Article
Biochemistry & Molecular Biology
Tanuja Joshi, Surbhi Garg, Alejandro Estana, Juan Cortes, Pau Bernado, Sayan Das, Anjana R. Kammath, Amin Sagar, Sabyasachi Rakshit
Summary: In polyproteins, the type of linker plays a significant role in the stability of domains. A linker rich in glycine can decrease domain stability, while interdomain interactions in glycine-rich linkers do not interfere with the stability of polyproteins. Flexible linkers are preferred for maintaining the independence of domains in a polyprotein.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(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
Multidisciplinary Sciences
Takanori Harashima, Shintaro Fujii, Yuki Jono, Tsuyoshi Terakawa, Noriyuki Kurita, Satoshi Kaneko, Manabu Kiguchi, Tomoaki Nishino
Summary: The electrical properties of DNA in the field of molecular electronics have been extensively studied, with a focus on the higher-order structures and design changes associated with single-molecule electronic devices. Researchers have developed a DNA zipper configuration to form a single-molecule junction, which exhibits high conductivity and an attractive self-restoring capability. This strategy provides a basis for novel designs of single-molecule junctions.
NATURE COMMUNICATIONS
(2021)
Article
Polymer Science
Xiaoye Zhang, Dandan Li, Yu Song, Wenke Zhang
Summary: In this study, the mechanical stability and melting pathway of highly stereoregular syndiotactic polypropylene (s-PP) were investigated using atomic force microscopy (AFM)-based single molecule force spectroscopy (SMFS). It was found that crystal thickness and structure have significant impacts on mechanical stability and melting pathway.
Article
Chemistry, Multidisciplinary
Qigang Zhong, Alexander Ihle, Sebastian Ahles, Hermann A. Wegner, Andre Schirmeisen, Daniel Ebeling
Summary: Constructing low-dimensional covalent assemblies with tailored size and connectivity is challenging but important in molecular electronics for tuning the properties of quantum materials. A versatile approach has been developed for building such structures block by block on a surface through highly selective tip-induced intermolecular reactions.
Review
Biochemistry & Molecular Biology
Rebeca Bocanegra, Ismael G. A. Plaza, Carlos R. Pulido, Borja Ibarra
Summary: The study reveals that the replisome machinery is stochastic, versatile, and highly dynamic, with transient protein-protein and protein-DNA interactions playing a key role in robust DNA replication.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Chemistry, Multidisciplinary
Qun Ma, Lichao Liu, Zeyue Yang, Peng Zheng
Summary: The successful synthesis of ultra-small gold nanoclusters via peptide conjugation was characterized using atomic force microscopy. Different peptides were conjugated to the nanoclusters, with their properties investigated through methods such as stretching tests.
Article
Polymer Science
Lu Qian, Kai Zhang, Xin Guo, Junyu Zhou, Miao Yu
Summary: The study found that there was almost no difference in the single-chain elasticity of gelatin in nonane and DI water. When a single gelatin chain is pulled into loose nonane, dehydration does not occur due to strong binding water interactions. Gelatin chains can only interact with water molecules at high temperatures.
Article
Chemistry, Multidisciplinary
Haipei Liu, Zhaowei Liu, Mariana Sa Santos, Michael A. A. Nash
Summary: Single-molecule force spectroscopy (SMFS) is a powerful tool for studying protein folding and mechanical properties. However, the traditional method of immobilization using lysine residues results in a heterogeneous distribution of tether positions. In this study, we compared lysine-based immobilization to site-specific immobilization using genetically encoded peptide tags (ybbR). Our results showed that lysine-based immobilization led to signal deterioration and incorrect classification of unfolding pathways. We also developed a mixed immobilization approach that partially recovered specific signals.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Biochemistry & Molecular Biology
Song Zhang, Miao Yu, Guoqiang Zhang, Guanmei He, Yunxu Ji, Juan Dong, Huayan Zheng, Lu Qian
Summary: The pH-responsive behavior of chitin molecules is essential for brewing and the design of chitin materials. Single-molecule studies have shown that chitin molecules exhibit different mechanical and conformational behaviors under different pH values.
Article
Biochemistry & Molecular Biology
Manish Bajaj, Mohd Muddassir, Bumjoon Choi, Priyanka Singh, Jong Bum Park, Surjeet Singh, Manisha Yadav, Rajesh Kumar, Kilho Eom, Deepak Sharma
Summary: This study investigates the effect of osmolytes on the mechanical unfolding properties of protein domain using atomic force microscopy. The results show that amines and methylamines enhance the mechanical stability of the protein, while polyols have no effect. Glycine betaine and trimethylamine-N-oxide increase the average unfolding force of the protein domain. These findings have potential applications in modulating the mechanical stability of proteins for nano-biotechnological purposes.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Polymer Science
Junpeng Wang, Tatiana B. Kouznetsova, Jianshe Xia, Felipe Jimenez Angeles, Monica Olvera de la Cruz, Stephen L. Craig
Summary: Single-molecule force spectroscopy is a powerful tool for studying the properties of individual polymer strands. However, the weak attachment between the atomic force microscope tip and the analyte limits its efficiency. In this study, we developed a polyelectrolyte handle that provides strong attachment, high success rate, non-fouling detachment, and specific attachment locations along the polymer strand.
