Article
Multidisciplinary Sciences
David R. Jacobson, Thomas T. Perkins
Summary: By using an atomic-force-microscope assay optimized for mechanical force to reversibly unfold local regions of an individual protein, researchers overcame limitations of chemical denaturation assays in understanding the energetics of membrane proteins. This approach provided quantitative insight into the Delta Delta G of single amino acid mutations in membrane proteins and highlighted the contribution of membrane protein-lipid contacts to folding energetics. The platform established allows for determining Delta Delta G for fully folded membrane proteins embedded in their native bilayers.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Chemistry, Multidisciplinary
Marc Mora, Stephanie Board, Olivier Languin-Cattoen, Laura Masino, Guillaume Stirnemann, Sergi Garcia-Manyes
Summary: Non-native disulfide bonds are dynamic covalent bridges formed in proteins, which can be detected using mechanical force and are associated with protein function and aggregation diseases.
Article
Multidisciplinary Sciences
Devin T. Edwards, Marc-Andre Leblanc, Thomas T. Perkins
Summary: Single-molecule force spectroscopy was used to study protein folding dynamics, revealing intrinsic changes in protein folding dynamics and transition state height under different pH conditions. Despite differences in destabilization mechanisms, constant-force landscapes showed minimal differences in transition state height, while force-dependent rates increased as pH decreased. This study provides insights for future AFM-based studies of mechanoresponsive proteins.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Chemistry, Multidisciplinary
Shinichiro Ido, Kei Kobayashi, Noriaki Oyabu, Yoshiki Hirata, Kazumi Matsushige, Hirofumi Yamada
Summary: Water structuring on the outer surface of protein molecules, known as the hydration shell, is crucial for the biological activities of protein molecules in vivo. The three-dimensional force mapping technique has been successfully used to investigate the molecular-scale hydration structure of native purple membrane patches.
Article
Multidisciplinary Sciences
Alyssa Miller, Jiapeng Wei, Sarah Meehan, Christopher M. Dobson, Mark E. Welland, David Klenerman, Michele Vendruscolo, Francesco Simone Ruggeri, Tuomas P. J. Knowles
Summary: Neurodegenerative diseases such as Alzheimer's disease are caused by protein misfolding and aggregation into amyloid fibrils. This study uses atomic force microscopy and statistical theory to characterize amyloid ring structures derived from the brains of AD patients and explains the diversity in the structures formed from protein aggregation. The results show that ex vivo protofibril chains possess greater flexibility than mature amyloid fibrils, allowing them to form end-to-end connections and shedding light on their role in disease.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Nanoscience & Nanotechnology
Keivan Asadi, Junghoon Yeom, Hanna Cho
Summary: Investigating internal resonance (IR) mechanisms in micro/nanoresonators reveals that intermodal coupling between second and third flexural modes in asymmetric structures provides an optimal condition for strong IR, with high energy transfer to the resonated mode. This study introduces design strategies that can be easily integrated into typical micro/nanoelectromechanical systems, offering potential for paradigm-shifting applications in micro/nanosystems.
MICROSYSTEMS & NANOENGINEERING
(2021)
Article
Chemistry, Multidisciplinary
Hai Lei, Junsheng Zhang, Ying Li, Xin Wang, Meng Qin, Wei Wang, Yi Cao
Summary: In this study, a histidine-specific phosphorylation strategy was developed to covalently anchor proteins to an atomic force microscopy. This method improved the data quality of single-molecule force spectroscopy experiments and was successfully applied to investigate the mechanical stability and unfolding process of proteins.
Article
Biology
Nicola Galvanetto, Zhongjie Ye, Arin Marchesi, Simone Mortal, Sourav Maity, Alessandro Laio, Vincent Torre
Summary: Single-molecule force spectroscopy (SMFS) is used to study protein unfolding, and we propose a pipeline for analyzing membrane proteins using SMFS. The pipeline involves isolating the plasma membrane of single cells and directly testing force-distance curves, combining information from mass spectrometry and proteomic databases to identify and characterize membrane proteins and classify their unfolding.
