1
|
Zhang X, Xie Y, Huang D, Zhang X, Tang X, Chen L, Luo SZ, Lou J, He C. Rapid and Mechanically Robust Immobilization of Proteins on Silica Studied at the Single-Molecule Level by Force Spectroscopy and Verified at the Macroscopic Level. ACS APPLIED MATERIALS & INTERFACES 2024; 16:16962-16972. [PMID: 38520330 DOI: 10.1021/acsami.3c18699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/25/2024]
Abstract
Typical methods for stable immobilization of proteins often involve time-consuming surface modification of silicon-based materials to enable specific binding, while the nonspecific adsorption method is faster but usually unstable. Herein, we fused a silica-binding protein, Si-tag, to target proteins so that the target proteins could attach directly to silica substrates in a single step, markedly streamlining the immobilization process. The adhesion force between the Si-tag and glass substrates was determined to be approximately 400-600 pN at the single-molecule level by atomic force microscopy, which is greater than the unfolding force of most proteins. The adhesion force of the Si-tag exhibits a slight increase when pulled from the C-terminus compared to that from the N-terminus. Furthermore, the Si-tag's adhesion force on a glass surface is marginally higher than that on a silicon nitride probe. The binding properties of the Si-tag are not obviously affected by environmental factors, including pH, salt concentration, and temperature. In addition, the macroscopic adhesion force between the Si-tag-coated hydrogel and glass substrates was ∼40 times higher than that of unmodified hydrogels. Therefore, the Si-tag, with its strong silica substrate binding ability, provides a useful tool as an excellent fusion tag for the rapid and mechanically robust immobilization of proteins on silica and for the surface coating of silica-binding materials.
Collapse
Affiliation(s)
- Xiaoxu Zhang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yayan Xie
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
- Sino Biological Inc., Building 9, Jing Dongbei Technology Park, No.18 Kechuang 10th St, BDA, Beijing 100176, China
| | - Duo Huang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xiaozhong Zhang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xiaoyu Tang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
- Sino Biological Inc., Building 9, Jing Dongbei Technology Park, No.18 Kechuang 10th St, BDA, Beijing 100176, China
| | - Long Chen
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Shi-Zhong Luo
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Jizhong Lou
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Chengzhi He
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
- Sino Biological Inc., Building 9, Jing Dongbei Technology Park, No.18 Kechuang 10th St, BDA, Beijing 100176, China
| |
Collapse
|
2
|
Tapia-Rojo R, Alonso-Caballero A, Badilla CL, Fernandez JM. Identical sequences, different behaviors: Protein diversity captured at the single-molecule level. Biophys J 2024; 123:814-823. [PMID: 38409780 PMCID: PMC10995423 DOI: 10.1016/j.bpj.2024.02.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 02/07/2024] [Accepted: 02/22/2024] [Indexed: 02/28/2024] Open
Abstract
The classical "one sequence, one structure, one function" paradigm has shaped much of our intuition of how proteins work inside the cell. Partially due to the insight provided by bulk biochemical assays, individual biomolecules are often assumed to behave as identical entities, and their characterization relies on ensemble averages that flatten any conformational diversity into a unique phenotype. While the emergence of single-molecule techniques opened the gates to interrogating individual molecules, technical shortcomings typically limit the duration of these measurements, which precludes a complete characterization of an individual protein and, hence, capturing the heterogeneity among molecular populations. Here, we introduce an ultrastable magnetic tweezers design, which enables us to measure the folding dynamics of a single protein during several uninterrupted days with high temporal and spatial resolution. Thanks to this instrumental development, we fully characterize the nanomechanics of two proteins with a very distinct force response, the talin R3IVVI domain and protein L. Days-long recordings on the same protein individual accumulate thousands of folding transitions with submicrosecond resolution, allowing us to reconstruct their free energy landscapes and describe how they evolve with force. By mapping the nanomechanical identity of many different protein individuals, we directly capture their molecular diversity as a quantifiable dispersion on their force response and folding kinetics. By significantly expanding the measurable timescales, our instrumental development offers a tool for profiling individual molecules, opening the gates to directly characterizing biomolecular heterogeneity.
Collapse
Affiliation(s)
- Rafael Tapia-Rojo
- Department of Biological Sciences, Columbia University, New York, New York.
| | | | - Carmen L Badilla
- Department of Biological Sciences, Columbia University, New York, New York
| | - Julio M Fernandez
- Department of Biological Sciences, Columbia University, New York, New York
| |
Collapse
|
3
|
Kim S, Cathey MVJ, Bounds BC, Scholl Z, Marszalek PE, Kim M. Ligand-Mediated Mechanical Enhancement in Protein Complexes at Nano- and Macro-Scale. ACS APPLIED MATERIALS & INTERFACES 2024; 16:272-280. [PMID: 38111156 DOI: 10.1021/acsami.3c14653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
Protein self-assembly plays a vital role in a myriad of biological functions and in the construction of biomaterials. Although the physical association underlying these assemblies offers high specificity, the advantage often compromises the overall durability of protein complexes. To address this challenge, we propose a novel strategy that reinforces the molecular self-assembly of protein complexes mediated by their ligand. Known for their robust noncovalent interactions with biotin, streptavidin (SAv) tetramers are examined to understand how the ligand influences the mechanical strength of protein complexes at the nanoscale and macroscale, employing atomic force microscopy-based single-molecule force spectroscopy, rheology, and bioerosion analysis. Our study reveals that biotin binding enhances the mechanical strength of individual SAv tetramers at the nanoscale. This enhancement translates into improved shear elasticity and reduced bioerosion rates when SAv tetramers are utilized as cross-linking junctions within hydrogel. This approach, which enhances the mechanical strength of protein-based materials without compromising specificity, is expected to open new avenues for advanced biotechnological applications, including self-assembled, robust biomimetic scaffolds and soft robotics.
Collapse
Affiliation(s)
- Samuel Kim
- Department of Biomedical Engineering, University of Arizona, Tucson, Arizona 85721, United States
| | - Marcus V J Cathey
- Department of Biomedical Engineering, University of Arizona, Tucson, Arizona 85721, United States
| | - Brandon C Bounds
- Department of Biomedical Engineering, University of Arizona, Tucson, Arizona 85721, United States
| | - Zackary Scholl
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
| | - Piotr E Marszalek
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
| | - Minkyu Kim
- Department of Biomedical Engineering, University of Arizona, Tucson, Arizona 85721, United States
- Department of Materials Science and Engineering, University of Arizona, Tucson, Arizona 85721, United States
- BIO5 Institute, University of Arizona, Tucson, Arizona 85719, United States
| |
Collapse
|
4
|
Sun H, Le S, Guo Z, Chen H. Exploring the free energy landscape of proteins using magnetic tweezers. Methods Enzymol 2024; 694:237-261. [PMID: 38492953 DOI: 10.1016/bs.mie.2023.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2024]
Abstract
Proteins fold to their native states by searching through the free energy landscapes. As single-domain proteins are the basic building block of multiple-domain proteins or protein complexes composed of subunits, the free energy landscapes of single-domain proteins are of critical importance to understand the folding and unfolding processes of proteins. To explore the free energy landscapes of proteins over large conformational space, the stability of native structure is perturbed by biochemical or mechanical means, and the conformational transition process is measured. In single molecular manipulation experiments, stretching force is applied to proteins, and the folding and unfolding transitions are recorded by the extension time course. Due to the broad force range and long-time stability of magnetic tweezers, the free energy landscape over large conformational space can be obtained. In this article, we describe the magnetic tweezers instrument design, protein construct design and preparation, fluid chamber preparation, common-used measuring protocols including force-ramp and force-jump measurements, and data analysis methods to construct the free energy landscape. Single-domain cold shock protein is introduced as an example to build its free energy landscape by magnetic tweezers measurements.
Collapse
Affiliation(s)
- Hao Sun
- Center of Biomedical Physics, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, P.R. China
| | - Shimin Le
- Department of Physics, Research Institute for Biomimetics and Soft Matter, Fujian Provincial Key Lab for Soft Functional Materials Research, Xiamen University, Xiamen, P.R. China
| | - Zilong Guo
- Center of Biomedical Physics, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, P.R. China.
| | - Hu Chen
- Center of Biomedical Physics, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, P.R. China; Department of Physics, Research Institute for Biomimetics and Soft Matter, Fujian Provincial Key Lab for Soft Functional Materials Research, Xiamen University, Xiamen, P.R. China.
| |
Collapse
|
5
|
Mora M, Tapia-Rojo R, Garcia-Manyes S. Unfolding and Refolding Proteins Using Single-Molecule AFM. Methods Mol Biol 2024; 2694:339-354. [PMID: 37824012 DOI: 10.1007/978-1-0716-3377-9_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
Single-molecule atomic force microscopy (AFM) allows capturing the conformational dynamics of an individual molecule under force. In this chapter, we describe a protocol for conducting a protein nanomechanical experiment using AFM, covering both the force-extension and force-clamp modes. Combined, these experiments provide an integrated vista of the molecular mechanisms-and their associated kinetics-underpinning the mechanical unfolding and refolding of individual proteins when exposed to mechanical load.
Collapse
Affiliation(s)
- Marc Mora
- Department of Physics, Randall Centre for Cell and Molecular Biophysics and London Centre for Nanotechnology, King's College London, London, UK
| | - Rafael Tapia-Rojo
- Department of Physics, Randall Centre for Cell and Molecular Biophysics and London Centre for Nanotechnology, King's College London, London, UK
| | - Sergi Garcia-Manyes
- Department of Physics, Randall Centre for Cell and Molecular Biophysics and London Centre for Nanotechnology, King's College London, London, UK.
| |
Collapse
|
6
|
Bu Y, Wu D, Zhao Y, Wang G, Dang X, Xie X, Wang S. Genetically Engineered Cell Membrane-Coated Nanoparticles with High-Density Customized Membrane Receptor for High-Performance Drug Lead Discovery. ACS APPLIED MATERIALS & INTERFACES 2023. [PMID: 37933874 DOI: 10.1021/acsami.3c10907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
Cell membrane coating strategies have been increasingly researched due to their unique capabilities of biomimicry and biointerfacing, which can mimic the functionality of the original source cells in vivo but fail to provide customized nanoparticle surfaces with new or enhanced capabilities beyond natural cells. However, the field of drug lead discovery necessitates the acquisition of sufficient surface density of specific target membrane receptors, presenting a heightened demand for this technology. In this study, we developed a novel approach to fabricate high density of fibroblast growth factor receptor 4 (FGFR4) cell membrane-coated nanoparticles through covalent site-specific immobilization between genetically engineered FGFR4 with HaloTag anchor on cell membrane and chloroalkane-functionalized magnetic nanoparticles. This technique enables efficient screening of tyrosine kinase inhibitors from natural products. And the enhanced density of FGFR4 on the surface of nanoparticles were successfully confirmed by Western blot assay and confocal laser scanning microscopy. Further, the customized nanoparticles demonstrated exceptional sensitivity (limit of detection = 0.3 × 10-3 μg mL-1). Overall, the proposed design of a high density of membrane receptors, achieved through covalent site-specific immobilization with a HaloTag anchor, demonstrates a promising strategy for the development of cell membrane surface engineering. This approach highlights the potential of cell membrane coating technology for facilitating the advanced extraction of small molecules for drug discovery.
