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
Chemistry, Multidisciplinary
Haiyan Hong, Zilong Guo, Hao Sun, Ping Yu, Huanhuan Su, Xuening Ma, Hu Chen
Summary: Research on Csp protein shows that it mainly folds and unfolds in a single step over a force range from 5 pN to 50 pN. The unfolding rates exhibit different force sensitivities below and above 8 pN, indicating a free energy landscape with two barriers and a transient intermediate state between them. These findings provide new insights into the protein folding mechanism of two-state proteins.
COMMUNICATIONS CHEMISTRY
(2021)
Article
Biochemical Research Methods
Qing Li, Dimitra Apostolidou, Piotr E. Marszalek
Summary: Most proteins in proteomes are large and structurally complex, making studying their mechanical unfolding pathways challenging. Proteins with tandem repeat domains display a saw-tooth pattern in their mechanical unfolding force profiles. The combination of experimental single-molecule force spectroscopy methods with computational simulations is powerful for understanding the unfolding and refolding of these proteins.
Article
Biochemistry & Molecular Biology
Xiangchao Pang, Bin Tang
Summary: Metalloproteins require metal cofactors to function properly, which can affect their folding and unfolding processes. The electronic configuration of the metal cofactors has a significant impact on the strength of organometallic bonds. Additionally, there is an intermediate state during the unfolding process of metalloproteins like PAZ.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
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
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
Vanni Doffini, Haipei Liu, Zhaowei Liu, Michael A. Nash
Summary: This study reports the application of machine learning techniques to classify and analyze protein unfolding trajectories. It demonstrates the potential of machine learning to accelerate data analysis and generate new insights.
Article
Chemistry, Physical
Pavel Zhuravlev, Michael Hinczewski, D. Thirumalai
Summary: Deviation from linearity in the dependence of protein unfolding rates on mechanical force may indicate multidimensionality and parallel pathways in the underlying energy landscape. Simulations show significant changes in unfolding kinetics and transition state structures as force increases, suggesting a switch in unfolding pathways. This indicates that the parallel unfolding of structurally unrelated single domain proteins can be determined based on the dependence of unfolding rates on force.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
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
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.
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
Biophysics
Dalton R. Gibbs, Roaa Mahmoud, Anisa Kaur, Soma Dhakal
Summary: This study used an optical-tweezers-based single-molecule manipulation assay to investigate the mechanical and thermodynamic properties of the RuvA-Holliday junction complex. The results showed that RuvA protein stabilizes the Holliday junction and increases its unfolding force, facilitating refolding under high force. This approach can be applied to study other junction-binding proteins involved in critical DNA repair processes.
BIOPHYSICAL JOURNAL
(2021)
Article
Chemistry, Medicinal
Petr Stadlbauer, Vojtech Mlynsky, Miroslav Krepl, Jiri Sponer
Summary: In this study, steered molecular dynamics simulations were performed to investigate the unfolding mechanism of human telomeric GQs. The results showed that the direction of force, pulling velocity, and pulling force all affected the unfolding process. Additionally, it was found that a GQ could continue to unfold after a force drop. Furthermore, the study revealed that different unfolding intermediates could have similar chain end-to-end distances, suggesting limitations in structural interpretations of single-molecule spectroscopic data.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
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
Biochemistry & Molecular Biology
Tianyu Duan, Hongbin Li
Article
Polymer Science
Linglan Fu, Hongbin Li
Article
Chemistry, Physical
Xiaoqing Gao, Yali Wang, Xuehao He, Mengjun Xu, Jintao Zhu, Xiaodong Hu, Xiaotang Hu, Hongbin Li, Chunguang Hu
Article
Biochemical Research Methods
Ruidi Wang, Miao Liu, Han Wang, Jiang Xia, Hongbin Li
Summary: Developing peptide tags that can bind target proteins covalently under mild conditions is crucial for various applications. The GB tags developed in this study show high specificity and yield in covalently labeling target proteins under oxidizing conditions, with improved thermodynamic stability and binding affinity. These new GB tags have potential applications in biochemical labeling and biomaterials such as protein hydrogels.
BIOCONJUGATE CHEMISTRY
(2021)
Article
Chemistry, Multidisciplinary
Tianyu Duan, Qingyuan Bian, Hongbin Li
Summary: Protein-based hydrogels can mimic native extracellular matrices and have diverse applications in cell proliferation, drug/cell delivery, and tissue engineering. Light can be utilized as a regulation stimulus for modifying the mechanical and/or biochemical properties of these hydrogels. LOVTRAP, a light-responsive interaction between LOV2 and zdk1, has been used to engineer protein hydrogels whose viscoelastic properties can change in response to light, showing shear-thinning and self-healing properties. This new class of light-responsive protein hydrogels is expected to broaden the scope of dynamic protein hydrogels for biomedical applications.
Article
Chemistry, Multidisciplinary
Jiacheng Zuo, Denghuang Zhan, Jiahao Xia, Hongbin Li
Summary: This study investigated the mechanical and thermodynamic effects of two missense mutations, R57C-I94 and S22P-I84, in the elastic I-band part of cardiac titin. Results showed that R57C significantly destabilized the I94 module, while S22P led to only modest destabilization of I84. It is suggested that R57C may have a larger impact on titin elasticity compared to S22P.
Article
Multidisciplinary Sciences
Han Wang, Guojun Chen, Hongbin Li
Summary: The folding of the RTX block-iv in adenylate cyclase is templated by the folded RTX block-v, which allows rapid folding and significant mutual stabilization. This finding provides insights into the mechanism of transmitting the folding signal within the RTX domain.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Analytical
Xiaoqing Gao, Cong Zhai, Zuzeng Lin, Yulu Chen, Hongbin Li, Chunguang Hu
Summary: This paper investigates the trapping process and steady position and orientation of Janus particles in a linearly polarized optical trap. The trapping trajectory and a practical simulation solution for more complex structures and trapping motions are revealed through simulation and experimentation.
Article
Biochemistry & Molecular Biology
Tianyu Duan, Qingyuan Bian, Hongbin Li
Summary: Fluorescent polymeric hydrogels are promising information storage media that can generate fluorescent patterns in a light-controlled and spatially defined manner. Grayscale patterning allows the generation of multi-dimensional fluorescent images. This method opens up new possibilities for developing protein-based smart materials for information storage and anti-counterfeit applications.
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.
Article
Engineering, Biomedical
Hongbin Li
Summary: SAE proteins are unique building blocks for engineering protein hydrogels with tailored mechanical properties. These proteins exhibit distinct mechanical properties due to force-induced unfolding of their globular domains during stretching, allowing for rational design of protein-based hydrogels at the molecular level.
ADVANCED NANOBIOMED RESEARCH
(2021)
Meeting Abstract
Biophysics
Han Wang, Hongbin Li
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS
(2021)
Article
Chemistry, Multidisciplinary
Jiayu Li, Guojun Chen, Yabin Guo, Han Wang, Hongbin Li
Summary: Top7 is a de novo designed protein with atomic level accuracy that shows a non-cooperative folding process and involves various folding intermediate states. Fragments of Top7 can fold independently in isolation, but their folding pathways are influenced by interactions with neighboring sequences. This context-dependent folding behavior highlights the importance of intra-chain interactions in shaping the folding landscape of Top7, which may have implications for the design of novel proteins.
Article
Chemistry, Multidisciplinary
Han Wang, Hongbin Li