1
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Khare E, Gonzalez Obeso C, Martín-Moldes Z, Talib A, Kaplan DL, Holten-Andersen N, Blank KG, Buehler MJ. Heterogeneous and Cooperative Rupture of Histidine-Ni 2+ Metal-Coordination Bonds on Rationally Designed Protein Templates. ACS Biomater Sci Eng 2024; 10:2945-2955. [PMID: 38669114 DOI: 10.1021/acsbiomaterials.3c01819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2024]
Abstract
Metal-coordination bonds, a highly tunable class of dynamic noncovalent interactions, are pivotal to the function of a variety of protein-based natural materials and have emerged as binding motifs to produce strong, tough, and self-healing bioinspired materials. While natural proteins use clusters of metal-coordination bonds, synthetic materials frequently employ individual bonds, resulting in mechanically weak materials. To overcome this current limitation, we rationally designed a series of elastin-like polypeptide templates with the capability of forming an increasing number of intermolecular histidine-Ni2+ metal-coordination bonds. Using single-molecule force spectroscopy and steered molecular dynamics simulations, we show that templates with three histidine residues exhibit heterogeneous rupture pathways, including the simultaneous rupture of at least two bonds with more-than-additive rupture forces. The methodology and insights developed improve our understanding of the molecular interactions that stabilize metal-coordinated proteins and provide a general route for the design of new strong, metal-coordinated materials with a broad spectrum of dissipative time scales.
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Affiliation(s)
- Eesha Khare
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Laboratory for Atomistic and Molecular Mechanics (LAMM), Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Mechano(bio)chemistry, Max Planck Institute of Colloids and Interfaces, Am Muehlenberg 1, 14476 Potsdam, Germany
| | | | - Zaira Martín-Moldes
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, United States
| | - Ayesha Talib
- Mechano(bio)chemistry, Max Planck Institute of Colloids and Interfaces, Am Muehlenberg 1, 14476 Potsdam, Germany
| | - David L Kaplan
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, United States
| | - Niels Holten-Andersen
- Department of Bioengineering and Materials Science and EngineeringLehigh University, 27 Memorial Dr W, Bethlehem, Pennsylvania 18015, United States
| | - Kerstin G Blank
- Mechano(bio)chemistry, Max Planck Institute of Colloids and Interfaces, Am Muehlenberg 1, 14476 Potsdam, Germany
- Department of Biomolecular & Selforganizing Matter, Institute of Experimental Physics, Johannes Kepler University, Altenberger Strasse 69, 4040 Linz, Austria
| | - Markus J Buehler
- Laboratory for Atomistic and Molecular Mechanics (LAMM), Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Center for Computational Science and Engineering, Schwarzman College of Computing, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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2
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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 Appl Mater 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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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
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3
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Wu Z, Bayón JL, Kouznetsova TB, Ouchi T, Barkovich KJ, Hsu SK, Craig SL, Steinmetz NF. Virus-like Particles Armored by an Endoskeleton. Nano Lett 2024; 24:2989-2997. [PMID: 38294951 DOI: 10.1021/acs.nanolett.3c03806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2024]
Abstract
Many virus-like particles (VLPs) have good chemical, thermal, and mechanical stabilities compared to those of other biologics. However, their stability needs to be improved for the commercialization and use in translation of VLP-based materials. We developed an endoskeleton-armored strategy for enhancing VLP stability. Specifically, the VLPs of physalis mottle virus (PhMV) and Qβ were used to demonstrate this concept. We built an internal polymer "backbone" using a maleimide-PEG15-maleimide cross-linker to covalently interlink viral coat proteins inside the capsid cavity, while the native VLPs are held together by only noncovalent bonding between subunits. Endoskeleton-armored VLPs exhibited significantly improved thermal stability (95 °C for 15 min), increased resistance to denaturants (i.e., surfactants, pHs, chemical denaturants, and organic solvents), and enhanced mechanical performance. Single-molecule force spectroscopy demonstrated a 6-fold increase in rupture distance and a 1.9-fold increase in rupture force of endoskeleton-armored PhMV. Overall, this endoskeleton-armored strategy provides more opportunities for the development and applications of materials.
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Affiliation(s)
- Zhuohong Wu
- Department of NanoEngineering, University of California, San Diego, La Jolla, California 92093, United States
- Center for Nano-ImmunoEngineering, University of California, San Diego, La Jolla, California 92093, United States
- Moores Cancer Center, University of California, San Diego, La Jolla, California 92093, United States
- Shu and K. C. Chien and Peter Farrell Collaboratory, University of California, San Diego, La Jolla, California 92093, United States
| | - Jorge L Bayón
- Department of NanoEngineering, University of California, San Diego, La Jolla, California 92093, United States
- Center for Nano-ImmunoEngineering, University of California, San Diego, La Jolla, California 92093, United States
- Moores Cancer Center, University of California, San Diego, La Jolla, California 92093, United States
- Shu and K. C. Chien and Peter Farrell Collaboratory, University of California, San Diego, La Jolla, California 92093, United States
| | - Tatiana B Kouznetsova
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Tetsu Ouchi
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Krister J Barkovich
- Center for Nano-ImmunoEngineering, University of California, San Diego, La Jolla, California 92093, United States
- Moores Cancer Center, University of California, San Diego, La Jolla, California 92093, United States
- Shu and K. C. Chien and Peter Farrell Collaboratory, University of California, San Diego, La Jolla, California 92093, United States
- Department of Radiology, University of California, San Diego, La Jolla, California 92093, United States
| | - Sean K Hsu
- Center for Nano-ImmunoEngineering, University of California, San Diego, La Jolla, California 92093, United States
- Moores Cancer Center, University of California, San Diego, La Jolla, California 92093, United States
- Shu and K. C. Chien and Peter Farrell Collaboratory, University of California, San Diego, La Jolla, California 92093, United States
- Department of Molecular Biology, University of California, San Diego, La Jolla, California 92093, United States
| | - Stephen L Craig
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Nicole F Steinmetz
- Department of NanoEngineering, University of California, San Diego, La Jolla, California 92093, United States
- Center for Nano-ImmunoEngineering, University of California, San Diego, La Jolla, California 92093, United States
- Moores Cancer Center, University of California, San Diego, La Jolla, California 92093, United States
- Shu and K. C. Chien and Peter Farrell Collaboratory, University of California, San Diego, La Jolla, California 92093, United States
- Department of Radiology, University of California, San Diego, La Jolla, California 92093, United States
- Department of Molecular Biology, University of California, San Diego, La Jolla, California 92093, United States
- Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, United States
- Institute for Materials Discovery and Design, University of California, San Diego, La Jolla, California 92093, United States
- Center for Engineering in Cancer, Institute for Engineering in Medicine, University of California, San Diego, La Jolla, California 92093, United States
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4
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Tang H, Xiao Y, Qian L, Wang Z, Lu M, Yao N, Zhou T, Tian F, Cao L, Zheng P, Dong X. Mechanistic insights into the C-type lectin receptor CLEC12A-mediated immune recognition of monosodium urate crystal. J Biol Chem 2024; 300:105765. [PMID: 38367667 PMCID: PMC10959670 DOI: 10.1016/j.jbc.2024.105765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 02/06/2024] [Accepted: 02/13/2024] [Indexed: 02/19/2024] Open
Abstract
CLEC12A, a member of the C-type lectin receptor family involved in immune homeostasis, recognizes MSU crystals released from dying cells. However, the molecular mechanism underlying the CLEC12A-mediated recognition of MSU crystals remains unclear. Herein, we reported the crystal structure of the human CLEC12A-C-type lectin-like domain (CTLD) and identified a unique "basic patch" site on CLEC12A-CTLD that is necessary for the binding of MSU crystals. Meanwhile, we determined the interaction strength between CLEC12A-CTLD and MSU crystals using single-molecule force spectroscopy. Furthermore, we found that CLEC12A clusters at the cell membrane and seems to serve as an internalizing receptor of MSU crystals. Altogether, these findings provide mechanistic insights for understanding the molecular mechanisms underlying the interplay between CLEC12A and MSU crystals.
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Affiliation(s)
- Hua Tang
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Biochemistry, School of Life Sciences, Nanjing University, Nanjing, China; Engineering Research Center of Protein and Peptide Medicine, Ministry of Education, Nanjing, China.
| | - Yuelong Xiao
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, China
| | - Lei Qian
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Biochemistry, School of Life Sciences, Nanjing University, Nanjing, China
| | - Zibin Wang
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Biochemistry, School of Life Sciences, Nanjing University, Nanjing, China
| | - Ming Lu
- Westlake laboratory, Westlake University, Hangzhou, Zhejiang, China
| | - Nan Yao
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Biochemistry, School of Life Sciences, Nanjing University, Nanjing, China
| | - Ting Zhou
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Biochemistry, School of Life Sciences, Nanjing University, Nanjing, 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, China
| | - Longxing Cao
- Westlake laboratory, Westlake University, Hangzhou, Zhejiang, 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, China.
| | - Xianchi Dong
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Biochemistry, School of Life Sciences, Nanjing University, Nanjing, China; Engineering Research Center of Protein and Peptide Medicine, Ministry of Education, Nanjing, China; Institute of Artificial Intelligence Biomedicine, Nanjing University, Nanjing, China.
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5
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Jacobson DR, Perkins TT. Quantifying a light-induced energetic change in bacteriorhodopsin by force spectroscopy. Proc Natl Acad Sci U S A 2024; 121:e2313818121. [PMID: 38324569 PMCID: PMC10873598 DOI: 10.1073/pnas.2313818121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 12/26/2023] [Indexed: 02/09/2024] Open
Abstract
Ligand-induced conformational changes are critical to the function of many membrane proteins and arise from numerous intramolecular interactions. In the photocycle of the model membrane protein bacteriorhodopsin (bR), absorption of a photon by retinal triggers a conformational cascade that results in pumping a proton across the cell membrane. While decades of spectroscopy and structural studies have probed this photocycle in intricate detail, changes in intramolecular energetics that underlie protein motions have remained elusive to experimental quantification. Here, we measured these energetics on the millisecond time scale using atomic-force-microscopy-based single-molecule force spectroscopy. Precisely, timed light pulses triggered the bR photocycle while we measured the equilibrium unfolding and refolding of the terminal 8-amino-acid region of bR's G-helix. These dynamics changed when the EF-helix pair moved ~9 Å away from this end of the G helix during the "open" portion of bR's photocycle. In ~60% of the data, we observed abrupt light-induced destabilization of 3.4 ± 0.3 kcal/mol, lasting 38 ± 3 ms. The kinetics and pH-dependence of this destabilization were consistent with prior measurements of bR's open phase. The frequency of light-induced destabilization increased with the duration of illumination and was dramatically reduced in the triple mutant (D96G/F171C/F219L) thought to trap bR in its open phase. In the other ~40% of the data, photoexcitation unexpectedly stabilized a longer-lived putative misfolded state. Through this work, we establish a general single-molecule force spectroscopy approach for measuring ligand-induced energetics and lifetimes in membrane proteins.
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Affiliation(s)
- David R. Jacobson
- JILA, National Institute of Standards and Technology and University of Colorado, Boulder, CO80309
| | - Thomas T. Perkins
- JILA, National Institute of Standards and Technology and University of Colorado, Boulder, CO80309
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO80309
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6
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Yu M, Jiang C, Lai B, Zhang K. Exploring Novel Sensor Design Ideas through Concentration-Induced Conformational Changes in PEG Single Chains. Sensors (Basel) 2024; 24:883. [PMID: 38339600 PMCID: PMC10856974 DOI: 10.3390/s24030883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 01/16/2024] [Accepted: 01/24/2024] [Indexed: 02/12/2024]
Abstract
Polyethylene glycol (PEG) is an artificial polymer with good biocompatibility and a low cost, which has a wide range of applications. In this study, the dynamic response of PEG single chains to different ion concentrations was investigated from a microscopic point of view based on single-molecule force spectroscopy, revealing unique interactions that go beyond the traditional sensor-design paradigm. Under low concentrations of potassium chloride, PEG single chains exhibit a gradual reduction in rigidity, while, conversely, high concentrations induce a progressive increase in rigidity. This dichotomy serves as the cornerstone for a profound understanding of PEG conformational dynamics under diverse ion environments. Capitalizing on the remarkable sensitivity of PEG single chains to ion concentration shifts, we introduce innovative sensor-design ideas. Rooted in the adaptive nature of PEG single chains, these sensor designs extend beyond the traditional applications, promising advancements in environmental monitoring, healthcare, and materials science.
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Affiliation(s)
- Miao Yu
- School of Mechanical Engineering, Sichuan University, Chengdu 610065, China; (M.Y.); (C.J.); (B.L.)
- Yibin Industrial Technology Research Institute, Sichuan University, Yibin 644000, China
| | - Chong Jiang
- School of Mechanical Engineering, Sichuan University, Chengdu 610065, China; (M.Y.); (C.J.); (B.L.)
- Yibin Industrial Technology Research Institute, Sichuan University, Yibin 644000, China
| | - Bing Lai
- School of Mechanical Engineering, Sichuan University, Chengdu 610065, China; (M.Y.); (C.J.); (B.L.)
