view of living cells can provide valuable insights into cell structure and function. Over the years, various microscopy techniques have been enrolled to obtain a window into biological specimens at the nanoscale but all with their limitations and challenges. Although scanning ion conductance microscopy has demonstrated the capability to image living biological samples in solution with nanoscale resolution, it has been hampered by challenges in reliably producing nanopipettes with the optimum geometry for the job. Now researchers led by Yasufumi Takahashi at Kanazawa University’s Nano LSI and Nagoya University have devised a protocol for reproducibly fabricating nanopipettes with the preferred geometry for high quality imaging.
So what is scanning ion conductance microscopy and what kind of nanopipette does it need?
Scanning ion conductance microscopy uses a nanopipette to control the distance between nanopipette and sample using an ion current as feedback signal. The shape of the nanopipette significantly influences the performance of the device. For instance, a wide aperture limits the possible resolution, a long shunt can lead to rectification effects that warp the ion current measurements, and if the glass of the nanopipette is too thick it can deform the sample before the proximity of the aperture has reached the point needed for constant ion current topographical mapping. As a result, the ideal nanopipette has a short shunt, small aperture and thin glass walls.
The standard procedure for fabricating the nanopipette is to pull a capillary tube with a laser puller that heats the capillary tube it is manipulating. The capillary then narrows where it lengthens until it is finally drawn into two separate pieces. Although quartz can allow a little more control in the process of drawing the capillary tube into shape it is hydrophobic, which raises complications in actually filling the nanopipette with the aqueous solution needed for the ion current. For this reason, the researchers developed a protocol by which they could draw nanopipettes from borosilicate glass capillaries with the required control and reproducibility.
Takahashi and his collaborators noted that ideally the starting capillary should have thick walls and a narrow inner diameter, however it is not easy to obtain capillary tubes to these requirements from commercial suppliers. Instead, they preheat the capillary for 5 s without pulling it, which causes the glass walls to the thicken and reduces the inner diameter. They also optimized the parameters for pulling the tube, such as the velocity.
So did it work? Apparently so
The researchers demonstrated the performance of the nanopipettes they produced by imaging a cell undergoing a type of endocytosis, where it engulfs and absorbs some external material. They were able to image the microvilli – that is, tiny cellular membrane protrusions – found on the cell surface, as well as the endocytic pits that form and the formation of a cap c
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Hydration matters: The interaction patterns of water and oxide crystals revealed
Transcript of this podcast
Hello and welcome to the NanoLSI podcast. Thank you for joining us today. In this episode we feature the latest research by Keisuke Miyazawa at the Kanazawa University NanoLSI.
The research described in this podcast was published in Nanoscale in July 2023
Kanazawa University NanoLSI website
https://nanolsi.kanazawa-u.ac.jp/en/
Hydration matters: The interaction patterns of water and oxide crystals revealed.
https://nanolsi.kanazawa-u.ac.jp/en/highlights/28428/
In a study recently published in the journal Nanoscale, researchers from Kanazawa University and AGC Inc. use three-dimensional atomic force microscopy to study the hydrated form and structure of commonly occurring oxide crystals.
While sapphire and quartz are oxide crystals used in a wide range of industrial applications, the atomic-scale structures of these materials are not well understood. The major chemical components of sapphire and quartz are aluminum oxide and silicon dioxide, respectively. These components have a high affinity for water, which affects the chemical reactivity of the crystals. Thus, a thorough knowledge of the water-binding properties of these oxides is important for further innovative applications.
To date, traditional microscopic methods have only provided insights into the two-dimensional topography of their surfaces. Now, a research team led by Keisuke Miyazawa from the NanoLSI at Kanazawa University has developed three-dimensional (3D) microscopy technique for a detailed study of the interaction of the surfaces of these materials with water.
So how did they do it?
The team started by looking at the surface structures and its hydration structures of sapphire and α-quartz in water. For this, they used an advanced form of microscopy known as 3D atomic force microscopy (3D-AFM). Oxide crystals usually have hydroxyl (OH) groups, which are the main “water-binding” molecules, closely linked with the oxides. Hence, the team studied the OH groups and its hydration structures on both crystals when immersed in water. They found that the hydration layer on sapphire was not uniform because of the nonuniform local distributions of the surface OH groups. On the other hand, the hydration layer on α-quartz was uniform because of the atomically flat distributions of the surface OH groups.
When the interaction force of these oxides with water was subsequently measured, it was found that a greater force was required to break the water-crystal bonds in sapphire than in α-quartz. Lastly, it was also discovered that this affinity was much higher in regions where the oxides were in close proximity to the OH groups.
This study showed that the hydration structures of oxides are dependent on the location and density of OH groups, in addition to the strength of the OH groups’ hydrogen bonding (the chemical bond used to bind to water). What’s more, it was successfully shown here that 3D-AFM can be used in unraveling the interaction of water with several surfaces, a potential avenue for understanding solid-liquid interactions better. “This study contributes to the application of 3D-AFM in exploring atomic scale hydration structures on various surfaces, and hence, to a wide range of solid–liquid interfacial research fields,” conclude the researchers.