Collapse
Affiliation(s)
- Yusi Bu
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an 710061, China
- Shaanxi Engineering Research Center of Cardiovascular Drugs Screening & Analysis, Xi'an 710061, China
| | - Dan Wu
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an 710061, China
- Shaanxi Engineering Research Center of Cardiovascular Drugs Screening & Analysis, Xi'an 710061, China
| | - Ying Zhao
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an 710061, China
- Shaanxi Engineering Research Center of Cardiovascular Drugs Screening & Analysis, Xi'an 710061, China
| | - Guoxiang Wang
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an 710061, China
| | - Xintao Dang
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an 710061, China
| | - Xiaoyu Xie
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an 710061, China
- Shaanxi Engineering Research Center of Cardiovascular Drugs Screening & Analysis, Xi'an 710061, China
| | - Sicen Wang
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an 710061, China
- Shaanxi Engineering Research Center of Cardiovascular Drugs Screening & Analysis, Xi'an 710061, China
- School of Medical, Tibet University, Lhasa 850000, China
| |
Collapse
|
7
|
Elias-Mordechai M, David N, Oren S, Georgia Pelah M, Jopp J, Fichtman B, Harel A, Berkovich R, Sal-Man N. A single filament biomechanical study of the enteropathogenic Escherichia coli Type III secretion system reveals a high elastic aspect ratio. NANOSCALE 2023; 15:15027-15037. [PMID: 37668452 DOI: 10.1039/d3nr01953e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
Abstract
Type III secretion systems (T3SSs) are syringe-like protein complexes used by some of the most harmful bacterial pathogens to infect host cells. While the T3SS filament, a long hollow conduit that bridges between bacteria and host cells, has been characterized structurally, very little is known about its physical properties. These filaments should endure shear and normal stresses imposed by the viscous mucosal flow during infection within the intestinal tract. We used atomic force microscopy (AFM) to probe the longitudinal and radial mechanical response of individual T3SS filaments by pulling on filaments extending directly from bacterial surfaces and later pressing into filaments that were detached from the bacteria. The measured longitudinal elastic moduli were higher by about two orders of magnitude than the radial elastic moduli. These proportions are commensurate with the role of the T3SS filament, which requires horizontal flexibility while maintaining its structural integrity to withstand intense stresses during infection.
Collapse
Affiliation(s)
- Moran Elias-Mordechai
- Department of Chemical Engineering, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel.
| | - Nofar David
- Department of Microbiology, Immunology, and Genetics, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel.
| | - Sonia Oren
- Department of Microbiology, Immunology, and Genetics, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel.
| | - Maya Georgia Pelah
- Department of Chemical Engineering, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel.
| | - Jürgen Jopp
- The Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel
| | - Boris Fichtman
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Amnon Harel
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Ronen Berkovich
- Department of Chemical Engineering, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel.
- The Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel
| | - Neta Sal-Man
- Department of Microbiology, Immunology, and Genetics, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel.
| |
Collapse
|
8
|
Beedle AEM, Garcia-Manyes S. The role of single protein elasticity in mechanobiology. NATURE REVIEWS. MATERIALS 2023; 8:10-24. [PMID: 37469679 PMCID: PMC7614781 DOI: 10.1038/s41578-022-00488-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 09/07/2022] [Indexed: 07/21/2023]
Abstract
In addition to biochemical signals and genetic considerations, mechanical forces are rapidly emerging as a master regulator of human physiology. Yet the molecular mechanisms that regulate force-induced functionalities across a wide range of scales, encompassing the cell, tissue or organ levels, are comparatively not so well understood. With the advent, development and refining of single molecule nanomechanical techniques, enabling to exquisitely probe the conformational dynamics of individual proteins under the effect of a calibrated force, we have begun to acquire a comprehensive knowledge on the rich plethora of physicochemical principles that regulate the elasticity of single proteins. Here we review the major advances underpinning our current understanding of how the elasticity of single proteins regulates mechanosensing and mechanotransduction. We discuss the present limitations and future challenges of such a prolific and burgeoning field.
Collapse
Affiliation(s)
- Amy EM Beedle
- Department of Physics, Randall Centre for Cell and Molecular Biophysics, Centre for the Physical Science of Life and London Centre for Nanotechnology, King’s College London, Strand, WC2R 2LS London, United Kingdom
- Institute for Bioengineering of Catalonia (IBEC), the Barcelona Institute of Technology (BIST), 08028 Barcelona, Spain
| | - Sergi Garcia-Manyes
- Department of Physics, Randall Centre for Cell and Molecular Biophysics, Centre for the Physical Science of Life and London Centre for Nanotechnology, King’s College London, Strand, WC2R 2LS London, United Kingdom
- Single Molecule Mechanobiology Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, London, UK
| |
Collapse
|
9
|
Ding X, Wang Z, Zheng B, Shi S, Deng Y, Yu H, Zheng P. One-step asparaginyl endopeptidase ( OaAEP1)-based protein immobilization for single-molecule force spectroscopy. RSC Chem Biol 2022; 3:1276-1281. [PMID: 36320890 PMCID: PMC9533667 DOI: 10.1039/d2cb00135g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 08/18/2022] [Indexed: 11/22/2022] Open
Abstract
Enzymatic protein ligation has become the most powerful and widely used method for high-precision atomic force microscopy single-molecule force spectroscopy (AFM-SMFS) study of protein mechanics. However, this methodology typically requires the functionalization of the glass surface with a corresponding peptide sequence/tag for enzymatic recognition and multiple steps are needed. Thus, it is time-consuming and a high level of experience is needed for reliable results. To solve this problem, we simplified the procedure using two strategies both based on asparaginyl endopeptidase (AEP). First, we designed a heterobifunctional peptide-based crosslinker, GL-peptide-propargylglycine, which links to an N 3-functionalized surface via the click reaction. Then, the target protein with a C-terminal NGL sequence can be immobilized via the AEP-mediated ligation. Furthermore, we took advantage of the direct ligation between primary amino in a small molecule and protein with C-terminal NGL by AEP. Thus, the target protein can be immobilized on an amino-functionalized surface via AEP in one step. Both approaches were successfully applied to the AFM-SMFS study of eGFP, showing consistent single-molecule results.
Collapse
Affiliation(s)
- Xuan Ding
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University 163 Xianlin Road Nanjing Jiangsu 210023 P. R. China
- State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University Nanjing Jiangsu 210023 P. R. China
| | - Ziyi Wang
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University Nanjing Jiangsu 210023 P. R. China
| | - Bin Zheng
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University Nanjing Jiangsu 210023 P. R. China
| | - Shengchao Shi
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University Nanjing Jiangsu 210023 P. R. China
| | - Yibing Deng
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University Nanjing Jiangsu 210023 P. R. China
| | - Hanyang Yu
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University 163 Xianlin Road Nanjing Jiangsu 210023 P. R. China
| | - Peng Zheng
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University Nanjing Jiangsu 210023 P. R. China
| |
Collapse
|
10
|
Lei H, Zhang J, Li Y, Wang X, Qin M, Wang W, Cao Y. Histidine-Specific Bioconjugation for Single-Molecule Force Spectroscopy. ACS NANO 2022; 16:15440-15449. [PMID: 35980082 DOI: 10.1021/acsnano.2c07298] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Atomic force microscopy (AFM) based single-molecule force spectroscopy (SMFS) is a powerful tool to study the mechanical properties of proteins. In these experiments, site-specific immobilization of proteins is critical, as the tether determines the direction and amplitude of forces applied to the protein of interest. However, existing methods are mainly based on thiol chemistry or specific protein tags, which cannot meet the need of many challenging experiments. Here, we developed a histidine-specific phosphorylation strategy to covalently anchor proteins to an AFM cantilever tip or the substrate via their histidine tag or surface-exposed histidine residues. The formed covalent linkage was mechanically stable with rupture forces of over 1.3 nN. This protein immobilization method considerably improved the pickup rate and data quality of SMFS experiments. We further demonstrated the use of this method to explore the pulling-direction-dependent mechanical stability of green fluorescent protein and the unfolding of the membrane protein archaerhodopsin-3.
Collapse
Affiliation(s)
- Hai Lei
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University 22 Hankou Road, Nanjing 210093, People's Republic of China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University 163 Xianlin Road, Nanjing 210023, People's Republic of China
| | - Junsheng Zhang
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University 22 Hankou Road, Nanjing 210093, People's Republic of China
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325001, People's Republic of China
| | - Ying Li
- Institute of Advanced Materials and Flexible Electronics (IAMFE), School of Chemistry and Materials Science, Nanjing University of Information Science & Technology 219 Ningliu Road, Nanjing, 210044, People's Republic of China
| | - Xin Wang
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325001, People's Republic of China
| | - Meng Qin
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University 22 Hankou Road, Nanjing 210093, People's Republic of China
| | - Wei Wang
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University 22 Hankou Road, Nanjing 210093, People's Republic of China
| | - Yi Cao
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University 22 Hankou Road, Nanjing 210093, People's Republic of China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University 163 Xianlin Road, Nanjing 210023, People's Republic of China
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325001, People's Republic of China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan 250021, People's Republic of China
| |
Collapse
|
11
|
Marques S, Slanska M, Chmelova K, Chaloupkova R, Marek M, Clark S, Damborsky J, Kool ET, Bednar D, Prokop Z. Mechanism-Based Strategy for Optimizing HaloTag Protein Labeling. JACS AU 2022; 2:1324-1337. [PMID: 35783171 PMCID: PMC9241015 DOI: 10.1021/jacsau.2c00002] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 04/08/2022] [Accepted: 04/08/2022] [Indexed: 06/15/2023]
Abstract
HaloTag labeling technology has introduced unrivaled potential in protein chemistry and molecular and cellular biology. A wide variety of ligands have been developed to meet the specific needs of diverse applications, but only a single protein tag, DhaAHT, is routinely used for their incorporation. Following a systematic kinetic and computational analysis of different reporters, a tetramethylrhodamine- and three 4-stilbazolium-based fluorescent ligands, we showed that the mechanism of incorporating different ligands depends both on the binding step and the efficiency of the chemical reaction. By studying the different haloalkane dehalogenases DhaA, LinB, and DmmA, we found that the architecture of the access tunnels is critical for the kinetics of both steps and the ligand specificity. We showed that highly efficient labeling with specific ligands is achievable with natural dehalogenases. We propose a simple protocol for selecting the optimal protein tag for a specific ligand from the wide pool of available enzymes with diverse access tunnel architectures. The application of this protocol eliminates the need for expensive and laborious protein engineering.
Collapse
Affiliation(s)
- Sérgio
M. Marques
- Loschmidt
Laboratories, Department of Experimental Biology and RECETOX, Faculty
of Science, Masaryk University, 625 00 Brno, Czech Republic
- International
Clinical Research Center, St. Anne’s
University Hospital, 656
91 Brno, Czech Republic
| | - Michaela Slanska
- Loschmidt
Laboratories, Department of Experimental Biology and RECETOX, Faculty
of Science, Masaryk University, 625 00 Brno, Czech Republic
| | - Klaudia Chmelova
- Loschmidt
Laboratories, Department of Experimental Biology and RECETOX, Faculty
of Science, Masaryk University, 625 00 Brno, Czech Republic
- International
Clinical Research Center, St. Anne’s
University Hospital, 656
91 Brno, Czech Republic
| | - Radka Chaloupkova
- Loschmidt
Laboratories, Department of Experimental Biology and RECETOX, Faculty
of Science, Masaryk University, 625 00 Brno, Czech Republic
- Enantis
Ltd., Biotechnology Incubator INBIT, 625 00 Brno, Czech Republic
| | - Martin Marek
- Loschmidt
Laboratories, Department of Experimental Biology and RECETOX, Faculty
of Science, Masaryk University, 625 00 Brno, Czech Republic
- International
Clinical Research Center, St. Anne’s
University Hospital, 656
91 Brno, Czech Republic
| | - Spencer Clark
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Jiri Damborsky
- Loschmidt
Laboratories, Department of Experimental Biology and RECETOX, Faculty
of Science, Masaryk University, 625 00 Brno, Czech Republic
- International
Clinical Research Center, St. Anne’s
University Hospital, 656
91 Brno, Czech Republic
| | - Eric T. Kool
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - David Bednar
- Loschmidt
Laboratories, Department of Experimental Biology and RECETOX, Faculty
of Science, Masaryk University, 625 00 Brno, Czech Republic
| | - Zbynek Prokop
- Loschmidt
Laboratories, Department of Experimental Biology and RECETOX, Faculty
of Science, Masaryk University, 625 00 Brno, Czech Republic
- International
Clinical Research Center, St. Anne’s
University Hospital, 656
91 Brno, Czech Republic
| |
Collapse
|
12
|
Chaudhuri D, Banerjee S, Chakraborty S, Chowdhury D, Haldar S. Direct Observation of the Mechanical Role of Bacterial Chaperones in Protein Folding. Biomacromolecules 2022; 23:2951-2967. [PMID: 35678300 DOI: 10.1021/acs.biomac.2c00451] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein folding under force is an integral source of generating mechanical energy in various cellular processes, ranging from protein translation to degradation. Although chaperones are well known to interact with proteins under mechanical force, how they respond to force and control cellular energetics remains unknown. To address this question, we introduce a real-time magnetic tweezer technology herein to mimic the physiological force environment on client proteins, keeping the chaperones unperturbed. We studied two structurally distinct client proteins--protein L and talin with seven different chaperones─independently and in combination and proposed a novel mechanical activity of chaperones. We found that chaperones behave differently, while these client proteins are under force, than their previously known functions. For instance, tunnel-associated chaperones (DsbA and trigger factor), otherwise working as holdase without force, assist folding under force. This process generates an additional mechanical energy up to ∼147 zJ to facilitate translation or translocation. However, well-known cytoplasmic foldase chaperones (PDI, thioredoxin, or DnaKJE) do not possess the mechanical folding ability under force. Notably, the transferring chaperones (DnaK, DnaJ, and SecB) act as holdase and slow down the folding process, both in the presence and absence of force, to prevent misfolding of the client proteins. This provides an emerging insight of mechanical roles of chaperones: they can generate or consume energy by shifting the energy landscape of the client proteins toward a folded or an unfolded state, suggesting an evolutionary mechanism to minimize energy consumption in various biological processes.
