1
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Kaur V, Garg S, Rakshit S. Polyprotein synthesis: a journey from the traditional pre-translational method to modern post-translational approaches for single-molecule force spectroscopy. Chem Commun (Camb) 2023. [PMID: 37183922 DOI: 10.1039/d3cc01756g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Polyproteins, an array of protein units of similar or differential functions in tandem, have been extensively utilized by organisms, unicellular or multicellular, as concentrators of the myriad of molecular activities. Most eukaryotic proteins, two-thirds in unicellular organisms, and more than 80% in metazoans, are polyproteins. Although the use of polyproteins continues to evolve in nature, our understanding of the structure-function-property of polyproteins is still limited. Cumbersome recombinant strategies and the lack of convenient in vitro synthetic routes of polyproteins have been rate-determining factors in the progress. However, in this review we have discussed the revolutionary journey of polyprotein synthesis with a major focus on surface-based structure-function-property studies, especially using force spectroscopy at the single-molecule level.
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Affiliation(s)
- Veerpal Kaur
- Department of Chemical Sciences, Indian Institute of Science Education and Research Mohali, 140306, Punjab, India.
| | - Surbhi Garg
- Department of Chemical Sciences, Indian Institute of Science Education and Research Mohali, 140306, Punjab, India.
| | - Sabyasachi Rakshit
- Department of Chemical Sciences, Indian Institute of Science Education and Research Mohali, 140306, Punjab, India.
- Centre for Protein Science Design and Engineering, Indian Institute of Science Education and Research Mohali, 140306, Punjab, India
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2
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Kaur V, Garg S, Rakshit S. Instantaneous splicing and excision of inteins to synthesize polyproteins on a substrate with tunable linkers. SOFT MATTER 2022; 18:602-608. [PMID: 34928293 DOI: 10.1039/d1sm01469b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Nature has adapted chimeric polyproteins to achieve superior and multiplexed functionality in a single protein. However, the hurdles in in vitro synthesis have restricted the biomimicry of and subsequent fundamental studies on the structure-function relationship of polyproteins. Recombinant expression of polyproteins and the synthesis of polyproteins via the enzyme-mediated repetitive digestion and ligation of individual protein domains have been widely practiced. However, recombinant expression often suffers from an in vitro refolding process, whereas enzyme-assisted peptide conjugation results in heterogeneous products, primarily due to enzymatic re-digestion, and prolonged and multistep reactions. Moreover, both methods incorporate enzyme-recognition residues of varying lengths as artifacts at interdomain linkers. The linkers, although tiny, regulate the spatiotemporal conformations of the polyproteins differentially and tune the folding dynamics, stability, and functions of the constituent protein. In an attempt to leave no string behind at the interdomain junctions, here, we develop a 'splice and excise' synthetic route for polyproteins on a substrate using two orthogonal split inteins. Inteins self-excise and conjugate the protein units covalently and instantaneously, without any cofactors, and incorporate a single cysteine or serine residue at the interdomain junctions.
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Affiliation(s)
- Veerpal Kaur
- Department of Chemical Sciences, Indian Institute of Science Education and Research Mohali, 140306, Punjab, India.
| | - Surbhi Garg
- Department of Chemical Sciences, Indian Institute of Science Education and Research Mohali, 140306, Punjab, India.
| | - Sabyasachi Rakshit
- Department of Chemical Sciences, Indian Institute of Science Education and Research Mohali, 140306, Punjab, India.
- Centre for Protein Science Design and Engineering, Indian Institute of Science Education and Research Mohali, 140306, Punjab, India
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3
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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 RESEARCH 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] [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
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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4
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Nie J, Tian F, Zheng B, Wang Z, Zheng P. Exploration of Metal-Ligand Coordination Bonds in Proteins by Single-molecule Force Spectroscopy. CHEM LETT 2021. [DOI: 10.1246/cl.210307] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Jingyuan Nie
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| | - Fang Tian
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| | - Bin Zheng
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| | - Ziyi Wang
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| | - Peng Zheng
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
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5
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Wang R, Li J, Li X, Guo J, Liu J, Li H. Engineering protein polymers of ultrahigh molecular weight via supramolecular polymerization: towards mimicking the giant muscle protein titin. Chem Sci 2019; 10:9277-9284. [PMID: 32055313 PMCID: PMC7003960 DOI: 10.1039/c9sc02128k] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 08/19/2019] [Indexed: 01/02/2023] Open
Abstract
Utilizing protein fragment reconstitution of a small protein GB1, we developed an efficient, supramolecular polymerization strategy to engineer protein polymers with ultrahigh molecular weight that mimic the giant muscle protein titin.
