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Kim S, Cathey MVJ, Bounds BC, Scholl Z, Marszalek PE, Kim M. Ligand-Mediated Mechanical Enhancement in Protein Complexes at Nano- and Macro-Scale. ACS APPLIED MATERIALS & INTERFACES 2024; 16:272-280. [PMID: 38111156 DOI: 10.1021/acsami.3c14653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
Protein self-assembly plays a vital role in a myriad of biological functions and in the construction of biomaterials. Although the physical association underlying these assemblies offers high specificity, the advantage often compromises the overall durability of protein complexes. To address this challenge, we propose a novel strategy that reinforces the molecular self-assembly of protein complexes mediated by their ligand. Known for their robust noncovalent interactions with biotin, streptavidin (SAv) tetramers are examined to understand how the ligand influences the mechanical strength of protein complexes at the nanoscale and macroscale, employing atomic force microscopy-based single-molecule force spectroscopy, rheology, and bioerosion analysis. Our study reveals that biotin binding enhances the mechanical strength of individual SAv tetramers at the nanoscale. This enhancement translates into improved shear elasticity and reduced bioerosion rates when SAv tetramers are utilized as cross-linking junctions within hydrogel. This approach, which enhances the mechanical strength of protein-based materials without compromising specificity, is expected to open new avenues for advanced biotechnological applications, including self-assembled, robust biomimetic scaffolds and soft robotics.
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Affiliation(s)
- Samuel Kim
- Department of Biomedical Engineering, University of Arizona, Tucson, Arizona 85721, United States
| | - Marcus V J Cathey
- Department of Biomedical Engineering, University of Arizona, Tucson, Arizona 85721, United States
| | - Brandon C Bounds
- Department of Biomedical Engineering, University of Arizona, Tucson, Arizona 85721, United States
| | - Zackary Scholl
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
| | - Piotr E Marszalek
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
| | - Minkyu Kim
- Department of Biomedical Engineering, University of Arizona, Tucson, Arizona 85721, United States
- Department of Materials Science and Engineering, University of Arizona, Tucson, Arizona 85721, United States
- BIO5 Institute, University of Arizona, Tucson, Arizona 85719, United States
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2
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Gupta M, Venkatramani R, Ainavarapu SRK. Role of Ligand Binding Site in Modulating the Mechanical Stability of Proteins with β-Grasp Fold. J Phys Chem B 2021; 125:1009-1019. [PMID: 33492970 DOI: 10.1021/acs.jpcb.0c08085] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Despite many studies on ligand-modulated protein mechanics, a comparative analysis of the role of ligand binding site on any specific protein fold is yet to be made. In this study, we explore the role of ligand binding site on the mechanical properties of β-grasp fold proteins, namely, ubiquitin and small ubiquitin related modifier 1 (SUMO1). The terminal segments directly connected through hydrogen bonds constitute the β-clamp geometry (or mechanical clamp), which confers high mechanical resilience to the β-grasp fold. Here, we study ubiquitin complexed with CUE2-1, a ubiquitin-binding domain (UBD) from yeast endonuclease protein Cue2, using a combination of single-molecule force spectroscopy (SMFS) and steered molecular dynamics (SMD) simulations. Our study reveals that CUE2-1 does not alter the mechanical properties of ubiquitin, despite directly interacting with its β-clamp. To explore the role of ligand binding site, we compare the mechanical properties of the ubiquitin/CUE2-1 complex with that of previously studied SUMO1/S12, another β-grasp protein complex, using SMD simulations. Simulations on the SUMO1/S12 complex corroborate previous experimentally observed enhancement in the mechanical stability of SUMO1, even though S12 binds away from the β-clamp. Differences in ligand binding-induced structural impact at the transition state of the two complexes explain the differences in ligand modulated protein mechanics. Contrary to previous reports, our study demonstrates that direct binding of ligands to the mechanical clamp does not necessarily alter the mechanical stability of β-grasp fold proteins. Rather, binding interactions away from the clamp can reinforce protein stability provided by the β-grasp fold. Our study highlights the importance of binding site and binding modes of ligands in modulating the mechanical stability of β-grasp fold proteins.
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Affiliation(s)
- Mona Gupta
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Dr Homi Bhabha Road, Colaba, Mumbai 400005, India
| | - Ravindra Venkatramani
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Dr Homi Bhabha Road, Colaba, Mumbai 400005, India
| | - Sri Rama Koti Ainavarapu
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Dr Homi Bhabha Road, Colaba, Mumbai 400005, India
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3
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Hughes MDG, Cussons S, Mahmoudi N, Brockwell DJ, Dougan L. Single molecule protein stabilisation translates to macromolecular mechanics of a protein network. SOFT MATTER 2020; 16:6389-6399. [PMID: 32578583 DOI: 10.1039/c9sm02484k] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Folded globular proteins are attractive building blocks for biopolymer-based materials, as their mechanically resistant structures carry out diverse biological functionality. While much is now understood about the mechanical response of single folded proteins, a major challenge is to understand and predictably control how single protein mechanics translates to the collective response of a network of connected folded proteins. Here, by utilising the binding of maltose to hydrogels constructed from photo-chemically cross-linked maltose binding protein (MBP), we investigate the effects of protein stabilisation at the molecular level on the macroscopic mechanical and structural properties of a protein-based hydrogel. Rheological measurements show an enhancement in the mechanical strength and energy dissipation of MBP hydrogels in the presence of maltose. Circular dichroism spectroscopy and differential scanning calorimetry measurements show that MBP remains both folded and functional in situ. By coupling these mechanical measurements with mesoscopic structural information obtained by small angle scattering, we propose an occupation model in which higher proportions of stabilised, ligand occupied, protein building blocks translate their increased stability to the macroscopic properties of the hydrogel network. This provides powerful opportunities to exploit environmentally responsive folded protein-based biomaterials for many broad applications.