Collapse
Affiliation(s)
- Deep Chaudhuri
- Department of Biological Sciences, Ashoka University, Sonepat, Haryana 131029, India
| | - Souradeep Banerjee
- Department of Biological Sciences, Ashoka University, Sonepat, Haryana 131029, India
| | - Soham Chakraborty
- Department of Biological Sciences, Ashoka University, Sonepat, Haryana 131029, India
| | - Debojyoti Chowdhury
- Department of Biological Sciences, Ashoka University, Sonepat, Haryana 131029, India
| | - Shubhasis Haldar
- Department of Biological Sciences, Ashoka University, Sonepat, Haryana 131029, India
| |
Collapse
|
13
|
Beaussart A, Canonico F, Mazon H, Hidalgo J, Cianférani S, Le Cordier H, Kriznik A, Rahuel-Clermont S. Probing the mechanism of the peroxiredoxin decamer interaction with its reductase sulfiredoxin from the single molecule to the solution scale. NANOSCALE HORIZONS 2022; 7:515-525. [PMID: 35234779 DOI: 10.1039/d2nh00037g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Peroxiredoxins from the Prx1 subfamily (Prx) are highly regulated multifunctional proteins involved in oxidative stress response, redox signaling and cell protection. Prx is a homodimer that associates into a decamer. The monomer C-terminus plays intricate roles in Prx catalytic functions, decamer stability and interaction with its redox partner, the small reductase sulfiredoxin (Srx), that regulates the switching between Prx cellular functions. As only static structures of covalent Prx-Srx complexes have been reported, whether Srx binding dissociates the decameric assembly and how Prx subunit flexibility impacts complex formation are unknown. Here, we assessed the non-covalent interaction mechanism and dynamics in the solution of Saccharomyces cerevisiae Srx with the ten subunits of Prx Tsa1 at the decamer level via a combination of multiscale biophysical approaches including native mass spectrometry. We show that the ten subunits of the decamer can be saturated by ten Srx molecules and that the Tsa1 decamer in complex with Srx does not dissociate in solution. Furthermore, the binding events of atomic force microscopy (AFM) tip-grafted Srx molecules to Tsa1 individual subunits were relevant to the interactions between free molecules in solution. Combined with protein engineering and rapid kinetics, the observation of peculiar AFM force-distance signatures revealed that Tsa1 C-terminus flexibility controls Tsa1/Srx two-step binding and dynamics and determines the force-induced dissociation of Srx from each subunit of the decameric complex in a sequential or concerted mode. This combined approach from the solution to the single-molecule level offers promising prospects for understanding oligomeric protein interactions with their partners.
Collapse
Affiliation(s)
| | | | - Hortense Mazon
- Université de Lorraine, CNRS, IMoPA, F-54000 Nancy, France
| | - Jorge Hidalgo
- Université de Lorraine, CNRS, IMoPA, F-54000 Nancy, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048 CNRS CEA, 67087 Strasbourg, France
| | | | - Alexandre Kriznik
- Université de Lorraine, CNRS, IMoPA, F-54000 Nancy, France
- Université de Lorraine, CNRS, INSERM, UMS2008 IBSLor, Biophysics and Structural Biology core facility, F-54000 Nancy, France.
| | - Sophie Rahuel-Clermont
- Université de Lorraine, CNRS, IMoPA, F-54000 Nancy, France
- Université de Lorraine, CNRS, INSERM, UMS2008 IBSLor, Biophysics and Structural Biology core facility, F-54000 Nancy, France.
| |
Collapse
|
14
|
Chetrit E, Sharma S, Maayan U, Pelah MG, Klausner Z, Popa I, Berkovich R. Nonexponential kinetics in captured in sequential unfolding of polyproteins over a range of loads. Curr Res Struct Biol 2022; 4:106-117. [PMID: 35540955 PMCID: PMC9079174 DOI: 10.1016/j.crstbi.2022.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 04/15/2022] [Accepted: 04/19/2022] [Indexed: 11/08/2022] Open
Abstract
While performing under mechanical loads in vivo, polyproteins are vitally involved in cellular mechanisms such as regulation of tissue elasticity and mechano-transduction by unfolding their comprising domains and extending them. It is widely thought that the process of sequential unfolding of polyproteins follows an exponential kinetics as the individual unfolding events exhibit identical and identically distributed (iid) Poisson behavior. However, it was shown that under high loads, the sequential unfolding kinetics displays nonexponential kinetics that alludes to aging by a subdiffusion process. Statistical order analysis of this kinetics indicated that the individual unfolding events are not iid, and cannot be defined as a Poisson (memoryless) process. Based on numerical simulations it was argued that this behavior becomes less pronounced with lowering the load, therefore it is to be expected that polyproteins unfolding under lower forces will follow a Poisson behavior. This expectation serves as the motivation of the current study, in which we investigate the effect of force lowering on the unfolding kinetics of Poly-L8 under varying loads, specifically high (150, 100 pN) and moderate-low (45, 30, 20 pN) forces. We found that a hierarchy among the unfolding events still exists even under low loads, again resulting in nonexponential behavior. We observe that analyzing the dwell-time distributions with stretched-exponentials and power laws give rise to different phenomenological trends. Using statistical order analysis, we demonstrated that even under the lowest load, the sequential unfolding cannot be considered as iid, in accord with the power law distribution. Additional free energy analysis revealed the contribution of the unfolded segments elasticity that scales with the force on the overall one-dimensional contour of the energy landscape, but more importantly, it discloses the hierarchy within the activation barriers during sequential unfolding that account for the observed nonexponentiality. Poly-L8 unfolding shows nonexponential kinetics at forces ranging from 150 to 20 pN. Different phenomenological trends are observed for the dwell-time distributions. The unfolding events were shown to be dependent and not identically distributed. Free energy analysis reveals elastic impact and hierarchy in the unfolding barriers.
Collapse
|
15
|
Nie J, Tian F, Zheng B, Wang Z, Zheng P. Exploration of Metal-Ligand Coordination Bonds in Proteins by Single-molecule Force Spectroscopy. CHEM LETT 2021. [DOI: 10.1246/cl.210307] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Jingyuan Nie
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| | - Fang Tian
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| | - Bin Zheng
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| | - Ziyi Wang
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| | - Peng Zheng
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| |
Collapse
|
16
|
Bowen CH, Sargent CJ, Wang A, Zhu Y, Chang X, Li J, Mu X, Galazka JM, Jun YS, Keten S, Zhang F. Microbial production of megadalton titin yields fibers with advantageous mechanical properties. Nat Commun 2021; 12:5182. [PMID: 34462443 PMCID: PMC8405620 DOI: 10.1038/s41467-021-25360-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 08/05/2021] [Indexed: 02/07/2023] Open
Abstract
Manmade high-performance polymers are typically non-biodegradable and derived from petroleum feedstock through energy intensive processes involving toxic solvents and byproducts. While engineered microbes have been used for renewable production of many small molecules, direct microbial synthesis of high-performance polymeric materials remains a major challenge. Here we engineer microbial production of megadalton muscle titin polymers yielding high-performance fibers that not only recapture highly desirable properties of natural titin (i.e., high damping capacity and mechanical recovery) but also exhibit high strength, toughness, and damping energy - outperforming many synthetic and natural polymers. Structural analyses and molecular modeling suggest these properties derive from unique inter-chain crystallization of folded immunoglobulin-like domains that resists inter-chain slippage while permitting intra-chain unfolding. These fibers have potential applications in areas from biomedicine to textiles, and the developed approach, coupled with the structure-function insights, promises to accelerate further innovation in microbial production of high-performance materials.
Collapse
Affiliation(s)
- Christopher H Bowen
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, One Brookings Drive, Saint Louis, MO, USA
| | - Cameron J Sargent
- Division of Biological & Biomedical Sciences, Washington University in St. Louis, One Brookings Drive, Saint Louis, MO, USA
| | - Ao Wang
- Department of Mechanical Engineering, Northwestern University, Evanston, IL, USA
| | - Yaguang Zhu
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, One Brookings Drive, Saint Louis, MO, USA
| | - Xinyuan Chang
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, One Brookings Drive, Saint Louis, MO, USA
| | - Jingyao Li
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, One Brookings Drive, Saint Louis, MO, USA
| | - Xinyue Mu
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, One Brookings Drive, Saint Louis, MO, USA
| | - Jonathan M Galazka
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, USA
| | - Young-Shin Jun
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, One Brookings Drive, Saint Louis, MO, USA
| | - Sinan Keten
- Department of Mechanical Engineering, Northwestern University, Evanston, IL, USA
| | - Fuzhong Zhang
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, One Brookings Drive, Saint Louis, MO, USA.
- Division of Biological & Biomedical Sciences, Washington University in St. Louis, One Brookings Drive, Saint Louis, MO, USA.
- Institute of Materials Science & Engineering, Washington University in St. Louis, One Brookings Drive, Saint Louis, MO, USA.
| |
Collapse
|
17
|
Eckels EC, Chaudhuri D, Chakraborty S, Echelman DJ, Haldar S. DsbA is a redox-switchable mechanical chaperone. Chem Sci 2021; 12:11109-11120. [PMID: 34522308 PMCID: PMC8386657 DOI: 10.1039/d1sc03048e] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 07/17/2021] [Indexed: 12/18/2022] Open
Abstract
DsbA is a ubiquitous bacterial oxidoreductase that associates with substrates during and after translocation, yet its involvement in protein folding and translocation remains an open question. Here we demonstrate a redox-controlled chaperone activity of DsbA, on both cysteine-containing and cysteine-free substrates, using magnetic tweezers-based single molecule force spectroscopy that enables independent measurements of oxidoreductase activity and chaperone behavior. Interestingly we found that this chaperone activity is tuned by the oxidation state of DsbA; oxidized DsbA is a strong promoter of folding, but the effect is weakened by the reduction of the catalytic CXXC motif. We further localize the chaperone binding site of DsbA using a seven-residue peptide which effectively blocks the chaperone activity. We found that the DsbA assisted folding of proteins in the periplasm generates enough mechanical work to decrease the ATP consumption needed for periplasmic translocation by up to 33%.
