1
|
Hang G, Liu W, Shakir U, Zhang T, Zheng S. Self-healable and reprocessable networks of Poly(propylene oxide) with POSS crosslinked with disulfide bonds. POLYMER 2022. [DOI: 10.1016/j.polymer.2022.125648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
|
2
|
Estrada P, Bañares-Hidalgo Á, Pérez-Gil J. Disulfide bonds in the SAPA domain of the pulmonary surfactant protein B precursor. J Proteomics 2022; 269:104722. [PMID: 36108905 DOI: 10.1016/j.jprot.2022.104722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 08/31/2022] [Accepted: 09/06/2022] [Indexed: 10/14/2022]
Abstract
The disulfide bonds formed in the SAPA domain of a recombinant version of the NH2-terminal propeptide (SP-BN) from the precursor of human pulmonary surfactant protein B (SP-B) were identified through sequential digestion of SP-BN with GluC/trypsin or thermolysin/GluC, followed by mass spectrometry (MS) analysis. MS spectra allowed identification of disulfide bonds between Cys32-Cys49 and Cys40-Cys55, and we propose a disulfide connectivity pattern of 1-3 and 2-4 within the SAPA domain, with the Cys residues numbered according to their position from the N-terminus of the propeptide sequence. The peaks with m/z ∼ 2136 and ∼ 1780 in the MS spectrum of the GluC/trypsin digest were assigned to peptides 24AWTTSSLACAQGPE37 and 45QALQCR50 linked by Cys32-Cys49 and 38FWCQSLE44 and 51ALGHCLQE58 linked by Cys40-Cys55 respectively. Tandem mass spectrometry (MS/MS) analysis verified the position of the bonds. The results of the series ions, immonium ions and internal fragment ions were all compatible with the proposed 1-3/2-4 position of the disulfide bonds in the SAPA domain. This X-pattern differs from the kringle-type found in the SAPB domain of the SAPLIP proteins, where the first Cys in the sequence links to the last, the second to the penultimate and the third to the fourth one. Regarding the SAPB domain of the SP-BN propeptide, the MS analysis of both digests identified the bond Cys100-Cys112, numbered 7-8, which is coincident with the bond position in the kringle motif. SIGNIFICANCE: The SAPLIP (saposin-like proteins) family encompasses several proteins with homology to saposins (sphingolipids activator proteins). These are proteins with mainly alpha-helical folds, compact packing including well conserved disulfide bonds and ability to interact with phospholipids and membranes. There are two types of saposin-like domains termed as Saposin A (SAPA) and Saposin B (SAPB) domains. While disulfide connectivity has been well established in several SAPB domains, the position of disulfide bonds in SAPA domains is still unknown. The present study approaches a detailed proteomic study to determine disulfide connectivity in the SAPA domain of the precursor of human pulmonary surfactant-associated protein SP-B. This task has been a challenge requiring the combination of different sequential proteolytic treatments followed by MS analysis including MALDI-TOF and tandem mass MS/MS spectrometry. The determination for first time of the position of disulfide bonds in SAPA domains is an important step to understand the structural determinants defining its biological functions.
Collapse
Affiliation(s)
- Pilar Estrada
- Dept. Biochemistry and Molecular Biology, Faculty of Biology, Complutense University, 28040 Madrid, Spain
| | - Ángeles Bañares-Hidalgo
- Dept. Biochemistry and Molecular Biology, Faculty of Biology, Complutense University, 28040 Madrid, Spain
| | - Jesús Pérez-Gil
- Dept. Biochemistry and Molecular Biology, Faculty of Biology, Complutense University, 28040 Madrid, Spain.