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Affiliation(s)
- Matt D G Hughes
- School of Physics and Astronomy, Faculty of Engineering and Physical Sciences, University of Leeds, Leeds, UK.
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4
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Wang YJ, Rico-Lastres P, Lezamiz A, Mora M, Solsona C, Stirnemann G, Garcia-Manyes S. DNA Binding Induces a Nanomechanical Switch in the RRM1 Domain of TDP-43. J Phys Chem Lett 2018; 9:3800-3807. [PMID: 29924934 DOI: 10.1021/acs.jpclett.8b01494] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Understanding the molecular mechanisms governing protein-nucleic acid interactions is fundamental to many nuclear processes. However, how nucleic acid binding affects the conformation and dynamics of the substrate protein remains poorly understood. Here we use a combination of single molecule force spectroscopy AFM and biochemical assays to show that the binding of TG-rich ssDNA triggers a mechanical switch in the RRM1 domain of TDP-43, toggling between an entropic spring devoid of mechanical stability and a shock absorber bound-form that resists unfolding forces of ∼40 pN. The fraction of mechanically resistant proteins correlates with an increasing length of the TG n oligonucleotide, demonstrating that protein mechanical stability is a direct reporter of nucleic acid binding. Steered molecular dynamics simulations on related RNA oligonucleotides reveal that the increased mechanical stability fingerprinting the holo-form is likely to stem from a unique scenario whereby the nucleic acid acts as a "mechanical staple" that protects RRM1 from mechanical unfolding. Our approach highlights nucleic acid binding as an effective strategy to control protein nanomechanics.
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Affiliation(s)
- Yong Jian Wang
- Department of Physics and Randall Centre for Cell and Molecular Biophysics , King's College London , WC2R 2LS , London , United Kingdom
| | - Palma Rico-Lastres
- Department of Physics and Randall Centre for Cell and Molecular Biophysics , King's College London , WC2R 2LS , London , United Kingdom
| | - Ainhoa Lezamiz
- Department of Physics and Randall Centre for Cell and Molecular Biophysics , King's College London , WC2R 2LS , London , United Kingdom
| | - Marc Mora
- Department of Physics and Randall Centre for Cell and Molecular Biophysics , King's College London , WC2R 2LS , London , United Kingdom
| | - Carles Solsona
- Department of Pathology and Experimental Therapeutics, Faculty of Medicine and Health Sciences , University of Barcelona and Bellvitge Biomedical Research Institute (IDIBELL) L'Hospitalet de Llobregat , Barcelona 08907 , Spain
| | - Guillaume Stirnemann
- CNRS Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique , Université Paris Denis Diderot, Sorbonne Paris Cité, PSL Research University , 75005 Paris , France
| | - Sergi Garcia-Manyes
- Department of Physics and Randall Centre for Cell and Molecular Biophysics , King's College London , WC2R 2LS , London , United Kingdom
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5
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Ni G, Wang Y, Cummins S, Walton S, Mounsey K, Liu X, Wei MQ, Wang T. Inhibitory mechanism of peptides with a repeating hydrophobic and hydrophilic residue pattern on interleukin-10. Hum Vaccin Immunother 2016; 13:518-527. [PMID: 27686406 DOI: 10.1080/21645515.2016.1238537] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Interleukin 10 (IL-10) is a cytokine that is able to downregulate inflammation. Its overexpression is directly associated with the difficulty in the clearance of chronic viral infections, such as chronic hepatitis B, hepatitis C and HIV infection, and infection-related cancer. IL-10 signaling blockade has been proposed as a promising way of clearing chronic viral infection and preventing tumor growth in animal models. Recently, we have reported that peptides with a helical repeating pattern of hydrophobic and hydrophilic residues are able to inhibit IL-10 significantly both in vitro and in vivo. 1 In this work, we seek to further study the inhibiting mechanism of these peptides using sequence-modified peptides. As evidenced by both experimental and molecular dynamics simulation in concert the N-terminal hydrophobic peptide constructed with repeating hydrophobic and hydrophilic pattern of residues is more likely to inhibit IL10. In addition, the sequence length and the ability of protonation are also important for inhibition activity.