Collapse
Affiliation(s)
- Edward C Eckels
- Department of Biological Sciences, Columbia University New York NY 10027 USA
- Department of Internal Medicine, Columbia University Medical Center New York NY 10032 USA
| | - Deep Chaudhuri
- Department of Biological Sciences, Ashoka University Sonepat Haryana 131029 India
| | - Soham Chakraborty
- Department of Biological Sciences, Ashoka University Sonepat Haryana 131029 India
| | - Daniel J Echelman
- Department of Biological Sciences, Columbia University New York NY 10027 USA
| | - Shubhasis Haldar
- Department of Biological Sciences, Ashoka University Sonepat Haryana 131029 India
| |
Collapse
|
18
|
Alegre-Cebollada J. Protein nanomechanics in biological context. Biophys Rev 2021; 13:435-454. [PMID: 34466164 PMCID: PMC8355295 DOI: 10.1007/s12551-021-00822-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 07/05/2021] [Indexed: 12/20/2022] Open
Abstract
How proteins respond to pulling forces, or protein nanomechanics, is a key contributor to the form and function of biological systems. Indeed, the conventional view that proteins are able to diffuse in solution does not apply to the many polypeptides that are anchored to rigid supramolecular structures. These tethered proteins typically have important mechanical roles that enable cells to generate, sense, and transduce mechanical forces. To fully comprehend the interplay between mechanical forces and biology, we must understand how protein nanomechanics emerge in living matter. This endeavor is definitely challenging and only recently has it started to appear tractable. Here, I introduce the main in vitro single-molecule biophysics methods that have been instrumental to investigate protein nanomechanics over the last 2 decades. Then, I present the contemporary view on how mechanical force shapes the free energy of tethered proteins, as well as the effect of biological factors such as post-translational modifications and mutations. To illustrate the contribution of protein nanomechanics to biological function, I review current knowledge on the mechanobiology of selected muscle and cell adhesion proteins including titin, talin, and bacterial pilins. Finally, I discuss emerging methods to modulate protein nanomechanics in living matter, for instance by inducing specific mechanical loss-of-function (mLOF). By interrogating biological systems in a causative manner, these new tools can contribute to further place protein nanomechanics in a biological context.
Collapse
|
19
|
Guo Z, Hong H, Sun H, Zhang X, Wu CX, Li B, Cao Y, Chen H. SpyTag/SpyCatcher tether as a fingerprint and force marker in single-molecule force spectroscopy experiments. NANOSCALE 2021; 13:11262-11269. [PMID: 34155491 DOI: 10.1039/d1nr01907d] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Single molecule force spectroscopy has emerged as a powerful tool to study protein folding dynamics, ligand-receptor interactions, and various mechanobiological processes. High force precision does not necessarily lead to high force accuracy, as the uncertainties in calibration can bring serious systematic errors. In the case of magnetic tweezers, accurate determination of the applied forces for short biomolecular tethers, by measuring thermal fluctuations of inhomogeneous magnetic beads, remains difficult. Here we address this challenge by showing that the SpyTag/SpyCatcher complex is not only a convenient and genetically encodable covalent linker but also an ideal molecular fingerprint and force marker in single molecule force spectroscopy experiments. By stretching the N-termini of both SpyCatcher and SpyTag, the complex unfolds locally up to the isopeptide bond position in an unzipping geometry, resulting in equilibrium transitions at ∼30 pN with step sizes of ∼3.4 nm. This mechanical feature can be used as the fingerprint to identify single-molecular events. Moreover, the transitions occur with a fast exchange rate and in a narrow force range. Therefore, the real applied forces can be determined accurately based on the force-dependent transitions. The equilibrium forces are insensitive to buffer conditions and temperature, making the calibration applicable to many complicated experimental systems. We provide an example to calibrate protein unfolding forces using this force marker and expect that this method can greatly simplify force calibration in single-molecule force spectroscopy experiments and improve the force accuracy.
Collapse
Affiliation(s)
- Zilong Guo
- Research Institute for Biomimetics and Soft Matter, Fujian Provincial Key Lab for Soft Functional Materials Research, Department of Physics, Xiamen University, Xiamen 361005, China.
| | | | | | | | | | | | | | | |
Collapse
|
20
|
Li Q, Apostolidou D, Marszalek PE. Reconstruction of mechanical unfolding and refolding pathways of proteins with atomic force spectroscopy and computer simulations. Methods 2021; 197:39-53. [PMID: 34020035 DOI: 10.1016/j.ymeth.2021.05.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 05/14/2021] [Accepted: 05/15/2021] [Indexed: 12/29/2022] Open
Abstract
Most proteins in proteomes are large, typically consist of more than one domain and are structurally complex. This often makes studying their mechanical unfolding pathways challenging. Proteins composed of tandem repeat domains are a subgroup of multi-domain proteins that, when stretched, display a saw-tooth pattern in their mechanical unfolding force extension profiles due to their repetitive structure. However, the assignment of force peaks to specific repeats undergoing mechanical unraveling is complicated because all repeats are similar and they interact with their neighbors and form a contiguous tertiary structure. Here, we describe in detail a combination of experimental and computational single-molecule force spectroscopy methods that proved useful for examining the mechanical unfolding and refolding pathways of ankyrin repeat proteins. Specifically, we explain and delineate the use of atomic force microscope-based single molecule force spectroscopy (SMFS) to record the mechanical unfolding behavior of ankyrin repeat proteins and capture their unusually strong refolding propensity that is responsible for generating impressive refolding force peaks. We also describe Coarse Grain Steered Molecular Dynamic (CG-SMD) simulations which complement the experimental observations and provide insights in understanding the unfolding and refolding of these proteins. In addition, we advocate the use of novel coiled-coils-based mechanical polypeptide probes which we developed to demonstrate the vectorial character of folding and refolding of these repeat proteins. The combination of AFM-based SMFS on native and CC-equipped proteins with CG-SMD simulations is powerful not only for ankyrin repeat polypeptides, but also for other repeat proteins and more generally to various multidomain, non-repetitive proteins with complex topologies.
Collapse
Affiliation(s)
- Qing Li
- Department of Mechanical Engineering and Materials Science, Duke University, 27708 Durham, NC, United States
| | - Dimitra Apostolidou
- Department of Mechanical Engineering and Materials Science, Duke University, 27708 Durham, NC, United States
| | - Piotr E Marszalek
- Department of Mechanical Engineering and Materials Science, Duke University, 27708 Durham, NC, United States.
| |
Collapse
|
21
|
Zhou S, He P, Dhindwal S, Grum-Tokars VL, Li Y, Parker K, Modica JA, Bleher R, Dos Reis R, Zuchniarz J, Dravid VP, Voth GA, Roux B, Mrksich M. Synthesis, Characterization, and Simulation of Four-Armed Megamolecules. Biomacromolecules 2021; 22:2363-2372. [PMID: 33979120 DOI: 10.1021/acs.biomac.1c00118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This paper describes the synthesis, characterization, and modeling of a series of molecules having four protein domains attached to a central core. The molecules were assembled with the "megamolecule" strategy, wherein enzymes react with their covalent inhibitors that are substituted on a linker. Three linkers were synthesized, where each had four oligo(ethylene glycol)-based arms terminated in a para-nitrophenyl phosphonate group that is a covalent inhibitor for cutinase. This enzyme is a serine hydrolase and reacts efficiently with the phosphonate to give a new ester linkage at the Ser-120 residue in the active site of the enzyme. Negative-stain transmission electron microscopy (TEM) images confirmed the architecture of the four-armed megamolecules. These cutinase tetramers were also characterized by X-ray crystallography, which confirmed the active-site serine-phosphonate linkage by electron-density maps. Molecular dynamics simulations of the tetracutinase megamolecules using three different force field setups were performed and compared with the TEM observations. Using the Amberff99SB-disp + pH7 force field, the two-dimensional projection distances of the megamolecules were found to agree with the measured dimensions from TEM. The study described here, which combines high-resolution characterization with molecular dynamics simulations, will lead to a comprehensive understanding of the molecular structures and dynamics for this new class of molecules.
Collapse
Affiliation(s)
- Shengwang Zhou
- School of Pharmacy, Jiangsu University, Zhenjiang 212013, P. R. China
| | - Peng He
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
| | - Sonali Dhindwal
- Department of Materials Science, Northwestern University, Evanston, Illinois 60208, United States
| | - Valerie L Grum-Tokars
- Department of Molecular Pharmacology and Biological Chemistry, Northwestern University, Chicago, Illinois 60611, United States
| | - Ying Li
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637, United States
| | - Kelly Parker
- Department of Materials Science, Northwestern University, Evanston, Illinois 60208, United States
| | - Justin A Modica
- Departments of Chemistry and Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Reiner Bleher
- Department of Materials Science, Northwestern University, Evanston, Illinois 60208, United States
| | - Roberto Dos Reis
- Department of Materials Science, Northwestern University, Evanston, Illinois 60208, United States
| | - Joshua Zuchniarz
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
| | - Vinayak P Dravid
- Department of Materials Science, Northwestern University, Evanston, Illinois 60208, United States
| | - Gregory A Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
| | - Benoît Roux
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637, United States
| | - Milan Mrksich
- Departments of Chemistry and Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States
| |
Collapse
|
22
|
Vilhena JG, Ortega M, Uhlig MR, Garcia R, Pérez R. Practical Guide to Single-Protein AFM Nanomechanical Spectroscopy Mapping: Insights and Pitfalls As Unraveled by All-Atom MD Simulations on Immunoglobulin G. ACS Sens 2021; 6:553-564. [PMID: 33503368 DOI: 10.1021/acssensors.0c02241] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Atomic force microscopy is an invaluable characterization tool in almost every biophysics laboratory. However, obtaining atomic/sub-nanometer resolution on single proteins has thus far remained elusive-a feat long achieved on hard substrates. In this regard, nanomechanical spectroscopy mapping may provide a viable approach to overcome this limitation. By complementing topography with mechanical properties measured locally, one may thus enhance spatial resolution at the single-protein level. In this work, we perform all-atom molecular dynamics simulations of the indentation process on a single immunoglobulin G (IgG) adsorbed on a graphene slab. Our simulations reveal three different stages as a function of strain: a noncontact regime-where the mechanical response is linked to the presence of the water environment- followed by an elastic response and a final plastic deformation regime. In the noncontact regime, we are able to identify hydrophobic/hydrophilic patches over the protein. This regime provides the most local mechanical information that allows one to discern different regions with similar height/topography and leads to the best spatial resolution. In the elastic regime, we conclude that the Young modulus is a well-defined property only within mechanically decoupled domains. This is caused by the fact that the elastic deformation is associated with a global reorganization of the domain. Differences in the mechanical response are large enough to clearly resolve domains within a single protein, such as the three subunits forming the IgG. Two events, unfolding or protein slipping, are observed in the plastic regime. Our simulations allow us to characterize these two processes and to provide a strategy to identify them in the force curves. Finally, we elaborate on possible challenges that could hamper the interpretation of such experiments/simulations and how to overcome them. All in all, our simulations provide a detailed picture of nanomechanical spectroscopy mapping on single proteins, showing its potential and the challenges that need to be overcome to unlock its full potential.
Collapse
Affiliation(s)
- J. G. Vilhena
- Department of Physics, University of Basel, Klingelbergstrasse 82, 4056 Basel, Switzerland
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
| | - Maria Ortega
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
| | - Manuel R. Uhlig
- Materials Science Factory, Instituto de Ciencia de Materiales de Madrid (ICMM), CSIC, 28049 Madrid, Spain
| | - Ricardo Garcia
- Materials Science Factory, Instituto de Ciencia de Materiales de Madrid (ICMM), CSIC, 28049 Madrid, Spain
| | - Rubén Pérez
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
- Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, E-28049 Madrid, Spain
| |
Collapse
|
23
|
Alonso-Caballero A, Echelman DJ, Tapia-Rojo R, Haldar S, Eckels EC, Fernandez JM. Protein folding modulates the chemical reactivity of a Gram-positive adhesin. Nat Chem 2021; 13:172-181. [PMID: 33257887 PMCID: PMC7858226 DOI: 10.1038/s41557-020-00586-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 09/29/2020] [Indexed: 01/30/2023]
Abstract
Gram-positive bacteria colonize mucosal tissues, withstanding large mechanical perturbations such as coughing, which generate shear forces that exceed the ability of non-covalent bonds to remain attached. To overcome these challenges, the pathogen Streptococcus pyogenes utilizes the protein Cpa, a pilus tip-end adhesin equipped with a Cys-Gln thioester bond. The reactivity of this bond towards host surface ligands enables covalent anchoring; however, colonization also requires cell migration and spreading over surfaces. The molecular mechanisms underlying these seemingly incompatible requirements remain unknown. Here we demonstrate a magnetic tweezers force spectroscopy assay that resolves the dynamics of the Cpa thioester bond under force. When folded at forces <6 pN, the Cpa thioester bond reacts reversibly with amine ligands, which are common in inflammation sites; however, mechanical unfolding and exposure to forces >6 pN block thioester reformation. We hypothesize that this folding-coupled reactivity switch (termed a smart covalent bond) could allow the adhesin to undergo binding and unbinding to surface ligands under low force and remain covalently attached under mechanical stress.