- Yibin Industrial Technology Research Institute, Sichuan University, Yibin 644000, China
| | - Kai Zhang
- School of Mechanical Engineering, Sichuan University, Chengdu 610065, China; (M.Y.); (C.J.); (B.L.)
- Yibin Industrial Technology Research Institute, Sichuan University, Yibin 644000, China
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7
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Mukherjee S, Goswami S, Dash S, Samanta D. Structural basis of molecular recognition among classical cadherins mediating cell adhesion. Biochem Soc Trans 2023; 51:2103-2115. [PMID: 37970977 DOI: 10.1042/bst20230356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 10/30/2023] [Accepted: 11/02/2023] [Indexed: 11/19/2023]
Abstract
Cadherins are type-I membrane glycoproteins that primarily participate in calcium-dependent cell adhesion and homotypic cell sorting in various stages of embryonic development. Besides their crucial role in cellular and physiological processes, increasing studies highlight their involvement in pathophysiological functions ranging from cancer progression and metastasis to being entry receptors for pathogens. Cadherins mediate these cellular processes through homophilic, as well as heterophilic interactions (within and outside the superfamily) by their membrane distal ectodomains. This review provides an in-depth structural perspective of molecular recognition among type-I and type-II classical cadherins. Furthermore, this review offers structural insights into different dimeric assemblies like the 'strand-swap dimer' and 'X-dimer' as well as mechanisms relating these dimer forms like 'two-step adhesion' and 'encounter complex'. Alongside providing structural details, this review connects structural studies to bond mechanics merging crystallographic and single-molecule force spectroscopic findings. Finally, the review discusses the recent discoveries on dimeric intermediates that uncover prospects of further research beyond two-step adhesion.
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Affiliation(s)
- Sarbartha Mukherjee
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India
| | - Saumyadeep Goswami
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India
| | - Sagarika Dash
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India
| | - Dibyendu Samanta
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India
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8
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Blaimschein N, Parameswaran H, Nagler G, Manioglu S, Helenius J, Ardelean C, Kuhn A, Guan L, Müller DJ. The insertase YidC chaperones the polytopic membrane protein MelB inserting and folding simultaneously from both termini. Structure 2023; 31:1419-1430.e5. [PMID: 37708891 PMCID: PMC10840855 DOI: 10.1016/j.str.2023.08.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 07/22/2023] [Accepted: 08/18/2023] [Indexed: 09/16/2023]
Abstract
The insertion and folding of proteins into membranes is crucial for cell viability. Yet, the detailed contributions of insertases remain elusive. Here, we monitor how the insertase YidC guides the folding of the polytopic melibiose permease MelB into membranes. In vivo experiments using conditionally depleted E. coli strains show that MelB can insert in the absence of SecYEG if YidC resides in the cytoplasmic membrane. In vitro single-molecule force spectroscopy reveals that the MelB substrate itself forms two folding cores from which structural segments insert stepwise into the membrane. However, misfolding dominates, particularly in structural regions that interface the pseudo-symmetric α-helical domains of MelB. Here, YidC takes an important role in accelerating and chaperoning the stepwise insertion and folding process of both MelB folding cores. Our findings reveal a great flexibility of the chaperoning and insertase activity of YidC in the multifaceted folding processes of complex polytopic membrane proteins.
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Affiliation(s)
- Nina Blaimschein
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, 4058 Basel, Basel-Stadt, Switzerland
| | - Hariharan Parameswaran
- Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Gisela Nagler
- Institute of Biology, University of Hohenheim, 70599 Stuttgart, Baden-Württemberg, Germany
| | - Selen Manioglu
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, 4058 Basel, Basel-Stadt, Switzerland
| | - Jonne Helenius
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, 4058 Basel, Basel-Stadt, Switzerland
| | | | - Andreas Kuhn
- Institute of Biology, University of Hohenheim, 70599 Stuttgart, Baden-Württemberg, Germany
| | - Lan Guan
- Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Daniel J Müller
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, 4058 Basel, Basel-Stadt, Switzerland.
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9
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Gresham IJ, Lilley SG, Nelson ARJ, Koynov K, Neto C. Nanostructure Explains the Behavior of Slippery Covalently Attached Liquid Surfaces. Angew Chem Int Ed Engl 2023; 62:e202308008. [PMID: 37550243 DOI: 10.1002/anie.202308008] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 08/05/2023] [Accepted: 08/07/2023] [Indexed: 08/09/2023]
Abstract
Slippery covalently-attached liquid surfaces (SCALS) with low contact angle hysteresis (CAH, <5°) and nanoscale thickness display impressive anti-adhesive properties, similar to lubricant-infused surfaces. Their efficacy is generally attributed to the liquid-like mobility of the constituent tethered chains. However, the precise physico-chemical properties that facilitate this mobility are unknown, hindering rational design. This work quantifies the chain length, grafting density, and microviscosity of a range of polydimethylsiloxane (PDMS) SCALS, elucidating the nanostructure responsible for their properties. Three prominent methods are used to produce SCALS, with characterization carried out via single-molecule force measurements, neutron reflectometry, and fluorescence correlation spectroscopy. CO2 snow-jet cleaning was also shown to reduce the CAH of SCALS via a modification of their grafting density. SCALS behavior can be predicted by reduced grafting density, Σ, with the lowest water CAH achieved at Σ≈2. This study provides the first direct examination of SCALS grafting density, chain length, and microviscosity and supports the hypothesis that SCALS properties stem from a balance of layer uniformity and mobility.
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Affiliation(s)
- Isaac J Gresham
- School of Chemistry and the University of Sydney Nano Institute, The University of Sydney, Sydney, NSW, Australia
| | - Seamus G Lilley
- School of Chemistry and the University of Sydney Nano Institute, The University of Sydney, Sydney, NSW, Australia
| | - Andrew R J Nelson
- Australian Center for Neutron Scattering, ANSTO, Sydney, NSW, Australia
| | - Kaloian Koynov
- Max Planck Institute for Polymer Research, Mainz, Germany
| | - Chiara Neto
- School of Chemistry and the University of Sydney Nano Institute, The University of Sydney, Sydney, NSW, Australia
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10
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Zhang S, Yu M, Zhang G, He G, Ji Y, Dong J, Zheng H, Qian L. Revealing the Control Mechanisms of pH on the Solution Properties of Chitin via Single-Molecule Studies. Molecules 2023; 28:6769. [PMID: 37836611 PMCID: PMC10574145 DOI: 10.3390/molecules28196769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 09/16/2023] [Accepted: 09/20/2023] [Indexed: 10/15/2023] Open
Abstract
Chitin is one of the most common polysaccharides and is abundant in the cell walls of fungi and the shells of insects and aquatic organisms as a skeleton. The mechanism of how chitin responds to pH is essential to the precise control of brewing and the design of smart chitin materials. However, this molecular mechanism remains a mystery. Results from single-molecule studies, including single-molecule force spectroscopy (SMFS), AFM imaging, and molecular dynamic (MD) simulations, have shown that the mechanical and conformational behaviors of chitin molecules show surprising pH responsiveness. This can be compared with how, in natural aqueous solutions, chitin tends to form a more relaxed spreading conformation and show considerable elasticity under low stretching forces in acidic conditions. However, its molecular chain collapses into a rigid globule in alkaline solutions. The results show that the chain state of chitin can be regulated by the proportions of inter- and intramolecular H-bonds, which are determined via the number of water bridges on the chain under different pH values. This basic study may be helpful for understanding the cellular activities of fungi under pH stress and the design of chitin-based drug carriers.
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Affiliation(s)
- Song Zhang
- Department of Food Science and Engineering, Moutai Institute, Renhuai 564502, China; (S.Z.); (G.Z.); (G.H.); (Y.J.); (J.D.)
| | - Miao Yu
- School of Mechanical Engineering, Sichuan University, Chengdu 610065, China;
| | - Guoqiang Zhang
- Department of Food Science and Engineering, Moutai Institute, Renhuai 564502, China; (S.Z.); (G.Z.); (G.H.); (Y.J.); (J.D.)
| | - Guanmei He
- Department of Food Science and Engineering, Moutai Institute, Renhuai 564502, China; (S.Z.); (G.Z.); (G.H.); (Y.J.); (J.D.)
| | - Yunxu Ji
- Department of Food Science and Engineering, Moutai Institute, Renhuai 564502, China; (S.Z.); (G.Z.); (G.H.); (Y.J.); (J.D.)
| | - Juan Dong
- Department of Food Science and Engineering, Moutai Institute, Renhuai 564502, China; (S.Z.); (G.Z.); (G.H.); (Y.J.); (J.D.)
| | - Huayan Zheng
- Department of Food Science and Engineering, Moutai Institute, Renhuai 564502, China; (S.Z.); (G.Z.); (G.H.); (Y.J.); (J.D.)
| | - Lu Qian
- School of Materials Science and Engineering, South China University of Technology, Guangzhou 510641, China
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11
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Lei H, Ma Q, Wang Z, Zhang D, Huang X, Qin M, Ma H, Wang W, Cao Y. Ester Bond: Chemically Labile Yet Mechanically Stable. ACS Nano 2023; 17:16870-16878. [PMID: 37646337 DOI: 10.1021/acsnano.3c03807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Due to the dynamic nature of ester linkages, ester-bond-containing materials are well known for their outstanding degradability and stimuli responsiveness. However, whether ester hydrolysis is affected by mechanical forces remains unclear. Here, we develop a single-molecule assay to quantitatively study the force-dependent ester hydrolysis using an engineered circular permutant protein with a caged ester bond as a model. Our single-molecule force spectroscopy results show that the ester hydrolysis rate is surprisingly insensitive to forces, with a ∼7 s-1 dissociation rate that remains almost unchanged in the force range of 80 to 200 pN. Quantum calculations reveal that the ester hydrolysis involves an intermediate state formed by either H3O+- or OH--bonded tetrahedral intermediates. The measured ester-hydrolysis kinetics at the single-molecule level may primarily correspond to the rupture of these intermediate states. However, the rate-limiting step appears to be the formation of the tetrahedral intermediates, which cannot be quantitatively characterized in our experiments. Nonetheless, based on the quantum calculations, this step is also insensitive to applied forces. Altogether, our study suggests that the ester bond is chemically labile yet mechanically stable, serving as the basis for the design of responsive materials using ester bonds as mechanically inert units.
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Affiliation(s)
- Hai Lei
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China
- School of Physics, Zhejiang University, Hangzhou 310027, China
- Institute for Advanced Study in Physics, Zhejiang University, Hangzhou 310027, China
| | - Quan Ma
- Zhejiang Laboratory, Hangzhou, Zhejiang 311121, China
| | - Zhangxia Wang
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Di Zhang
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China
| | - Xiaoyu Huang
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China
| | - Meng Qin
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China
| | - Haibo Ma
- Qingdao Institute for Theoretical and Computational Sciences, Qingdao Institute of Frontier and Interdisciplinary Science, Shandong University, Qingdao 266237, China
| | - Wei Wang
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China
| | - Yi Cao
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan 250021, China
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12
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Xu Z, Li Q, Huang Y, Guo K, Xue B, Cao Y, Li Y. Blocking Nonspecific Interactions Using Y-Shape Poly(ethylene glycol). Int J Mol Sci 2023; 24:12414. [PMID: 37569789 PMCID: PMC10419274 DOI: 10.3390/ijms241512414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 07/27/2023] [Accepted: 07/31/2023] [Indexed: 08/13/2023] Open
Abstract
Nonspecific interactions play a significant role in physiological activities, surface chemical modification, and artificial adhesives. However, nonspecificity sometimes causes sticky problems, including surface fouling, decreased target specificity, and artifacts in single-molecule measurements. Adjusting the liquid pH, using protein-blocking additives, adding nonionic surfactants, or increasing the salt concentration are common methods to minimize nonspecific binding to achieve high-quality data. Here, we report that grafting heteromorphic polyethylene glycol (Y-shape PEG) with two inert terminates could noticeably decrease nonspecific binding. As a proof-of-concept, we performed single-molecule force spectroscopy and fluorescence staining imaging experiments to verify the feasibility of Y-shape PEG in blocking nonspecific interactions. Our results indicate that Y-shape PEG could serve as a prominent and efficient candidate to minimize nonspecificity for scientific and biomedical applications.
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Affiliation(s)
- Zhengyu Xu
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China; (Z.X.); (Q.L.); (Y.H.); (K.G.); (B.X.)
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan 250021, China
| | - Qingtai Li
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China; (Z.X.); (Q.L.); (Y.H.); (K.G.); (B.X.)
| | - Yaying Huang
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China; (Z.X.); (Q.L.); (Y.H.); (K.G.); (B.X.)
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan 250021, China
| | - Kaiqiang Guo
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China; (Z.X.); (Q.L.); (Y.H.); (K.G.); (B.X.)
| | - Bin Xue
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China; (Z.X.); (Q.L.); (Y.H.); (K.G.); (B.X.)
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan 250021, China
| | - Yi Cao
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China; (Z.X.); (Q.L.); (Y.H.); (K.G.); (B.X.)