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Affiliation(s)
- Guoying Ni
- a Genecology Research Centre , University of the Sunshine Coast , Maroochydore , DC , Australia.,b School of Medical Science, Griffith Health Institute , Griffith University , Gold Coast , Australia
| | - Yuejian Wang
- c Cancer Research Institute, Foshan First People's Hospital , Foshan , Guangdong , China
| | - Scott Cummins
- a Genecology Research Centre , University of the Sunshine Coast , Maroochydore , DC , Australia
| | - Shelley Walton
- d Inflammation and Healing Research Cluster, School of Health and Sport Sciences , University of Sunshine Coast , Maroochydore , DC , Australia
| | - Kate Mounsey
- d Inflammation and Healing Research Cluster, School of Health and Sport Sciences , University of Sunshine Coast , Maroochydore , DC , Australia
| | - Xiaosong Liu
- c Cancer Research Institute, Foshan First People's Hospital , Foshan , Guangdong , China.,d Inflammation and Healing Research Cluster, School of Health and Sport Sciences , University of Sunshine Coast , Maroochydore , DC , Australia
| | - Ming Q Wei
- b School of Medical Science, Griffith Health Institute , Griffith University , Gold Coast , Australia
| | - Tianfang Wang
- a Genecology Research Centre , University of the Sunshine Coast , Maroochydore , DC , Australia
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6
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Zhang X, Jia R, Zhou J, Wang M, Yin Z, Cheng A. Capsid-Targeted Viral Inactivation: A Novel Tactic for Inhibiting Replication in Viral Infections. Viruses 2016; 8:E258. [PMID: 27657114 PMCID: PMC5035972 DOI: 10.3390/v8090258] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 09/08/2016] [Accepted: 09/15/2016] [Indexed: 12/18/2022] Open
Abstract
Capsid-targeted viral inactivation (CTVI), a conceptually powerful new antiviral strategy, is attracting increasing attention from researchers. Specifically, this strategy is based on fusion between the capsid protein of a virus and a crucial effector molecule, such as a nuclease (e.g., staphylococcal nuclease, Barrase, RNase HI), lipase, protease, or single-chain antibody (scAb). In general, capsid proteins have a major role in viral integration and assembly, and the effector molecule used in CTVI functions to degrade viral DNA/RNA or interfere with proper folding of viral key proteins, thereby affecting the infectivity of progeny viruses. Interestingly, such a capsid-enzyme fusion protein is incorporated into virions during packaging. CTVI is more efficient compared to other antiviral methods, and this approach is promising for antiviral prophylaxis and therapy. This review summarizes the mechanism and utility of CTVI and provides some successful applications of this strategy, with the ultimate goal of widely implementing CTVI in antiviral research.
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Affiliation(s)
- Xingcui Zhang
- Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Wenjiang District, Chengdu 611130, Sichuan Province, China.
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu 611130, Sichuan Province, China.
| | - Renyong Jia
- Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Wenjiang District, Chengdu 611130, Sichuan Province, China.
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Wenjiang District, Chengdu 611130, Sichuan Province, China.
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu 611130, Sichuan Province, China.
| | - Jiakun Zhou
- Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Wenjiang District, Chengdu 611130, Sichuan Province, China.
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu 611130, Sichuan Province, China.
| | - Mingshu Wang
- Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Wenjiang District, Chengdu 611130, Sichuan Province, China.
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Wenjiang District, Chengdu 611130, Sichuan Province, China.
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu 611130, Sichuan Province, China.
| | - Zhongqiong Yin
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Wenjiang District, Chengdu 611130, Sichuan Province, China.
| | - Anchun Cheng
- Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Wenjiang District, Chengdu 611130, Sichuan Province, China.
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Wenjiang District, Chengdu 611130, Sichuan Province, China.
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu 611130, Sichuan Province, China.
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7
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Scholl ZN, Josephs EA, Marszalek PE. Modular, Nondegenerate Polyprotein Scaffolds for Atomic Force Spectroscopy. Biomacromolecules 2016; 17:2502-5. [PMID: 27276010 PMCID: PMC4940236 DOI: 10.1021/acs.biomac.6b00548] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Zackary N. Scholl
- Computational Biology and Bioinformatics Program, Edmund
T. Pratt, Jr. School of Engineering, Duke University, Durham, North Carolina, United
States
| | - Eric A. Josephs
- Department of Mechanical Engineering and Materials
Science, Edmund T. Pratt, Jr. School of Engineering, Duke University, Durham, North
Carolina, United States
| | - Piotr E. Marszalek
- Department of Mechanical Engineering and Materials
Science, Edmund T. Pratt, Jr. School of Engineering, Duke University, Durham, North
Carolina, United States
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8
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Shahverdi AR, Mirzaie S, Rafii F, Kakavand M, Foroumadi A. Monoterpenes as nitrofurantoin resistance modulating agents: minimal structural requirements, molecular dynamics simulations, and the effect of piperitone on the emergence of nitrofurantoin resistance in Enterobacteriaceae. J Mol Model 2015; 21:198. [PMID: 26174760 DOI: 10.1007/s00894-015-2741-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 06/24/2015] [Indexed: 01/10/2023]
Abstract
The effects of different monoterpenes and 2-cyclohexen-1-one on the antibacterial activity of nitrofurantoin against resistant Enterobacter cloacae, were compared and the minimal structural component of monoterpene required for the highest level of resistance-modulating activity was determined. Subinhibitory concentrations of all compounds tested enhanced the antibacterial activity of nitrofurantoin against E. cloacae to different extents. The highest synergistic effect was observed for the monoterpenes, like piperitone, which contained a conjugated ketone and C=C bond in their carbon ring structure. Piperitone also suppressed the emergence of nitrofurantoin-resistant strains of Enterobacteriaceae that were mutagenized by ethyl methanesulfonate. The modes of interaction of carvone, piperitone, and an enzyme inhibitor, benzoate, with nitroreductase were investigated by molecular docking and molecular dynamic (MD) simulation for 20 ns. MD simulation supported greater stability of the benzoate and monoterpene-nitroreductase (NR) complexes than of free NR. The results of this investigation are promising for the synthesis of more effective lead compounds to enhance the antibacterial activity of nitro drugs against resistant Enterobacter strains.