Reference
Sho Nagai, Shingo Urata, Kent Suga, Takeshi Fukuma, Yasuo Hayashi and Keisuke Miyazawa. Three-dimensional ordering of water molecules reflecting hydroxyl groups on sapphire (001) and α-quartz (100) surfaces
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Ion channel block unraveled
Transcript of this podcast
Hello and welcome to the NanoLSI podcast. Thank you for joining us today. In this episode we feature the latest research by Takashi Sumikama at the Kanazawa University NanoLSI in collaboration with Katsumasa Irie from Wakayama Medical University and colleagues.
The research described in this podcast was published in Nature Communications in July 2023
Kanazawa University NanoLSI website
https://nanolsi.kanazawa-u.ac.jp/en/
Ion channel block unraveled
Researchers at Kanazawa University report in Nature Communications how calcium ions can block sodium ion channels located in cell membranes. Structural analysis and computer simulations made it possible to identify where and why calcium ions get stuck.
Ion channels are structures within cell membranes that enable specific ions to travel to and from the cell. Such transfer is essential for a variety of physiological processes like muscle cell contraction and nerve excitation. In so-called tetrameric cation channels, the ion selectivity results from the unique structural and chemical environment of the part referred to as the selectivity filter, which is located between two intertwined helical structures. Tetrameric ion channels are prone to ‘divalent cation block’, the blocking of the channel by ions like calcium (as in Ca2+). Such blocking regulates the ionic current, which is involved in various neural activities such as memory formation. How divalent cation block happens exactly is still unclear at the moment — in particular, a direct observation of the cation actually blocking the ion pathway has not been reported yet. Now, Takashi Sumikama from Kanazawa University in collaboration with Katsumasa Irie from Wakayama Medical University and colleagues has discovered the mechanism behind divalent cation block in NavAb, a well-known tetrameric sodium (Na) channel. Through structural analysis and computer simulations, the researchers were able to reveal the relevant structural features and molecular processes at play.
So how did they go about this structural analysis?
NavAb is a sodium channel cloned from a bacterium (Arcobacter butzleri) and has a well-known structure. Sumikama and Irie’s colleagues performed experiments with NavAb and three mutants. The structures of the mutants were determined for environments with and without calcium. The scientists focused on the differences in electron densities for the different structures, as these provide insights into the locations of the calcium ions. They found that for the mutants displaying calcium blocking, one or two calcium ions are located at the bottom of the selectivity filter. They also discovered that two other divalent cations — magnesium (as in Mg2+) and strontium (Sr2+) ions — blocked the calcium-blocking mutant sodium channels.
The researchers then performed computer simulations to obtain a detailed understanding of the interaction between the calcium ions and the mutated NavAb channels. The simulations reproduce the dynamics of ions passing — or not passing — the channel. In the absence of calcium ions, sodium ions were observed to penetrate the channel. In the presence of calcium ions, penetration significantly decreased in the calcium-blocking mutants. The simulations also confirmed that the blocking calcium ions are ‘stuck’ at the bottom of the selectivity filter, and revealed that this ‘sticking’ is related to the increased hydrophilicity (affinity to water) of relevant structural parts of the mutated channels.
The results of Sumikama and Irie’s colleagues provide an important step forward towards a full understanding of the mechanism of divalent cation block in NavAb, an important and representa
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Brain cancer linked to nuclear pore alterations
Transcript of this podcast
Hello and welcome to the NanoLSI podcast. Thank you for joining us today. In this episode we feature the latest research by Masaharu Hazawa and Richard Wong at the Kanazawa University NanoLSI, alongside Mitsutoshi Nakada and colleagues at Kanazawa University.
The research described in this podcast was published in Cell Reports in August 2023
Kanazawa University NanoLSI website
https://nanolsi.kanazawa-u.ac.jp/en/
Brain cancer linked to nuclear pore alterations
Researchers at Kanazawa University report in Cell Reports how alterations in nuclear pores lead to the degradation of anti-tumor proteins.
Several types of cancer are believed to be linked to alterations of macromolecular structures known as nuclear pore complexes. These structures are embedded in the nuclear envelope, a membrane barrier that separates the nucleus of a cell from the cytoplasm (the liquid filling the rest of the cell). They consist of proteins called nucleoporins, which regulate the transport of molecules across the nuclear envelope, including enzymes that enable the synthesis of DNA. Whether nuclear pore complex alterations play a role in glioblastoma, the most common type of cancer originating in the brain, is unclear at the moment. Now, Masaharu Hazawa, Mitsutoshi Nakada and Richard Wong from Kanazawa University and colleagues have found a link between the functioning of nuclear pore complexes and glioblastoma — specifically, they demonstrated the inactivation of a tumor-suppressing protein called p53.
The protein p53 is crucial in cancer prevention. The corresponding gene TP53 encodes proteins that prevent mutations of the genome and is the most frequently mutated gene in human cancers. Gaining insights into how p53 inactivation happens is crucial for understanding tumorigenesis in general and glioblastoma in particular.