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan 250021, China
| | - Yiran Li
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China; (Z.X.); (Q.L.); (Y.H.); (K.G.); (B.X.)
- Medical School, Nanjing University, Nanjing 210093, China
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13
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Zheng B, Xiao Y, Tong B, Mao Y, Ge R, Tian F, Dong X, Zheng P. S373P Mutation Stabilizes the Receptor-Binding Domain of the Spike Protein in Omicron and Promotes Binding. JACS Au 2023; 3:1902-1910. [PMID: 37502147 PMCID: PMC10369413 DOI: 10.1021/jacsau.3c00142] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 06/12/2023] [Accepted: 06/12/2023] [Indexed: 07/29/2023]
Abstract
A cluster of several newly occurring mutations on Omicron is found at the β-core region of the spike protein's receptor-binding domain (RBD), where mutation rarely happened before. Notably, the binding of SARS-CoV-2 to human receptor ACE2 via RBD happens in a dynamic airway environment, where mechanical force caused by coughing or sneezing occurs. Thus, we used atomic force microscopy-based single-molecule force spectroscopy (AFM-SMFS) to measure the stability of RBDs and found that the mechanical stability of Omicron RBD increased by ∼20% compared with the wild type. Molecular dynamics (MD) simulations revealed that Omicron RBD showed more hydrogen bonds in the β-core region due to the closing of the α-helical motif caused primarily by the S373P mutation. In addition to a higher unfolding force, we showed a higher dissociation force between Omicron RBD and ACE2. This work reveals the mechanically stabilizing effect of the conserved mutation S373P for Omicron and the possible evolution trend of the β-core region of RBD.
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Affiliation(s)
- 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, China
| | - Yuelong Xiao
- State
Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine
Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Bei Tong
- Institute
of Botany, Jiangsu Province and Chinese
Academy of Sciences, Nanjing, Jiangsu 210014, China
| | - Yutong Mao
- State
Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine
Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Rui Ge
- State
Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine
Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, 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, China
| | - Xianchi Dong
- State
Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210023, China
- Engineering
Research Center of Protein and Peptide Medicine, Ministry of Education, Nanjing, Jiangsu 210023, 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, China
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14
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Deptuła P, Fiedoruk K, Wasilewska M, Suprewicz Ł, Cieśluk M, Żeliszewska P, Oćwieja M, Adamczyk Z, Pogoda K, Bucki R. Physicochemical Nature of SARS-CoV-2 Spike Protein Binding to Human Vimentin. ACS Appl Mater Interfaces 2023. [PMID: 37413693 PMCID: PMC10360031 DOI: 10.1021/acsami.3c03347] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/08/2023]
Abstract
Vimentin, a protein that builds part of the cytoskeleton and is involved in many aspects of cellular function, was recently identified as a cell surface attachment site for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The present study investigated the physicochemical nature of the binding between the SARS-CoV-2 S1 glycoprotein receptor binding domain (S1 RBD) and human vimentin using atomic force microscopy and a quartz crystal microbalance. The molecular interactions of S1 RBD and vimentin proteins were quantified using vimentin monolayers attached to the cleaved mica or a gold microbalance sensor as well as in its native extracellular form present on the live cell surface. The presence of specific interactions between vimentin and S1 RBD was also confirmed using in silico studies. This work provides new evidence that cell-surface vimentin (CSV) functions as a site for SARS-CoV-2 virus attachment and is involved in the pathogenesis of Covid-19, providing a potential target for therapeutic countermeasures.
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Affiliation(s)
- Piotr Deptuła
- Independent Laboratory of Nanomedicine, Medical University of Bialystok, PL-15222 Białystok, Poland
| | - Krzysztof Fiedoruk
- Department of Medical Microbiology and Nanobiomedical Engineering, Medical University of Bialystok, PL-15222 Białystok, Poland
| | - Monika Wasilewska
- J. Haber Institute of Catalysis and Surface Chemistry Polish Academy of Science, Niezapominajek 8, PL-30239 Krakow, Poland
| | - Łukasz Suprewicz
- Department of Medical Microbiology and Nanobiomedical Engineering, Medical University of Bialystok, PL-15222 Białystok, Poland
| | - Mateusz Cieśluk
- Department of Medical Microbiology and Nanobiomedical Engineering, Medical University of Bialystok, PL-15222 Białystok, Poland
| | - Paulina Żeliszewska
- J. Haber Institute of Catalysis and Surface Chemistry Polish Academy of Science, Niezapominajek 8, PL-30239 Krakow, Poland
| | - Magdalena Oćwieja
- J. Haber Institute of Catalysis and Surface Chemistry Polish Academy of Science, Niezapominajek 8, PL-30239 Krakow, Poland
| | - Zbigniew Adamczyk
- J. Haber Institute of Catalysis and Surface Chemistry Polish Academy of Science, Niezapominajek 8, PL-30239 Krakow, Poland
| | - Katarzyna Pogoda
- Institute of Nuclear Physics Polish Academy of Sciences, PL-31342 Krakow, Poland
| | - Robert Bucki
- Department of Medical Microbiology and Nanobiomedical Engineering, Medical University of Bialystok, PL-15222 Białystok, Poland
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15
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Liu H, Liu Z, Santos M, Nash M. Direct Comparison of Lysine versus Site-Specific Protein Surface Immobilization in Single-molecule Mechanical Assays. Angew Chem Int Ed Engl 2023:e202304136. [PMID: 37285322 DOI: 10.1002/anie.202304136] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 05/24/2023] [Accepted: 06/06/2023] [Indexed: 06/09/2023]
Abstract
Single-molecule force spectroscopy (SMFS) is powerful for studying folding states and mechanical properties of proteins, however, it requires protein immobilization onto force-transducing probes such as cantilevers or microbeads. A common immobilization method relies on coupling lysine residues to carboxylated surfaces using 1-ethyl-3-(3-dimethyl-aminopropyl) carbodiimide and N-hydroxysuccinimide (EDC/NHS). Because proteins typically contain many lysine groups, this strategy results in a heterogeneous distribution of tether positions. Genetically encoded peptide tags (e.g., ybbR) provide alternative chemistries for achieving site-specific immobilization, but thus far a direct comparison of site-specific vs. lysine-based immobilization strategies to assess effects on the observed mechanical properties was lacking. Here, we compared lysine- vs. ybbR-based protein immobilization in SMFS assays using several model polyprotein systems. Our results show that lysine-based immobilization results in significant signal deterioration for monomeric streptavidin-biotin interactions, and loss of the ability to correctly classify unfolding pathways in a multipathway Cohesin-Dockerin system. We developed a mixed immobilization approach where a site-specifically tethered ligand was used to probe surface-bound proteins immobilized through lysine groups, and found partial recovery of specific signals. The mixed immobilization approach represents a viable alternative for mechanical assays on in vivo-derived samples or other proteins of interest where genetically encoded tags are not feasible.
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Affiliation(s)
- Haipei Liu
- University of Basel/ETH Zurich, Chemistry / Biosystems Engineering, SWITZERLAND
| | - Zhaowei Liu
- Delft University of Technology: Technische Universiteit Delft, Bionanoscience, NETHERLANDS
| | - Mariana Santos
- University of Basel/ETH Zurich, Chemistry / Biosystems Engineering, SWITZERLAND
| | - Michael Nash
- ETH Zurich: Eidgenossische Technische Hochschule Zurich, Mattenstrasse 24a, Box 3350, 4058, Basel, SWITZERLAND
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16
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Kerkhoff Y, Azizi L, Mykuliak VV, Hytönen VP, Block S. Microfluidics-Based Force Spectroscopy Enables High-Throughput Force Experiments with Sub-Nanometer Resolution and Sub-Piconewton Sensitivity. Small 2023; 19:e2206713. [PMID: 36631276 DOI: 10.1002/smll.202206713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/23/2022] [Indexed: 06/17/2023]
Abstract
Several techniques have been established to quantify the mechanicals of single molecules. However, most of them show only limited capabilities of parallelizing the measurement by performing many individual measurements simultaneously. Herein, a microfluidics-based single-molecule force spectroscopy method, which achieves sub-nanometer spatial resolution and sub-piconewton sensitivity and is capable of simultaneously quantifying hundreds of single-molecule targets in parallel, is presented. It relies on a combination of total internal reflection microscopy and microfluidics, in which monodisperse fluorescent beads are immobilized on the bottom of a microfluidic channel by macromolecular linkers. Application of a flow generates a well-defined shear force acting on the beads, whereas the nanomechanical linker response is quantified based on the force-induced displacement of individual beads. To handle the high amount of data generated, a cluster analysis which is capable of a semi-automatic identification of measurement artifacts and molecular populations is implemented. The method is validated by probing the mechanical response polyethylene glycol linkers and binding strength of biotin-NeutrAvidin complexes. Two energy barriers (at 3 and 5.7 Å, respectively) in the biotin-NeutrAvidin interaction are resolved and the unfolding behavior of talin's rod domain R3 in the force range between 1 to ≈10 pN is probed.
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Affiliation(s)
- Yannic Kerkhoff
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany
| | - Latifeh Azizi
- Faculty of Medicine and Health Technology, Tampere University, Arvo Ylpön katu 34, Tampere, FI-33520, Finland
| | - Vasyl V Mykuliak
- Faculty of Medicine and Health Technology, Tampere University, Arvo Ylpön katu 34, Tampere, FI-33520, Finland
| | - Vesa P Hytönen
- Faculty of Medicine and Health Technology, Tampere University, Arvo Ylpön katu 34, Tampere, FI-33520, Finland
- Fimlab Laboratories, Biokatu 4, Tampere, FI-33520, Finland
| | - Stephan Block
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany
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17
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Tsirigoni AM, Goktas M, Atris Z, Valleriani A, Vila Verde A, Blank KG. Chain Sliding versus β-Sheet Formation upon Shearing Single α-Helical Coiled Coils. Macromol Biosci 2023; 23:e2200563. [PMID: 36861255 DOI: 10.1002/mabi.202200563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/20/2023] [Indexed: 03/03/2023]
Abstract
Coiled coils (CCs) are key building blocks of biogenic materials and determine their mechanical response to large deformations. Of particular interest is the observation that CC-based materials display a force-induced transition from α-helices to mechanically stronger β-sheets (αβT). Steered molecular dynamics simulations predict that this αβT requires a minimum, pulling speed-dependent CC length. Here, de novo designed CCs with a length between four to seven heptads are utilized to probe if the transition found in natural CCs can be mimicked with synthetic sequences. Using single-molecule force spectroscopy and molecular dynamics simulations, these CCs are mechanically loaded in shear geometry and their rupture forces and structural responses to the applied load are determined. Simulations at the highest pulling speed (0.01 nm ns-1 ) show the appearance of β-sheet structures for the five- and six-heptad CCs and a concomitant increase in mechanical strength. The αβT is less probable at a lower pulling speed of 0.001 nm ns-1 and is not observed in force spectroscopy experiments. For CCs loaded in shear geometry, the formation of β-sheets competes with interchain sliding. β-sheet formation is only possible in higher-order CC assemblies or in tensile-loading geometries where chain sliding and dissociation are prohibited.
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Affiliation(s)
- Anna-Maria Tsirigoni
- Max Planck Institute of Colloids and Interfaces, Mechano(bio)chemistry, Am Mühlenberg 1, 14476, Potsdam, Germany.,Max Planck Institute of Colloids and Interfaces, Department of Biomaterials, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Melis Goktas
- Max Planck Institute of Colloids and Interfaces, Mechano(bio)chemistry, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Zeynep Atris
- Max Planck Institute of Colloids and Interfaces, Mechano(bio)chemistry, Am Mühlenberg 1, 14476, Potsdam, Germany.,Max Planck Institute of Colloids and Interfaces, Department of Biomaterials, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Angelo Valleriani
- Max Planck Institute of Colloids and Interfaces, Department of Biomaterials, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Ana Vila Verde
- University of Duisburg-Essen, Faculty of Physics, Lotharstrasse 1, 47057, Duisburg, Germany
| | - Kerstin G Blank
- Max Planck Institute of Colloids and Interfaces, Mechano(bio)chemistry, Am Mühlenberg 1, 14476, Potsdam, Germany.,Johannes Kepler University Linz, Institute of Experimental Physics, Department of Biomolecular & Selforganizing Matter, Altenberger Strasse 69, Linz, 4040, Austria
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18
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Wang Z, Wang M, Zhao Z, Zheng P. Quantification of carboxylate-bridged di-zinc site stability in protein due ferri by single-molecule force spectroscopy. Protein Sci 2023; 32:e4583. [PMID: 36718829 PMCID: PMC9926469 DOI: 10.1002/pro.4583] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 01/16/2023] [Accepted: 01/27/2023] [Indexed: 02/01/2023]
Abstract
Carboxylate-bridged diiron proteins belong to a protein family involved in different physiological processes. These proteins share the conservative EXXH motif, which provides the carboxylate bridge and is critical for metal binding. Here, we choose de novo-designed single-chain due ferri protein (DFsc), a four-helical protein with two EXXH motifs as a model protein, to study the stability of the carboxylate-bridged di-metal binding site. The mechanical and kinetic properties of the di-Zn site in DFsc were obtained by atomic force microscopy-based single-molecule force spectroscopy. Zn-DFsc showed a considerable rupture force of ~200 pN, while the apo-protein is mechanically labile. In addition, multiple rupture pathways were observed with different probabilities, indicating the importance of the EXXH-based carboxylate-bridged metal site. These results demonstrate carboxylate-bridged di-metal site is mechanically stable and improve our understanding of this important type of metalloprotein.