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Affiliation(s)
- Ahmad R Shahverdi
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy and Biotechnology Research Center, Tehran University of Medical Sciences, Tehran, 1417614411, Iran,
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9
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Rivas-Pardo JA, Alegre-Cebollada J, Ramírez-Sarmiento CA, Fernandez JM, Guixé V. Identifying sequential substrate binding at the single-molecule level by enzyme mechanical stabilization. ACS NANO 2015; 9:3996-4005. [PMID: 25840594 PMCID: PMC4467879 DOI: 10.1021/nn507480v] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Enzyme-substrate binding is a dynamic process intimately coupled to protein structural changes, which in turn changes the unfolding energy landscape. By the use of single-molecule force spectroscopy (SMFS), we characterize the open-to-closed conformational transition experienced by the hyperthermophilic adenine diphosphate (ADP)-dependent glucokinase from Thermococcus litoralis triggered by the sequential binding of substrates. In the absence of substrates, the mechanical unfolding of TlGK shows an intermediate 1, which is stabilized in the presence of Mg·ADP(-), the first substrate to bind to the enzyme. However, in the presence of this substrate, an additional unfolding event is observed, intermediate 1*. Finally, in the presence of both substrates, the unfolding force of intermediates 1 and 1* increases as a consequence of the domain closure. These results show that SMFS can be used as a powerful experimental tool to investigate binding mechanisms of different enzymes with more than one ligand, expanding the repertoire of protocols traditionally used in enzymology.
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Affiliation(s)
- Jaime Andrés Rivas-Pardo
- Department of Biological Sciences, Columbia University, Northwest Corner Building, 550 West 120 Street, New York, New York 10027, USA
- Laboratorio de Bioquímica y Biología Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago, Chile
| | - Jorge Alegre-Cebollada
- Department of Biological Sciences, Columbia University, Northwest Corner Building, 550 West 120 Street, New York, New York 10027, USA
| | - César A. Ramírez-Sarmiento
- Laboratorio de Bioquímica y Biología Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago, Chile
| | - Julio M. Fernandez
- Department of Biological Sciences, Columbia University, Northwest Corner Building, 550 West 120 Street, New York, New York 10027, USA
| | - Victoria Guixé
- Laboratorio de Bioquímica y Biología Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago, Chile
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10
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Scholl ZN, Yang W, Marszalek PE. Direct observation of multimer stabilization in the mechanical unfolding pathway of a protein undergoing oligomerization. ACS NANO 2015; 9:1189-97. [PMID: 25639698 DOI: 10.1021/nn504686f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Understanding how protein oligomerization affects the stability of monomers in self-assembled structures is crucial to the development of new protein-based nanomaterials and protein cages for drug delivery. Here, we use single-molecule force spectroscopy (AFM-SMFS), protein engineering, and computer simulations to evaluate how dimerization and tetramerization affects the stability of the monomer of Streptavidin, a model homotetrameric protein. The unfolding force directly relates to the folding stability, and we find that monomer of Streptavidin is mechanically stabilized by 40% upon dimerization, and that it is stabilized an additional 24% upon tetramerization. We also find that biotin binding increases stability by another 50% as compared to the apo-tetrameric form. We used the distribution of unfolding forces to extract properties of the underlying energy landscape and found that the distance to the transition state is decreased and the barrier height is increased upon multimerization. Finally, we investigated the origin of the strengthening by ligand binding. We found that, rather than being strengthened through intramolecular contacts, it is strengthened due to the contacts provided by the biotin-binding loop that crosses the interface between the dimers.