Editorial Material
Multidisciplinary Sciences
Telmo O. Paiva, Albertus Viljoen, Yves F. Dufrene
Summary: Advancements in atomic force microscopy (AFM) techniques and methodologies in microbiology have enhanced our understanding of microbial cell surfaces. Recent studies have shown that AFM imaging of cells and membranes at or near molecular resolution enables detailed visualization of membrane-drug interactions.
NATURE COMMUNICATIONS
(2022)
Article
Physics, Applied
Shiquan Lin, Zhong Lin Wang
Summary: Inspired by TENG, scanning TENG is proposed for local surface charge density measurement using atomic force microscopy. The technique taps a conductive tip above a charged dielectric surface to induce an AC, with Fourier analysis showing a linear relation to surface charge density. Results demonstrate its power in probing nanoscale charge transfer in contact-electrification.
APPLIED PHYSICS LETTERS
(2021)
Article
Chemistry, Physical
Miles F. Beaux, Reuben J. Peterson, Igor O. Usov
Summary: Atomic force microscopy was used to map the topography and qualitative mechanical characteristics of gallium-stabilized delta-phase plutonium coupons. The initial rough and heterogeneous surface of plutonium was observed, along with distinct striation patterns in qualitative nanomechanical mapping. Investigation suggested that the striations were not measurement artifacts or plutonium-specific features, and were influenced by mechanical working of the surface.
SURFACES AND INTERFACES
(2021)
Article
Chemistry, Physical
Francisco J. Solis, Monica Olvera de la Cruz
Summary: This article discusses the interactions between charged particles and induced polarization charge on solid-liquid or liquid-liquid interfaces with dielectric contrast, as well as the self-energy of charged particles near rough surfaces. Results show that the local convexity and concavity of the surface affect the repulsion of ions.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Cell Biology
Elma Sakinatus Sajidah, Keesiang Lim, Tomoyoshi Yamano, Goro Nishide, Yujia Qiu, Takeshi Yoshida, Hanbo Wang, Akiko Kobayashi, Masaharu Hazawa, Firli R. P. Dewi, Rikinari Hanayama, Toshio Ando, Richard W. Wong
Summary: Small extracellular vesicles (sEVs) play a crucial role in cell communication and can be used for drug delivery and structural characterization of nanoparticles. The high-speed atomic force microscopy (HS-AFM) can evaluate the structural changes of sEVs under different physicochemical stresses.
JOURNAL OF EXTRACELLULAR VESICLES
(2022)
Article
Mechanics
Abbasali Abouei Mehrizi, Qiao Liu, Hao Wang
Summary: The extended thin-film region adjacent to the contact line plays a crucial role in heat transfer and wetting dynamics by enhancing heat transfer and influencing contact line morphology. The study focused on advancing contact line morphology induced by water vapor condensation at low rates. Results showed that the morphology of the liquid film in this process differs from nonvolatile cases, with a precursor nanofilm and nanodroplets detected beyond the contact line.
Article
Chemistry, Analytical
Xinyu Li, Li Zhao, Rongrong Feng, Xiaowei Du, Zelin Guo, Yu Meng, Yulan Zou, Wenchao Liao, Qiyuan Liu, Yaohuan Sheng, Gaowei Zhao, Haijian Zhong, Weidong Zhao
Summary: Using atomic force microscopy, it was found that Na(V)1.5 is irregularly distributed on the surfaces of both normal and cancer breast cells, with higher expression on cancer cells. The stability of the Na(V)1.5-antibody complex is higher on normal breast cells compared to cancer breast cells. These findings provide insights into the interactions of ion channel-antibody systems and the role of sodium channels in tumor metastasis and invasion.
ANALYTICAL METHODS
(2023)
Article
Hematology
Volker Huck, Po-Chia Chen, Emma-Ruoqi Xu, Alexander Tischer, Ulrike Klemm, Camilo Aponte-Santamaria, Christian Mess, Tobias Obser, Fabian Kutzki, Gesa Koenig, Cecile V. Denis, Frauke Graeter, Matthias Wilmanns, Matthew Auton, Stefan W. Schneider, Reinhard Schneppenheim, Janosch Hennig, Maria A. Brehm
Summary: This study uncovered a prothrombotic gain of function associated with a VWF variant located in the C4 domain, leading to an increase in platelet aggregate size and affecting the structural flexibility. The research highlights the uniqueness of this VWF variant and its significance for vascular health.