The giant muscle protein titin is the largest protein in cells and responsible for the passive elasticity of muscles. Titin, made of hundreds of individually folded globular domains, is a protein polymer with folded globular domains as its macromonomers. Due to titin's ultrahigh molecular weight, it has been challenging to engineer high molecular weight artificial protein polymers that mimic titin. Taking advantage of protein fragment reconstitution (PFR) of a small protein GB1, which can be reconstituted from its two split fragments GN and GC, here we report the development of an efficient, PFR-based supramolecular polymerization strategy to engineer protein polymers with ultrahigh molecular weight. We found that the engineered bifunctional protein macromonomers (GC-macromonomer-GN) can undergo supramolecular polymerization, in a way similar to condensation polymerization, via the reconstitution of GN and GC to produce protein polymers with ultrahigh molecular weight (with an average molecular weight of 0.5 MDa). Such high molecular weight linear protein polymers closely mimic titin and provide protein polymer building blocks for the construction of biomaterials with improved physical and mechanical properties.
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Affiliation(s)
- Ruidi Wang
- State Key Laboratory of Supramolecular Structure and Materials , College of Chemistry , Jilin University , Changchun 130012 , P. R. China.,Department of Chemistry , The University of British Columbia , Vancouver , BC V6T 1Z1 , Canada .
| | - Jiayu Li
- Department of Chemistry , The University of British Columbia , Vancouver , BC V6T 1Z1 , Canada .
| | - Xiumei Li
- State Key Laboratory of Supramolecular Structure and Materials , College of Chemistry , Jilin University , Changchun 130012 , P. R. China
| | - Jin Guo
- Department of Chemistry , The University of British Columbia , Vancouver , BC V6T 1Z1 , Canada .
| | - Junqiu Liu
- State Key Laboratory of Supramolecular Structure and Materials , College of Chemistry , Jilin University , Changchun 130012 , P. R. China
| | - Hongbin Li
- Department of Chemistry , The University of British Columbia , Vancouver , BC V6T 1Z1 , Canada .
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6
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Deng Y, Wu T, Wang M, Shi S, Yuan G, Li X, Chong H, Wu B, Zheng P. Enzymatic biosynthesis and immobilization of polyprotein verified at the single-molecule level. Nat Commun 2019; 10:2775. [PMID: 31235796 PMCID: PMC6591319 DOI: 10.1038/s41467-019-10696-x] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 05/23/2019] [Indexed: 11/09/2022] Open
Abstract
The recent development of chemical and bio-conjugation techniques allows for the engineering of various protein polymers. However, most of the polymerization process is difficult to control. To meet this challenge, we develop an enzymatic procedure to build polyprotein using the combination of a strict protein ligase OaAEP1 (Oldenlandia affinis asparaginyl endopeptidases 1) and a protease TEV (tobacco etch virus). We firstly demonstrate the use of OaAEP1-alone to build a sequence-uncontrolled ubiquitin polyprotein and covalently immobilize the coupled protein on the surface. Then, we construct a poly-metalloprotein, rubredoxin, from the purified monomer. Lastly, we show the feasibility of synthesizing protein polymers with rationally-controlled sequences by the synergy of the ligase and protease, which are verified by protein unfolding using atomic force microscopy-based single-molecule force spectroscopy (AFM-SMFS). Thus, this study provides a strategy for polyprotein engineering and immobilization.
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Affiliation(s)
- Yibing Deng
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 210023, P. R. China
| | - Tao Wu
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 210023, P. R. China
| | - Mengdi Wang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 210023, P. R. China
| | - Shengchao Shi
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 210023, P. R. China
| | - Guodong Yuan
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 210023, P. R. China
| | - Xi Li
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 210023, P. R. China
| | - Hanchung Chong
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore, 636921, Singapore
| | - Bin Wu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore, 636921, Singapore
| | - Peng Zheng
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 210023, P. R. China.
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7
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Abstract
Polyproteins, individual protein units joined covalently in tandem, have evolved as a promising tool for measuring the dynamic folding of biomacromolecules in single-molecule force spectroscopy. However, the synthetic routes to prepare polyproteins have been a bottleneck, and urge development of in vitro methods to knit individual protein units covalently into polyprotein. Employing two enzymes of orthogonal functionalities periodically in sequence, we synthesized monodispersed polyproteins on a solid surface. We used Sortase A (SrtA), the enzyme known for sequence specific transpeptidation, to staple protein units covalently through peptide bonds. Exploiting the sequence-specific peptide cleaving ability of TEV protease, we controlled the progress of the reaction to one attachment at a time. Finally, with unique design of the unit proteins we control the orientation of proteins in polyprotein. This simple conjugation has the potential to staple proteins with different functionalities and from different expression systems, in any number in the polyprotein and, above all, via irreversible peptide bonds. Multiple chimeric constructs can also be synthesized with interchangeable protein units.