So how did the researchers go about it?
Mitsutoshi Nakada and Richard Wong and colleagues first checked whether any nuclear pore complex proteins were amplified (that is ‘overexpressed’) in glioblastoma. They found that one such protein, called NUP107, showed overexpression. Further investigations revealed that NUP107 is a potential oncoprotein in glioblastoma; its overexpression degrades the function of the cancer-suppressing p53 protein. They also found that MDM2, another protein, is overexpressed simultaneously with NUP107. MDM2 is also known to mediate p53 protein degradation.
Further studies will be necessary to uncover the full molecular pathways at play, but the scientists speculate that the increased amount of NUP107 proteins in the nuclear pore complexes of glioblastoma cells results in nuclear pore complex structures that regulate the transport of molecules from the nucleus to the cytoplasm in a way that promotes p53 degradation. This scenario is referred to as nuclear transport surveillance. Experiments in which NUP107 proteins were depleted re-activated p53, consistent with NUP107 providing the structural stability of glioblastoma NPCs.
The findings of Mitsutoshi Nakada and Richard Wong and colleagues confirm that alterations of nuclear pore complexes contribute to the pathogenesis of glioblastoma. As Mitsutoshi Nakada and Richard Wong put it : “Together, our findings establish roles of nuclear pore complexes in transport surveillance and provide insights into p53 inactivation in glioblastoma.”
Reference
Dini Kurnia Ikliptikawati, Nozomi Hirai, Kei Makiyama, Hemragul Sabit, Masashi Kinoshita, Koki Matsumoto, Keesiang Lim, Makiko Meguro-Horike, Shin-ichi Horike, Masaharu Hazawa, Mitsutoshi Nakada, and Richard&
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Researchers define a protocol for narrow nanoneedle fabrication and high-resolution imaging of living cells using AFM
Transcript of this podcast
Hello and welcome to the NanoLSI podcast. Thank you for joining us today. In this episode we feature the latest research by Takehiko Ichikawa and Takeshi Fukuma at the Kanazawa University NanoLSI.
The research described in this podcast was published in STAR Protocols in September 2023
Kanazawa University NanoLSI website
https://nanolsi.kanazawa-u.ac.jp/en/
Researchers define a protocol for narrow nanoneedle fabrication and high-resolution imaging of living cells using AFM
Researchers at Kanazawa University report in STAR Protocols procedural details and tips for nanoendoscopy-AFM, for capturing images of nanoscale structures inside living cells.
Images of nanoscale structures inside living cells are in increasing demand for the insights into cellular structure and function they can reveal. So far, the tools for capturing such images have been limited in various ways, but researchers led by Takeshi Fukuma and Takehiko Ichikawa at Kanazawa University have now devised and reported a full protocol for using atomic force microscopy (AFM) to image inside living cells.
AFM was first developed in the 1980s and uses the changes in the forces between a sample surface and a nanoscale tip attached to a cantilever to “feel” surfaces and produce images of the topography with nanoscale resolution. The technique has grown increasingly sophisticated for extracting information about samples and at speeds sufficient for the tool to capture moving images of dynamics at the nanoscale. However, so far, it has been limited to surfaces. Other techniques exist that can provide a view of the inside of a cell but with limitations. For instance, there is electron microscopy, which is capable of resolving details at the nanoscale and smaller, but the required operating conditions are not compatible with living cells. Alternatively, fluorescence microscopy is regularly used on living cells, but while fluorescence techniques exist to increase the resolution, there are practical challenges that inhibit fluorescence imaging at the nanoscale. AFM suffers from neither limitation and by embellishing the tool with a nanoneedle to penetrate cells, Fukuma, Ichikawa and their collaborators have recently demonstrated the capability to image inside cells at the nanoscale, which they describe as nanoendoscopy-AFM.
So how does it work?
In their protocol, the researchers break down the method for nanoendoscopy-AFM into 4 stages. The first few steps involve cell preparation and staining with a fluorescent dye and checking the fluorescence, which is used to identify the imaging area quickly. Next is the fabrication of the nanoneedles themselves, for which there are two options – either etching away a nanoneedle structure with a focused ion beam or building one up with electron beam deposition. Then comes the nanoendoscopy stage itself, and in the report, the researchers describe the approach for both 2D and 3D nanoendoscopy. There are even details outlined to describe the best way to clean up after the nanoendoscopy images are captured before finally outlining the data processing needed to visualize the measured data. The method is replete with tips for successfully accomplishing each stage, as well as a guide for troubleshooting when things are not quite working out.
This technique should be suitable for the observation of intact intracellular structures, including mitochondria, focal adhesions, endoplasmic reticulum, lysosomes, Golgi apparatus, organelle connections, and liquid-liquid phase-separated structures. They conclude, “This protocol can
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High-speed atomic force microscopy takes on intrinsically disordered proteins
Transcript of this podcast
Hello and welcome to the NanoLSI podcast. Thank you for joining us today. In this episode we feature the latest research by Toshio Ando at the Kanazawa University NanoLSI, alongside Sonia Longhi at Aix-Marseille University and CNRS in France.