THROMBOSIS AND HAEMOSTASIS
(2022)
Article
Chemistry, Physical
Claudia L. Gomez-Flores, Denis Maag, Mayukh Kansari, Van-Quan Vuong, Stephan Irle, Frauke Graeter, Tomas Kubar, Marcus Elstner
Summary: This paper investigates the generation of free energy surfaces in complex reactions using the semiempirical method DFTB and improves its accuracy by developing a specific reaction parametrization (SRP). Through the implementation of an artificial neural network (ANN), the authors successfully generate highly accurate free energy surfaces for thiol-disulfide exchange in two molecular complexes.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Review
Chemistry, Physical
Feng Wang, Rui Ma, Senbo Xiao, Niall J. English, Jianying He, Zhiliang Zhang
Summary: It is critical to understand the intrinsic interactions between a solid surface and gas hydrate to solve the complex role of surface properties in hydrate nucleation. Additionally, mechanisms to suppress hydrate deposition and surfaces that can manipulate these mechanisms need to be well-understood. Furthermore, research on correlating and understanding hydrate adhesion on different scales will help in designing surfaces with low hydrate adhesion.
JOURNAL OF MATERIALS CHEMISTRY A
(2022)
Article
Multidisciplinary Sciences
Isabel M. Martin, Michele M. Nava, Sara A. Wickstroem, Frauke Graeter
Summary: This study investigates the mechanotransducing functions of the essential adhesion component integrin-linked kinase (ILK) using force-probe molecular-dynamics simulations. The results suggest that ATP plays a role in facilitating cellular force generation and migration.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Shumeng Ma, Shymaa Damfo, Jiaqi Lou, Nikos Pinotsis, Matthew W. Bowler, Shozeb Haider, Frank Kozielski
Summary: The regular reappearance of coronavirus outbreaks has caused significant consequences globally. The ongoing pandemic caused by SARS-CoV-2 has highlighted the need for safe and effective antiviral drugs. The study identified fragment hits against the N-terminal domain of SARS-CoV-2 nsp1 and determined ligand-binding sites, providing a starting point for the development of more potent nsp1-targeting inhibitors.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Uladzimir Barayeu, Danny Schilling, Mohammad Eid, Thamara Nishida Xavier da Silva, Lisa Schlicker, Nikolina Mitreska, Christopher Zapp, Frauke Graeter, Aubry K. Miller, Reinhard Kappl, Almut Schulze, Jose Pedro Friedmann Angeli, Tobias P. Dick
Summary: Ferroptosis is a type of cell death caused by radical-driven lipid peroxidation. Our study shows that sulfane sulfur species, particularly hydropersulfides, scavenge free radicals and suppress ferroptosis. Cysteine can support ferroptosis resistance independently of the GPX4 pathway by providing sulfur for S-0 biosynthesis.
NATURE CHEMICAL BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Christopher A. Waudby, Saul Alvarez-Teijeiro, E. Josue Ruiz, Simon Suppinger, Nikos Pinotsis, Paul R. Brown, Axel Behrens, John Christodoulou, Anastasia Mylona
Summary: Protein phosphorylation regulates cellular signaling, and the phosphorylation of c-JUN at multiple sites controls various functional states in signal response.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Jerome Buergi, Pascal Lill, Evdokia-Anastasia Giannopoulou, Cy M. Jeffries, Grzegorz Chojnowski, Stefan Raunser, Christos Gatsogiannis, Matthias Wilmanns
Summary: Oxalyl-CoA synthetase from Saccharomyces cerevisiae, a peroxisomal protein, assembles into concentration-dependent dimers, tetramers and hexamers by self-association. The hexameric assembly has an asymmetric horseshoe-like arrangement, different from other protein structures. A single mutation in the self-association interface abolishes higher-level oligomerization, resulting in a homogenous dimeric assembly. The data provide a basis to mechanistically study peroxisomal translocation of this target.