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Affiliation(s)
- S. Garg
- Department of Chemical Sciences, Indian Institute of Science Education and Research Mohali, Punjab, India
| | - G. S. Singaraju
- Department of Chemical Sciences, Indian Institute of Science Education and Research Mohali, Punjab, India
| | - S. Yenghkom
- Department of Chemical Sciences, Indian Institute of Science Education and Research Mohali, Punjab, India
| | - S. Rakshit
- Department of Chemical Sciences, Indian Institute of Science Education and Research Mohali, Punjab, India
- Centre for Protein Science Design and Engineering, Indian Institute of Science Education and Research Mohali, Punjab, India
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8
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Nunes-Alves A, Arantes GM. Mechanical Unfolding of Macromolecules Coupled to Bond Dissociation. J Chem Theory Comput 2017; 14:282-290. [DOI: 10.1021/acs.jctc.7b00805] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Ariane Nunes-Alves
- Department of Biochemistry,
Instituto de Quı́mica, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, 05508-900 São Paulo, SP, Brazil
| | - Guilherme Menegon Arantes
- Department of Biochemistry,
Instituto de Quı́mica, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, 05508-900 São Paulo, SP, Brazil
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9
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Lei H, Guo Y, Hu X, Hu C, Hu X, Li H. Reversible Unfolding and Folding of the Metalloprotein Ferredoxin Revealed by Single-Molecule Atomic Force Microscopy. J Am Chem Soc 2017; 139:1538-1544. [DOI: 10.1021/jacs.6b11371] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hai Lei
- State
Key Laboratory of Precision Measurements Technology and Instruments,
School of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin 300072, People’s Republic of China
- Department
of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Yabin Guo
- Department
of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Xiaodong Hu
- State
Key Laboratory of Precision Measurements Technology and Instruments,
School of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin 300072, People’s Republic of China
| | - Chunguang Hu
- State
Key Laboratory of Precision Measurements Technology and Instruments,
School of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin 300072, People’s Republic of China
| | - Xiaotang Hu
- State
Key Laboratory of Precision Measurements Technology and Instruments,
School of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin 300072, People’s Republic of China
| | - Hongbin Li
- State
Key Laboratory of Precision Measurements Technology and Instruments,
School of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin 300072, People’s Republic of China
- Department
of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
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10
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Hoffmann T, Tych KM, Crosskey T, Schiffrin B, Brockwell DJ, Dougan L. Rapid and Robust Polyprotein Production Facilitates Single-Molecule Mechanical Characterization of β-Barrel Assembly Machinery Polypeptide Transport Associated Domains. ACS NANO 2015; 9:8811-21. [PMID: 26284289 DOI: 10.1021/acsnano.5b01962] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Single-molecule force spectroscopy by atomic force microscopy exploits the use of multimeric protein constructs, namely, polyproteins, to decrease the impact of nonspecific interactions, to improve data accumulation, and to allow the accommodation of benchmarking reference domains within the construct. However, methods to generate such constructs are either time- and labor-intensive or lack control over the length or the domain sequence of the obtained construct. Here, we describe an approach that addresses both of these shortcomings that uses Gibson assembly (GA) to generate a defined recombinant polyprotein rapidly using linker sequences. To demonstrate the feasibility of this approach, we used GA to make a polyprotein composed of alternating domains of I27 and TmCsp, (I27-TmCsp)3-I27)(GA), and showed the mechanical fingerprint, mechanical strength, and pulling speed dependence are the same as an analogous polyprotein constructed using the classical approach. After this benchmarking, we exploited this approach to facilitiate the mechanical characterization of POTRA domain 2 of BamA from E. coli (EcPOTRA2) by assembling the polyprotein (I27-EcPOTRA2)3-I27(GA). We show that, as predicted from the α + β topology, EcPOTRA2 domains are mechanically robust over a wide range of pulling speeds. Furthermore, we identify a clear correlation between mechanical robustness and brittleness for a range of other α + β proteins that contain the structural feature of proximal terminal β-strands in parallel geometry. We thus demonstrate that the GA approach is a powerful tool, as it circumvents the usual time- and labor-intensive polyprotein production process and allows for rapid production of new constructs for single-molecule studies. As shown for EcPOTRA2, this approach allows the exploration of the mechanical properties of a greater number of proteins and their variants. This improves our understanding of the relationship between structure and mechanical strength, increasing our ability to design proteins with tailored mechanical properties.