The research described in this podcast was published in Nature Nanotechnology in November 2020
Kanazawa University NanoLSI website
https://nanolsi.kanazawa-u.ac.jp/en/
High-speed atomic force microscopy takes on intrinsically disordered proteins
Kanazawa University’s pioneering high-speed atomic force microscope technology has now shed light on the structure and dynamics of some of life’s most ubiquitous and inscrutable molecules – intrinsically disordered proteins. The study is reported in Nature Nanotechnology.
Our understanding of biological proteins does not always correlate with how common or important they are. Half of all proteins, molecules that play an integral role in cell processes, are intrinsically disordered, which means many of the standard techniques for probing biomolecules don’t work on them. Now researchers at Kanazawa University in Japan have shown that their home-grown high-speed atomic force microscopy technology can provide information not just on the structures of these proteins but also their dynamics.
Understanding how a protein is put together provides valuable clues to its functions. The development of protein crystallography in the 1930s and 1950s brought several protein structures into view for the first time, but it gradually became apparent that a large fraction of proteins lack a single set structure making them intractable to xray crystallography. As they are too thin for electron microscopy, the only viable alternatives for many of these intrinsically disordered proteins are nuclear magnetic resonance imaging and small angle xray scattering. Data collected from these techniques are averaged over ensembles and so give no clear indication of individual protein conformations or how often they occur. Atomic force microscopy on the other hand is capable of nanoscale resolution biological imaging at high-speed, so it can capture dynamics as well as protein structures.
So what kind of insights can high-speed AFM offer for these proteins?
In this latest work researchers at Kanazawa University alongside collaborators in Japan, France and Italy applied the technique to study several intrinsically disordered proteins. They identified parameters defining the shape, size and chain length of protein regions, as well as a power law relating the protein size to the protein length. Not only that but they got a quantitative description of the effect of the mica surface on protein dimensions. The dynamics of the protein conformations captured thanks to the high-speed capabilities of the technique revealed globules that appear and disappear, and transformations between fully unstructured and loosely folded conformations in segments up to 160 amino acids long.
Studies of the measles virus nucleoprotein in particular helped identify not just the shape and dimensions but also characteristics of the order-disorder transitions in the region responsible for molecular recognition, which allows viruses to identify host factors so that they can reproduce. They could also determine larger scale structures of the virus’s phosphoprotein that are not accessible to nuclear magnetic resonance (which can only give an indication of distances between amino acids separated by less than 2 nm). The researchers suggest that the formation of certain compact shapes observed may explain the resistance to proteolysis – protein break
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Kanazawa University NanoLSI Podcast:Heat and manipulate, one cell at a time
Transcript of this podcast
Hello and welcome to the NanoLSI podcast. Thank you for joining us today. In this episode we feature the latest research by Satoshi Arai at the Kanazawa University NanoLSI.The research described in this podcast was published in ACS Nano in June 2022
Kanazawa University NanoLSI website
https://nanolsi.kanazawa-u.ac.jp/en/
Heat and manipulate, one cell at a time
Researchers at Kanazawa University report in ACS Nano the development of a nanoparticle that acts as a heater and a thermometer. Inserting the nanoparticle in living cells results in a heat spot that, by switching it on and off, enables the controlled modulation of local cellular activities.
Being able to heat nano-sized regions in biological tissues is key to several biomedical applications. Indeed, many biological processes are temperature-sensitive, and the ability to locally modify temperature provides a way to manipulate cellular activity. A notable purpose is the destruction of cancer cells by heating them. Beside the need for an in-tissue local heating mechanism, it also important to be able to instantaneously measure the generated temperature. Satoshi Arai from Kanazawa University and colleagues have now engineered a nanoparticle that is both a nanoheater and a nanothermometer at the same time. They successfully showed that the insertion of a single, controllable heat spot in tissue can be very effective in modifying cellular function.
The nanoparticle, called “nanoHT” by the scientists — an abbreviation of “nanoheater-thermometer” — is essentially a polymer matrix embedding a dye molecule (called EuDT) used for sensing temperature, and another dye molecule (called V-Nc) for releasing heat. The latter happens through the conversion of light into thermal energy (the photothermal effect, which is also exploited in solar cells): shining a near-infrared laser (with a wavelength of 808 nanometer) onto V-Nc results in fast heating, with a stronger increase in temperature for higher laser power.
The temperature sensing is based on the thermal fluorescence effect of EuDT. When irradiated with light of one wavelength, the molecule emits light at another wavelength — that is, it fluoresces. The higher the temperature, the less intense the fluorescence becomes. This inverse relationship can be used to measure temperature. Arai and colleagues tested the performance of nanoHT as a thermometer, and established that it can determine temperatures with a resolution of 0.8 °C and less.
So what could you use this nanoHT for?