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Affiliation(s)
- Zackary N Scholl
- Program in Computational Biology and Bioinformatics, Duke University , Durham, North Carolina 27708, United States
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11
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Hu X, Li H. Force spectroscopy studies on protein-ligand interactions: a single protein mechanics perspective. FEBS Lett 2014; 588:3613-20. [PMID: 24747422 DOI: 10.1016/j.febslet.2014.04.009] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2014] [Revised: 04/07/2014] [Accepted: 04/08/2014] [Indexed: 01/04/2023]
Abstract
Protein-ligand interactions are ubiquitous and play important roles in almost every biological process. The direct elucidation of the thermodynamic, structural and functional consequences of protein-ligand interactions is thus of critical importance to decipher the mechanism underlying these biological processes. A toolbox containing a variety of powerful techniques has been developed to quantitatively study protein-ligand interactions in vitro as well as in living systems. The development of atomic force microscopy-based single molecule force spectroscopy techniques has expanded this toolbox and made it possible to directly probe the mechanical consequence of ligand binding on proteins. Many recent experiments have revealed how ligand binding affects the mechanical stability and mechanical unfolding dynamics of proteins, and provided mechanistic understanding on these effects. The enhancement effect of mechanical stability by ligand binding has been used to help tune the mechanical stability of proteins in a rational manner and develop novel functional binding assays for protein-ligand interactions. Single molecule force spectroscopy studies have started to shed new lights on the structural and functional consequence of ligand binding on proteins that bear force under their biological settings.
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Affiliation(s)
- Xiaotang Hu
- State Key Laboratory of Precision Measurements Technology and Instruments, School of Precision Instrument and Opto-Electronics Engineering, Tianjin University, Tianjin 300072, PR China
| | - Hongbin Li
- State Key Laboratory of Precision Measurements Technology and Instruments, School of Precision Instrument and Opto-Electronics Engineering, Tianjin University, Tianjin 300072, PR China; Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada.
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12
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Scholl ZN, Marszalek PE. Improving single molecule force spectroscopy through automated real-time data collection and quantification of experimental conditions. Ultramicroscopy 2013; 136:7-14. [PMID: 24001740 DOI: 10.1016/j.ultramic.2013.07.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Revised: 07/17/2013] [Accepted: 07/25/2013] [Indexed: 12/30/2022]
Abstract
The benefits of single molecule force spectroscopy (SMFS) clearly outweigh the challenges which include small sample sizes, tedious data collection and introduction of human bias during the subjective data selection. These difficulties can be partially eliminated through automation of the experimental data collection process for atomic force microscopy (AFM). Automation can be accomplished using an algorithm that triages usable force-extension recordings quickly with positive and negative selection. We implemented an algorithm based on the windowed fast Fourier transform of force-extension traces that identifies peaks using force-extension regimes to correctly identify usable recordings from proteins composed of repeated domains. This algorithm excels as a real-time diagnostic because it involves <30 ms computational time, has high sensitivity and specificity, and efficiently detects weak unfolding events. We used the statistics provided by the automated procedure to clearly demonstrate the properties of molecular adhesion and how these properties change with differences in the cantilever tip and protein functional groups and protein age.
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Affiliation(s)
- Zackary N Scholl
- Program in Computational Biology and Bioinformatics, Duke University, Durham, NC 27708, USA.
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13
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Xie T, Feng Y, Shan L, Wang J. Modeling of the [E43S]SNase-ssDNA–Cd2+ complex: Structural insight into the action of nuclease on ssDNA. Arch Biochem Biophys 2013; 532:103-13. [DOI: 10.1016/j.abb.2013.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 02/04/2013] [Accepted: 02/06/2013] [Indexed: 11/30/2022]
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14
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15
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Hoffmann T, Tych KM, Brockwell DJ, Dougan L. Single-molecule force spectroscopy identifies a small cold shock protein as being mechanically robust. J Phys Chem B 2013; 117:1819-26. [PMID: 23293964 DOI: 10.1021/jp310442s] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Single-molecule force spectroscopy has emerged as a powerful approach to examine the stability and dynamics of single proteins. We have completed force extension experiments on the small cold shock protein B from Thermotoga maritima, using a specially constructed chimeric polyprotein. The protein's simple topology, which is distinct from the mechanically well-characterized β-grasp and immunoglobulin (Ig)-like folds, in addition to the wide range of structural homologues resulting from its ancient origin, provides an attractive model protein for single-molecule force spectroscopy studies. We have determined that the protein has mechanical stability, unfolding at greater than 70 pN at a pulling velocity of 100 nm s(-1). We reveal features of the unfolding energy landscape by measuring the dependence of the mechanical stability on pulling velocity, in combination with Monte Carlo simulations. We show that the cold shock protein has mechanically robust, yet malleable, features that may be important in providing the protein with stability and flexibility to function over a range of environmental conditions. These results provide insights into the relationship between the secondary structure and topology of a protein and its mechanical strength. This lays the foundation for the investigation of the effects of changes in environmental conditions on the mechanical and dynamic properties of cold shock proteins.