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Affiliation(s)
- Toni Hoffmann
- School of Physics and Astronomy, ‡Astbury Centre for Structural and Molecular Biology, and §School of Molecular and Cellular Biology, University of Leeds , Leeds, LS2 9JT, U.K
| | - Katarzyna M Tych
- School of Physics and Astronomy, ‡Astbury Centre for Structural and Molecular Biology, and §School of Molecular and Cellular Biology, University of Leeds , Leeds, LS2 9JT, U.K
| | - Thomas Crosskey
- School of Physics and Astronomy, ‡Astbury Centre for Structural and Molecular Biology, and §School of Molecular and Cellular Biology, University of Leeds , Leeds, LS2 9JT, U.K
| | - Bob Schiffrin
- School of Physics and Astronomy, ‡Astbury Centre for Structural and Molecular Biology, and §School of Molecular and Cellular Biology, University of Leeds , Leeds, LS2 9JT, U.K
| | - David J Brockwell
- School of Physics and Astronomy, ‡Astbury Centre for Structural and Molecular Biology, and §School of Molecular and Cellular Biology, University of Leeds , Leeds, LS2 9JT, U.K
| | - Lorna Dougan
- School of Physics and Astronomy, ‡Astbury Centre for Structural and Molecular Biology, and §School of Molecular and Cellular Biology, University of Leeds , Leeds, LS2 9JT, U.K
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11
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Zheng P, Arantes GM, Field MJ, Li H. Force-induced chemical reactions on the metal centre in a single metalloprotein molecule. Nat Commun 2015; 6:7569. [PMID: 26108369 PMCID: PMC4491811 DOI: 10.1038/ncomms8569] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 05/19/2015] [Indexed: 02/06/2023] Open
Abstract
Metalloproteins play indispensable roles in biology owing to the versatile chemical reactivity of metal centres. However, studying their reactivity in many metalloproteins is challenging, as protein three-dimensional structure encloses labile metal centres, thus limiting their access to reactants and impeding direct measurements. Here we demonstrate the use of single-molecule atomic force microscopy to induce partial unfolding to expose metal centres in metalloproteins to aqueous solution, thus allowing for studying their chemical reactivity in aqueous solution for the first time. As a proof-of-principle, we demonstrate two chemical reactions for the FeS4 centre in rubredoxin: electrophilic protonation and nucleophilic ligand substitution. Our results show that protonation and ligand substitution result in mechanical destabilization of the FeS4 centre. Quantum chemical calculations corroborated experimental results and revealed detailed reaction mechanisms. We anticipate that this novel approach will provide insights into chemical reactivity of metal centres in metalloproteins under biologically more relevant conditions. The investigation of the chemical reactivity of metal centres in metalloproteins in aqueous solution is challenging. Here, the authors demonstrate the use of single molecule force spectroscopy to study the chemical reactivity of the iron-sulfur centre in rubredoxin in aqueous solution.
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Affiliation(s)
- Peng Zheng
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z1.,School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210063, P. R. China
| | - Guilherme M Arantes
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Avenue Lineu Prestes 748, São Paulo SP 05508-900, Brazil
| | - Martin J Field
- Institut de Biologie Structurale (IBS) Jean-Pierre Ebel, CEA/CNRS/Universite Joseph Fourier, 71 Avenue des Martyrs, CS 10090, Grenoble 9 38044, France
| | - Hongbin Li
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z1
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12
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Protein misfolding occurs by slow diffusion across multiple barriers in a rough energy landscape. Proc Natl Acad Sci U S A 2015; 112:8308-13. [PMID: 26109573 DOI: 10.1073/pnas.1419197112] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The timescale for the microscopic dynamics of proteins during conformational transitions is set by the intrachain diffusion coefficient, D. Despite the central role of protein misfolding and aggregation in many diseases, it has proven challenging to measure D for these processes because of their heterogeneity. We used single-molecule force spectroscopy to overcome these challenges and determine D for misfolding of the prion protein PrP. Observing directly the misfolding of individual dimers into minimal aggregates, we reconstructed the energy landscape governing nonnative structure formation. Remarkably, rather than displaying multiple pathways, as typically expected for aggregation, PrP dimers were funneled into a thermodynamically stable misfolded state along a single pathway containing several intermediates, one of which blocked native folding. Using Kramers' rate theory, D was found to be 1,000-fold slower for misfolding than for native folding, reflecting local roughening of the misfolding landscape, likely due to increased internal friction. The slow diffusion also led to much longer transit times for barrier crossing, allowing transition paths to be observed directly for the first time to our knowledge. These results open a new window onto the microscopic mechanisms governing protein misfolding.