The researchers then performed experiments with a type of human cells called HeLa cells. They looked at the effect of heating through nanoHT, and found that at a temperature increment of about 11.4 °C, the heated HeLa cells died after only a few seconds. This finding suggests that nanoHT could be used to induce cell death in cancer cells.
Arai and colleagues also studied how nanoHT can be used to affect the behavior of muscles. They introduced the nanoparticle into a myotube, a type of fiber present in muscle tissue. Upon heating the myotube by approximately 10.5 °C, the muscle tissue contracted. The procedure worked reversibly; letting the myotube cool again led to muscle relaxation.
The work of Arai and colleagues shows that local heating at a subcellular scale by means of nanoHT enables the controlled manipulation of a single cell’s activity. Regarding applications, the scientists believe that – to quote them from their paper - “the targeted application of nanoHT has a diverse and versatile range of capabilities to regulate cellular activities that w
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Xiabing Lyu: Exosomes to regulate the human immune system
(Kanazawa/ Recorded in June 2023)
Xiabing Lyu is an Assistant Professor at the Nano Life Science Institute (WPI-NanoLSI), Kanazawa University.
Here, she describes her research on engineering exosomes that regulate anti-viral and anti-tumor immune system responses.
Details here:
https://nanolsi.kanazawa-u.ac.jp/en/about/members/life-science/
The Kanazawa University NanoLSI Podcast offers updates of the latest news and research at the WPI-NanoLSI Kanazawa University.
The Nano Life Science Institute (NanoLSI) at Kanazawa University was established in 2017 as part of the World Premier International (WPI) Research Center Initiative of the Ministry of Education, Culture, Sports, Science and Technology (MEXT).
Researchers at the NanoLSI are combining their cutting-edge expertise in scanning probe microscopy to establish ‘nano-endoscopic techniques’ to directly image, analyze, and manipulate biomolecules for insights into mechanisms governing life phenomena such as diseases.
Further information
WPI-NanoLSI Kanazawa University website
https://nanolsi.kanazawa-u.ac.jp/en/
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Endoscopy of a living cell on the nanoscale
Transcript of this podcast
Hello and welcome to the NanoLSI podcast. Thank you for joining us today. In this episode we feature the latest research by Takeshi Fukuma at the Kanazawa University NanoLSI.
The research described in this podcast was published in Science Advances in December 2021
Kanazawa University NanoLSI website
https://nanolsi.kanazawa-u.ac.jp/en/
Endoscopy of a living cell on the nanoscale
Researchers at Kanazawa University report in Science Advances a new technique for visualizing the inside of a biological cell. The method is an extension of atomic force microscopy and offers the promise of studying nanoscale inner cell dynamics at high resolution in a non-destructive way.
In order to advance our understanding of how biological cells function, visualizing the dynamics of intra-cellular components on the nanoscale is of key importance. Current techniques for imaging such dynamics are not optimal — for example, fluorescence microscopy can visualize ‘labeled’ molecules but not the target components themselves. Now Takeshi Fukuma from Kanazawa University and his colleagues have developed a label-free, non-destructive nanoimaging method, which they call nanoendoscopy-AFM – it’s a version of atomic-force microscopy that can be deployed within a living cell. The research was carried out as a collaboration between Kanazawa University and the National Institute of Advanced Industrial Science and Technology (AIST), with Marcos Penedo, the lead author of the publication reporting the new method, recently moving from Kanazawa University’s Nano Life Science Institute (WPI-NanoLSI) to the École Polytechnique Fédérale de Lausanne, Switzerland.
So what is AFM in the first place?
The principle of AFM – or atomic force microscopy ti give its full title - is to have a very small tip move over the surface of a sample. During this ‘xy’ scanning motion, the tip, attached to a small cantilever, will follow the sample’s height, that is, the (‘z’) dimension or profile, producing a measurable force on the cantilever. The magnitude of the force can be back-converted into a height value; the resulting height map provides structural information about the sample’s surface.
The researchers designed a novel AFM setup where the needle-like tip is brought in and out of the interior of a cell. The process is reminiscent of an endoscopy — the procedure of looking at an organ from the inside, by inserting a small camera attached to a thin tube into the body — which is why Fukuma and colleagues call their technique nanoendoscopy-AFM. Letting the nanoneedle travel in an ‘xyz’ trajectory, and going in and out of the cell results in a 3D map of its structure. They tested the technique on a cell from the so-called HeLa cell line commonly used in medical research, and could clearly identify internal granular structures in a scanned volume of 10 x 10 x 6 µm3.
But how does the cell fare under this kind of interrogation?
During a scan, the nanoneedle penetrates the cell membrane (and the nuclear membrane) many times. The scientists checked whether this repeated penetration causes any damage to the cell. They performed a viability test on HeLa cells by using two fluorescent marker molecules. One molecule emits green fluorescence from a living cell, the other red fluorescence from (the nucleus of) a dead cell. The researchers found that when using nanoprobes smaller than 200 nm, nanoendoscopy-AFM does not severely damage cells.