| |
Collapse
|
3
|
Liu W, Ge W, Mei H, Hang G, Li L, Zheng S. Poly(hydroxyurethane‐
co
‐thiourethane)s cross‐linked with disulfide bonds: Synthesis via isocyanate‐free approach, thermomechanical and reprocessing properties. JOURNAL OF POLYMER SCIENCE 2022. [DOI: 10.1002/pol.20220121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Weiming Liu
- Department of Polymer Science and Engineering and the State Key Laboratory of Metal Matrix Composites Shanghai Jiao Tong University Shanghai PR China
| | - Wenming Ge
- Department of Polymer Science and Engineering and the State Key Laboratory of Metal Matrix Composites Shanghai Jiao Tong University Shanghai PR China
| | - Honggang Mei
- Department of Polymer Science and Engineering and the State Key Laboratory of Metal Matrix Composites Shanghai Jiao Tong University Shanghai PR China
| | - Guohua Hang
- Department of Polymer Science and Engineering and the State Key Laboratory of Metal Matrix Composites Shanghai Jiao Tong University Shanghai PR China
| | - Lei Li
- Department of Polymer Science and Engineering and the State Key Laboratory of Metal Matrix Composites Shanghai Jiao Tong University Shanghai PR China
| | - Sixun Zheng
- Department of Polymer Science and Engineering and the State Key Laboratory of Metal Matrix Composites Shanghai Jiao Tong University Shanghai PR China
| |
Collapse
|
4
|
Molecular scaffolds: when DNA becomes the hardware for single-molecule investigations. Curr Opin Chem Biol 2019; 53:192-203. [DOI: 10.1016/j.cbpa.2019.09.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 09/21/2019] [Accepted: 09/24/2019] [Indexed: 01/14/2023]
|
5
|
Disulfide isomerization reactions in titin immunoglobulin domains enable a mode of protein elasticity. Nat Commun 2018; 9:185. [PMID: 29330363 PMCID: PMC5766482 DOI: 10.1038/s41467-017-02528-7] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 12/04/2017] [Indexed: 12/31/2022] Open
Abstract
The response of titin to mechanical forces is a major determinant of the function of the heart. When placed under a pulling force, the unstructured regions of titin uncoil while its immunoglobulin (Ig) domains unfold and extend. Using single-molecule atomic force microscopy, we show that disulfide isomerization reactions within Ig domains enable a third mechanism of titin elasticity. Oxidation of Ig domains leads to non-canonical disulfide bonds that stiffen titin while enabling force-triggered isomerization reactions to more extended states of the domains. Using sequence and structural analyses, we show that 21% of titin’s I-band Ig domains contain a conserved cysteine triad that can engage in disulfide isomerization reactions. We propose that imbalance of the redox status of myocytes can have immediate consequences for the mechanical properties of the sarcomere via alterations of the oxidation state of titin domains. Titin regulates myocyte stiffness through uncoiling and unfolding but these two processes cannot fully explain its elasticity. Here, the authors use atomic force microscopy to study the properties of titin disulfide bonds, showing that disulfide isomerization represents a third mode of titin elasticity.
Collapse
|
6
|
|
7
|
Lee J, Kim M, Seo Y, Lee Y, Park H, Byun SJ, Kwon MH. The catalytic activity of a recombinant single chain variable fragment nucleic acid-hydrolysing antibody varies with fusion tag and expression host. Arch Biochem Biophys 2017; 633:110-117. [PMID: 28888872 DOI: 10.1016/j.abb.2017.09.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 08/31/2017] [Accepted: 09/05/2017] [Indexed: 12/12/2022]
Abstract
The antigen-binding properties of single chain Fv antibodies (scFvs) can vary depending on the position and type of fusion tag used, as well as the host cells used for expression. The issue is even more complicated with a catalytic scFv antibody that binds and hydrolyses a specific antigen. Herein, we investigated the antigen-binding and -hydrolysing activities of the catalytic anti-nucleic acid antibody 3D8 scFv expressed in Escherichia coli or HEK293f cells with or without additional amino acid residues at the N- and C-termini. DNA-binding activity was retained in all recombinant forms. However, the DNA-hydrolysing activity varied drastically between forms. The DNA-hydrolysing activity of E. coli-derived 3D8 scFvs was not affected by the presence of a C-terminal human influenza haemagglutinin (HA) or His tag. By contrast, the activity of HEK293f-derived 3D8 scFvs was completely lost when additional residues were included at the N-terminus and/or when a His tag was incorporated at the C-terminus, whereas a HA tag at the C-terminus did not diminish activity. Thus, we demonstrate that the antigen-binding and catalytic activities of a catalytic antibody can be separately affected by the presence of additional residues at the N- and C-termini, and by the host cell type.
Collapse
Affiliation(s)
- Joungmin Lee
- Department of Biomedical Sciences, Graduate School, Ajou University, 206 World Cup-ro, Yeongtong-gu, Suwon 16499, South Korea
| | - Minjae Kim
- Department of Biomedical Sciences, Graduate School, Ajou University, 206 World Cup-ro, Yeongtong-gu, Suwon 16499, South Korea
| | - Youngsil Seo
- Department of Biomedical Sciences, Graduate School, Ajou University, 206 World Cup-ro, Yeongtong-gu, Suwon 16499, South Korea
| | - Yeonjin Lee
- Department of Biomedical Sciences, Graduate School, Ajou University, 206 World Cup-ro, Yeongtong-gu, Suwon 16499, South Korea
| | - Hyunjoon Park
- Department of Biomedical Sciences, Graduate School, Ajou University, 206 World Cup-ro, Yeongtong-gu, Suwon 16499, South Korea
| | - Sung June Byun
- Animal Biotechnology Division, National Institute of Animal Science, Rural Development Administration, 1500, Kongjwipatjwi-ro, Iseo-myeon, Wanju-gun, Jeollabuk-do, 55365, South Korea
| | - Myung-Hee Kwon
- Department of Biomedical Sciences, Graduate School, Ajou University, 206 World Cup-ro, Yeongtong-gu, Suwon 16499, South Korea; Department of Microbiology, Ajou University School of Medicine, 206 World Cup-ro, Yeongtong-gu, Suwon 16499, South Korea.