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Affiliation(s)
- Zhiyi Wang
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical EngineeringNanjing UniversityNanjingPeople's Republic of China
| | - Mengdie Wang
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical EngineeringNanjing UniversityNanjingPeople's Republic of China
| | - Zhongxin Zhao
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical EngineeringNanjing UniversityNanjingPeople's Republic of China
| | - Peng Zheng
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical EngineeringNanjing UniversityNanjingPeople's Republic of China
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19
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Blaimschein N, Hariharan P, Manioglu S, Guan L, Müller DJ. Substrate-binding guides individual melibiose permeases MelB to structurally soften and to destabilize cytoplasmic middle-loop C3. Structure 2023; 31:58-67.e4. [PMID: 36525976 PMCID: PMC9825662 DOI: 10.1016/j.str.2022.11.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 11/06/2022] [Accepted: 11/18/2022] [Indexed: 12/23/2022]
Abstract
The melibiose permease MelB is a well-studied Na+-coupled transporter of the major facilitator superfamily. However, the symport mechanism of galactosides and cations is still not fully understood, especially at structural levels. Here, we use single-molecule force spectroscopy to investigate substrate-induced structural changes of MelB from Salmonella typhimurium. In the absence of substrate, MelB equally populates two different states, from which one shows higher mechanical structural stability with additional stabilization of the cytoplasmic middle-loop C3. In the presence of either melibiose or a coupling Na+-cation, however, MelB increasingly populates the mechanically less stable state, which shows a destabilized middle-loop C3. In the presence of both substrate and co-substrate, this mechanically less stable state of MelB is predominant. Our findings describe how both substrates guide MelB transporters to populate two different mechanically stabilized states, and contribute mechanistic insights to the alternating-access action for the galactoside/cation symport catalyzed by MelB.
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Affiliation(s)
- Nina Blaimschein
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, 4058 Basel, Switzerland
| | - Parameswaran Hariharan
- Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Selen Manioglu
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, 4058 Basel, Switzerland
| | - Lan Guan
- Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA.
| | - Daniel J Müller
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, 4058 Basel, Switzerland.
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20
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Boonrod K, Kuaguim L, Braun M, Müller-Renno C, Ziegler C, Krczal G. Identification of the Actin-Binding Region and Binding to Host Plant Apple Actin of Immunodominant Transmembrane Protein of 'Candidatus Phytoplasma mali'. Int J Mol Sci 2023; 24. [PMID: 36674483 DOI: 10.3390/ijms24020968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/21/2022] [Accepted: 12/28/2022] [Indexed: 01/07/2023] Open
Abstract
'Candidatus Phytoplasma mali' ('Ca. P. mali') has only one major membrane protein, the immunodominant membrane protein (Imp), which is regarded as being close to the ancestor of all phytoplasma immunodominant membrane proteins. Imp binds to actin and possibly facilitates its movement in the plant or insect host cells. However, protein sequences of Imp are quite diverse among phytoplasma species, thus resulting in difficulties in identifying conserved domains across species. In this work, we compare Imp protein sequences of 'Ca. P. mali' strain PM19 (Imp-PM19) with Imp of different strains of 'Ca. P. mali' and identify its actin-binding domain. Moreover, we show that Imp binds to the actin of apple (Malus x domestica), which is the host plant of 'Ca. P. mali'. Using molecular and scanning force spectroscopy analysis, we find that the actin-binding domain of Imp-PM19 contains a highly positively charged amino acid cluster. Our result could allow investigating a possible correlation between Imp variants and the infectivity of the corresponding 'Ca. P. mali' isolates.
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21
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Arce NA, Liu Y, Chen W, Zhang XF, Li R. Autoinhibitory module underlies species difference in shear activation of von Willebrand factor. J Thromb Haemost 2022; 20:2686-2696. [PMID: 36031939 PMCID: PMC9588639 DOI: 10.1111/jth.15837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 07/05/2022] [Accepted: 07/22/2022] [Indexed: 11/30/2022]
Abstract
BACKGROUND Von Willebrand factor (VWF) is a multimeric plasma protein that bridges the gap between vessel injury and platelet capture at high shear rates. Under high shear or tension, VWF can become activated upon the unfolding of its autoinhibitory module (AIM). AIM unfolding exposes the A1 domain, allowing for binding to platelet glycoprotein (GP)Ibα to initiate primary hemostasis. The characteristics of the AIM and its inhibitory properties within mouse VWF are unknown. OBJECTIVES To determine and characterize the autoinhibitory properties of mouse VWF. METHODS Recombinant mouse VWF A1 fragments containing or lacking the flanking regions around the A1 domain were generated. We tested the ability of these fragments to bind to human or mouse GPIbα and platelets. We compared the unfolding of mouse AIM-A1 to human AIM-A1 by single-molecule force spectroscopy. RESULTS Recombinant mouse AIM-A1 binds with higher affinity to GPIbα than its human counterpart. Recombinant mouse proteins lacking part of the AIM show increased binding to GPIbα. Activated A1 fragments lacking the AIM can effectively agglutinate platelets across the species barrier. Using single-molecule force spectroscopy, we determined that the mouse AIM unfolds under forces similar to the human AIM. Additionally, the human AIM paired with mouse A1 largely recapitulates the behavior of human AIM-A1. CONCLUSIONS Our results suggest that the regulation of VWF-GPIbα binding has been specifically tuned to work optimally in different rheological architectures. Differences in the AIM sequence may contribute to the difference in VWF shear response between human and mice.
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Affiliation(s)
- Nicholas A. Arce
- Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Yi Liu
- Department of Bioengineering, Lehigh University, Bethlehem, Pennsylvania, USA
| | - Wenchun Chen
- Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - X. Frank Zhang
- Department of Bioengineering, Lehigh University, Bethlehem, Pennsylvania, USA
| | - Renhao Li
- Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
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22
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Chan JFW, Oh YJ, Yuan S, Chu H, Yeung ML, Canena D, Chan CCS, Poon VKM, Chan CCY, Zhang AJ, Cai JP, Ye ZW, Wen L, Yuen TTT, Chik KKH, Shuai H, Wang Y, Hou Y, Luo C, Chan WM, Qin Z, Sit KY, Au WK, Legendre M, Zhu R, Hain L, Seferovic H, Tampé R, To KKW, Chan KH, Thomas DG, Klausberger M, Xu C, Moon JJ, Stadlmann J, Penninger JM, Oostenbrink C, Hinterdorfer P, Yuen KY, Markovitz DM. A molecularly engineered, broad-spectrum anti-coronavirus lectin inhibits SARS-CoV-2 and MERS-CoV infection in vivo. Cell Rep Med 2022; 3:100774. [PMID: 36195094 PMCID: PMC9519379 DOI: 10.1016/j.xcrm.2022.100774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 08/08/2022] [Accepted: 09/19/2022] [Indexed: 11/30/2022]
Abstract
"Pan-coronavirus" antivirals targeting conserved viral components can be designed. Here, we show that the rationally engineered H84T-banana lectin (H84T-BanLec), which specifically recognizes high mannose found on viral proteins but seldom on healthy human cells, potently inhibits Middle East respiratory syndrome coronavirus (MERS-CoV), severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (including Omicron), and other human-pathogenic coronaviruses at nanomolar concentrations. H84T-BanLec protects against MERS-CoV and SARS-CoV-2 infection in vivo. Importantly, intranasally and intraperitoneally administered H84T-BanLec are comparably effective. Mechanistic assays show that H84T-BanLec targets virus entry. High-speed atomic force microscopy depicts real-time multimolecular associations of H84T-BanLec dimers with the SARS-CoV-2 spike trimer. Single-molecule force spectroscopy demonstrates binding of H84T-BanLec to multiple SARS-CoV-2 spike mannose sites with high affinity and that H84T-BanLec competes with SARS-CoV-2 spike for binding to cellular ACE2. Modeling experiments identify distinct high-mannose glycans in spike recognized by H84T-BanLec. The multiple H84T-BanLec binding sites on spike likely account for the drug compound's broad-spectrum antiviral activity and the lack of resistant mutants.
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Affiliation(s)
- Jasper Fuk-Woo Chan
- State Key Laboratory of Emerging Infectious Diseases, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China; Department of Infectious Disease and Microbiology, the University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, China; Academician Workstation of Hainan Province, Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, China; Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, China; Guangzhou Laboratory, Guangdong Province, China
| | - Yoo Jin Oh
- Department of Experimental Applied Biophysics, Johannes Kepler University Linz, Linz, Austria
| | - Shuofeng Yuan
- State Key Laboratory of Emerging Infectious Diseases, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China; Department of Infectious Disease and Microbiology, the University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, China
| | - Hin Chu
- State Key Laboratory of Emerging Infectious Diseases, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China; Department of Infectious Disease and Microbiology, the University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, China
| | - Man-Lung Yeung
- State Key Laboratory of Emerging Infectious Diseases, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China; Department of Infectious Disease and Microbiology, the University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, China; Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Daniel Canena
- Department of Experimental Applied Biophysics, Johannes Kepler University Linz, Linz, Austria
| | - Chris Chung-Sing Chan
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
| | - Vincent Kwok-Man Poon
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
| | - Chris Chun-Yiu Chan
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Anna Jinxia Zhang
- State Key Laboratory of Emerging Infectious Diseases, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
| | - Jian-Piao Cai
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Zi-Wei Ye
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Lei Wen
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Terrence Tsz-Tai Yuen
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Kenn Ka-Heng Chik
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
| | - Huiping Shuai
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
| | - Yixin Wang
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Yuxin Hou
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Cuiting Luo
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Wan-Mui Chan
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Zhenzhi Qin
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Ko-Yung Sit
- Department of Surgery, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Wing-Kuk Au
- Department of Surgery, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Maureen Legendre
- Division of Infectious Diseases, Department of Internal Medicine, and the Programs in Immunology, Cellular and Molecular Biology, and Cancer Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Rong Zhu
- Department of Experimental Applied Biophysics, Johannes Kepler University Linz, Linz, Austria
| | - Lisa Hain
- Department of Experimental Applied Biophysics, Johannes Kepler University Linz, Linz, Austria
| | - Hannah Seferovic
- Department of Experimental Applied Biophysics, Johannes Kepler University Linz, Linz, Austria
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt, Germany
| | - Kelvin Kai-Wang To
- State Key Laboratory of Emerging Infectious Diseases, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China; Department of Infectious Disease and Microbiology, the University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, China; Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, China; Guangzhou Laboratory, Guangdong Province, China
| | - Kwok-Hung Chan
- State Key Laboratory of Emerging Infectious Diseases, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China; Department of Infectious Disease and Microbiology, the University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, China
| | | | - Miriam Klausberger
- Institute of Molecular Biotechnology, Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
| | - Cheng Xu
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI 48109, USA; Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - James J Moon
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI 48109, USA; Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Johannes Stadlmann
- Department of Chemistry, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
| | - Josef M Penninger
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria; Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
| | - Chris Oostenbrink
- Institute for Molecular Modelling and Simulation, Department of Material Science and Process Engineering, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Peter Hinterdorfer
- Department of Experimental Applied Biophysics, Johannes Kepler University Linz, Linz, Austria.
| | - Kwok-Yung Yuen
- State Key Laboratory of Emerging Infectious Diseases, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China; Department of Infectious Disease and Microbiology, the University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, China; Academician Workstation of Hainan Province, Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, China; Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, China; Guangzhou Laboratory, Guangdong Province, China.
| | - David M Markovitz
- Division of Infectious Diseases, Department of Internal Medicine, and the Programs in Immunology, Cellular and Molecular Biology, and Cancer Biology, University of Michigan, Ann Arbor, MI 48109, USA.