The method is also particularly useful for probing surfaces within the cell, for example the inner side of the cell membrane or the surface of the cell nucleus. Fukuma and colleagues call this application 2D
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Kanazawa University NanoLSI Podcast: Enhancing carbon dioxide reduction
Transcript of this podcast
Hello and welcome to the NanoLSI podcast. Thank you for joining us today. In this episode we feature the latest research by Yasafumi Takahashi at the Kanazawa University NanoLSI and Yoshikazu Ito and Yuta Hori at the University of Tsukuba.
The research described in this podcast was published in ACS Nano in June 2023
Kanazawa University NanoLSI website
https://nanolsi.kanazawa-u.ac.jp/en/
Enhancing carbon dioxide reduction
Researchers at Kanazawa University report in ACS Nano how ultrathin layers of tin disulfide can be used to accelerate the chemical reduction of carbon dioxide — a finding that is highly relevant for our quest towards a carbon-neutral society.
Recycling carbon dioxide released by industrial processes is a must in humanity’s urgent quest for a sustainable, carbon-neutral society. For this purpose, electrocatalysts that can efficiently convert carbon dioxide into other, less impactful chemical products are widely researched today. A category of materials known as two-dimensional (2D) metal dichalcogenides are candidate electrocatalysts for carbon dioxide conversion, but these materials also typically facilitate competing reactions, which compromises their efficiency. Yasufumi Takahashi from Nano Life Science Institute (WPI-NanoLSI), at Kanazawa University and colleagues have now identified a 2D metal dichalcogenide that can efficiently reduce carbon dioxide to formic acid, a compound that not only occurs naturally but is also an intermediate product in chemical synthesis.
Takahashi and colleagues compared the catalytic performance of 2D sheets of molybdenum disulfide and tin disulfide. Both are 2D metal dichalcogenides, with the latter of particular interest because pure tin is a known catalyst for the production of formic acid. Electrochemical tests of these compounds revealed that with molybdenum disulfide, instead of carbon dioxide conversion, hydrogen evolution reactions were promoted. Hydrogen evolution reactions refer to reactions yielding hydrogen, which can be useful when the production of hydrogen gas fuel is intended, but in the context of carbon dioxide reduction it is an unwanted competing process. Tin disulphide, on the other hand, showed good carbon dioxide reduction activity and suppressed hydrogen evolution reactions. The researchers also carried out electrochemical measurements for bulk tin dioxide powder, which was found to have less catalytic carbon dioxide reduction activity.
So how is tin disulphide facilitating carbon dioxide reduction?
To understand where the catalytically active sites are in tin disulphide, and why the 2D material performs better than the bulk compound, the scientists applied a method called scanning electrochemical cell microscopy (SECCM). SECCM is used as a nanopipette to form the meniscus shape nanoscale electrochemical cell for the surface reactivity sensing probe on the sample. The measurements revealed that the whole surface of the tin disulphide sheet is catalytically active, not only ‘terrace’ or ‘edge’ features in the structure. This also explains why 2D tin disulphide has enhanced activity compared to bulk tin disulphide.
Calculations provided further insights into the chemical reactions at play. Specifically, the formation of formic acid was confirmed as an energetically favorable reaction pathway when using 2D tin disulphide as catalyst.
The results of Takahashi and colleagues signify an important step forward towards the use of 2D electrocatalysts in electrochemical carbon dioxide reduction applications. Quoting the scientists: “These findings will provide a better understanding and desig
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Kanazawa University NanoLSI Podcast: Experiments provide insights into the molecular mechanism for memory and learning
Transcript of this podcastHello and welcome to the NanoLSI podcast. Thank you for joining us today. In this episode we feature the latest research by Mikihiro Shibata at the Kanazawa University NanoLSI alongside Hideji Murakoshi at The Graduate University for Advanced Studies and the National Institute for Physiological Sciences, and their colleagues.
The research described in this podcast was published in Science Advances in June 2023
Kanazawa University NanoLSI website
https://nanolsi.kanazawa-u.ac.jp/en/
Experiments provide insights into the molecular mechanism for memory and learning
Researchers at Kanazawa University report in Science Advances high-speed atomic force microscopy experiments that show the structural and chemical changes in an enzyme thought to play a vital role in modulating the strength of neural connections.
Synapses connect neurons allowing the transmission of signals around the neural network. The strength of these connections varies – for instance strengthening or weakening depending on the signals received and how. This synaptic “plasticity” underlies learning and memory and the Ca2+/calmodulin-dependent protein kinase II (CaMKII) is known to play a key role. Previous studies have provided some clues to the mechanisms of CaMKII protein activity in these functions but no-one had seen these proteins in action. Now Hideji Murakoshi at the Graduate University of Advanced Studies and the National Institute for Physiological Sciences and Mikihiro Shibata at Kanazawa University and their colleagues have used high speed atomic force microscopy (HS-AFM) to observe the structural dynamics of these proteins for the first time, not only in various states but in three different species.