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Affiliation(s)
- Toni Hoffmann
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, United Kingdom
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16
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Settanni G, Serquera D, Marszalek PE, Paci E, Itzhaki LS. Effects of ligand binding on the mechanical properties of ankyrin repeat protein gankyrin. PLoS Comput Biol 2013; 9:e1002864. [PMID: 23341763 PMCID: PMC3547791 DOI: 10.1371/journal.pcbi.1002864] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Accepted: 11/11/2012] [Indexed: 11/30/2022] Open
Abstract
Ankyrin repeat proteins are elastic materials that unfold and refold sequentially, repeat by repeat, under force. Herein we use atomistic molecular dynamics to compare the mechanical properties of the 7-ankyrin-repeat oncoprotein Gankyrin in isolation and in complex with its binding partner S6-C. We show that the bound S6-C greatly increases the resistance of Gankyrin to mechanical stress. The effect is specific to those repeats of Gankyrin directly in contact with S6-C, and the mechanical ‘hot spots’ of the interaction map to the same repeats as the thermodynamic hot spots. A consequence of stepwise nature of unfolding and the localized nature of ligand binding is that it impacts on all aspects of the protein's mechanical behavior, including the order of repeat unfolding, the diversity of unfolding pathways accessed, the nature of partially unfolded intermediates, the forces required and the work transferred to the system to unfold the whole protein and its parts. Stepwise unfolding thus provides the means to buffer repeat proteins and their binding partners from mechanical stress in the cell. Our results illustrate how ligand binding can control the mechanical response of proteins. The data also point to a cellular mechano-switching mechanism whereby binding between two partner macromolecules is regulated by mechanical stress. Here we use molecular dynamics simulation to compare the mechanical properties of the 7-ankyrin-repeat oncoprotein Gankyrin in isolation and in complex with binding partner S6-C. Tandem repeat proteins like Gankyrin comprise tandem arrays of small structural motifs that pack linearly to produce elongated architectures. They are elastic, mechanically weak molecules and they unfold and refold repeat by repeat under force. We show that S6-C binding greatly increases the resistance of Gankyrin to mechanical stress. The enhanced mechanical stability is specific to those ankyrin repeats in contact with S6-C, and the localized nature of the effect results in fundamental changes in the way the protein responds to force. Thus, the forced unfolding of isolated Gankryin involves a diverse set of pathways with a preference for a C- to N-terminus unfolding mechanism whereas this diversity is reduced upon complex formation with the central repeats, which are those most tightly bound to the ligand, tending to unfold last. Our study shows how stepwise unfolding can buffer repeat proteins and their binding partners from mechanical stress in the cell. It also points to a mechano-switching mechanism whereby binding between two partner macromolecules is regulated by mechanical stress.
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Affiliation(s)
- Giovanni Settanni
- Physics Department, Johannes Gutenberg University, Mainz, Germany
- * E-mail: (GS); (EP); (LSI)
| | - David Serquera
- MRC Cancer Cell Unit, Hutchison/MRC Research Centre, Cambridge, United Kingdom
| | - Piotr E. Marszalek
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina, United States of America
| | - Emanuele Paci
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
- * E-mail: (GS); (EP); (LSI)
| | - Laura S. Itzhaki
- University of Cambridge Department of Chemistry, Cambridge, United Kingdom
- * E-mail: (GS); (EP); (LSI)
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Brantley JN, Bailey CB, Wiggins KM, Keatinge-Clay AT, Bielawski CW. Mechanobiochemistry: harnessing biomacromolecules for force-responsive materials. Polym Chem 2013. [DOI: 10.1039/c3py00001j] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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18
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Zoldák G, Rief M. Force as a single molecule probe of multidimensional protein energy landscapes. Curr Opin Struct Biol 2012; 23:48-57. [PMID: 23279960 DOI: 10.1016/j.sbi.2012.11.007] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Revised: 11/26/2012] [Accepted: 11/26/2012] [Indexed: 01/06/2023]
Abstract
Force spectroscopy has developed into an indispensable tool for studying folding and binding of proteins on a single molecule level in real time. Design of the pulling geometry allows tuning the reaction coordinate in a very precise manner. Many recent experiments have taken advantage of this possibility and have provided detailed insight the folding pathways on the complex high dimensional energy landscape. Beyond its potential to provide control over the reaction coordinate, force is also an important physiological parameter that affects protein conformation under in vivo conditions. Single molecule force spectroscopy studies have started to unravel the response and adaptation of force bearing protein structures to mechanical loads.
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Affiliation(s)
- Gabriel Zoldák
- Physik Department E22, Technische Universität München, James-Franck-Strasse, 85748 Garching, Germany
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19
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Gao X, Qin M, Yin P, Liang J, Wang J, Cao Y, Wang W. Single-molecule experiments reveal the flexibility of a Per-ARNT-Sim domain and the kinetic partitioning in the unfolding pathway under force. Biophys J 2012; 102:2149-57. [PMID: 22824279 DOI: 10.1016/j.bpj.2012.03.042] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2011] [Revised: 02/21/2012] [Accepted: 03/20/2012] [Indexed: 10/28/2022] Open
Abstract
Per-ARNT-Sim (PAS) domains serve as versatile binding motifs in many signal-transduction proteins and are able to respond to a wide spectrum of chemical or physical signals. Despite their diverse functions, PAS domains share a conserved structure. It has been suggested that the structure of PAS domains is flexible and thus adaptable to many binding partners. However, direct measurement of the flexibility of PAS domains has not yet been provided. Here, we quantitatively measure the mechanical unfolding of a PAS domain, ARNT PAS-B, using single-molecule atomic force microscopy. Our force spectroscopy results indicate that the structure of ARNT PAS-B can be unraveled under mechanical forces as low as ~30 pN due to its broad potential well for the mechanical unfolding transition of ~2 nm. This allows the PAS-B domain to extend by up to 75% of its resting end-to-end distance without unfolding. Moreover, we found that the ARNT PAS-B domain unfolds in two distinct pathways via a kinetic partitioning mechanism. Sixty-seven percent of ARNT PAS-B unfolds through a simple two-state pathway, whereas the other 33% unfolds with a well-defined intermediate state in which the C-terminal β-hairpin is detached. We propose that the structural flexibility and force-induced partial unfolding of PAS-B domains may provide a unique mechanism for them to recruit diverse binding partners and lower the free-energy barrier for the formation of the binding interface.