Collapse
Affiliation(s)
- Alvaro Alonso-Caballero
- Department of Biological Sciences, Columbia University, NY
10027, USA,Correspondence and request of material should be
addressed to A.A-C.:
| | | | - Rafael Tapia-Rojo
- Department of Biological Sciences, Columbia University, NY
10027, USA
| | - Shubhasis Haldar
- Department of Biological Sciences, Columbia University, NY
10027, USA
| | - Edward C. Eckels
- Department of Biological Sciences, Columbia University, NY
10027, USA
| | | |
Collapse
|
24
|
Ding Y, Apostolidou D, Marszalek P. Mechanical Stability of a Small, Highly-Luminescent Engineered Protein NanoLuc. Int J Mol Sci 2020; 22:E55. [PMID: 33374567 PMCID: PMC7801952 DOI: 10.3390/ijms22010055] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 12/19/2020] [Accepted: 12/20/2020] [Indexed: 11/16/2022] Open
Abstract
NanoLuc is a bioluminescent protein recently engineered for applications in molecular imaging and cellular reporter assays. Compared to other bioluminescent proteins used for these applications, like Firefly Luciferase and Renilla Luciferase, it is ~150 times brighter, more thermally stable, and smaller. Yet, no information is known with regards to its mechanical properties, which could introduce a new set of applications for this unique protein, such as a novel biomaterial or as a substrate for protein activity/refolding assays. Here, we generated a synthetic NanoLuc derivative protein that consists of three connected NanoLuc proteins flanked by two human titin I91 domains on each side and present our mechanical studies at the single molecule level by performing Single Molecule Force Spectroscopy (SMFS) measurements. Our results show each NanoLuc repeat in the derivative behaves as a single domain protein, with a single unfolding event occurring on average when approximately 72 pN is applied to the protein. Additionally, we performed cyclic measurements, where the forces applied to a single protein were cyclically raised then lowered to allow the protein the opportunity to refold: we observed the protein was able to refold to its correct structure after mechanical denaturation only 16.9% of the time, while another 26.9% of the time there was evidence of protein misfolding to a potentially non-functional conformation. These results show that NanoLuc is a mechanically moderately weak protein that is unable to robustly refold itself correctly when stretch-denatured, which makes it an attractive model for future protein folding and misfolding studies.
Collapse
Affiliation(s)
- Yue Ding
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA; (Y.D.); (D.A.)
- Department of Engineering Mechanics, SVL, Xi’an Jiaotong University, Xi’an 710049, China
| | - Dimitra Apostolidou
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA; (Y.D.); (D.A.)
| | - Piotr Marszalek
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA; (Y.D.); (D.A.)
| |
Collapse
|
25
|
Avestan MS, Javidi A, Ganote LP, Brown JM, Stan G. Kinetic effects in directional proteasomal degradation of the green fluorescent protein. J Chem Phys 2020; 153:105101. [DOI: 10.1063/5.0015191] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
| | - Alex Javidi
- Data Sciences, Janssen Research and Development, Spring House, Pennsylvania 19477, USA
| | | | | | - George Stan
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, USA
| |
Collapse
|
26
|
Straková K, López-Andarias J, Jiménez-Rojo N, Chambers JE, Marciniak SJ, Riezman H, Sakai N, Matile S. HaloFlippers: A General Tool for the Fluorescence Imaging of Precisely Localized Membrane Tension Changes in Living Cells. ACS CENTRAL SCIENCE 2020; 6:1376-1385. [PMID: 32875078 PMCID: PMC7453570 DOI: 10.1021/acscentsci.0c00666] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Indexed: 05/03/2023]
Abstract
Tools to image membrane tension in response to mechanical stimuli are badly needed in mechanobiology. We have recently introduced mechanosensitive flipper probes to report quantitatively global membrane tension changes in fluorescence lifetime imaging microscopy (FLIM) images of living cells. However, to address specific questions on physical forces in biology, the probes need to be localized precisely in the membrane of interest (MOI). Herein we present a general strategy to image the tension of the MOI by tagging our newly introduced HaloFlippers to self-labeling HaloTags fused to proteins in this membrane. The critical challenge in the construction of operational HaloFlippers is the tether linking the flipper and the HaloTag: It must be neither too taut nor too loose, be hydrophilic but lipophilic enough to passively diffuse across membranes to reach the HaloTags, and allow partitioning of flippers into the MOI after the reaction. HaloFlippers with the best tether show localized and selective fluorescence after reacting with HaloTags that are close enough to the MOI but remain nonemissive if the MOI cannot be reached. Their fluorescence lifetime in FLIM images varies depending on the nature of the MOI and responds to myriocin-mediated sphingomyelin depletion as well as to osmotic stress. The response to changes in such precisely localized membrane tension follows the validated principles, thus confirming intact mechanosensitivity. Examples covered include HaloTags in the Golgi apparatus, peroxisomes, endolysosomes, and the ER, all thus becoming accessible to the selective fluorescence imaging of membrane tension.
Collapse
Affiliation(s)
- Karolína Straková
- School
of Chemistry and Biochemistry and National Centre of Competence in
Research (NCCR) Chemical Biology, University
of Geneva, Geneva 1211, Switzerland
| | - Javier López-Andarias
- School
of Chemistry and Biochemistry and National Centre of Competence in
Research (NCCR) Chemical Biology, University
of Geneva, Geneva 1211, Switzerland
- (J.L.-A.)
| | - Noemi Jiménez-Rojo
- School
of Chemistry and Biochemistry and National Centre of Competence in
Research (NCCR) Chemical Biology, University
of Geneva, Geneva 1211, Switzerland
| | - Joseph E. Chambers
- Cambridge
Institute for Medical Research, University
of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - Stefan J. Marciniak
- Cambridge
Institute for Medical Research, University
of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - Howard Riezman
- School
of Chemistry and Biochemistry and National Centre of Competence in
Research (NCCR) Chemical Biology, University
of Geneva, Geneva 1211, Switzerland
| | - Naomi Sakai
- School
of Chemistry and Biochemistry and National Centre of Competence in
Research (NCCR) Chemical Biology, University
of Geneva, Geneva 1211, Switzerland
| | - Stefan Matile
- School
of Chemistry and Biochemistry and National Centre of Competence in
Research (NCCR) Chemical Biology, University
of Geneva, Geneva 1211, Switzerland
- (S.M.)
| |
Collapse
|
27
|
Sharma S, Subramani S, Popa I. Does protein unfolding play a functional role in vivo? FEBS J 2020; 288:1742-1758. [PMID: 32761965 DOI: 10.1111/febs.15508] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/09/2020] [Accepted: 08/03/2020] [Indexed: 12/21/2022]
Abstract
Unfolding and refolding of multidomain proteins under force have yet to be recognized as a major mechanism of function for proteins in vivo. In this review, we discuss the inherent properties of multidomain proteins under a force vector from a structural and functional perspective. We then characterize three main systems where multidomain proteins could play major roles through mechanical unfolding: muscular contraction, cellular mechanotransduction, and bacterial adhesion. We analyze how key multidomain proteins for each system can produce a gain-of-function from the perspective of a fine-tuned quantized response, a molecular battery, delivery of mechanical work through refolding, elasticity tuning, protection and exposure of cryptic sites, and binding-induced mechanical changes. Understanding how mechanical unfolding and refolding affect function will have important implications in designing mechano-active drugs against conditions such as muscular dystrophy, cancer, or novel antibiotics.
Collapse
Affiliation(s)
- Sabita Sharma
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Smrithika Subramani
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Ionel Popa
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| |
Collapse
|
28
|
Keeble AH, Howarth M. Power to the protein: enhancing and combining activities using the Spy toolbox. Chem Sci 2020; 11:7281-7291. [PMID: 33552459 PMCID: PMC7844731 DOI: 10.1039/d0sc01878c] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 06/30/2020] [Indexed: 12/27/2022] Open
Abstract
Proteins span an extraordinary range of shapes, sizes and functionalities. Therefore generic approaches are needed to overcome this diversity and stream-line protein analysis or application. Here we review SpyTag technology, now used in hundreds of publications or patents, and its potential for detecting and controlling protein behaviour. SpyTag forms a spontaneous and irreversible isopeptide bond upon binding its protein partner SpyCatcher, where both parts are genetically-encoded. New variants of this pair allow reaction at a rate approaching the diffusion limit, while reversible versions allow purification of SpyTagged proteins or tuned dynamic interaction inside cells. Anchoring of SpyTag-linked proteins has been established to diverse nanoparticles or surfaces, including gold, graphene and the air/water interface. SpyTag/SpyCatcher is mechanically stable, so is widely used for investigating protein folding and force sensitivity. A toolbox of scaffolds allows SpyTag-fusions to be assembled into defined multimers, from dimers to 180-mers, or unlimited 1D, 2D or 3D networks. Icosahedral multimers are being evaluated for vaccination against malaria, HIV and cancer. For enzymes, Spy technology has increased resilience, promoted substrate channelling, and assembled hydrogels for continuous flow biocatalysis. Combinatorial increase in functionality has been achieved through modular derivatisation of antibodies, light-emitting diodes or viral vectors. In living cells, SpyTag allowed imaging of protein trafficking, retargeting of CAR-T cell killing, investigation of heart contraction, and control of nucleosome position. The simple genetic encoding and rapid irreversible reaction provide diverse opportunities to enhance protein function. We describe limitations as well as future directions.
Collapse
Affiliation(s)
- Anthony H Keeble
- Department of Biochemistry , University of Oxford , South Parks Road , Oxford , OX1 3QU , UK . ; Tel: +44 (0)1865 613200
| | - Mark Howarth
- Department of Biochemistry , University of Oxford , South Parks Road , Oxford , OX1 3QU , UK . ; Tel: +44 (0)1865 613200
| |
Collapse
|
29
|
Jiang Y, Feldman T, Bakx JA, Yang D, Wong WP. Stretching DNA to twice the normal length with single-molecule hydrodynamic trapping. LAB ON A CHIP 2020; 20:1780-1791. [PMID: 32301470 PMCID: PMC7239757 DOI: 10.1039/c9lc01028a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Single-molecule force spectroscopy has brought many new insights into nanoscale biology, from the functioning of molecular motors to the mechanical response of soft materials within the cell. To expand the single-molecule toolbox, we have developed a surface-free force spectroscopy assay based on a high-speed hydrodynamic trap capable of applying extremely high tensions for long periods of time. High-speed single-molecule trapping is enabled by a rigid and gas-impermeable microfluidic chip, rapidly and inexpensively fabricated out of glass, double-sided tape and UV-curable adhesive. Our approach does not require difficult covalent attachment chemistries, and enables simultaneous force application and single-molecule fluorescence. Using this approach, we have induced a highly extended state with twice the contour length of B-DNA in regions of partially intercalated double-stranded (dsDNA) by applying forces up to 250 pN. This highly extended state resembles the hyperstretched state of dsDNA, which was initially discovered as a structure fully intercalated by dyes under high tension. It has been hypothesized that hyperstretched DNA could also be induced without the aid of intercalators if high-enough forces were applied, which matches our observation. Combining force application with single-molecule fluorescence imaging is critical for distinguishing hyperstretched DNA from single-stranded DNA that can result from peeling. High-speed hydrodynamic trapping is a powerful yet accessible force spectroscopy method that enables the mechanics of biomolecules to be probed in previously difficult to access regimes.