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13
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Tych KM, Hughes ML, Bourke J, Taniguchi Y, Kawakami M, Brockwell DJ, Dougan L. Optimizing the calculation of energy landscape parameters from single-molecule protein unfolding experiments. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 91:012710. [PMID: 25679645 DOI: 10.1103/physreve.91.012710] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Indexed: 06/04/2023]
Abstract
Single-molecule force spectroscopy using an atomic force microscope (AFM) can be used to measure the average unfolding force of proteins in a constant velocity experiment. In combination with Monte Carlo simulations and through the application of the Zhurkov-Bell model, information about the parameters describing the underlying unfolding energy landscape of the protein can be obtained. Using this approach, we have completed protein unfolding experiments on the polyprotein (I27)(5) over a range of pulling velocities. In agreement with previous work, we find that the observed number of protein unfolding events observed in each approach-retract cycle varies between one and five, due to the nature of the interactions between the polyprotein, the AFM tip, and the substrate, and there is an unequal unfolding probability distribution. We have developed a Monte Carlo simulation that incorporates the impact of this unequal unfolding probability distribution on the median unfolding force and the calculation of the protein unfolding energy landscape parameters. These results show that while there is a significant, unequal unfolding probability distribution, the unfolding energy landscape parameters obtained from use of the Zhurkov-Bell model are not greatly affected. This result is important because it demonstrates that the minimum acceptance criteria typically used in force extension experiments are justified and do not skew the calculation of the unfolding energy landscape parameters. We further validate this approach by determining the error in the energy landscape parameters for two extreme cases, and we provide suggestions for methods that can be employed to increase the level of accuracy in single-molecule experiments using polyproteins.
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Affiliation(s)
- Katarzyna M Tych
- Astbury Centre for Structural Molecular Biology and School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Megan L Hughes
- Astbury Centre for Structural Molecular Biology and School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - James Bourke
- School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Yukinori Taniguchi
- School of Materials Science, Japan Advanced Institute of Science and Technology (JAIST), 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
| | - Masaru Kawakami
- School of Materials Science, Japan Advanced Institute of Science and Technology (JAIST), 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
| | - David J Brockwell
- Astbury Centre for Structural Molecular Biology and School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Lorna Dougan
- Astbury Centre for Structural Molecular Biology and School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, United Kingdom
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14
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Zheng P, Wang Y, Li H. Reversible Unfolding-Refolding of Rubredoxin: A Single-Molecule Force Spectroscopy Study. Angew Chem Int Ed Engl 2014; 53:14060-3. [DOI: 10.1002/anie.201408105] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Indexed: 11/11/2022]
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15
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Zheng P, Wang Y, Li H. Reversible Unfolding-Refolding of Rubredoxin: A Single-Molecule Force Spectroscopy Study. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201408105] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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16
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Janissen R, Berghuis BA, Dulin D, Wink M, van Laar T, Dekker NH. Invincible DNA tethers: covalent DNA anchoring for enhanced temporal and force stability in magnetic tweezers experiments. Nucleic Acids Res 2014; 42:e137. [PMID: 25140010 PMCID: PMC4191378 DOI: 10.1093/nar/gku677] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Magnetic tweezers are a powerful single-molecule technique that allows real-time quantitative investigation of biomolecular processes under applied force. High pulling forces exceeding tens of picoNewtons may be required, e.g. to probe the force range of proteins that actively transcribe or package the genome. Frequently, however, the application of such forces decreases the sample lifetime, hindering data acquisition. To provide experimentally viable sample lifetimes in the face of high pulling forces, we have designed a novel anchoring strategy for DNA in magnetic tweezers. Our approach, which exploits covalent functionalization based on heterobifunctional poly(ethylene glycol) crosslinkers, allows us to strongly tether DNA while simultaneously suppressing undesirable non-specific adhesion. A complete force and lifetime characterization of these covalently anchored DNA-tethers demonstrates that, compared to more commonly employed anchoring strategies, they withstand 3-fold higher pulling forces (up to 150 pN) and exhibit up to 200-fold higher lifetimes (exceeding 24 h at a constant force of 150 pN). This advance makes it possible to apply the full range of biologically relevant force scales to biomolecular processes, and its straightforward implementation should extend its reach to a multitude of applications in the field of single-molecule force spectroscopy.