BIOLOGICAL CHEMISTRY
(2023)
Article
Engineering, Environmental
Rui Ma, Senbo Xiao, Yuanhao Chang, Yuequn Fu, Jianying He, Zhiliang Zhang
Summary: This study investigates the mechanisms and influencing factors of hydrate adhesion using molecular dynamics simulations. It is found that enriching gas content near solid surfaces is crucial for reducing hydrate adhesion strength and enabling automatic detachment. The results provide insights for the design of passive anti-hydrate surfaces using an interfacial gas-enrichment strategy (IGES).
CHEMICAL ENGINEERING JOURNAL
(2023)
Article
Physics, Applied
Yu Ding, Kai Zhao, Meichao Lin, Haiyang Yu, Senbo Xiao, Jianying He, Zhiliang Zhang
Summary: The effect of solute hydrogen on shear-coupled grain boundary migration was studied and the dual role of hydrogen on grain boundary mobility was revealed. At low temperature and high loading rate, where hydrogen diffusion is slower than grain boundary motion, the grain boundary breaks away from the hydrogen atmosphere and transforms into a new stable phase with enhanced mobility. In the reverse regime, hydrogen atoms move along with the grain boundary, exerting a drag force and decreasing its mobility. These findings provide a rationale for the coexistence of hydrogen hardening and softening observed experimentally in polycrystalline materials.
JOURNAL OF APPLIED PHYSICS
(2023)
Article
Biochemistry & Molecular Biology
Po-Chia Chen, Fabian Kutzki, Angelika Mojzisch, Bernd Simon, Emma-Ruoqi Xu, Camilo Aponte-Santamaria, Kai Horny, Cy Jeffries, Reinhard Schneppenheim, Matthias Wilmanns, Maria A. Brehm, Frauke Graeter, Janosch Hennig
Summary: Von Willebrand disease is a bleeding disorder associated with mutations in the VWF gene. This study investigates the structure and dynamics of the C6 domain and the G2705R variant in C6, using nuclear magnetic resonance spectroscopy, molecular dynamics simulations and aggregometry. The findings show that the G2705R mutation destabilizes VWF by promoting hinging between the subdomains of C6.
JOURNAL OF STRUCTURAL BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Benedikt Rennekamp, Christoph Karfusehr, Markus Kurth, Aysecan uenal, Debora Monego, Kai Riedmiller, Ganna Gryn'ova, David M. Hudson, Frauke Graeter
Summary: The authors used scale-bridging simulations to identify breakage points in collagen and studied the mechanical and chemical impact of these ruptures on the tissue. They found that collagen has a unique failure mode that helps prevent material ageing and macroscopic failure.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Shumeng Ma, Vitaliy Mykhaylyk, Matthew W. Bowler, Nikos Pinotsis, Frank Kozielski
Summary: The authors propose a method to identify binding orientations of 2-dimensional fragments containing sulphur or chloro substituents using tunable beamlines. They successfully validate previously reported conformations and determine the positions of sulphur and chlorine in fragments bound to their protein target.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Multidisciplinary
Wojtek Treyde, Kai Riedmiller, Frauke Graeter
Summary: Knowledge of reliable X-H bond dissociation energies is crucial for studying the radical chemistry of proteins. By computing the X-H bond dissociation energies of model dipeptides, our work provides a highly valuable and unprecedented data set with accuracy and comprehensiveness. This dataset is likely to be useful for predicting protein biochemistry involving radicals.
Article
Chemistry, Physical
Matthias Brosz, Nicholas Michelarakis, Uwe H. F. Bunz, Camilo Aponte-Santamaria, Frauke Graeter
Summary: Poly(para-phenylene ethynylene)s (PPEs) are a class of conjugated and semi-flexible polymers with a wide range of technological applications. In this study, a coarse-grained model for PPEs was developed using the Martini 3 force field to study large-scale assemblies computationally. The model successfully reproduced key structural and thermodynamic properties of single PPE chains and mixtures. It was found that chain entanglement increased with PPE chain length, while nematic ordering decreased. The Martini 3 PPE model allows for investigation of the structural organization of PPE bulk systems at large spatio-temporal scales and is predicted to be applicable for studying out-of-equilibrium behavior under mechanical force.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