CaMKII is common to a vast range of species from mammals like rats to older, non-mammalian species like the roundworms (C. elegans) and hydra. In particular, certain structural features of the protein are particularly well preserved, including the kinase domain, the regulatory segment that inhibits the activity of the kinase domain and the hub domain. In addition, the protein has binding sites, phosphorylation sites and linker regions – however, the linker region shows a little more variability across species suggesting that its function and activation mechanisms are more bespoke for the different species.
So what did we know about how this protein works? (3min)
Previous studies had suggested that the regulatory segment’s inhibition of the kinase domain is released when Ca2+/calmodulin binds to the regulatory segment. The activated kinase domains then phosphorylate each other, activity that persists even after the Ca2+/calmodulin becomes dissociated, which has been “hypothesized to be a form of molecular memory”, as the researchers describe in their report.
Murakoshi, Shibata and their colleagues studied the protein using atomic force microscopy, which feels topologies using a nanoscale tip like a needle reading a vinyl record, raster scanning the image plane to build up a picture of the sample structure. With HS-AFM, these images are collected quickly enough to record movies of how these structures change. The researchers noted various measures of the proteins size and motion – the gyrus of rotation – as well as reactions such as kinase domain oligomerization (that is, where there is a limited level of polymerization to join molecules into chains) and phosphorylation – the addition of a phosphoryl group (PO3), which can activate enzymes like kinase.
They found that the kinase domain was quite mobile, although this decreased with Ca2+/calmodulin binding. Th
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Kanazawa University NanoLSI Podcast:Zooming in on neurotoxic aggregates
Transcript of this podcastHello and welcome to the NanoLSI podcast. Thank you for joining us today. In this episode we feature the latest research led by Kenjiro Ono at the Kanazawa University NanoLSI.
The research described in this podcast was published in Nano Letters in May 2023
Kanazawa University NanoLSI website
https://nanolsi.kanazawa-u.ac.jp/en/
Zooming in on neurotoxic aggregates
Researchers at Kanazawa University report in Nano Letters how high-speed atomic force microscopy leads to insights into processes relevant to Alzheimer’s disease. Moreover, the technique is shown to be an excellent tool for studying the effect of drugs against the disease.
According to the amyloid hypothesis, Alzheimer’s disease — the most common type of dementia — is caused by flaws in the production, accumulation, and disposal of amyloid-beta in the brain. Amyloid-beta refers to a group of peptides (protein fragments) that over time form plaques in the brain of a person with Alzheimer’s disease. Drugs aiming to reduce the aggregation of amyloid-beta have been developed, but recent findings show that different types of amyloid-beta aggregates have different contributions to the development of Alzheimer’s disease. In particular, intermediate aggregates such as protofibrils are more toxic than the actual final fibrils, the main component of amyloid-beta plaques. A precise understanding of the complex aggregation pathways is therefore necessary for the further development of efficient drugs against Alzheimer’s disease. Kenjiro Ono from Kanazawa University and colleagues have now succeeded in visualizing the structural dynamics of protofibrils, as well as the effect of a recently developed drug based on anti-amyloiide-beta antibodies.
So how did they go about it?
The scientists looked at the formation and the structure of amyloid-beta protofibrils by means of high-speed atomic force microscopy (AFM). The latter method has in recent years emerged as a powerful nanoimaging tool for studying biomolecules and their dynamics at high spatiotemporal resolution. High-speed AFM observations showed that protofibrils have a nodal structure, with stable structural features — specifically, the binding angle between nodes — across several samples. Importantly, this nodal structure is distinct from proper, mature fibrils, which have a helical structure.
Ono and colleagues then investigated the dissociation of protofibrils. They found that the length of protofibrils depends on their concentration, suggesting that aggregates can dissociate spontaneously.
Now onto the interaction with drugs
To obtain detailed insights into the functioning of anti-amyloid-beta antibody drugs, the researchers examined the binding between amyloid-beta protofibrils and a new drug known as lecanemab. They found that the binding ability – termed the affinity - of lecanemab for protofibrils is almost independent of the size of the protofibrils — in other words, the affinity does not substantially vary throughout the aggregation process. High-speed AFM observations further revealed that lecanemab covers the surface of small, pre-protofibril aggregates. In doing so, the drug inhibits the further aggregation into protofibrils, which in turn prevents the formation of proper amyloid-beta fibrils and plaques.
The results of Ono and colleagues provide direct evidence of a mechanism through which an antibody drug interferes with the amyloid-beta aggregation process. More generally, the work confirms the versatility of high-speed-AFM as a tool for studying biochemical pathways.
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Kanazawa University NanoLSI Podcast:Experiments reveal chilli-sensitive molecular structure fluctuation changes in TRPV1
Transcript of this podcastHello and welcome to the NanoLSI podcast. Thank you for joining us today. In this episode we feature the latest research by Ayumi Sumino at the Kanazawa University NanoLSI alongside Motoyuki Hattori at Fudan University in China, and their colleagues.