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23
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Hackl M, Contrada EV, Ash JE, Kulkarni A, Yoon J, Cho HY, Lee KB, Yarbrough JM, López CA, Gnanakaran S, Chundawat SPS. Acoustic force spectroscopy reveals subtle differences in cellulose unbinding behavior of carbohydrate-binding modules. Proc Natl Acad Sci U S A 2022; 119:e2117467119. [PMID: 36215467 DOI: 10.1073/pnas.2117467119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Protein adsorption to solid carbohydrate interfaces is critical to many biological processes, particularly in biomass deconstruction. To engineer more-efficient enzymes for biomass deconstruction into sugars, it is necessary to characterize the complex protein-carbohydrate interfacial interactions. A carbohydrate-binding module (CBM) is often associated with microbial surface-tethered cellulosomes or secreted cellulase enzymes to enhance substrate accessibility. However, it is not well known how CBMs recognize, bind, and dissociate from polysaccharides to facilitate efficient cellulolytic activity, due to the lack of mechanistic understanding and a suitable toolkit to study CBM-substrate interactions. Our work outlines a general approach to study the unbinding behavior of CBMs from polysaccharide surfaces using a highly multiplexed single-molecule force spectroscopy assay. Here, we apply acoustic force spectroscopy (AFS) to probe a Clostridium thermocellum cellulosomal scaffoldin protein (CBM3a) and measure its dissociation from nanocellulose surfaces at physiologically relevant, low force loading rates. An automated microfluidic setup and method for uniform deposition of insoluble polysaccharides on the AFS chip surfaces are demonstrated. The rupture forces of wild-type CBM3a, and its Y67A mutant, unbinding from nanocellulose surfaces suggests distinct multimodal CBM binding conformations, with structural mechanisms further explored using molecular dynamics simulations. Applying classical dynamic force spectroscopy theory, the single-molecule unbinding rate at zero force is extrapolated and found to agree with bulk equilibrium unbinding rates estimated independently using quartz crystal microbalance with dissipation monitoring. However, our results also highlight critical limitations of applying classical theory to explain the highly multivalent binding interactions for cellulose-CBM bond rupture forces exceeding 15 pN.
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24
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Liu H, Liu Z, Yang B, Lopez Morales J, Nash MA. Optimal Sacrificial Domains in Mechanical Polyproteins: S. epidermidis Adhesins Are Tuned for Work Dissipation. JACS Au 2022; 2:1417-1427. [PMID: 35783175 PMCID: PMC9241160 DOI: 10.1021/jacsau.2c00121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 04/27/2022] [Accepted: 04/27/2022] [Indexed: 06/15/2023]
Abstract
The opportunistic pathogen Staphylococcus epidermidis utilizes a multidomain surface adhesin protein to bind host components and adhere to tissues. While it is known that the interaction between the SdrG receptor and its fibrinopeptide target (FgB) is exceptionally mechanostable (∼2 nN), the influence of downstream B domains (B1 and B2) is unclear. Here, we studied the mechanical relationships between folded B domains and the SdrG receptor bound to FgB. We used protein engineering, single-molecule force spectroscopy (SMFS) with an atomic force microscope (AFM), and Monte Carlo simulations to understand how the mechanical properties of folded sacrificial domains, in general, can be optimally tuned to match the stability of a receptor-ligand complex. Analogous to macroscopic suspension systems, sacrificial shock absorber domains should neither be too weak nor too strong to optimally dissipate mechanical energy. We built artificial molecular shock absorber systems based on the nanobody (VHH) scaffold and studied the competition between domain unfolding and receptor unbinding. We quantitatively determined the optimal stability of shock absorbers that maximizes work dissipation on average for a given receptor and found that natural sacrificial domains from pathogenic S. epidermidis and Clostridium perfringens adhesins exhibit stabilities at or near this optimum within a specific range of loading rates. These findings demonstrate how tuning the stability of sacrificial domains in adhesive polyproteins can be used to maximize mechanical work dissipation and serve as an adhesion strategy by bacteria.
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Affiliation(s)
- Haipei Liu
- Department
of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
| | - Zhaowei Liu
- Department
of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
| | - Byeongseon Yang
- Department
of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
| | - Joanan Lopez Morales
- Department
of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
| | - Michael A. Nash
- Department
of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
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25
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Nie JY, Song GB, Deng YB, Zheng P. Single-Molecule Force Spectroscopy Reveals Stability of mitoNEET and its [2Fe2Se] Cluster in Weakly Acidic and Basic Solutions. Chemistry 2022; 11:e202200056. [PMID: 35608094 PMCID: PMC9127745 DOI: 10.1002/open.202200056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/21/2022] [Indexed: 11/05/2022]
Abstract
The outer mitochondrial membrane protein mitoNEET (mNT) is a recently identified iron-sulfur protein containing a unique Fe2 S2 (His)1 (Cys)3 metal cluster with a single Fe-N(His87) coordinating bond. This labile Fe-N bond led to multiple unfolding/rupture pathways of mNT and its cluster by atomic force microscopy-based single-molecule force spectroscopy (AFM-SMFS), one of most common tools for characterizing the molecular mechanics. Although previous ensemble studies showed that this labile Fe-N(His) bond is essential for protein function, they also indicated that the protein and its [2Fe2S] cluster are stable under acidic conditions. Thus, we applied AFM-SMFS to measure the stability of mNT and its cluster at pH values of 6, 7, and 8. Indeed, all previous multiple unfolding pathways of mNT were still observed. Moreover, single-molecule measurements revealed that the stabilities of the protein and the [2Fe2S] cluster are consistent at these pH values with only ≈20 pN force differences. Thus, we found that the behavior of the protein is consistent in both weakly acidic and basic solutions despite a labile Fe-N bond.
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Affiliation(s)
- Jing-Yuan 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
| | - Guo-Bin Song
- 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
| | - Yi-Bing 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
| | - 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
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26
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Mora M, Board S, Languin-Cattoën O, Masino L, Stirnemann G, Garcia-Manyes S. A Single-Molecule Strategy to Capture Non-native Intramolecular and Intermolecular Protein Disulfide Bridges. Nano Lett 2022; 22:3922-3930. [PMID: 35549281 PMCID: PMC9136921 DOI: 10.1021/acs.nanolett.2c00043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 02/23/2022] [Indexed: 05/04/2023]
Abstract
Non-native disulfide bonds are dynamic covalent bridges that form post-translationally between two cysteines within the same protein (intramolecular) or with a neighboring protein (intermolecular), frequently due to changes in the cellular redox potential. The reversible formation of non-native disulfides is intimately linked to alterations in protein function; while they can provide a mechanism to protect against cysteine overoxidation, they are also involved in the early stages of protein multimerization, a hallmark of several protein aggregation diseases. Yet their identification using current protein chemistry technology remains challenging, mainly because of their fleeting reactivity. Here, we use single-molecule spectroscopy AFM and molecular dynamics simulations to capture both intra- and intermolecular disulfide bonds in γD-crystallin, a cysteine-rich, structural human lens protein involved in age-related eye cataracts. Our approach showcases the power of mechanical force as a conformational probe in dynamically evolving proteins and presents a platform to detect non-native disulfide bridges with single-molecule resolution.
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Affiliation(s)
- Marc Mora
- Department
of Physics, Randall Centre for Cell and Molecular Biophysics 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 United
Kingdom
| | - Stephanie Board
- Department
of Physics, Randall Centre for Cell and Molecular Biophysics 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 United
Kingdom
| | - Olivier Languin-Cattoën
- CNRS
Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Université Paris Diderot,
Sorbonne Paris Cité, PSL Research University, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Laura Masino
- Structural
Biology Science Technology Platform, The
Francis Crick Institute, 1 Midland Road London, NW1 1AT, United Kingdom
| | - Guillaume Stirnemann
- CNRS
Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Université Paris Diderot,
Sorbonne Paris Cité, PSL Research University, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Sergi Garcia-Manyes
- Department
of Physics, Randall Centre for Cell and Molecular Biophysics 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 United
Kingdom
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27
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Qian L, Zhang K, Guo X, Zhou J, Yu M. Single-Chain Mechanical Properties of Gelatin: A Single-Molecule Study. Polymers (Basel) 2022; 14:polym14050869. [PMID: 35267692 PMCID: PMC8912665 DOI: 10.3390/polym14050869] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 02/18/2022] [Accepted: 02/21/2022] [Indexed: 01/27/2023] Open
Abstract
Gelatin is an important natural biological resource with a wide range of applications in the pharmaceutical, industrial and food industries. We investigated the single-chain behaviors of gelatin by atomic force microscopy (AFM)-based single-molecule force spectroscopy (SMFS), and found that gelatin exists as long chains by fitting with the M-FJC model. By comparing the single-chain elasticity in a nonpolar organic solvent (nonane) and DI water, it was surprising to find that there was almost no difference in the single-chain elasticity of gelatin in nonane and DI water. Considering the specificity of gelatin solubility and the solvent size effect of nonane molecules, when a single gelatin chain is pulled into loose nonane, dehydration does not occur due to strong binding water interactions. Gelatin chains can only interact with water molecules at high temperatures; therefore, no further interaction of single gelatin chains with water molecules occurred at the experimental temperature. This eventually led to almost no difference in the single-chain F-E curves under the two conditions. It is expected that our study will enable the deep exploration of the interaction between water molecules and gelatin and provide a theoretical basis and experimental foundation for the design of gelatin-based materials with more functionalities.
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Affiliation(s)
- Lu Qian
- School of Materials Science and Engineering, South China University of Technology, Guangzhou 510000, China;
| | - Kai Zhang
- School of Mechanical Engineering, Sichuan University, Chengdu 610065, China; (K.Z.); (X.G.); (J.Z.)
| | - Xin Guo
- School of Mechanical Engineering, Sichuan University, Chengdu 610065, China; (K.Z.); (X.G.); (J.Z.)
| | - Junyu Zhou
- School of Mechanical Engineering, Sichuan University, Chengdu 610065, China; (K.Z.); (X.G.); (J.Z.)
| | - Miao Yu
- School of Mechanical Engineering, Sichuan University, Chengdu 610065, China; (K.Z.); (X.G.); (J.Z.)
- Correspondence: ; Tel.: +86-28-85405307
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28
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Abstract
Methylation changes at cytosine-guanine dinucleotide (CpG) sites in genes are closely related to cancer development. Thus, detection and quantification of low-abundance methylated DNA is critical for early diagnosis. Here, we report an atomic force microscopy (AFM)-based quantification method for DNA that contains methyl-CpG at a specific site, without any treatment to the target DNA such as chemical labeling, fluorescence tagging, or amplification. We employed AFM-tip-tethered methyl-CpG-binding proteins to probe surface-captured methylated DNA. We observed a linear correlation (R2 = 0.982) between the input copy number and detected copy number, in the low copy number regime (10 or fewer; subattomolar concentrations). For a mixture of methylated and nonmethylated DNA that resembles clinical samples, we were still able to quantify the methylated DNA. These results highlight the potential of our force-mapping-based quantification method for wide applications in early detection of diseases associated with methylated DNA.
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Affiliation(s)
- Woo Cheol Shim
- Department of Chemistry, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Republic of Korea
| | - Sungwook Woo
- Department of Chemistry, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Republic of Korea
| | - Joon Won Park
- Department of Chemistry, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Republic of Korea
- Institute of Convergence Science, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
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29
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Liu Z, Moreira RA, Dujmović A, Liu H, Yang B, Poma AB, Nash MA. Mapping Mechanostable Pulling Geometries of a Therapeutic Anticalin/CTLA-4 Protein Complex. Nano Lett 2022; 22:179-187. [PMID: 34918516 PMCID: PMC8759085 DOI: 10.1021/acs.nanolett.1c03584] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 11/03/2021] [Indexed: 05/27/2023]
Abstract
We used single-molecule AFM force spectroscopy (AFM-SMFS) in combination with click chemistry to mechanically dissociate anticalin, a non-antibody protein binding scaffold, from its target (CTLA-4), by pulling from eight different anchor residues. We found that pulling on the anticalin from residue 60 or 87 resulted in significantly higher rupture forces and a decrease in koff by 2-3 orders of magnitude over a force range of 50-200 pN. Five of the six internal anchor points gave rise to complexes significantly more stable than N- or C-terminal anchor points, rupturing at up to 250 pN at loading rates of 0.1-10 nN s-1. Anisotropic network modeling and molecular dynamics simulations helped to explain the geometric dependency of mechanostability. These results demonstrate that optimization of attachment residue position on therapeutic binding scaffolds can provide large improvements in binding strength, allowing for mechanical affinity maturation under shear stress without mutation of binding interface residues.
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Affiliation(s)
- Zhaowei Liu
- Institute
of Physical Chemistry, Department of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
| | - Rodrigo A. Moreira
- Biosystems
and Soft Matter Division, Institute of Fundamental
Technological Research, Polish Academy of Sciences, Pawińskiego 5B, 02-106 Warsaw, Poland
| | - Ana Dujmović
- Institute
of Physical Chemistry, Department of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
| | - Haipei Liu
- Institute
of Physical Chemistry, Department of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
| | - Byeongseon Yang
- Institute
of Physical Chemistry, Department of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
| | - Adolfo B. Poma
- Biosystems
and Soft Matter Division, Institute of Fundamental
Technological Research, Polish Academy of Sciences, Pawińskiego 5B, 02-106 Warsaw, Poland
- International
Center for Research on Innovative Biobased Materials (ICRI-BioM)—International
Research Agenda, Lodz University of Technology, Żeromskiego 116, 90-924 Lodz, Poland
| | - Michael A. Nash
- Institute
of Physical Chemistry, Department of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
- National
Center for Competence in Research (NCCR) Molecular Systems Engineering, 4058 Basel, Switzerland
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30
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Espinosa FM, Uhlig MR, Garcia R. Molecular Recognition by Silicon Nanowire Field-Effect Transistor and Single-Molecule Force Spectroscopy. Micromachines (Basel) 2022; 13:97. [PMID: 35056261 DOI: 10.3390/mi13010097] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 12/31/2021] [Accepted: 01/05/2022] [Indexed: 11/16/2022]
Abstract
Silicon nanowire (SiNW) field-effect transistors (FETs) have been developed as very sensitive and label-free biomolecular sensors. The detection principle operating in a SiNW biosensor is indirect. The biomolecules are detected by measuring the changes in the current through the transistor. Those changes are produced by the electrical field created by the biomolecule. Here, we have combined nanolithography, chemical functionalization, electrical measurements and molecular recognition methods to correlate the current measured by the SiNW transistor with the presence of specific molecular recognition events on the surface of the SiNW. Oxidation scanning probe lithography (o-SPL) was applied to fabricate sub-12 nm SiNW field-effect transistors. The devices were applied to detect very small concentrations of proteins (500 pM). Atomic force microscopy (AFM) single-molecule force spectroscopy (SMFS) experiments allowed the identification of the protein adsorption sites on the surface of the nanowire. We detected specific interactions between the biotin-functionalized AFM tip and individual avidin molecules adsorbed to the SiNW. The measurements confirmed that electrical current changes measured by the device were associated with the deposition of avidin molecules.