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Affiliation(s)
- Richard Janissen
- Department of Bionanoscience, Kavli Institute of Nanoscience, Faculty of Applied Sciences, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
| | - Bojk A Berghuis
- Department of Bionanoscience, Kavli Institute of Nanoscience, Faculty of Applied Sciences, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
| | - David Dulin
- Department of Bionanoscience, Kavli Institute of Nanoscience, Faculty of Applied Sciences, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
| | - Max Wink
- Department of Bionanoscience, Kavli Institute of Nanoscience, Faculty of Applied Sciences, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
| | - Theo van Laar
- Department of Bionanoscience, Kavli Institute of Nanoscience, Faculty of Applied Sciences, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
| | - Nynke H Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Faculty of Applied Sciences, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
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17
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Li Y, Qin M, Li Y, Cao Y, Wang W. Single molecule evidence for the adaptive binding of DOPA to different wet surfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:4358-4366. [PMID: 24716607 DOI: 10.1021/la501189n] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
3,4-Dihydroxyphenylalanine (DOPA) is the noncanonical amino acid widely found in mussel holdfast proteins, which is proposed to be responsible for their strong wet adhesion. This feature has also inspired the successful development of a range of DOPA-containing synthetic polymers for wet adhesions and surface coating. Despite the increasing applications of DOPA in material science, the underlying mechanism of DOPA-wet surface interactions remains unclear. In this work, we studied DOPA-surface interactions one bond at a time using atomic force microscope (AFM) based single molecule force spectroscopy. With our recently developed "multiple fishhook" protocol, we were able to perform high-throughput quantification of the binding strength of DOPA to various types of surfaces for the first time. We found that the dissociation forces between DOPA and nine different types of organic and inorganic surfaces are all in the range of 60-90 pN at a pulling speed of 1000 nm s(-1), suggesting the strong and versatile binding capability of DOPA to different types of surfaces. Moreover, by constructing the free energy landscape for the rupture events, we revealed several distinct binding modes between DOPA and different surfaces, which are directly related to the chemistry nature of the surfaces. These results explain the molecular origin of the versatile binding ability of DOPA. Moreover, we could quantitatively predict the relationship between DOPA contents and the binding strength based on the measured rupture kinetics. These serve as the bases for the quantitative prediction of the relationship between DOPA contents and adhesion strength to different wet surfaces, which is important for the design of novel DOPA based materials.
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Affiliation(s)
- Yiran Li
- National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University , 22 Hankou Road, Nanjing, Jiangsu, China 210093
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18
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Scholl ZN, Li Q, Marszalek PE. Single molecule mechanical manipulation for studying biological properties of proteins,
DNA
, and sugars. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2013; 6:211-29. [DOI: 10.1002/wnan.1253] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Revised: 10/10/2013] [Accepted: 10/17/2013] [Indexed: 11/07/2022]
Affiliation(s)
- Zackary N. Scholl
- Department of Computational Biology and Bioinformatics Duke University Durham NC USA
| | - Qing Li
- Department of Mechanical Engineering and Materials Science Duke University Durham NC USA
| | - Piotr E. Marszalek
- Department of Mechanical Engineering and Materials Science, Center for Biologically Inspired Materials and Material Systems Duke University Durham NC USA
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19
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Li YD, Lamour G, Gsponer J, Zheng P, Li H. The molecular mechanism underlying mechanical anisotropy of the protein GB1. Biophys J 2013; 103:2361-8. [PMID: 23283235 DOI: 10.1016/j.bpj.2012.10.035] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Revised: 10/19/2012] [Accepted: 10/26/2012] [Indexed: 10/27/2022] Open
Abstract
Mechanical responses of elastic proteins are crucial for their biological function and nanotechnological use. Loading direction has been identified as one key determinant for the mechanical responses of proteins. However, it is not clear how a change in pulling direction changes the mechanical unfolding mechanism of the protein. Here, we combine protein engineering, single-molecule force spectroscopy, and steered molecular dynamics simulations to systematically investigate the mechanical response of a small globular protein GB1. Force versus extension profiles from both experiments and simulations reveal marked mechanical anisotropy of GB1. Using native contact analysis, we relate the mechanically robust shearing geometry with concurrent rupture of native contacts. This clearly contrasts the sequential rupture observed in simulations for the mechanically labile peeling geometry. Moreover, we identify multiple distinct mechanical unfolding pathways in two loading directions. Implications of such diverse unfolding mechanisms are discussed. Our results may also provide some insights for designing elastomeric proteins with tailored mechanical properties.
