Article
Chemistry, Multidisciplinary
Zhaowei Liu, Rodrigo A. Moreira, Ana Dujmovic, Haipei Liu, Byeongseon Yang, Adolfo B. Poma, Michael A. Nash
Summary: Using single-molecule AFM force spectroscopy in combination with click chemistry, the mechanical interactions between anticalin and its target CTLA-4 were studied. Results showed that pulling from different anchor residues significantly affected rupture forces and dissociation rates. Molecular dynamics simulations revealed a geometric dependency of mechanostability.
Article
Biochemistry & Molecular Biology
Shengchao Shi, Tao Wu, Peng Zheng
Summary: Cobalt is a trace transition metal that exists in numerous cobalt-containing proteins in living organisms. The Co(II) ion can be used as a powerful tool to characterize metal-binding proteins through the formation of cobalt-ligand bonds. This study used atomic force microscopy-based single-molecule force spectroscopy to directly measure the rupture force of the Co(II)-thiolate bond in cobalt-substituted rubredoxin. The results showed that the Co(II)-thiolate bond is a mechanically stable chemical bond, and the Co-S bond is less stable compared to the Zn-S bond in proteins.
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
Multidisciplinary Sciences
Eric M. Mulhall, Andrew Ward, Darren Yang, Mounir A. Koussa, David P. Corey, Wesley P. Wong
Summary: Researchers characterized the strength of the tip-link connection at single-molecule resolution and found that a single tip-link bond is more mechanically stable relative to classic cadherins, and that the double stranded tip-link connection is stabilized by single strand rebinding facilitated by strong cis-dimerization domains.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Multidisciplinary
Hai Lei, Quan Ma, Zhangxia Wang, Di Zhang, Xiaoyu Huang, Meng Qin, Haibo Ma, Wei Wang, Yi Cao
Summary: This study developed a single-molecule assay to investigate the force-dependent ester hydrolysis. The results showed that the ester hydrolysis rate is surprisingly insensitive to forces. The study revealed that the rate-limiting step for the formation of intermediate states is not affected by applied forces.
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.
Article
Chemistry, Multidisciplinary
Patricia Lopez-Garcia, Aline D. de Araujo, Ana E. Bergues-Pupo, Isabell Tunn, David P. Fairlie, Kerstin G. Blank
Summary: Coiled coils can be stabilized and fine-tuned for thermodynamic and mechanical stability by introducing helix-inducing macrocyclic constraints known as staples. The number of staples affects thermodynamic stabilization against helix uncoiling, while the positioning of staples controls mechanical stability of CCs. Different types, positions, and numbers of staples are key design parameters for using helical macrocyclic templates in emerging biomaterials to adjust CC properties.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Chemistry, Multidisciplinary
Albert A. Smith, Emelyne M. Pacull, Sabrina Stecher, Peter W. Hildebrand, Alexander Vogel, Daniel Huster
Summary: G protein-coupled receptors initiate signal transduction by binding with ligands. In this study, we focus on the growth hormone secretagogue receptor (GHSR), which binds with the 28 residue peptide ghrelin. We compared the dynamics of apo and ghrelin-bound GHSR using long molecular dynamics simulation trajectories and identified differences in dynamics in specific regions. We also investigated the traversal of GHSR over a rugged energy landscape via principal component analysis.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Editorial Material
Biochemical Research Methods
Dominika T. Gruszka
Summary: Single-molecule methods allow researchers to directly probe individual behaviors of biological macromolecules, uncovering unexpected modes of action and offering a deeper understanding of the mechanistic basis of biological processes. By studying molecular behaviors beyond the ensemble level, this approach highlights the intrinsic molecular heterogeneity of biological systems.
BIOCHEMISTRY: ONE MOLECULE AT A TIME
(2021)
Article
Chemistry, Multidisciplinary
Jiacheng Zuo, Hongbin Li
Summary: Scientists have developed an atomic force microscopy (AFM)-based two-molecule force spectroscopy method to directly probe the mechanical properties of parallelly arranged elastomeric proteins. By using a twin-molecule approach, they were able to pick up and stretch two parallelly arranged elastomeric proteins simultaneously in an AFM experiment, revealing the mechanical features and determining the mechanical unfolding forces of proteins in such an experimental setting.
Editorial Material
Optics
Zhiyuan Zhang, Daniel Ahmed
Summary: Researchers have developed a new optical technique for high-precision measurement of cell lateral adhesion kinetics in complex clinical samples.