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31
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Nie J, Deng Y, Tian F, Shi S, Zheng P. Detection of weak non-covalent cation-π interactions in NGAL by single-molecule force spectroscopy. Nano Res 2022; 15:4251-4257. [PMID: 35574260 PMCID: PMC9077643 DOI: 10.1007/s12274-021-4065-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 11/23/2021] [Accepted: 12/09/2021] [Indexed: 05/14/2023]
Abstract
UNLABELLED Cation-π interaction is an electrostatic interaction between a cation and an electron-rich arene. It plays an essential role in many biological systems as a vital driving force for protein folding, stability, and receptor-ligand interaction/recognition. To date, the discovery of most cation-π interactions in proteins relies on the statistical analyses of available three-dimensional (3D) protein structures and corresponding computational calculations. However, their experimental verification and quantification remain sparse at the molecular level, mainly due to the limited methods to dynamically measure such a weak non-covalent interaction in proteins. Here, we use atomic force microscopy-based single-molecule force spectroscopy (AFM-SMFS) to measure the stability of protein neutrophil gelatinase-associated lipocalin (also known as NGAL, siderocalin, lipocalin 2) that can bind iron through the cation-π interactions between its three cationic residues and the iron-binding tri-catechols. Based on a site-specific cysteine engineering and anchoring method, we first characterized the stability and unfolding pathways of apo-NGAL. Then, the same NGAL but bound with the iron-catechol complexes through the cation-π interactions as a holo-form was characterized. AFM measurements demonstrated stronger stabilities and kinetics of the holo-NGAL from two pulling sites, F122 and F133. Here, NGAL is stretched from the designed cysteine close to the cationic residues for a maximum unfolding effect. Thus, our work demonstrates high-precision detection of the weak cation-π interaction in NGAL. ELECTRONIC SUPPLEMENTARY MATERIAL Supplementary material (additional SDS-PAGE, UV-vis, protein sequences, and more experimental methods) is available in the online version of this article at 10.1007/s12274-021-4065-9.
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Affiliation(s)
- Jingyuan Nie
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Road, Nanjing, 210023 China
| | - Yibing Deng
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Road, Nanjing, 210023 China
| | - Fang Tian
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Road, Nanjing, 210023 China
| | - Shengchao Shi
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Road, Nanjing, 210023 China
| | - Peng Zheng
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Road, Nanjing, 210023 China
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32
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Ritzmann N, Manioglu S, Hiller S, Müller DJ. Monitoring the antibiotic darobactin modulating the β-barrel assembly factor BamA. Structure 2021; 30:350-359.e3. [PMID: 34875215 DOI: 10.1016/j.str.2021.11.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/30/2021] [Accepted: 11/11/2021] [Indexed: 12/15/2022]
Abstract
The β-barrel assembly machinery (BAM) complex is an essential component of Escherichia coli that inserts and folds outer membrane proteins (OMPs). The natural antibiotic compound darobactin inhibits BamA, the central unit of BAM. Here, we employ dynamic single-molecule force spectroscopy (SMFS) to better understand the structure-function relationship of BamA and its inhibition by darobactin. The five N-terminal polypeptide transport (POTRA) domains show low mechanical, kinetic, and energetic stabilities. In contrast, the structural region linking the POTRA domains to the transmembrane β-barrel exposes the highest mechanical stiffness and lowest kinetic stability within BamA, thus indicating a mechano-functional role. Within the β-barrel, the four N-terminal β-hairpins H1-H4 expose the highest mechanical stabilities and stiffnesses, while the four C-terminal β-hairpins H5-H6 show lower stabilities and higher flexibilities. This asymmetry within the β-barrel suggests that substrates funneling into the lateral gate formed by β-hairpins H1 and H8 can force the flexible C-terminal β-hairpins to change conformations.
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Affiliation(s)
- Noah Ritzmann
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Selen Manioglu
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Sebastian Hiller
- Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Daniel J Müller
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, Mattenstrasse 26, 4058 Basel, Switzerland.
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33
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Rico-Pasto M, Zaltron A, Ritort F. Force Dependence of Proteins' Transition State Position and the Bell-Evans Model. Nanomaterials (Basel) 2021; 11:3023. [PMID: 34835787 DOI: 10.3390/nano11113023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/06/2021] [Accepted: 11/08/2021] [Indexed: 01/27/2023]
Abstract
Single-molecule force spectroscopy has opened a new field of research in molecular biophysics and biochemistry. Pulling experiments on individual proteins permit us to monitor conformational transitions with high temporal resolution and measure their free energy landscape. The force–extension curves of single proteins often present large hysteresis, with unfolding forces that are higher than refolding ones. Therefore, the high energy of the transition state (TS) in these molecules precludes kinetic rates measurements in equilibrium hopping experiments. In irreversible pulling experiments, force-dependent kinetic rates measurements show a systematic discrepancy between the sum of the folding and unfolding TS distances derived by the kinetic Bell–Evans model and the full molecular extension predicted by elastic models. Here, we show that this discrepancy originates from the force-induced movement of TS. Specifically, we investigate the highly kinetically stable protein barnase, using pulling experiments and the Bell–Evans model to characterize the position of its kinetic barrier. Experimental results show that while the TS stays at a roughly constant distance relative to the native state, it shifts with force relative to the unfolded state. Interestingly, a conversion of the protein extension into amino acid units shows that the TS position follows the Leffler–Hammond postulate: the higher the force, the lower the number of unzipped amino acids relative to the native state. The results are compared with the quasi-reversible unfolding–folding of a short DNA hairpin.
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34
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Ma Q, Liu L, Yang Z, Zheng P. Facile Synthesis of Peptide-Conjugated Gold Nanoclusters with Different Lengths. Nanomaterials (Basel) 2021; 11:2932. [PMID: 34835696 DOI: 10.3390/nano11112932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 10/26/2021] [Accepted: 10/29/2021] [Indexed: 11/17/2022]
Abstract
The synthesis of ultra-small gold nanoclusters (Au NCs) with sizes down to 2 nm has received increasing interest due to their unique optical and electronic properties. Like many peptide-coated gold nanospheres synthesized before, modified gold nanoclusters with peptide conjugation are potentially significant in biomedical and catalytic fields. Here, we explore whether such small-sized gold nanoclusters can be conjugated with peptides also and characterize them using atomic force microscopy. Using a long and flexible elastin-like polypeptide (ELP)20 as the conjugated peptide, (ELP)20-Au NCs was successfully synthesized via a one-pot synthesis method. The unique optical and electronic properties of gold nanoclusters are still preserved, while a much larger size was obtained as expected due to the peptide conjugation. In addition, a short and rigid peptide (EAAAK)3 was conjugated to the gold nanoclusters. Their Yong’s modulus was characterized using atomic force microscopy (AFM). Moreover, the coated peptide on the nanoclusters was pulled using AFM-based single molecule-force spectroscopy (SMFS), showing expected properties as one of the first force spectroscopy experiments on peptide-coated nanoclusters. Our results pave the way for further modification of nanoclusters based on the conjugated peptides and show a new method to characterize these materials using AFM-SMFS.
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35
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Bauer J, Žoldák G. Interpretation of Single-Molecule Force Experiments on Proteins Using Normal Mode Analysis. Nanomaterials (Basel) 2021; 11:nano11112795. [PMID: 34835560 PMCID: PMC8624234 DOI: 10.3390/nano11112795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/20/2021] [Accepted: 10/20/2021] [Indexed: 11/25/2022]
Abstract
Single-molecule force spectroscopy experiments allow protein folding and unfolding to be explored using mechanical force. Probably the most informative technique for interpreting the results of these experiments at the structural level makes use of steered molecular dynamics (MD) simulations, which can explicitly model the protein under load. Unfortunately, this technique is computationally expensive for many of the most interesting biological molecules. Here, we find that normal mode analysis (NMA), a significantly cheaper technique from a computational perspective, allows at least some of the insights provided by MD simulation to be gathered. We apply this technique to three non-homologous proteins that were previously studied by force spectroscopy: T4 lysozyme (T4L), Hsp70 and the glucocorticoid receptor domain (GCR). The NMA results for T4L and Hsp70 are compared with steered MD simulations conducted previously, and we find that we can recover the main results. For the GCR, which did not undergo MD simulation, our approach identifies substructures that correlate with experimentally identified unfolding intermediates. Overall, we find that NMA can make a valuable addition to the analysis toolkit for the structural analysis of single-molecule force experiments on proteins.
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Affiliation(s)
- Jacob Bauer
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovakia
- Correspondence: (J.B.); (G.Ž.); Tel.: +421-55-234-2242 (G.Ž.)
| | - Gabriel Žoldák
- Center for Interdisciplinary Biosciences, P. J. Šafárik University, Technology and Innovation Park, Trieda SNP 1, 041 54 Košice, Slovakia
- Correspondence: (J.B.); (G.Ž.); Tel.: +421-55-234-2242 (G.Ž.)
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36
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van der Sleen LM, Tych KM. Bioconjugation Strategies for Connecting Proteins to DNA-Linkers for Single-Molecule Force-Based Experiments. Nanomaterials (Basel) 2021; 11:2424. [PMID: 34578744 PMCID: PMC8464727 DOI: 10.3390/nano11092424] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/13/2021] [Accepted: 09/15/2021] [Indexed: 01/10/2023]
Abstract
The mechanical properties of proteins can be studied with single molecule force spectroscopy (SMFS) using optical tweezers, atomic force microscopy and magnetic tweezers. It is common to utilize a flexible linker between the protein and trapped probe to exclude short-range interactions in SMFS experiments. One of the most prevalent linkers is DNA due to its well-defined properties, although attachment strategies between the DNA linker and protein or probe may vary. We will therefore provide a general overview of the currently existing non-covalent and covalent bioconjugation strategies to site-specifically conjugate DNA-linkers to the protein of interest. In the search for a standardized conjugation strategy, considerations include their mechanical properties in the context of SMFS, feasibility of site-directed labeling, labeling efficiency, and costs.
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Affiliation(s)
| | - Katarzyna M. Tych
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands;
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37
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Tian F, Tong B, Sun L, Shi S, Zheng B, Wang Z, Dong X, Zheng P. N501Y mutation of spike protein in SARS-CoV-2 strengthens its binding to receptor ACE2. eLife 2021; 10:e69091. [PMID: 34414884 PMCID: PMC8455130 DOI: 10.7554/elife.69091] [Citation(s) in RCA: 196] [Impact Index Per Article: 65.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 08/19/2021] [Indexed: 12/18/2022] Open
Abstract
SARS-CoV-2 has been spreading around the world for the past year. Recently, several variants such as B.1.1.7 (alpha), B.1.351 (beta), and P.1 (gamma), which share a key mutation N501Y on the receptor-binding domain (RBD), appear to be more infectious to humans. To understand the underlying mechanism, we used a cell surface-binding assay, a kinetics study, a single-molecule technique, and a computational method to investigate the interaction between these RBD (mutations) and ACE2. Remarkably, RBD with the N501Y mutation exhibited a considerably stronger interaction, with a faster association rate and a slower dissociation rate. Atomic force microscopy (AFM)-based single-molecule force microscopy (SMFS) consistently quantified the interaction strength of RBD with the mutation as having increased binding probability and requiring increased unbinding force. Molecular dynamics simulations of RBD-ACE2 complexes indicated that the N501Y mutation introduced additional π-π and π-cation interactions that could explain the changes observed by force microscopy. Taken together, these results suggest that the reinforced RBD-ACE2 interaction that results from the N501Y mutation in the RBD should play an essential role in the higher rate of transmission of SARS-CoV-2 variants, and that future mutations in the RBD of the virus should be under surveillance.