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Affiliation(s)
- Yongnan Devin Li
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
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20
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Zheng P, Takayama SIJ, Mauk AG, Li H. Single Molecule Force Spectroscopy Reveals That Iron Is Released from the Active Site of Rubredoxin by a Stochastic Mechanism. J Am Chem Soc 2013; 135:7992-8000. [DOI: 10.1021/ja402150q] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Peng Zheng
- Department of Chemistry, University of British Columbia, Vancouver, British
Columbia V6T 1Z1, Canada
| | - Shin-ichi J. Takayama
- Department of Biochemistry and
Molecular Biology and the Center for Blood Research, University of British Columbia, Vancouver, British
Columbia V6T 1Z3, Canada
| | - A. Grant Mauk
- Department of Biochemistry and
Molecular Biology and the Center for Blood Research, University of British Columbia, Vancouver, British
Columbia V6T 1Z3, Canada
| | - Hongbin Li
- Department of Chemistry, University of British Columbia, Vancouver, British
Columbia V6T 1Z1, Canada
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21
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Mora MF, Stockton AM, Willis PA. Analysis of thiols by microchip capillary electrophoresis for in situ planetary investigations. Electrophoresis 2012; 34:309-16. [PMID: 23161601 DOI: 10.1002/elps.201200379] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Revised: 08/30/2012] [Accepted: 09/01/2012] [Indexed: 11/09/2022]
Abstract
The detection of thiols on extraterrestrial bodies could provide evidence for life, as well as a host of potential prebiological or abiological processes. Here, we report a novel protocol to analyze organic thiols by microchip CE with LIF detection. Thiols were labeled with Pacific Blue C5 maleimide and analyzed by MEKC. The separation buffer consisted of 15 mM tetraborate pH 9.2 and 25 mM SDS. The optimized method provided LODs ranging from 1.4 to 15 nM. The method was validated using samples collected from geothermal pools at Hot Creek Gorge, California, which were found to contain 2-propanethiol and 1-butanethiol in the nanomolar concentration range. These samples serve as chemical analogues to material potentially present in the reducing environment of primitive Earth and also at sulfurous regions of Mars. Hence, the protocol developed here enables highly sensitive thiol analysis in samples with complexity comparable to that expected in astrobiologically relevant extraterrestrial settings. This new protocol could be readily added to the existing suite of microfluidic chemical analyses developed for in situ planetary exploration; all that is required is the incorporation of two new reagents to the payload of an existing instrument concept.
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Affiliation(s)
- Maria F Mora
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA
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22
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Oohora K, Onoda A, Hayashi T. Supramolecular assembling systems formed by heme-heme pocket interactions in hemoproteins. Chem Commun (Camb) 2012; 48:11714-26. [PMID: 23079761 DOI: 10.1039/c2cc36376c] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A native protein in a biological system spontaneously produces large and elegant assemblies via self-assembly or assembly with various biomolecules which provide non-covalent interactions. In this context, the protein plays a key role in construction of a unique supramolecular structure operating as a functional system. Our group has recently highlighted the structure and function of hemoproteins reconstituted with artificially created heme analogs. The heme molecule is a replaceable cofactor of several hemoproteins. Here, we focus on the successive supramolecular protein assemblies driven by heme-heme pocket interactions to afford various examples of protein fibers, networks and three-dimensional clusters in which an artificial heme moiety is introduced onto the surface of a hemoprotein via covalent linkage and the native heme cofactor is removed from the heme pocket. This strategy is found to be useful for constructing hybrid materials with an electrode or with nanoparticles. The new systems described herein are expected to lead to the generation of various biomaterials with functions and characteristic physicochemical properties similar to those of hemoproteins.
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Affiliation(s)
- Koji Oohora
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Yamadaoka 2-1, Suita, Osaka, 565-0871, Japan
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23
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Han X, Qin M, Pan H, Cao Y, Wang W. A versatile "multiple fishhooks" approach for the study of ligand-receptor interactions using single-molecule atomic force microscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:10020-10025. [PMID: 22690829 DOI: 10.1021/la301903z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Despite the powerfulness of atomic force microscopy (AFM)-based single-molecule force spectroscopy in the study of ligand-receptor interactions, complicated cantilever functionalization and data interpretation have often been a great hurdle for its widespread application. Here, we present a much simplified experimental scheme by using a "multiple fishhooks" approach. In this strategy, multiple ligands are labeled on a single polymer chain, which forms complexes with receptors anchored on the substrate surface. Therefore, multiple single-bond rupture events can be captured in the same force-extension curves, similar to the widely used polyprotein approach. This method also allows nonsingle-molecule events and nonspecific interactions between cantilever and surface to be readily excluded from real data pool and greatly increases the quality and quantity of single-molecule data. The biggest advantage of our approach over the previously reported one is the choice of a naturally occurring polysaccharide, hyaluronan, the conformation of which in solution can be fine-tuned by pH, as the polymer backbone of the "multiple fishhooks" handle. Furthermore, our approach greatly simplifies the chemical synthesis of the polymer handle, allowing bioactive molecules to be easily one-step labeled on the handles in aqueous solution. We validate this strategy using the widely studied streptavidin-biotin system, and our single-molecule AFM results are in good agreement with previously reported ones. We anticipate that this novel strategy can be used as a versatile tool to study other complex and challenging ligand-receptor interactions.