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Affiliation(s)
- Xiang Gao
- National Laboratory of Solid State Microstructure and Department of Physics, Nanjing University, Nanjing, People's Republic of China
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20
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Taniguchi Y, Kawakami M. Variation in the mechanical unfolding pathway of p53DBD induced by interaction with p53 N-terminal region or DNA. PLoS One 2012; 7:e49003. [PMID: 23145047 PMCID: PMC3493487 DOI: 10.1371/journal.pone.0049003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Accepted: 10/03/2012] [Indexed: 12/04/2022] Open
Abstract
The tumor suppressor p53 plays a crucial role in the cell cycle checkpoints, DNA repair, and apoptosis. p53 consists of a natively unfolded N-terminal region (NTR), central DNA binding domain (DBD), C-terminal tetramerization domain, and regulatory region. In this paper, the interactions between the DBD and the NTR, and between the DBD and DNA were investigated by measuring changes in the mechanical unfolding trajectory of the DBD using atomic force microscopy (AFM)-based single molecule force spectroscopy. In the absence of DNA, the DBD (94–293, 200 amino acids (AA)) showed two different mechanical unfolding patterns. One indicated the existence of an unfolding intermediate consisting of approximately 60 AA, and the other showed a 100 AA intermediate. The DBD with the NTR did not show such unfolding patterns, but heterogeneous unfolding force peaks were observed. Of the heterogeneous patterns, we observed a high frequency of force peaks indicating the unfolding of a domain consisting of 220 AA, which is apparently larger than that of a sole DBD. This observation implies that a part of NTR binds to the DBD, and the mechanical unfolding happens not solely on the DBD but also accompanying a part of NTR. When DNA is bound, the mechanical unfolding trajectory of p53NTR+DBD showed a different pattern from that without DNA. The pattern was similar to that of the DBD alone, but two consecutive unfolding force peaks corresponding to 60 and 100 AA sub-domains were observed. These results indicate that interactions with the NTR or DNA alter the mechanical stability of DBD and result in drastic changes in the mechanical unfolding trajectory of the DBD.
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Affiliation(s)
- Yukinori Taniguchi
- School of Materials Science, Japan Advanced Institute of Science and Technology (JAIST), Nomi, Ishikawa, Japan
| | - Masaru Kawakami
- School of Materials Science, Japan Advanced Institute of Science and Technology (JAIST), Nomi, Ishikawa, Japan
- * E-mail:
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21
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Tiryaki VM, Khan AA, Ayres VM. AFM feature definition for neural cells on nanofibrillar tissue scaffolds. SCANNING 2012; 34:316-324. [PMID: 22585747 DOI: 10.1002/sca.21013] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2011] [Accepted: 12/23/2011] [Indexed: 05/31/2023]
Abstract
A diagnostic approach is developed and implemented that provides clear feature definition in atomic force microscopy (AFM) images of neural cells on nanofibrillar tissue scaffolds. Because the cellular edges and processes are on the same order as the background nanofibers, this imaging situation presents a feature definition problem. The diagnostic approach is based on analysis of discrete Fourier transforms of standard AFM section measurements. The diagnostic conclusion that the combination of dynamic range enhancement with low-frequency component suppression enhances feature definition is shown to be correct and to lead to clear-featured images that could change previously held assumptions about the cell-cell interactions present. Clear feature definition of cells on scaffolds extends the usefulness of AFM imaging for use in regenerative medicine.
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Affiliation(s)
- Volkan M Tiryaki
- Department of Electrical and Computer Engineering, Michigan State University, East Lansing, MI, USA.
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22
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Dynamics of protein folding and cofactor binding monitored by single-molecule force spectroscopy. Biophys J 2012; 101:2009-17. [PMID: 22004755 DOI: 10.1016/j.bpj.2011.08.051] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2011] [Revised: 08/23/2011] [Accepted: 08/26/2011] [Indexed: 12/24/2022] Open
Abstract
Many proteins in living cells require cofactors to carry out their biological functions. To reach their functional states, these proteins need to fold into their unique three-dimensional structures in the presence of their cofactors. Two processes, folding of the protein and binding of cofactors, intermingle with each other, making the direct elucidation of the folding mechanism of proteins in the presence of cofactors challenging. Here we use single-molecule atomic force microscopy to directly monitor the folding and cofactor binding dynamics of an engineered metal-binding protein G6-53 at the single-molecule level. Using the mechanical stability of different conformers of G6-53 as sensitive probes, we directly identified different G6-53 conformers (unfolded, apo- and Ni(2+)-bound) populated along the folding pathway of G6-53 in the presence of its cofactor Ni(2+). By carrying out single-molecule atomic force microscopy refolding experiments, we monitored kinetic evolution processes of these different conformers. Our results suggested that the majority of G6-53 folds through a binding-after-folding mechanism, whereas a small fraction follows a binding-before-folding pathway. Our study opens an avenue to utilizing force spectroscopy techniques to probe the folding dynamics of proteins in the presence of cofactors at the single-molecule level, and we anticipated that this method can be used to study a wide variety of proteins requiring cofactors for their function.