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Affiliation(s)
- Fang Tian
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing UniversityNanjingChina
| | - Bei Tong
- Institute of Botany, Jiangsu Province and Chinese Academy of SciencesNanjingChina
| | - Liang Sun
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing UniversityNanjingChina
| | - Shengchao Shi
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing UniversityNanjingChina
| | - Bin Zheng
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing UniversityNanjingChina
| | - Zibin Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing UniversityNanjingChina
| | - Xianchi Dong
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing UniversityNanjingChina
- Engineering Research Center of Protein and Peptide Medicine, Ministry of EducationNanjingChina
| | - Peng Zheng
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing UniversityNanjingChina
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38
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Wypijewska Del Nogal A, Sundar Rajan V, Westerlund F, Wilhelmsson LM. Complex Conformational Dynamics of the Heart Failure-Associated Pre-miRNA-377 Hairpin Revealed by Single-Molecule Optical Tweezers. Int J Mol Sci 2021; 22:9008. [PMID: 34445712 DOI: 10.3390/ijms22169008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 08/13/2021] [Accepted: 08/18/2021] [Indexed: 11/17/2022] Open
Abstract
Pre-miRNA-377 is a hairpin-shaped regulatory RNA associated with heart failure. Here, we use single-molecule optical tweezers to unzip pre-miRNA-377 and study its stability and dynamics. We show that magnesium ions have a strong stabilizing effect, and that sodium ions stabilize the hairpin more than potassium ions. The hairpin unfolds in a single step, regardless of buffer composition. Interestingly, hairpin folding occurs either in a single step (type 1) or through the formation of intermediates, in multiple steps (type 2) or gradually (type 3). Type 3 occurs only in the presence of both sodium and magnesium, while type 1 and 2 take place in all buffers, with type 1 being the most prevalent. By reducing the size of the native hairpin loop from fourteen to four nucleotides, we demonstrate that the folding heterogeneity originates from the large size of the hairpin loop. Further, while efficient pre-miRNA-377 binders are lacking, we demonstrate that the recently developed C2 ligand displays bimodal activity: it enhances the mechanical stability of the pre-miRNA-377 hairpin and perturbs its folding. The knowledge regarding pre-miRNA stability and dynamics that we provide is important in understanding its regulatory function and how it can be modulated to achieve a therapeutic effect, e.g., in heart failure treatment.
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39
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Rajput SS, Deopa SPS, Ajith VJ, Kamerkar SC, Patil S. Validity of point-mass model in off-resonance dynamic atomic force microscopy. Nanotechnology 2021; 32:405702. [PMID: 34144547 DOI: 10.1088/1361-6528/ac0cb1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 06/18/2021] [Indexed: 06/12/2023]
Abstract
The quantitative measurement of viscoelasticity of nano-scale entities is an important goal of nanotechnology research and there is considerable progress with advent of dynamic atomic force microscopy. The hydrodynamics of cantilever, the force sensor in AFM measurements, plays a pivotal role in quantitative estimates of nano-scale viscoelasticity. The point-mass (PM) model, wherein the AFM cantilever is approximated as a point-mass with mass-less spring is widely used in dynamic AFM analysis and its validity, particularly in liquid environments, is debated. It is suggested that the cantilever must be treated as a continuous rectangular beam to obtain accurate estimates of nano-scale viscoelasticity of materials it is probing. Here, we derived equations, which relate stiffness and damping coefficient of the material under investigation to measured parameters, by approximating cantilever as a point-mass and also considering the full geometric details. These equations are derived for both tip-excited as well as base-excited cantilevers. We have performed off-resonance dynamic atomic force spectroscopy on a single protein molecule to investigate the validity of widely used PM model. We performed measurements with AFMs equipped with different cantilever excitation methods as well as detection schemes to measure cantilever response. The data was analyzed using both, continuous beam model and the PM model. We found that both models yield same results when the experiments are performed in truly off-resonance regime with small amplitudes and the cantilever stiffness is much higher than the interaction stiffness. Our findings suggest that a simple PM approximation based model is adequate to describe the dynamics, provided care is taken while performing experiments so that the approximations used in these models are valid.
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Affiliation(s)
- Shatruhan Singh Rajput
- Department of Physics, Indian Institute of Science Education and Research Pune, Dr Homi Bhabha Road, Pashan, Pune 411008, India
| | - Surya Pratap S Deopa
- Department of Physics, Indian Institute of Science Education and Research Pune, Dr Homi Bhabha Road, Pashan, Pune 411008, India
| | - V J Ajith
- Department of Physics, Indian Institute of Science Education and Research Pune, Dr Homi Bhabha Road, Pashan, Pune 411008, India
| | - Sukrut C Kamerkar
- Department of Biology, Indian Institute of Science Education and Research Pune, Dr Homi Bhabha Road, Pashan, Pune 411008, India
| | - Shivprasad Patil
- Department of Physics, Indian Institute of Science Education and Research Pune, Dr Homi Bhabha Road, Pashan, Pune 411008, India
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40
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Dumitru AC, Stommen A, Koehler M, Cloos AS, Yang J, Leclercqz A, Tyteca D, Alsteens D. Probing PIEZO1 Localization upon Activation Using High-Resolution Atomic Force and Confocal Microscopy. Nano Lett 2021; 21:4950-4958. [PMID: 34125553 DOI: 10.1021/acs.nanolett.1c00599] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
PIEZO1 ion channels are activated by mechanical stimuli, triggering intracellular chemical signals. Recent structural studies suggest that plasma membrane tension or local curvature changes modulate PIEZO1 channel gating and activation. However, whether PIEZO1 localization is governed by tension gradients or long-range mechanical perturbations across the cells is still unclear. Here, we probe the nanoscale localization of PIEZO1 on red blood cells (RBCs) at high resolution (∼30 nm), and we report for the first time the existence of submicrometric PIEZO1 clusters in native conditions. Upon interaction with Yoda1, an allosteric modulator, PIEZO1 clusters increase in abundance in regions of higher membrane tension and lower curvature. We further show that PIEZO1 ion channels interact with the spectrin cytoskeleton in both resting and activated states. Our results point toward a strong interplay between plasma membrane tension gradients, curvature, and cytoskeleton association of PIEZO1.
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Affiliation(s)
- Andra C Dumitru
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Louvain-la-Neuve 1348, Belgium
| | - Amaury Stommen
- de Duve Institute, Université Catholique de Louvain, Brussels 1200, Belgium
| | - Melanie Koehler
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Louvain-la-Neuve 1348, Belgium
| | - Anne-Sophie Cloos
- de Duve Institute, Université Catholique de Louvain, Brussels 1200, Belgium
| | - Jinsung Yang
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Louvain-la-Neuve 1348, Belgium
| | - Arnaud Leclercqz
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Louvain-la-Neuve 1348, Belgium
| | - Donatienne Tyteca
- de Duve Institute, Université Catholique de Louvain, Brussels 1200, Belgium
| | - David Alsteens
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Louvain-la-Neuve 1348, Belgium
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41
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Dai L, Xiao X, Pan L, Shi L, Xu N, Zhang Z, Feng X, Ma L, Dou S, Wang P, Zhu B, Li W, Zhou Z. Recognition of the inherently unstable H2A nucleosome by Swc2 is a major determinant for unidirectional H2A.Z exchange. Cell Rep 2021; 35:109183. [PMID: 34038732 DOI: 10.1016/j.celrep.2021.109183] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 03/29/2021] [Accepted: 05/05/2021] [Indexed: 12/24/2022] Open
Abstract
The multisubunit chromatin remodeler SWR1/SRCAP/p400 replaces the nucleosomal H2A-H2B dimer with the free-form H2A.Z-H2B dimer, but the mechanism governing the unidirectional H2A-to-H2A.Z exchange remains elusive. Here, we perform single-molecule force spectroscopy to dissect the disassembly/reassembly processes of the H2A nucleosome and H2A.Z nucleosome. We find that the N-terminal 1-135 residues of yeast SWR1 complex protein 2 (previously termed Swc2-Z) facilitate the disassembly of nucleosomes containing H2A but not H2A.Z. The Swc2-mediated nucleosome disassembly/reassembly requires the inherently unstable H2A nucleosome, whose instability is conferred by three H2A α2-helical residues, Gly47, Pro49, and Ile63, as they selectively weaken the structural rigidity of the H2A-H2B dimer. It also requires Swc2-ZN (residues 1-37) that directly anchors to the H2A nucleosome and functions in the SWR1-catalyzed H2A.Z replacement in vitro and yeast H2A.Z deposition in vivo. Our findings provide mechanistic insights into how the SWR1 complex discriminates between the H2A nucleosome and H2A.Z nucleosome, establishing a simple paradigm for the governance of unidirectional H2A.Z exchange.
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Affiliation(s)
- Linchang Dai
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xue Xiao
- National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lu Pan
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Liuxin Shi
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ning Xu
- Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zhuqiang Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaoli Feng
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Lu Ma
- National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Shuoxing Dou
- National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Pengye Wang
- National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China; Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
| | - Bing Zhu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Li
- National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China; Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China.
| | - Zheng Zhou
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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42
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Urbanska M, Lüdecke A, Walter WJ, van Oijen AM, Duderstadt KE, Diez S. Highly-Parallel Microfluidics-Based Force Spectroscopy on Single Cytoskeletal Motors. Small 2021; 17:e2007388. [PMID: 33759372 DOI: 10.1002/smll.202007388] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 02/22/2021] [Indexed: 06/12/2023]
Abstract
Cytoskeletal motors transform chemical energy into mechanical work to drive essential cellular functions. Optical trapping experiments have provided crucial insights into the operation of these molecular machines under load. However, the throughput of such force spectroscopy experiments is typically limited to one measurement at a time. Here, a highly-parallel, microfluidics-based method that allows for rapid collection of force-dependent motility parameters of cytoskeletal motors with two orders of magnitude improvement in throughput compared to currently available methods is introduced. Tunable hydrodynamic forces to stepping kinesin-1 motors via DNA-tethered beads and utilize a large field of view to simultaneously track the velocities, run lengths, and interaction times of hundreds of individual kinesin-1 molecules under varying resisting and assisting loads are applied. Importantly, the 16 µm long DNA tethers between the motors and the beads significantly reduces the vertical component of the applied force pulling the motors away from the microtubule. The approach is readily applicable to other molecular systems and constitutes a new methodology for parallelized single-molecule force studies on cytoskeletal motors.
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Affiliation(s)
- Marta Urbanska
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, 01069, Dresden, Germany
| | - Annemarie Lüdecke
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, 01069, Dresden, Germany
| | - Wilhelm J Walter
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, 01069, Dresden, Germany
| | - Antoine M van Oijen
- Zernike Institute for Advanced Materials, University of Groningen, Groningen, AE, 9700, Netherlands
- Molecular Horizons, University of Wollongong, Illawarra Health and Medical Research Institute, Wollongong, NSW, 2522, Australia
| | - Karl E Duderstadt
- Zernike Institute for Advanced Materials, University of Groningen, Groningen, AE, 9700, Netherlands
- Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
- Physics Department, Technische Universität München, 85748, Garching, Germany
| | - Stefan Diez
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, 01069, Dresden, Germany
- Cluster of Excellence Physics of Life, Technische Universität Dresden, 01062, Dresden, Germany
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307, Dresden, Germany
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43
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Jacobson DR, Perkins TT. Free-energy changes of bacteriorhodopsin point mutants measured by single-molecule force spectroscopy. Proc Natl Acad Sci U S A 2021; 118:e2020083118. [PMID: 33753487 DOI: 10.1073/pnas.2020083118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Single amino acid mutations provide quantitative insight into the energetics that underlie the dynamics and folding of membrane proteins. Chemical denaturation is the most widely used assay and yields the change in unfolding free energy (ΔΔG). It has been applied to >80 different residues of bacteriorhodopsin (bR), a model membrane protein. However, such experiments have several key limitations: 1) a nonnative lipid environment, 2) a denatured state with significant secondary structure, 3) error introduced by extrapolation to zero denaturant, and 4) the requirement of globally reversible refolding. We overcame these limitations by reversibly unfolding local regions of an individual protein with mechanical force using an atomic-force-microscope assay optimized for 2 μs time resolution and 1 pN force stability. In this assay, bR was unfolded from its native bilayer into a well-defined, stretched state. To measure ΔΔG, we introduced two alanine point mutations into an 8-amino-acid region at the C-terminal end of bR's G helix. For each, we reversibly unfolded and refolded this region hundreds of times while the rest of the protein remained folded. Our single-molecule-derived ΔΔG for mutant L223A (-2.3 ± 0.6 kcal/mol) quantitatively agreed with past chemical denaturation results while our ΔΔG for mutant V217A was 2.2-fold larger (-2.4 ± 0.6 kcal/mol). We attribute the latter result, in part, to contact between Val217 and a natively bound squalene lipid, highlighting the contribution of membrane protein-lipid contacts not present in chemical denaturation assays. More generally, we established a platform for determining ΔΔG for a fully folded membrane protein embedded in its native bilayer.