Collapse
Affiliation(s)
- Yan Jiang
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Theodore Feldman
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- VA Boston Healthcare System, Boston, MA 02130, USA
| | - Julia A.M. Bakx
- Department of Physics and Astronomy and LaserLaB, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Darren Yang
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Wesley P. Wong
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| |
Collapse
|
30
|
Yang B, Liu Z, Liu H, Nash MA. Next Generation Methods for Single-Molecule Force Spectroscopy on Polyproteins and Receptor-Ligand Complexes. Front Mol Biosci 2020; 7:85. [PMID: 32509800 PMCID: PMC7248566 DOI: 10.3389/fmolb.2020.00085] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 04/16/2020] [Indexed: 12/31/2022] Open
Abstract
Single-molecule force spectroscopy with the atomic force microscope provides molecular level insights into protein function, allowing researchers to reconstruct energy landscapes and understand functional mechanisms in biology. With steadily advancing methods, this technique has greatly accelerated our understanding of force transduction, mechanical deformation, and mechanostability within single- and multi-domain polyproteins, and receptor-ligand complexes. In this focused review, we summarize the state of the art in terms of methodology and highlight recent methodological improvements for AFM-SMFS experiments, including developments in surface chemistry, considerations for protein engineering, as well as theory and algorithms for data analysis. We hope that by condensing and disseminating these methods, they can assist the community in improving data yield, reliability, and throughput and thereby enhance the information that researchers can extract from such experiments. These leading edge methods for AFM-SMFS will serve as a groundwork for researchers cognizant of its current limitations who seek to improve the technique in the future for in-depth studies of molecular biomechanics.
Collapse
Affiliation(s)
- Byeongseon Yang
- Department of Chemistry, University of Basel, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Zhaowei Liu
- Department of Chemistry, University of Basel, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Haipei Liu
- Department of Chemistry, University of Basel, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Michael A. Nash
- Department of Chemistry, University of Basel, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| |
Collapse
|
31
|
Rivas-Pardo JA, Li Y, Mártonfalvi Z, Tapia-Rojo R, Unger A, Fernández-Trasancos Á, Herrero-Galán E, Velázquez-Carreras D, Fernández JM, Linke WA, Alegre-Cebollada J. A HaloTag-TEV genetic cassette for mechanical phenotyping of proteins from tissues. Nat Commun 2020; 11:2060. [PMID: 32345978 PMCID: PMC7189229 DOI: 10.1038/s41467-020-15465-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Accepted: 03/09/2020] [Indexed: 11/09/2022] Open
Abstract
Single-molecule methods using recombinant proteins have generated transformative hypotheses on how mechanical forces are generated and sensed in biological tissues. However, testing these mechanical hypotheses on proteins in their natural environment remains inaccesible to conventional tools. To address this limitation, here we demonstrate a mouse model carrying a HaloTag-TEV insertion in the protein titin, the main determinant of myocyte stiffness. Using our system, we specifically sever titin by digestion with TEV protease, and find that the response of muscle fibers to length changes requires mechanical transduction through titin's intact polypeptide chain. In addition, HaloTag-based covalent tethering enables examination of titin dynamics under force using magnetic tweezers. At pulling forces < 10 pN, titin domains are recruited to the unfolded state, and produce 41.5 zJ mechanical work during refolding. Insertion of the HaloTag-TEV cassette in mechanical proteins opens opportunities to explore the molecular basis of cellular force generation, mechanosensing and mechanotransduction.
Collapse
Affiliation(s)
- Jaime Andrés Rivas-Pardo
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
- Center for Genomics and Bioinformatics, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
| | - Yong Li
- Institute of Physiology II, University of Muenster, Muenster, Germany
| | - Zsolt Mártonfalvi
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - Rafael Tapia-Rojo
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
| | - Andreas Unger
- Institute of Physiology II, University of Muenster, Muenster, Germany
| | | | | | | | - Julio M Fernández
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
| | - Wolfgang A Linke
- Institute of Physiology II, University of Muenster, Muenster, Germany.
| | | |
Collapse
|
32
|
Deng Y, Shi S, Zheng B, Wu T, Zheng P. Enzymatic Construction of Protein Polymer/Polyprotein Using OaAEP1 and TEV Protease. Bio Protoc 2020; 10:e3596. [PMID: 33659562 PMCID: PMC7842765 DOI: 10.21769/bioprotoc.3596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 02/24/2020] [Accepted: 02/26/2020] [Indexed: 04/01/2024] Open
Abstract
The development of chemical and biological coupling technologies in recent years has made possible of protein polymers engineering. We have developed an enzymatic method for building polyproteins using a protein ligase OaAEP1 (asparagine endopeptidase 1) and protease TEV (tobacco etching virus). Using a mobile TEV protease site compatible with the OaAEP1 ligation, we achieved a stepwise polymerization of the protein on the surface. The produced polyprotein can be verified by protein unfolding scenario using atomic force microscopy-based single-molecule force spectroscopy (AFM-SMFS). Thus, this study provides an alternative method for polyprotein engineering and immobilization.
Collapse
Affiliation(s)
- Yibing Deng
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 21002, China
| | - Shengchao Shi
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 21002, China
| | - Bin Zheng
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 21002, China
| | - Tao Wu
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 21002, China
| | - Peng Zheng
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 21002, China
| |
Collapse
|
33
|
Lanzicher T, Zhou T, Saripalli C, Keschrumrus V, Smith III JE, Mayans O, Sbaizero O, Granzier H. Single-Molecule Force Spectroscopy on the N2A Element of Titin: Effects of Phosphorylation and CARP. Front Physiol 2020; 11:173. [PMID: 32256378 PMCID: PMC7093598 DOI: 10.3389/fphys.2020.00173] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Accepted: 02/13/2020] [Indexed: 01/08/2023] Open
Abstract
Titin is a large filamentous protein that forms a sarcomeric myofilament with a molecular spring region that develops force in stretched sarcomeres. The molecular spring has a complex make-up that includes the N2A element. This element largely consists of a 104-residue unique sequence (N2A-Us) flanked by immunoglobulin domains (I80 and I81). The N2A element is of interest because it assembles a signalosome with CARP (Cardiac Ankyrin Repeat Protein) as an important component; CARP both interacts with the N2A-Us and I81 and is highly upregulated in response to mechanical stress. The mechanical properties of the N2A element were studied using single-molecule force spectroscopy, including how these properties are affected by CARP and phosphorylation. Three protein constructs were made that consisted of 0, 1, or 2 N2A-Us elements with flanking I80 and I81 domains and with specific handles at their ends for study by atomic force microscopy (AFM). The N2A-Us behaved as an entropic spring with a persistence length (Lp) of ∼0.35 nm and contour length (Lc) of ∼39 nm. CARP increased the Lp of the N2A-Us and the unfolding force of the Ig domains; force clamp experiments showed that CARP reduced the Ig domain unfolding kinetics. These findings suggest that CARP might function as a molecular chaperone that protects I81 from unfolding when mechanical stress is high. The N2A-Us was found to be a PKA substrate, and phosphorylation was blocked by CARP. Mass spectrometry revealed a PKA phosphosite (Ser-9895 in NP_001254479.2) located at the border between the N2A-Us and I81. AFM studies showed that phosphorylation affected neither the Lp of the N2A-Us nor the Ig domain unfolding force (Funfold). Simulating the force-sarcomere length relation of a single titin molecule containing all spring elements showed that the compliance of the N2A-Us only slightly reduces passive force (1.4%) with an additional small reduction by CARP (0.3%). Thus, it is improbable that the compliance of the N2A element has a mechanical function per se. Instead, it is likely that this compliance has local effects on binding of signaling molecules and that it contributes thereby to strain- and phosphorylation- dependent mechano-signaling.
Collapse
Affiliation(s)
- Thomas Lanzicher
- Department of Cellular & Molecular Medicine, The University of Arizona, Tucson, AZ, United States
- Department of Engineering and Architecture, University of Trieste, Trieste, Italy
| | - Tiankun Zhou
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Chandra Saripalli
- Department of Cellular & Molecular Medicine, The University of Arizona, Tucson, AZ, United States
| | - Vic Keschrumrus
- Department of Cellular & Molecular Medicine, The University of Arizona, Tucson, AZ, United States
| | - John E. Smith III
- Department of Cellular & Molecular Medicine, The University of Arizona, Tucson, AZ, United States
| | - Olga Mayans
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Orfeo Sbaizero
- Department of Engineering and Architecture, University of Trieste, Trieste, Italy
| | - Henk Granzier
- Department of Cellular & Molecular Medicine, The University of Arizona, Tucson, AZ, United States
| |
Collapse
|
34
|
Dahal N, Nowitzke J, Eis A, Popa I. Binding-Induced Stabilization Measured on the Same Molecular Protein Substrate Using Single-Molecule Magnetic Tweezers and Heterocovalent Attachments. J Phys Chem B 2020; 124:3283-3290. [DOI: 10.1021/acs.jpcb.0c00167] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Narayan Dahal
- Department of Physics, University of Wisconsin-Milwaukee, 3135 North Maryland Avenue, Milwaukee, Wisconsin 53211, United States
| | - Joel Nowitzke
- Department of Physics, University of Wisconsin-Milwaukee, 3135 North Maryland Avenue, Milwaukee, Wisconsin 53211, United States
| | - Annie Eis
- Department of Physics, University of Wisconsin-Milwaukee, 3135 North Maryland Avenue, Milwaukee, Wisconsin 53211, United States
| | - Ionel Popa
- Department of Physics, University of Wisconsin-Milwaukee, 3135 North Maryland Avenue, Milwaukee, Wisconsin 53211, United States
| |
Collapse
|
35
|
Wagner AM, Knipe JM, Orive G, Peppas NA. Quantum dots in biomedical applications. Acta Biomater 2019; 94:44-63. [PMID: 31082570 PMCID: PMC6642839 DOI: 10.1016/j.actbio.2019.05.022] [Citation(s) in RCA: 169] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 04/10/2019] [Accepted: 05/08/2019] [Indexed: 01/14/2023]
Abstract
Semiconducting nanoparticles, more commonly known as quantum dots, possess unique size and shape dependent optoelectronic properties. In recent years, these unique properties have attracted much attention in the biomedical field to enable real-time tissue imaging (bioimaging), diagnostics, single molecule probes, and drug delivery, among many other areas. The optical properties of quantum dots can be tuned by size and composition, and their high brightness, resistance to photobleaching, multiplexing capacity, and high surface-to-volume ratio make them excellent candidates for intracellular tracking, diagnostics, in vivo imaging, and therapeutic delivery. We discuss recent advances and challenges in the molecular design of quantum dots are discussed, along with applications of quantum dots as drug delivery vehicles, theranostic agents, single molecule probes, and real-time in vivo deep tissue imaging agents. We present a detailed discussion of the biodistribution and toxicity of quantum dots, and highlight recent advances to improve long-term stability in biological buffers, increase quantum yield following bioconjugation, and improve clearance from the body. Last, we present an outlook on future challenges and strategies to further advance translation to clinical application. STATEMENT OF SIGNIFICANCE: Semiconducting nanoparticles, commonly known as quantum dots, possess unique size and shape dependent electrical and optical properties. In recent years, they have attracted much attention in biomedical imaging to enable diagnostics, single molecule probes, and real-time imaging of tumors. This review discusses recent advances and challenges in the design of quantum dots, and highlights how these strategies can further advance translation to clinical applications.