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24
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Kim M, Wang CC, Benedetti F, Marszalek PE. A nanoscale force probe for gauging intermolecular interactions. Angew Chem Int Ed Engl 2012; 51:1903-6. [PMID: 22253141 DOI: 10.1002/anie.201107210] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Revised: 12/16/2011] [Indexed: 11/07/2022]
Affiliation(s)
- Minkyu Kim
- Center for Biologically Inspired Materials and Material Systems, Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA
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25
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Kim M, Wang CC, Benedetti F, Rabbi M, Bennett V, Marszalek PE. Nanomechanics of streptavidin hubs for molecular materials. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2011; 23:5684-8. [PMID: 22102445 PMCID: PMC3837471 DOI: 10.1002/adma.201103316] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Indexed: 05/24/2023]
Abstract
A new strategy is reported for creating protein-based nanomaterials by genetically fusing large polypeptides to monomeric streptavidin and exploiting the propensity of streptavidin monomers(SM) to self-assemble into stable tetramers. We have characterized the mechanical properties of streptavidin-linked structures and measured, for the first time, the mechanical strength of streptavidin tetramers themselves. Using streptavidin tetramers as molecular hubs offers a unique opportunity to create a variety of well-defined, self-assembled protein-based (nano)materials with unusual mechanical properties.
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Affiliation(s)
- Minkyu Kim
- Department of Mechanical Engineering and Materials Science, Center for Biologically Inspired Materials and Material Systems, Center for Biomolecular and Tissue Engineering, Duke University, Durham, NC 27708, USA
| | - Chien-Chung Wang
- Graduate Insititute of Biotechnology, National Chung-Hsing University, Taichung, Taiwan (R.O.C)
| | - Fabrizio Benedetti
- Laboratory of Physics of Living Matter, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Mahir Rabbi
- Department of Mechanical Engineering and Materials Science, Center for Biologically Inspired Materials and Material Systems, Center for Biomolecular and Tissue Engineering, Duke University, Durham, NC 27708, USA
| | - Vann Bennett
- Howard Hughes Medical Institute, Department of Biochemistry and Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Piotr E. Marszalek
- Department of Mechanical Engineering and Materials Science, Center for Biologically Inspired Materials and Material Systems, Center for Biomolecular and Tissue Engineering, Duke University, Durham, NC 27708, USA
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26
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Horejs C, Ristl R, Tscheliessnig R, Sleytr UB, Pum D. Single-molecule force spectroscopy reveals the individual mechanical unfolding pathways of a surface layer protein. J Biol Chem 2011; 286:27416-24. [PMID: 21690085 PMCID: PMC3149335 DOI: 10.1074/jbc.m111.251322] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2011] [Revised: 06/15/2011] [Indexed: 12/14/2022] Open
Abstract
Surface layers (S-layers) represent an almost universal feature of archaeal cell envelopes and are probably the most abundant bacterial cell proteins. S-layers are monomolecular crystalline structures of single protein or glycoprotein monomers that completely cover the cell surface during all stages of the cell growth cycle, thereby performing their intrinsic function under a constant intra- and intermolecular mechanical stress. In gram-positive bacteria, the individual S-layer proteins are anchored by a specific binding mechanism to polysaccharides (secondary cell wall polymers) that are linked to the underlying peptidoglycan layer. In this work, atomic force microscopy-based single-molecule force spectroscopy and a polyprotein approach are used to study the individual mechanical unfolding pathways of an S-layer protein. We uncover complex unfolding pathways involving the consecutive unfolding of structural intermediates, where a mechanical stability of 87 pN is revealed. Different initial extensibilities allow the hypothesis that S-layer proteins adapt highly stable, mechanically resilient conformations that are not extensible under the presence of a pulling force. Interestingly, a change of the unfolding pathway is observed when individual S-layer proteins interact with secondary cell wall polymers, which is a direct signature of a conformational change induced by the ligand. Moreover, the mechanical stability increases up to 110 pN. This work demonstrates that single-molecule force spectroscopy offers a powerful tool to detect subtle changes in the structure of an individual protein upon binding of a ligand and constitutes the first conformational study of surface layer proteins at the single-molecule level.
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Affiliation(s)
| | - Robin Ristl
- From the Department for Nanobiotechnology and
| | - Rupert Tscheliessnig
- the Austrian Centre of Industrial Biotechnology, c/o Institute for Biotechnology, University of Natural Resources and Life Sciences, 1190 Vienna, Austria
| | | | - Dietmar Pum
- From the Department for Nanobiotechnology and
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