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Affiliation(s)
- Xiaotian Han
- National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing, Jiangsu, People's Republic of China
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24
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He C, Genchev GZ, Lu H, Li H. Mechanically untying a protein slipknot: multiple pathways revealed by force spectroscopy and steered molecular dynamics simulations. J Am Chem Soc 2012; 134:10428-35. [PMID: 22626004 PMCID: PMC3663486 DOI: 10.1021/ja3003205] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein structure is highly diverse when considering a wide range of protein types, helping to give rise to the multitude of functions that proteins perform. In particular, certain proteins are known to adopt a knotted or slipknotted fold. How such proteins undergo mechanical unfolding was investigated utilizing a combination of single molecule atomic force microscopy (AFM), protein engineering, and steered molecular dynamics (SMD) simulations to show the mechanical unfolding mechanism of the slipknotted protein AFV3-109. Our results reveal that the mechanical unfolding of AFV3-109 can proceed via multiple parallel unfolding pathways that all cause the protein slipknot to untie and the polypeptide chain to completely extend. These distinct unfolding pathways proceed via either a two- or three-state unfolding process involving the formation of a well-defined, stable intermediate state. SMD simulations predict the same contour length increments for different unfolding pathways as single molecule AFM results, thus providing a plausible molecular mechanism for the mechanical unfolding of AFV3-109. These SMD simulations also reveal that two-state unfolding is initiated from both the N- and C-termini, while three-state unfolding is initiated only from the C-terminus. In both pathways, the protein slipknot was untied during unfolding, and no tightened slipknot conformation was observed. Detailed analysis revealed that interactions between key structural elements lock the knotting loop in place, preventing it from shrinking and the formation of a tightened slipknot conformation. Our results demonstrate the bifurcation of the mechanical unfolding pathway of AFV3-109 and point to the generality of a kinetic partitioning mechanism for protein folding/unfolding.
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Affiliation(s)
- Chengzhi He
- Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | - Georgi Z. Genchev
- Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, U. S. A
| | - Hui Lu
- Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, U. S. A
| | - Hongbin Li
- Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada
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25
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Zheng P, Takayama SIJ, Mauk AG, Li H. Hydrogen Bond Strength Modulates the Mechanical Strength of Ferric-Thiolate Bonds in Rubredoxin. J Am Chem Soc 2012; 134:4124-31. [DOI: 10.1021/ja2078812] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Peng Zheng
- Department of Chemistry, University of British Columbia, Vancouver,
BC V6T 1Z1 Canada
| | - Shin-ichi J. Takayama
- Department of Biochemistry
and Molecular Biology and the Center for Blood Research, University of British Columbia, Vancouver,
BC V6T 1Z3 Canada
| | - A. Grant Mauk
- Department of Biochemistry
and Molecular Biology and the Center for Blood Research, University of British Columbia, Vancouver,
BC V6T 1Z3 Canada
| | - Hongbin Li
- Department of Chemistry, University of British Columbia, Vancouver,
BC V6T 1Z1 Canada
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26
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Hoffmann T, Dougan L. Single molecule force spectroscopy using polyproteins. Chem Soc Rev 2012; 41:4781-96. [DOI: 10.1039/c2cs35033e] [Citation(s) in RCA: 139] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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27
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Zheng P, Li H. Direct measurements of the mechanical stability of zinc-thiolate bonds in rubredoxin by single-molecule atomic force microscopy. Biophys J 2011; 101:1467-73. [PMID: 21943428 DOI: 10.1016/j.bpj.2011.08.021] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2011] [Revised: 07/28/2011] [Accepted: 08/09/2011] [Indexed: 01/09/2023] Open
Abstract
Zinc (Zn) is one of the most abundant metals and is essential for life. Through ligand interactions, often with thiolate from cysteine residues in proteins, Zn can play important structural roles in organizing protein structure and augmenting protein folding and stability. However, it is difficult to separate the contributions of Zn-ligand interactions from those originating from intrinsic protein folding in experimental studies of Zn-containing metalloproteins, which makes the study of Zn-ligand interactions in proteins challenging. Here, we used single-molecule force spectroscopy to directly measure the mechanical rupture force of the Zn-thiolate bond in Zn-rubredoxin. Our results show that considerable force is needed to rupture Zn-thiolate bonds (~170 pN, which is significantly higher than the force necessary to rupture the coordination bond between Zn and histidines). To our knowledge, our study not only provides new information about Zn-thiolate bonds in rubredoxin, it also opens a new avenue for studying metal-ligand bonds in proteins using single-molecule force spectroscopy.
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Affiliation(s)
- Peng Zheng
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
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