Collapse
Affiliation(s)
- Angela M Wagner
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA; Institute for Biomaterials, Drug Delivery, and Regenerative Medicine, The University of Texas at Austin, Austin, TX, USA
| | - Jennifer M Knipe
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA; Institute for Biomaterials, Drug Delivery, and Regenerative Medicine, The University of Texas at Austin, Austin, TX, USA
| | - Gorka Orive
- NanoBioCel Group, Laboratory of Pharmaceutics, School of Pharmacy, University of the Basque Country UPV/EHU, Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain; Biomedical Research Networking Centre in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Vitoria-Gasteiz, Spain; University Institute for Regenerative Medicine and Oral Implantology - UIRMI (UPV/EHU-Fundación Eduardo Anitua), Vitoria, Spain
| | - Nicholas A Peppas
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA; Institute for Biomaterials, Drug Delivery, and Regenerative Medicine, The University of Texas at Austin, Austin, TX, USA; Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, USA; Department of Pediatrics, Dell Medical School, The University of Texas at Austin, Austin, TX, USA; Department of Surgery and Perioperative Care, Dell Medical School, The University of Texas at Austin, Austin, TX, USA; Division of Molecular Pharmaceutics and Drug Delivery, College of Pharmacy, The University of Texas at Austin, Austin, TX, USA.
| |
Collapse
|
36
|
Berki T, Bakunts A, Duret D, Fabre L, Ladavière C, Orsi A, Charreyre MT, Raimondi A, van Anken E, Favier A. Advanced Fluorescent Polymer Probes for the Site-Specific Labeling of Proteins in Live Cells Using the HaloTag Technology. ACS OMEGA 2019; 4:12841-12847. [PMID: 31460409 PMCID: PMC6682114 DOI: 10.1021/acsomega.9b01643] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 07/16/2019] [Indexed: 06/01/2023]
Abstract
We report the site-specific and covalent bioconjugation of fluorescent polymer chains to proteins in live cells using the HaloTag technology. Polymer chains bearing a Halo-ligand precisely located at their α-chain-end were synthesized in a controlled manner owing to the RAFT polymerization process. They were labeled in lateral position by several organic fluorophores such as AlexaFluor 647. The resulting Halo-ligand polymer probe was finally shown to selectively recognize and label HaloTag proteins present at the membrane of live cells using confocal fluorescence microscopy. Such a polymer bioconjugation approach holds great promises for various applications ranging from cell imaging to cell surface functionalization.
Collapse
Affiliation(s)
- Thomas Berki
- Univ
Lyon, Université Lyon 1, INSA de Lyon, CNRS, Laboratoire Ingénierie
des Matériaux Polymères, UMR5223, F-69621 Villeurbanne, France
- Univ
Lyon, Ens de Lyon, CNRS, Laboratoire Joliot-Curie, USR3010, F-69364 Lyon, France
| | - Anush Bakunts
- Division of Genetics and Cell Biology and Experimental
Imaging Center, San Raffaele Scientific
Institute, Milan 20132, Italy
| | - Damien Duret
- Univ
Lyon, Université Lyon 1, INSA de Lyon, CNRS, Laboratoire Ingénierie
des Matériaux Polymères, UMR5223, F-69621 Villeurbanne, France
- Univ
Lyon, Ens de Lyon, CNRS, Laboratoire Joliot-Curie, USR3010, F-69364 Lyon, France
| | - Laura Fabre
- Univ
Lyon, Université Lyon 1, INSA de Lyon, CNRS, Laboratoire Ingénierie
des Matériaux Polymères, UMR5223, F-69621 Villeurbanne, France
| | - Catherine Ladavière
- Univ
Lyon, Université Lyon 1, INSA de Lyon, CNRS, Laboratoire Ingénierie
des Matériaux Polymères, UMR5223, F-69621 Villeurbanne, France
| | - Andrea Orsi
- Division of Genetics and Cell Biology and Experimental
Imaging Center, San Raffaele Scientific
Institute, Milan 20132, Italy
- Università
Vita-Salute San Raffaele, Milan 20132, Italy
| | - Marie-Thérèse Charreyre
- Univ
Lyon, Université Lyon 1, INSA de Lyon, CNRS, Laboratoire Ingénierie
des Matériaux Polymères, UMR5223, F-69621 Villeurbanne, France
- Univ
Lyon, Ens de Lyon, CNRS, Laboratoire Joliot-Curie, USR3010, F-69364 Lyon, France
| | - Andrea Raimondi
- Division of Genetics and Cell Biology and Experimental
Imaging Center, San Raffaele Scientific
Institute, Milan 20132, Italy
| | - Eelco van Anken
- Division of Genetics and Cell Biology and Experimental
Imaging Center, San Raffaele Scientific
Institute, Milan 20132, Italy
- Università
Vita-Salute San Raffaele, Milan 20132, Italy
| | - Arnaud Favier
- Univ
Lyon, Université Lyon 1, INSA de Lyon, CNRS, Laboratoire Ingénierie
des Matériaux Polymères, UMR5223, F-69621 Villeurbanne, France
- Univ
Lyon, Ens de Lyon, CNRS, Laboratoire Joliot-Curie, USR3010, F-69364 Lyon, France
| |
Collapse
|
37
|
Eckels EC, Tapia-Rojo R, Rivas-Pardo JA, Fernández JM. The Work of Titin Protein Folding as a Major Driver in Muscle Contraction. Annu Rev Physiol 2019; 80:327-351. [PMID: 29433413 DOI: 10.1146/annurev-physiol-021317-121254] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Single-molecule atomic force microscopy and magnetic tweezers experiments have demonstrated that titin immunoglobulin (Ig) domains are capable of folding against a pulling force, generating mechanical work that exceeds that produced by a myosin motor. We hypothesize that upon muscle activation, formation of actomyosin cross bridges reduces the force on titin, causing entropic recoil of the titin polymer and triggering the folding of the titin Ig domains. In the physiological force range of 4-15 pN under which titin operates in muscle, the folding contraction of a single Ig domain can generate 200% of the work of entropic recoil and occurs at forces that exceed the maximum stalling force of single myosin motors. Thus, titin operates like a mechanical battery, storing elastic energy efficiently by unfolding Ig domains and delivering the charge back by folding when the motors are activated during a contraction. We advance the hypothesis that titin folding and myosin activation act as inextricable partners during muscle contraction.
Collapse
Affiliation(s)
- Edward C Eckels
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA; , .,Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University Medical Center, New York, NY 10032, USA
| | - Rafael Tapia-Rojo
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA; ,
| | | | - Julio M Fernández
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA; ,
| |
Collapse
|
38
|
Ephemeral states in protein folding under force captured with a magnetic tweezers design. Proc Natl Acad Sci U S A 2019; 116:7873-7878. [PMID: 30936303 DOI: 10.1073/pnas.1821284116] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Magnetic tape heads are ubiquitously used to read and record on magnetic tapes in technologies as diverse as old VHS tapes, modern hard-drive disks, or magnetic bands on credit cards. Their design highlights the ability to convert electric signals into fluctuations of the magnetic field at very high frequencies, which is essential for the high-density storage demanded nowadays. Here, we twist this conventional use of tape heads to implement one in a magnetic tweezers design, which offers the unique capability of changing the force with a bandwidth of ∼10 kHz. We calibrate our instrument by developing an analytical expression that predicts the magnetic force acting on a superparamagnetic bead based on the Karlqvist approximation of the magnetic field created by a tape head. This theory is validated by measuring the force dependence of protein L unfolding/folding step sizes and the folding properties of the R3 talin domain. We demonstrate the potential of our instrument by carrying out millisecond-long quenches to capture the formation of the ephemeral molten globule state in protein L, which has never been observed before. Our instrument provides the capability of interrogating individual molecules under fast-changing forces with a control and resolution below a fraction of a piconewton, opening a range of force spectroscopy protocols to study protein dynamics under force.
Collapse
|
39
|
Mechanobiology: protein refolding under force. Emerg Top Life Sci 2018; 2:687-699. [PMID: 33530665 DOI: 10.1042/etls20180044] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 09/19/2018] [Accepted: 09/19/2018] [Indexed: 02/03/2023]
Abstract
The application of direct force to a protein enables to probe wide regions of its energy surface through conformational transitions as unfolding, extending, recoiling, collapsing, and refolding. While unfolding under force typically displayed a two-state behavior, refolding under force, from highly extended unfolded states, displayed a more complex behavior. The first recording of protein refolding at a force quench step displayed an initial rapid elastic recoil, followed by a plateau phase at some extension, concluding with a collapse to a final state, at which refolding occurred. These findings stirred a lively discussion, which led to further experimental and theoretical investigation of this behavior. It was demonstrated that the polymeric chain of the unfolded protein is required to fully collapse to a globular conformation for the maturation of native structure. This behavior was modeled using one-dimensional free energy landscape over the end-to-end length reaction coordinate, the collective measured variable. However, at low forces, conformational space is not well captured by such models, and using two-dimensional energy surfaces provides further insight into the dynamics of this process. This work reviews the main concepts of protein refolding under constant force, which is essential for understanding how mechanotransducing proteins operate in vivo.
Collapse
|
40
|
Nathwani B, Shih WM, Wong WP. Force Spectroscopy and Beyond: Innovations and Opportunities. Biophys J 2018; 115:2279-2285. [PMID: 30447991 PMCID: PMC6302248 DOI: 10.1016/j.bpj.2018.10.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 10/08/2018] [Accepted: 10/25/2018] [Indexed: 12/26/2022] Open
Abstract
Life operates at the intersection of chemistry and mechanics. Over the years, we have made remarkable progress in understanding life from a biochemical perspective and the mechanics of life at the single-molecule scale. Yet the full integration of physical and mechanical models into mainstream biology has been impeded by technical and conceptual barriers, including limitations in our ability to 1) easily measure and apply mechanical forces to biological systems, 2) scale these measurements from single-molecule characterization to more complex biomolecular systems, and 3) model and interpret biophysical data in a coherent way across length scales that span single molecules to cells to multicellular organisms. In this manuscript, through a look at historical and recent developments in force spectroscopy techniques and a discussion of a few exemplary open problems in cellular biomechanics, we aim to identify research opportunities that will help us reach our goal of a more complete and integrated understanding of the role of force and mechanics in biological systems.
Collapse
Affiliation(s)
- Bhavik Nathwani
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts.
| | - William M Shih
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts
| | - Wesley P Wong
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts.
| |
Collapse
|
41
|
Sutherland AR, Alam MK, Geyer CR. Post‐translational Assembly of Protein Parts into Complex Devices by Using SpyTag/SpyCatcher Protein Ligase. Chembiochem 2018; 20:319-328. [DOI: 10.1002/cbic.201800538] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Indexed: 01/21/2023]
Affiliation(s)
- Ashley R. Sutherland
- Department of BiochemistryUniversity of Saskatchewan Saskatoon SK S7N 5E5 Canada
| | - Md. Kausar Alam
- Donnelly Centre for Cellular and Biomolecular ResearchUniversity of Toronto Toronto ON M5S3E1 Canada
| | - C. Ronald Geyer
- Department of Pathology and Laboratory MedicineUniversity of Saskatchewan Saskatoon SK S7N 5E5 Canada
| |
Collapse
|
42
|
Conformational entropy of a single peptide controlled under force governs protease recognition and catalysis. Proc Natl Acad Sci U S A 2018; 115:11525-11530. [PMID: 30341218 DOI: 10.1073/pnas.1803872115] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
An immense repertoire of protein chemical modifications catalyzed by enzymes is available as proteomics data. Quantifying the impact of the conformational dynamics of the modified peptide remains challenging to understand the decisive kinetics and amino acid sequence specificity of these enzymatic reactions in vivo, because the target peptide must be disordered to accommodate the specific enzyme-binding site. Here, we were able to control the conformation of a single-molecule peptide chain by applying mechanical force to activate and monitor its specific cleavage by a model protease. We found that the conformational entropy impacts the reaction in two distinct ways. First, the flexibility and accessibility of the substrate peptide greatly increase upon mechanical unfolding. Second, the conformational sampling of the disordered peptide drives the specific recognition, revealing force-dependent reaction kinetics. These results support a mechanism of peptide recognition based on conformational selection from an ensemble that we were able to quantify with a torsional free-energy model. Our approach can be used to predict how entropy affects site-specific modifications of proteins and prompts conformational and mechanical selectivity.