The research described in this podcast was published in the journal Proceedings of the National Academy of Science in May 2023
Kanazawa University NanoLSI website
https://nanolsi.kanazawa-u.ac.jp/en/Experiments reveal chilli-sensitive molecular structure fluctuation changes in TRPV1
Researchers at Kanazawa University report high-speed atomic force microscopy experiments that show how ligands associated with stimulating and suppressing activation of the TRPV1 protein increase and decrease the molecule’s structural variations. The observations provide insights into how these heat- and chilli-sensing proteins function.
The skin senses heat – both from increased temperature and molecules like capsaicin in chillies – through the activation of protein receptors called Transient receptor potential vanilloid member 1 or TRPV1. However, the mechanisms behind the function of TRPV1 have not been clear. Now Ayumi Sumino at Kanazawa University in Japan and Motoyuki Hattori at the Fudan University in China and their colleagues provide important insights into this mechanism. Using high-speed atomic force microscopy to compare the protein with and without stimulating or suppressing molecules – ligands – bound to it, they obtain what they describe as “the first experimental evidence showing the correlation between molecular fluctuation and the gating state (ligand binding)”.
So what was already known about this mechanism?
Well once activated, the TRPV1 channel opens, allowing ions to permeate and signalling to the nervous system that a noxious stimulant is present. And in 2011 researchers at the Howard Hughes Medical Institute in the US put forward a theoretical basis for the activation of the receptor derived from thermodynamics, a theoretical framework that has since been corroborated by experiment. The idea was that the molecule would respond to heat with a change in heat capacity, which is related to the fluctuations in the molecule’s conformation. Structures for the TRPV1 protein were known from previous cryo electron microscopy studies but these did not clarify how the fluctuations in protein conformation might change with stimulating or suppressing molecules, or even whether temperature and chilli sensing shared the same molecular mechanism.
Here's where the high-speed atomic force microscopy comes in
Atomic force microscopy (AFM) senses the topology of surfaces through the effect of distance on the forces on a nanosized tip positioned directly above the surface. The microscope was first invented in 1986 but gained a new lease of life through work at Kanazawa University that enabled it to capture topologies at high speed thereby providing a window into the dynamics of structures.
Sumino, Hattori and colleagues used high-speed AFM to image the TRPV1 receptor both in its unbound state and when bound to ligand molecules that either stimulate, that is agonist molecules, or suppress - antagonist molecules - the protein’s activity. They used the molecule resiniferatoxin, which is 1000 times hotter than capsaicin, as the agonist and for the antagonist they used capsazepine, which blocks the pain of capsaicin.
From the structures captured the researchers were able to observe fluctuations in the conformation of both the bound and unbound states of TRPV1. They found that resinifera
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Kanazawa Univesity NanoLSI Podcast:Dynamic 3D structure extraction from HS-AFM images
Transcript of this podcast
Hello and welcome to the NanoLSI podcast. Thank you for joining us today. In this episode we feature the latest research by Holger Flechsig and Toshio Ando at the Kanazawa University NanoLSI.The research described in this podcast was published in the journal Current Opinion in Structural Biology in April 2023
Kanazawa University NanoLSI website
https://nanolsi.kanazawa-u.ac.jp/en/Dynamic 3D structure extraction from high-speed atomic force microscopy images
By allowing the direct observation of biomolecules in dynamic action, high-speed atomic force microscopy or AFM has opened a new avenue to dynamic structural biology. A vast number of successful applications within the past 15 years have provided unique insights into essential biological processes at the nanoscale – visualizing, for example, how molecular motors execute their specific functions.Some intrinsic limitations of AFM imaging are that only the surface topography can be acquired, and that the AFM tip is too large to resolve details below the nanometer scale. To facilitate the interpretation and understanding of high-speed AFM observations, post-experimental analysis and computational methods play an increasingly important role.
In their review paper published in the Current Opinion in Structural Biology journal Holger Flechsig a computational scientist at the NanoLSI at Kanazawa University and Toshio Ando, a Distinguished Professor at NanoLSI, provide an overview of developments in this topical field of interdisciplinary research. Computational modeling and simulations already allow the reconstruction of 3D conformations with atomistic resolution from topographic resolution-limited AFM images. Furthermore, quantitative analysis methods allow for example automated recognition of biomolecular shape changes from topographic images, or feature assignment including the identification of amino acid residues on the molecular surface.
So how is all this implemented?
The developed computational methods are often implemented in open-access software, allowing for convenient applications by the broad Bio-AFM community to complement experimental observations. In that regard, the BioAFMviewer software project initiated at Kanazawa University in 2020 has gained significant attention and plays an important role in a plethora of collaboration projects.
Combining high-speed AFM and computational modeling will elevate the understanding of how proteins function in atomistic detail. An ambitious future goal is the application of molecular modeling to reconstruct atomistic-level 3D molecular movies from high-speed AFM topographic movies.
Reference
Holger Flechsig and Toshio Ando. Protein dynamics by the combination of high-speed AFM and computational modelingNanoLSI Podcast website
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