JOURNAL OF POLYMER SCIENCE
(2023)
Review
Biochemistry & Molecular Biology
Rafayel Petrosyan, Abhishek Narayan, Michael T. Woodside
Summary: Single-molecule force spectroscopy (SMFS) is a powerful tool for studying protein folding dynamics, uncovering energy landscapes of folding, complex folding pathways, mechanisms of chaperones in assisting folding, effects of ribosomes on co-translational folding, and monitoring membrane protein folding.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Marta Urbanska, Annemarie Ludecke, Wilhelm J. Walter, Antoine M. van Oijen, Karl E. Duderstadt, Stefan Diez
Summary: This study introduces a highly-parallel, microfluidics-based method for rapid collection of force-dependent motility parameters of cytoskeletal motors, significantly improving throughput. DNA-tethered beads are used to apply tunable hydrodynamic forces to stepping kinesin-1 motors, allowing for simultaneous tracking of various motility parameters of hundreds of individual molecules. The approach, applicable to other molecular systems, represents a new methodology for parallelized single-molecule force studies on cytoskeletal motors.
Review
Chemistry, Multidisciplinary
Lyan M. van der Sleen, Katarzyna M. Tych
Summary: Research on the mechanical properties of proteins often involves the use of various connectors and techniques, with DNA being a common choice. When site-specifically conjugating DNA-linkers to proteins of interest, considerations include mechanical properties, labeling efficiency, and costs associated with different conjugation strategies.
Article
Biochemistry & Molecular Biology
Jie Gu, Yu Guo, Yiran Li, Juan Wang, Wei Wang, Yi Cao, Bin Xue
Summary: By adjusting the surface charge of proteins in hydrogels, the strain-stiffening amplitudes of protein hydrogels can be quantitatively regulated, even up to a 5-fold enhancement under high deformations. This method can maintain the bulk property, recovery ability, and biocompatibility of hydrogels almost unchanged.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Wenting Yu, Wenxu Sun, Huiyan Chen, Juan Wang, Bin Xue, Yi Cao
Summary: There is growing evidence that the mechanical properties of extracellular matrices greatly influence the function and form of residing cells. However, the study of the effect of stress-relaxation on cellular behaviors has been difficult due to the correlation between elasticity and stress-relaxation. In this study, a hybrid network hydrogel with a controllable stress-relaxation gradient and constant elasticity was designed, and the influence of hydrogel stress-relaxation on cell spreading was investigated.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Multidisciplinary
Yuehai Mei, Wenmao Huang, Weishuai Di, Xin Wang, Zhenshu Zhu, Yanyan Zhou, Fengwei Huo, Wei Wang, Yi Cao
Summary: The study proposes a mechanochemical lithography (MCL) method based on compressive force-triggered reactions for creating surfaces with patterned biomolecules. The method allows printing in physiological conditions and enables the creation of complex structures. The researchers discovered that amino groups in biomolecules can react with maleimide through a force-triggered reaction, resulting in mechanically and chemically stable covalent linkages.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Multidisciplinary Sciences
Mengxue Li, Lili Chen, Yiran Li, Xiaobin Dai, Zhekai Jin, Yucheng Zhang, Wenwen Feng, Li-Tang Yan, Yi Cao, Chao Wang
Summary: A new type of elastomer with superior mechanical properties, obtained through hierarchical crosslinking design, can be used as artificial ligaments in soft robotics.
NATURE COMMUNICATIONS
(2022)
Review
Biochemistry & Molecular Biology
Quan Ma, Hai Lei, Yi Cao
Summary: This article summarizes the relationship between the mechanical stability and function of intramolecular covalent bonds in Gram-positive bacterial surface proteins, and highlights the potential impact of these discoveries on the development of novel antibiotics and chemical biology tools.
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
Biochemistry & Molecular Biology
Qun Ma, Boqiang He, Guojin Tang, Ran Xie, Peng Zheng
Summary: The immobilization of proteins on nanoparticles has gained attention in recent years. Enzymatic protein immobilization, particularly using the peptide ligase OaAEP1, shows advantages due to site-specific connection. Our study demonstrates the successful C-terminal site-specific protein immobilization on amino-functionalized Fe3O4 nanoparticles mediated by OaAEP1. This provides a new method for site-specific protein immobilization on nanoparticles.