Collapse
|
43
|
Haining AWM, Rahikainen R, Cortes E, Lachowski D, Rice A, von Essen M, Hytönen VP, del Río Hernández A. Mechanotransduction in talin through the interaction of the R8 domain with DLC1. PLoS Biol 2018; 16:e2005599. [PMID: 30028837 PMCID: PMC6054372 DOI: 10.1371/journal.pbio.2005599] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2018] [Accepted: 06/19/2018] [Indexed: 11/19/2022] Open
Abstract
The mechanical unfolding of proteins is a cellular mechanism for force transduction with potentially broad implications in cell fate. Despite this, the mechanism by which protein unfolding elicits differential downstream signalling pathways remains poorly understood. Here, we used protein engineering, atomic force microscopy, and biophysical tools to delineate how protein unfolding controls cell mechanics. Deleted in liver cancer 1 (DLC1) is a negative regulator of Ras homolog family member A (RhoA) and cell contractility that regulates cell behaviour when localised to focal adhesions bound to folded talin. Using a talin mutant resistant to force-induced unfolding of R8 domain, we show that talin unfolding determines DLC1 downstream signalling and, consequently, cell mechanics. We propose that this new mechanism of mechanotransduction may have implications for a wide variety of associated cellular processes.
Collapse
Affiliation(s)
- Alexander William M. Haining
- Cellular and Molecular Biomechanics Laboratory, Department of Bioengineering, Imperial College London, London, United Kingdom
| | - Rolle Rahikainen
- Faculty of Medicine and Life Sciences and BioMediTech, University of Tampere, Finland and Fimlab Laboratories, Tampere, Finland
| | - Ernesto Cortes
- Cellular and Molecular Biomechanics Laboratory, Department of Bioengineering, Imperial College London, London, United Kingdom
| | - Dariusz Lachowski
- Cellular and Molecular Biomechanics Laboratory, Department of Bioengineering, Imperial College London, London, United Kingdom
| | - Alistair Rice
- Cellular and Molecular Biomechanics Laboratory, Department of Bioengineering, Imperial College London, London, United Kingdom
| | - Magdalena von Essen
- Faculty of Medicine and Life Sciences and BioMediTech, University of Tampere, Finland and Fimlab Laboratories, Tampere, Finland
| | - Vesa P. Hytönen
- Faculty of Medicine and Life Sciences and BioMediTech, University of Tampere, Finland and Fimlab Laboratories, Tampere, Finland
| | - Armando del Río Hernández
- Cellular and Molecular Biomechanics Laboratory, Department of Bioengineering, Imperial College London, London, United Kingdom
| |
Collapse
|
44
|
Nadler H, Shaulov L, Blitsman Y, Mordechai M, Jopp J, Sal-Man N, Berkovich R. Deciphering the Mechanical Properties of Type III Secretion System EspA Protein by Single Molecule Force Spectroscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:6261-6270. [PMID: 29726683 DOI: 10.1021/acs.langmuir.8b01198] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Bacterial pathogens inject virulence factors into host cells during bacterial infections using type III secretion systems. In enteropathogenic Escherichia coli, this system contains an external filament, formed by a self-oligomerizing protein called E. coli secreted protein A (EspA). The EspA filament penetrates the thick viscous mucus layer to facilitate the attachment of the bacteria to the gut-epithelium. To do that, the EspA filament requires noteworthy mechanical endurance considering the mechanical shear stresses found within the intestinal tract. To date, the mechanical properties of the EspA filament and the structural and biophysical knowledge of monomeric EspA are very limited, mostly due to the strong tendency of the protein to self-oligomerize. To overcome this limitation, we employed a single molecule force spectroscopy (SMFS) technique and studied the mechanical properties of EspA. Force extension dynamic of (I91)4-EspA-(I91)4 chimera revealed two structural unfolding events occurring at low forces during EspA unfolding, thus indicating no unique mechanical stability of the monomeric protein. SMFS examination of purified monomeric EspA protein, treated by a gradually refolding protocol, exhibited similar mechanical properties as the EspA protein within the (I91)4-EspA-(I91)4 chimera. Overall, our results suggest that the mechanical integrity of the EspA filament likely originates from the interactions between EspA monomers and not from the strength of an individual monomer.
Collapse
Affiliation(s)
- Hila Nadler
- Department of Chemical Engineering , Ben-Gurion University of the Negev , Beer Sheva 8410501 , Israel
| | - Lihi Shaulov
- Department of Microbiology, Immunology and Genetics , Ben-Gurion University of the Negev , Beer Sheva 8410501 , Israel
| | - Yossi Blitsman
- Department of Chemical Engineering , Ben-Gurion University of the Negev , Beer Sheva 8410501 , Israel
| | - Moran Mordechai
- Department of Chemical Engineering , Ben-Gurion University of the Negev , Beer Sheva 8410501 , Israel
| | - Jürgen Jopp
- The Ilse Katz Institute for Nanoscale Science and Technology , Ben-Gurion University of the Negev , Beer Sheva 8410501 , Israel
| | - Neta Sal-Man
- Department of Microbiology, Immunology and Genetics , Ben-Gurion University of the Negev , Beer Sheva 8410501 , Israel
| | - Ronen Berkovich
- Department of Chemical Engineering , Ben-Gurion University of the Negev , Beer Sheva 8410501 , Israel
- The Ilse Katz Institute for Nanoscale Science and Technology , Ben-Gurion University of the Negev , Beer Sheva 8410501 , Israel
| |
Collapse
|
45
|
Wang GF, Qin H, Gao X, Cao Y, Wang W, Wang FC, Wu HA, Cong HP, Yu SH. Graphene Thin Films by Noncovalent-Interaction-Driven Assembly of Graphene Monolayers for Flexible Supercapacitors. Chem 2018. [DOI: 10.1016/j.chempr.2018.01.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
|
46
|
Sumbul F, Marchesi A, Rico F. History, rare, and multiple events of mechanical unfolding of repeat proteins. J Chem Phys 2018; 148:123335. [PMID: 29604819 DOI: 10.1063/1.5013259] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Mechanical unfolding of proteins consisting of repeat domains is an excellent tool to obtain large statistics. Force spectroscopy experiments using atomic force microscopy on proteins presenting multiple domains have revealed that unfolding forces depend on the number of folded domains (history) and have reported intermediate states and rare events. However, the common use of unspecific attachment approaches to pull the protein of interest holds important limitations to study unfolding history and may lead to discarding rare and multiple probing events due to the presence of unspecific adhesion and uncertainty on the pulling site. Site-specific methods that have recently emerged minimize this uncertainty and would be excellent tools to probe unfolding history and rare events. However, detailed characterization of these approaches is required to identify their advantages and limitations. Here, we characterize a site-specific binding approach based on the ultrastable complex dockerin/cohesin III revealing its advantages and limitations to assess the unfolding history and to investigate rare and multiple events during the unfolding of repeated domains. We show that this approach is more robust, reproducible, and provides larger statistics than conventional unspecific methods. We show that the method is optimal to reveal the history of unfolding from the very first domain and to detect rare events, while being more limited to assess intermediate states. Finally, we quantify the forces required to unfold two molecules pulled in parallel, difficult when using unspecific approaches. The proposed method represents a step forward toward more reproducible measurements to probe protein unfolding history and opens the door to systematic probing of rare and multiple molecule unfolding mechanisms.
Collapse
Affiliation(s)
- Fidan Sumbul
- U1006, Aix-Marseille Université and INSERM, 163 Avenue de Luminy, 13009 Marseille, France
| | - Arin Marchesi
- U1006, Aix-Marseille Université and INSERM, 163 Avenue de Luminy, 13009 Marseille, France
| | - Felix Rico
- U1006, Aix-Marseille Université and INSERM, 163 Avenue de Luminy, 13009 Marseille, France
| |
Collapse
|
47
|
Khoury LR, Nowitzke J, Shmilovich K, Popa I. Study of Biomechanical Properties of Protein-Based Hydrogels Using Force-Clamp Rheometry. Macromolecules 2018. [DOI: 10.1021/acs.macromol.7b02160] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Luai R. Khoury
- Department of Physics, University of Wisconsin—Milwaukee, 3135 North Maryland Ave., Milwaukee, Wisconsin 53211, United States
| | - Joel Nowitzke
- Department of Physics, University of Wisconsin—Milwaukee, 3135 North Maryland Ave., Milwaukee, Wisconsin 53211, United States
| | - Kirill Shmilovich
- Department of Physics, University of Wisconsin—Milwaukee, 3135 North Maryland Ave., Milwaukee, Wisconsin 53211, United States
| | - Ionel Popa
- Department of Physics, University of Wisconsin—Milwaukee, 3135 North Maryland Ave., Milwaukee, Wisconsin 53211, United States
| |
Collapse
|
48
|
Walder R, Van Patten WJ, Adhikari A, Perkins TT. Going Vertical To Improve the Accuracy of Atomic Force Microscopy Based Single-Molecule Force Spectroscopy. ACS NANO 2018; 12:198-207. [PMID: 29244486 DOI: 10.1021/acsnano.7b05721] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Single-molecule force spectroscopy (SMFS) is a powerful technique to characterize the energy landscape of individual proteins, the mechanical properties of nucleic acids, and the strength of receptor-ligand interactions. Atomic force microscopy (AFM)-based SMFS benefits from ongoing progress in improving the precision and stability of cantilevers and the AFM itself. Underappreciated is that the accuracy of such AFM studies remains hindered by inadvertently stretching molecules at an angle while measuring only the vertical component of the force and extension, degrading both measurements. This inaccuracy is particularly problematic in AFM studies using double-stranded DNA and RNA due to their large persistence length (p ≈ 50 nm), often limiting such studies to other SMFS platforms (e.g., custom-built optical and magnetic tweezers). Here, we developed an automated algorithm that aligns the AFM tip above the DNA's attachment point to a coverslip. Importantly, this algorithm was performed at low force (10-20 pN) and relatively fast (15-25 s), preserving the connection between the tip and the target molecule. Our data revealed large uncorrected lateral offsets for 100 and 650 nm DNA molecules [24 ± 18 nm (mean ± standard deviation) and 180 ± 110 nm, respectively]. Correcting this offset yielded a 3-fold improvement in accuracy and precision when characterizing DNA's overstretching transition. We also demonstrated high throughput by acquiring 88 geometrically corrected force-extension curves of a single individual 100 nm DNA molecule in ∼40 min and versatility by aligning polyprotein- and PEG-based protein-ligand assays. Importantly, our software-based algorithm was implemented on a commercial AFM, so it can be broadly adopted. More generally, this work illustrates how to enhance AFM-based SMFS by developing more sophisticated data-acquisition protocols.
Collapse
Affiliation(s)
- Robert Walder
- JILA, National Institute of Standards and Technology , and University of Colorado, Boulder, Colorado 80309, United States
| | - William J Van Patten
- JILA, National Institute of Standards and Technology , and University of Colorado, Boulder, Colorado 80309, United States
| | - Ayush Adhikari
- JILA, National Institute of Standards and Technology , and University of Colorado, Boulder, Colorado 80309, United States
| | - Thomas T Perkins
- JILA, National Institute of Standards and Technology , and University of Colorado, Boulder, Colorado 80309, United States
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado , Boulder, Colorado 80309, United States
| |
Collapse
|
49
|
Abstract
Single-molecule force spectroscopy (SMFS) measurements allow for quantification of the molecular forces required to unfold individual protein domains. Atomic force microscopy (AFM) is one of the long-established techniques for force spectroscopy (FS). Although FS at conventional AFM pulling rates provides valuable information on protein unfolding, in order to get a more complete picture of the mechanism, explore new regimes, and combine and compare experiments with simulations, we need higher pulling rates and μs-time resolution, now accessible via high-speed force spectroscopy (HS-FS). In this chapter, we provide a step-by-step protocol of HS-FS including sample preparation, measurements and analysis of the acquired data using HS-AFM with an illustrative example on unfolding of a well-studied concatamer made of eight repeats of the titin I91 domain.
Collapse
|
50
|
|