LIGHT-SCIENCE & APPLICATIONS
(2022)
Article
Multidisciplinary Sciences
Markus Hackl, Edward V. Contrada, Jonathan E. Ash, Atharv Kulkarni, Jinho Yoon, Hyeon-Yeol Cho, Ki-Bum Lee, John M. Yarbrough, Cesar A. Lopez, Sandrasegaram Gnanakaran, Shishir P. S. Chundawat
Summary: Protein adsorption to solid carbohydrate interfaces is crucial in biological processes such as biomass deconstruction. This study focuses on understanding the interactions between carbohydrate-binding modules (CBMs) and polysaccharides to improve enzymatic efficiency in biomass deconstruction. The research presents a method using single-molecule force spectroscopy to study the unbinding behavior of CBMs from polysaccharide surfaces. The results reveal distinct CBM binding conformations and provide insights into the structural mechanisms through molecular dynamics simulations.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Olena Synhaivska, Shayon Bhattacharya, Silvia Campioni, Damien Thompson, Peter Niraj Nirmalraj
Summary: This study investigates the concentration-dependent effect of Cu2+ ions on the aggregation pathway of alpha-synuclein (α-Syn) proteins. The results show that Cu2+ ions induce the formation of annular oligomers, highlighting their potential as therapeutic targets and biomarkers for Parkinson's disease and neurodegeneration.
ACS CHEMICAL NEUROSCIENCE
(2022)
Review
Biotechnology & Applied Microbiology
Ipek Simay Gokulu, Scott Banta
Summary: The functionalization of proteins with DNA through covalent bond formation enables various biotechnology advancements. DNA labeling of proteins allows for easy identification, organization, and control within DNA-protein networks. Bioconjugation reactions can target different amino acids within proteins, and further protein engineering methods can be used for conjugation reactions. The choice of technique depends on factors such as yield, selectivity, conjugation position, cost, and potential impact on protein function.
TRENDS IN BIOTECHNOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Kaushik Pal, Ying Tu, Xuefeng Wang
Summary: Podosomes are integrin-mediated cell adhesion units involved in various cellular and physiological processes. Their formation is influenced by actomyosin contractility and actin polymerization, while extracellular integrin-ligand tensions are not crucial for their formation.
Article
Chemistry, Physical
Jingyuan Nie, Yibing Deng, Fang Tian, Shengchao Shi, Peng Zheng
Summary: Cation-pi interaction plays a crucial role in biological systems but its experimental verification and quantification at the molecular level are limited. In this study, atomic force microscopy-based single-molecule force spectroscopy was used to measure the stability and kinetics of NGAL protein with cation-pi interactions. The results demonstrated the high-precision detection of weak cation-pi interaction in NGAL.
Article
Chemistry, Physical
Dongdong Wu, Hai Lei, Xian Xie, Liang Zhou, Peng Zheng, Yi Cao, Yan Zhang
Summary: This study developed a double network hydrogel that mimics protein assemblies in the extracellular matrix (ECM) and defines its mechanical and biochemical cues using advanced chemical biology tools.
Article
Chemistry, Multidisciplinary
Shengchao Shi, Ziyi Wang, Yibing Deng, Fang Tian, Qingsong Wu, Peng Zheng
Summary: In this study, a protein immobilization method combining SPAAC click reaction and enzymatic ligation is developed to overcome the issues of NHS hydrolysis and nonspecific reaction of maleimide with the protein. The successful immobilization of eGFP and verification of its correct folding and stability demonstrate that this method is stable, efficient, and site-specific.
Article
Biochemistry & Molecular Biology
Shengchao Shi, Tao Wu, Peng Zheng
Summary: Cobalt is a trace transition metal that exists in numerous cobalt-containing proteins in living organisms. The Co(II) ion can be used as a powerful tool to characterize metal-binding proteins through the formation of cobalt-ligand bonds. This study used atomic force microscopy-based single-molecule force spectroscopy to directly measure the rupture force of the Co(II)-thiolate bond in cobalt-substituted rubredoxin. The results showed that the Co(II)-thiolate bond is a mechanically stable chemical bond, and the Co-S bond is less stable compared to the Zn-S bond in proteins.
Article
Chemistry, Physical
Ziyi Wang, Zhongxing Zhao, Guoqiang Li, Peng Zheng
Summary: The de novo-designed metalloprotein alpha 3DIV binds to mercury via three cysteine residues under dynamic conditions. An unusual trigonal three-coordinate HgS3 site is formed in the protein in basic solution, whereas a linear two-coordinate HgS2 site is formed in acidic solution. It is found that any two of the three cysteines in the protein bind to mercury in the HgS2 site.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Biochemistry & Molecular Biology
Bei Tong, Fang Tian, Peng Zheng
Summary: Titin, the largest protein in humans, plays a critical role in muscle's elasticity. The study investigates the mechanical stability of Ig domains and shows that the interdomain linker affects their stability in a complex and domain-specific manner.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
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
Zhangwei Lu, Yutong Liu, Yibing Deng, Bin Jia, Xuan Ding, Peng Zheng, Zhe Li
Summary: We describe the use of a protein ligase for covalently attaching a protein to a peptide nucleic acid (PNA). This approach only requires a GL dipeptide at the N-terminus of the target protein and an NGL tripeptide at the C-terminus of the PNA. Our study demonstrates the versatility of this method by successfully attaching a PNA strand to three different proteins. Additionally, we show the feasibility of erasable imaging of EGFR on HEK293 cell membranes using DNA origami nanostructures and toehold-mediated strand displacement.
CHEMICAL COMMUNICATIONS
(2022)
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.