Article
Biochemistry & Molecular Biology
Zhiyi Wang, Mengdie Wang, Zhongxin Zhao, Peng Zheng
Summary: Carboxylate-bridged diiron proteins are a family of proteins involved in various physiological processes. These proteins have a conserved EXXH motif that forms the carboxylate bridge and is crucial for metal binding. In this study, we used a de novo-designed single-chain di-ferri protein (DFsc) with two EXXH motifs as a model protein to investigate the stability of the carboxylate-bridged di-metal binding site. By using atomic force microscopy-based single-molecule force spectroscopy, we obtained the mechanical and kinetic properties of the di-Zn site in DFsc. The results demonstrate the mechanical stability of the carboxylate-bridged di-metal site and enhance our understanding of this important type of metalloprotein.
Article
Chemistry, Physical
Ziyi Wang, Zhongxing Zhao, Zeyue Yang, Guoqiang Li, Peng Zheng
Summary: Lead is a toxic metal widely used in human society, but its interaction with proteins and formation of Pb-S bonds can cause toxicity. In this study, we used a de novo designed protein alpha 3DIV as a model protein to study Pb-S bonds. By detecting specific Pb-S bond rupture signals using atomic force microscopy-based single-molecule force spectroscopy (AFM-SMFS), we confirmed the formation of a triangular pyramidal PbS3 site in alpha 3DIV, including the previously undetected Pb-S(Cys67) bond. We also revealed and quantified the pH-dependent weakening of Pb-S bond strength, resulting in the dissociation of the PbS3 site at pH 4.5.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Chemistry, Physical
Jingyuan Nie, Ziyi Wang, Mengdie Wang, Peng Zheng
Summary: The specific interaction between Ni-nitrilotriaceticacid and the six-histidine tag is widely used in biological research for recombinant protein purification. The stability of this interaction is crucial for target protein binding, while the mechanochemistry between the system and the competing ligand imidazole/proton remains unclear. In this study, an AFM-SMFS system was used to characterize the system and reveal the destabilizing effect of imidazole and proton on the interaction, leading to a 3-fold increase in the bond dissociation rate.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Engineering, Electrical & Electronic
Songlin Zhang, Yihao Zhou, Alberto Libanori, Yibing Deng, Mingyang Liu, Mengjuan Zhou, Hao Qu, Xun Zhao, Peng Zheng, You-Liang Zhu, Jun Chen, Swee Ching Tan
Summary: Soft, conductive fibres for electronic textiles can be made using a spontaneous phase separation technique inspired by spider silk formation. These fibres are mechanically stretchable, strong, and electrically conductive, making them suitable for various applications including energy, sensing, and therapeutic uses.
NATURE ELECTRONICS
(2023)
Article
Chemistry, Multidisciplinary
Bin Zheng, Yuelong Xiao, Bei Tong, Yutong Mao, Rui Ge, Fang Tian, Xianchi Dong, Peng Zheng
Summary: A cluster of newly occurring mutations on Omicron was found in the β-core region of the spike protein's receptor-binding domain, where mutations rarely occurred before. The mechanical stability of Omicron RBD was found to increase by approximately 20% compared to the wild type. Molecular dynamics simulations showed that Omicron RBD had more hydrogen bonds in the β-core region due to the closing of the α-helical motif caused by the S373P mutation. In addition, the dissociation force between Omicron RBD and ACE2 was higher. This study reveals the mechanically stabilizing effect of the conserved S373P mutation in Omicron and the possible evolutionary trend of the β-core region of the receptor-binding domain.
Article
Chemistry, Physical
Ziyi Wang, Zhongxing Zhao, Zeyue Yang, Guoqiang Li, Peng Zheng
Summary: Lead is a toxic metal that is harmful to human beings due to its long history and wide use in human society. It exerts toxicity through its interaction with proteins, particularly by targeting thiol-rich proteins and forming stable Pb-S bonds. A study was conducted using a de novo designed protein alpha 3DIV as a model protein to investigate Pb-S bonds. Atomic force microscopy-based single-molecule force spectroscopy (AFM-SMFS) was used to detect specific Pb-S bond rupture signals, revealing the formation of a triangular pyramidal PbS3 site in alpha 3DIV and the pH-dependent weakening of Pb-S bond strength.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Chemistry, Multidisciplinary
Jiahao Xia, Jiacheng Zuo, Hongbin Li
Summary: In this study using single molecule force spectroscopy, it was found that the small globular protein GB1 exhibits molecular homogeneity in its mechanical unfolding reaction, with ensemble averages and time averages of physical quantities showing no differences among individual molecules. This suggests that the ergodic hypothesis holds true for GB1 on the time scale of the force spectroscopy experiments.
Article
Chemistry, Multidisciplinary
Jiayu Li, Hongbin Li
Summary: Metalloproteins play important roles in biological processes and understanding their folding mechanisms is challenging. This study used single-molecule optical tweezers to investigate the folding of horse heart cytochrome C (cytc), revealing new insights into its folding mechanism and the existence of intermediate states. The study also showed that apo-cytc is not a true random coil and has weak interactions within the unfolded polypeptide chain.