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44
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LeBlanc MA, Fink MR, Perkins TT, Sousa MC. Type III secretion system effector proteins are mechanically labile. Proc Natl Acad Sci U S A 2021; 118:e2019566118. [PMID: 33723050 DOI: 10.1073/pnas.2019566118] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Multiple gram-negative bacteria encode type III secretion systems (T3SS) that allow them to inject effector proteins directly into host cells to facilitate colonization. To be secreted, effector proteins must be at least partially unfolded to pass through the narrow needle-like channel (diameter <2 nm) of the T3SS. Fusion of effector proteins to tightly packed proteins-such as GFP, ubiquitin, or dihydrofolate reductase (DHFR)-impairs secretion and results in obstruction of the T3SS. Prior observation that unfolding can become rate-limiting for secretion has led to the model that T3SS effector proteins have low thermodynamic stability, facilitating their secretion. Here, we first show that the unfolding free energy ([Formula: see text]) of two Salmonella effector proteins, SptP and SopE2, are 6.9 and 6.0 kcal/mol, respectively, typical for globular proteins and similar to published [Formula: see text] for GFP, ubiquitin, and DHFR. Next, we mechanically unfolded individual SptP and SopE2 molecules by atomic force microscopy (AFM)-based force spectroscopy. SptP and SopE2 unfolded at low force (F unfold ≤ 17 pN at 100 nm/s), making them among the most mechanically labile proteins studied to date by AFM. Moreover, their mechanical compliance is large, as measured by the distance to the transition state (Δx ‡ = 1.6 and 1.5 nm for SptP and SopE2, respectively). In contrast, prior measurements of GFP, ubiquitin, and DHFR show them to be mechanically robust (F unfold > 80 pN) and brittle (Δx ‡ < 0.4 nm). These results suggest that effector protein unfolding by T3SS is a mechanical process and that mechanical lability facilitates efficient effector protein secretion.
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45
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Kotamarthi HC, Sauer RT, Baker TA. The Non-dominant AAA+ Ring in the ClpAP Protease Functions as an Anti-stalling Motor to Accelerate Protein Unfolding and Translocation. Cell Rep 2021; 30:2644-2654.e3. [PMID: 32101742 DOI: 10.1016/j.celrep.2020.01.110] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 11/25/2019] [Accepted: 01/30/2020] [Indexed: 10/24/2022] Open
Abstract
ATP-powered unfoldases containing D1 and D2 AAA+ rings play important roles in protein homeostasis, but uncertainty about the function of each ring remains. Here we use single-molecule optical tweezers to assay mechanical unfolding and translocation by a variant of the ClpAP protease containing an ATPase-inactive D1 ring. This variant displays substantial mechanical defects in both unfolding and translocation of protein substrates. Notably, when D1 is hydrolytically inactive, ClpAP often stalls for times as long as minutes, and the substrate can back-slip through the enzyme when ATP concentrations are low. The inactive D1 variant also has more difficulty traveling in the N-to-C direction on a polypeptide track than it does moving in a C-to-N direction. These results indicate that D1 normally functions as an auxiliary/regulatory motor to promote uninterrupted enzyme advancement that is fueled largely by the D2 ring.
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Affiliation(s)
- Hema Chandra Kotamarthi
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Robert T Sauer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Tania A Baker
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA.
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46
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Banerjee S, Chakraborty S, Sreepada A, Banerji D, Goyal S, Khurana Y, Haldar S. Cutting-Edge Single-Molecule Technologies Unveil New Mechanics in Cellular Biochemistry. Annu Rev Biophys 2021; 50:419-445. [PMID: 33646813 DOI: 10.1146/annurev-biophys-090420-083836] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Single-molecule technologies have expanded our ability to detect biological events individually, in contrast to ensemble biophysical technologies, where the result provides averaged information. Recent developments in atomic force microscopy have not only enabled us to distinguish the heterogeneous phenomena of individual molecules, but also allowed us to view up to the resolution of a single covalent bond. Similarly, optical tweezers, due to their versatility and precision, have emerged as a potent technique to dissect a diverse range of complex biological processes, from the nanomechanics of ClpXP protease-dependent degradation to force-dependent processivity of motor proteins. Despite the advantages of optical tweezers, the time scales used in this technology were inconsistent with physiological scenarios, which led to the development of magnetic tweezers, where proteins are covalently linked with the glass surface, which in turn increases the observation window of a single biomolecule from minutes to weeks. Unlike optical tweezers, magnetic tweezers use magnetic fields to impose torque, which makes them convenient for studying DNA topology and topoisomerase functioning. Using modified magnetic tweezers, researchers were able to discover the mechanical role of chaperones, which support their substrate proteinsby pulling them during translocation and assist their native folding as a mechanical foldase. In this article, we provide a focused review of many of these new roles of single-molecule technologies, ranging from single bond breaking to complex chaperone machinery, along with the potential to design mechanomedicine, which would be a breakthrough in pharmacological interventions against many diseases.
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Affiliation(s)
- Souradeep Banerjee
- Department of Biological Sciences, Ashoka University, Sonipat, Haryana 131029, India;
| | - Soham Chakraborty
- Department of Biological Sciences, Ashoka University, Sonipat, Haryana 131029, India;
| | - Abhijit Sreepada
- Department of Biological Sciences, Ashoka University, Sonipat, Haryana 131029, India;
| | - Devshuvam Banerji
- Department of Biological Sciences, Ashoka University, Sonipat, Haryana 131029, India;
| | - Shashwat Goyal
- Department of Biological Sciences, Ashoka University, Sonipat, Haryana 131029, India;
| | - Yajushi Khurana
- Department of Biological Sciences, Ashoka University, Sonipat, Haryana 131029, India;
| | - Shubhasis Haldar
- Department of Biological Sciences, Ashoka University, Sonipat, Haryana 131029, India;
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47
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López‐García P, de Araujo AD, Bergues‐Pupo AE, Tunn I, Fairlie DP, Blank KG. Fortified Coiled Coils: Enhancing Mechanical Stability with Lactam or Metal Staples. Angew Chem Int Ed Engl 2021; 60:232-236. [PMID: 32940968 PMCID: PMC7821110 DOI: 10.1002/anie.202006971] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Indexed: 12/19/2022]
Abstract
Coiled coils (CCs) are powerful supramolecular building blocks for biomimetic materials, increasingly used for their mechanical properties. Here, we introduce helix-inducing macrocyclic constraints, so-called staples, to tune thermodynamic and mechanical stability of CCs. We show that thermodynamic stabilization of CCs against helix uncoiling primarily depends on the number of staples, whereas staple positioning controls CC mechanical stability. Inserting a covalent lactam staple at one key force application point significantly increases the barrier to force-induced CC dissociation and reduces structural deformity. A reversible His-Ni2+ -His metal staple also increases CC stability, but ruptures upon mechanical loading to allow helix uncoiling. Staple type, position and number are key design parameters in using helical macrocyclic templates for fine-tuning CC properties in emerging biomaterials.
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Affiliation(s)
- Patricia López‐García
- Mechano(bio)chemistryMax Planck Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
| | - Aline D. de Araujo
- ARC Centre of Excellence for Innovations in Peptide and Protein ScienceInstitute for Molecular BioscienceThe University of QueenslandBrisbaneQld4072Australia
| | - Ana E. Bergues‐Pupo
- Department of Theory and Bio-SystemsMax Planck Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
- Present address: Berlin Institute for Medical Systems BiologyMax Delbrück Center for Molecular Medicine10115BerlinGermany
| | - Isabell Tunn
- Mechano(bio)chemistryMax Planck Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
| | - David P. Fairlie
- ARC Centre of Excellence for Innovations in Peptide and Protein ScienceInstitute for Molecular BioscienceThe University of QueenslandBrisbaneQld4072Australia
| | - Kerstin G. Blank
- Mechano(bio)chemistryMax Planck Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
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48
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Yang B, Liu H, Liu Z, Doenen R, Nash MA. Influence of Fluorination on Single-Molecule Unfolding and Rupture Pathways of a Mechanostable Protein Adhesion Complex. Nano Lett 2020; 20:8940-8950. [PMID: 33191756 PMCID: PMC7729889 DOI: 10.1021/acs.nanolett.0c04178] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/08/2020] [Indexed: 05/25/2023]
Abstract
We investigated the influence of fluorination on unfolding and unbinding reaction pathways of a mechanostable protein complex comprising the tandem dyad XModule-Dockerin bound to Cohesin. Using single-molecule atomic force spectroscopy, we mapped the energy landscapes governing the unfolding and unbinding reactions. We then used sense codon suppression to substitute trifluoroleucine in place of canonical leucine globally in XMod-Doc. Although TFL substitution thermally destabilized XMod-Doc, it had little effect on XMod-Doc:Coh binding affinity at equilibrium. When we mechanically dissociated global TFL-substituted XMod-Doc from Coh, we observed the emergence of a new unbinding pathway with a lower energy barrier. Counterintuitively, when fluorination was restricted to Doc, we observed mechano-stabilization of the non-fluorinated neighboring XMod domain. This suggests that intramolecular deformation is modulated by fluorination and highlights the differences between equilibrium thermostability and non-equilibrium mechanostability. Future work is poised to investigate fluorination as a means to modulate mechanical properties of synthetic proteins and hydrogels.
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Affiliation(s)
- Byeongseon Yang
- Department
of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
| | - Haipei Liu
- Department
of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
| | - Zhaowei Liu
- Department
of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
| | - Regina Doenen
- Department
of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
| | - Michael A. Nash
- Department
of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
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49
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Leicher R, Ge EJ, Lin X, Reynolds MJ, Xie W, Walz T, Zhang B, Muir TW, Liu S. Single-molecule and in silico dissection of the interaction between Polycomb repressive complex 2 and chromatin. Proc Natl Acad Sci U S A 2020; 117:30465-30475. [PMID: 33208532 PMCID: PMC7720148 DOI: 10.1073/pnas.2003395117] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Polycomb repressive complex 2 (PRC2) installs and spreads repressive histone methylation marks on eukaryotic chromosomes. Because of the key roles that PRC2 plays in development and disease, how this epigenetic machinery interacts with DNA and nucleosomes is of major interest. Nonetheless, the mechanism by which PRC2 engages with native-like chromatin remains incompletely understood. In this work, we employ single-molecule force spectroscopy and molecular dynamics simulations to dissect the behavior of PRC2 on polynucleosome arrays. Our results reveal an unexpectedly diverse repertoire of PRC2 binding configurations on chromatin. Besides reproducing known binding modes in which PRC2 interacts with bare DNA, mononucleosomes, and adjacent nucleosome pairs, our data also provide direct evidence that PRC2 can bridge pairs of distal nucleosomes. In particular, the "1-3" bridging mode, in which PRC2 engages two nucleosomes separated by one spacer nucleosome, is a preferred low-energy configuration. Moreover, we show that the distribution and stability of different PRC2-chromatin interaction modes are modulated by accessory subunits, oncogenic histone mutations, and the methylation state of chromatin. Overall, these findings have implications for the mechanism by which PRC2 spreads histone modifications and compacts chromatin. The experimental and computational platforms developed here provide a framework for understanding the molecular basis of epigenetic maintenance mediated by Polycomb-group proteins.
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Affiliation(s)
- Rachel Leicher
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, NY 10065
- Tri-Institutional PhD Program in Chemical Biology, New York, NY 10065
| | - Eva J Ge
- Department of Chemistry, Princeton University, Princeton, NJ 08544
| | - Xingcheng Lin
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Matthew J Reynolds
- Laboratory of Structural Biophysics and Mechanobiology, The Rockefeller University, New York, NY 10065
| | - Wenjun Xie
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Thomas Walz
- Laboratory of Molecular Electron Microscopy, The Rockefeller University, New York, NY 10065
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139;
| | - Tom W Muir
- Department of Chemistry, Princeton University, Princeton, NJ 08544
| | - Shixin Liu
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, NY 10065;
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50
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Wu J, Cao C, Loch RA, Tiiman A, Luo J. Single-molecule studies of amyloid proteins: from biophysical properties to diagnostic perspectives. Q Rev Biophys 2020; 53:e12. [PMID: 33148356 DOI: 10.1017/S0033583520000086] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In neurodegenerative diseases, a wide range of amyloid proteins or peptides such as amyloid-beta and α-synuclein fail to keep native functional conformations, followed by misfolding and self-assembling into a diverse array of aggregates. The aggregates further exert toxicity leading to the dysfunction, degeneration and loss of cells in the affected organs. Due to the disordered structure of the amyloid proteins, endogenous molecules, such as lipids, are prone to interact with amyloid proteins at a low concentration and influence amyloid cytotoxicity. The heterogeneity of amyloid proteinscomplicates the understanding of the amyloid cytotoxicity when relying only on conventional bulk and ensemble techniques. As complementary tools, single-molecule techniques (SMTs) provide novel insights into the different subpopulations of a heterogeneous amyloid mixture as well as the cytotoxicity, in particular as involved in lipid membranes. This review focuses on the recent advances of a series of SMTs, including single-molecule fluorescence imaging, single-molecule force spectroscopy and single-nanopore electrical recording, for the understanding of the amyloid molecular mechanism. The working principles, benefits and limitations of each technique are discussed and compared in amyloid protein related studies.. We also discuss why SMTs show great potential and are worthy of further investigation with feasibility studies as diagnostic tools of neurodegenerative diseases and which limitations are to be addressed.
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