| |
Collapse
|
8
|
Jian X, Hu Y, Zhou W, Xiao L. Self-healing polyurethane based on disulfide bond and hydrogen bond. POLYM ADVAN TECHNOL 2017. [DOI: 10.1002/pat.4135] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Xiaoxia Jian
- School of Chemical Engineering; Nanjing University of Science and Technology; 210094 Nanjing China
| | - Yiwen Hu
- School of Chemical Engineering; Nanjing University of Science and Technology; 210094 Nanjing China
| | - Weiliang Zhou
- School of Chemical Engineering; Nanjing University of Science and Technology; 210094 Nanjing China
| | - Leqin Xiao
- School of Chemical Engineering; Nanjing University of Science and Technology; 210094 Nanjing China
| |
Collapse
|
9
|
Manteca A, Alonso-Caballero Á, Fertin M, Poly S, De Sancho D, Perez-Jimenez R. The influence of disulfide bonds on the mechanical stability of proteins is context dependent. J Biol Chem 2017. [PMID: 28642368 DOI: 10.1074/jbc.m117.784934] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Disulfide bonds play a crucial role in proteins, modulating their stability and constraining their conformational dynamics. A particularly important case is that of proteins that need to withstand forces arising from their normal biological function and that are often disulfide bonded. However, the influence of disulfides on the overall mechanical stability of proteins is poorly understood. Here, we used single-molecule force spectroscopy (smFS) to study the role of disulfide bonds in different mechanical proteins in terms of their unfolding forces. For this purpose, we chose the pilus protein FimG from Gram-negative bacteria and a disulfide-bonded variant of the I91 human cardiac titin polyprotein. Our results show that disulfide bonds can alter the mechanical stability of proteins in different ways depending on the properties of the system. Specifically, disulfide-bonded FimG undergoes a 30% increase in its mechanical stability compared with its reduced counterpart, whereas the unfolding force of I91 domains experiences a decrease of 15% relative to the WT form. Using a coarse-grained simulation model, we rationalized that the increase in mechanical stability of FimG is due to a shift in the mechanical unfolding pathway. The simple topology-based explanation suggests a neutral effect in the case of titin. In summary, our results indicate that disulfide bonds in proteins act in a context-dependent manner rather than simply as mechanical lockers, underscoring the importance of considering disulfide bonds both computationally and experimentally when studying the mechanical properties of proteins.
Collapse
Affiliation(s)
- Aitor Manteca
- From the Nanobiomechanics Laboratory, CIC nanoGUNE, 20018 Donostia-San Sebastián, Spain
| | | | - Marie Fertin
- From the Nanobiomechanics Laboratory, CIC nanoGUNE, 20018 Donostia-San Sebastián, Spain
| | - Simon Poly
- the Interfaculty Institute of Biochemistry, University of Tübingen, 72076 Tübingen, Germany, and
| | - David De Sancho
- From the Nanobiomechanics Laboratory, CIC nanoGUNE, 20018 Donostia-San Sebastián, Spain, .,the IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain
| | - Raul Perez-Jimenez
- From the Nanobiomechanics Laboratory, CIC nanoGUNE, 20018 Donostia-San Sebastián, Spain, .,the IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain
| |
Collapse
|
10
|
Beedle AEM, Mora M, Lynham S, Stirnemann G, Garcia-Manyes S. Tailoring protein nanomechanics with chemical reactivity. Nat Commun 2017; 8:15658. [PMID: 28585528 PMCID: PMC5467162 DOI: 10.1038/ncomms15658] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Accepted: 04/13/2017] [Indexed: 12/22/2022] Open
Abstract
The nanomechanical properties of elastomeric proteins determine the elasticity of a variety of tissues. A widespread natural tactic to regulate protein extensibility lies in the presence of covalent disulfide bonds, which significantly enhance protein stiffness. The prevalent in vivo strategy to form disulfide bonds requires the presence of dedicated enzymes. Here we propose an alternative chemical route to promote non-enzymatic oxidative protein folding via disulfide isomerization based on naturally occurring small molecules. Using single-molecule force-clamp spectroscopy, supported by DFT calculations and mass spectrometry measurements, we demonstrate that subtle changes in the chemical structure of a transient mixed-disulfide intermediate adduct between a protein cysteine and an attacking low molecular-weight thiol have a dramatic effect on the protein's mechanical stability. This approach provides a general tool to rationalize the dynamics of S-thiolation and its role in modulating protein nanomechanics, offering molecular insights on how chemical reactivity regulates protein elasticity. Post-translational modifications modulate nanomechanics of proteins. Here the authors use single-molecule force-clamp spectroscopy supported by density functional theory calculations to show how reactive low-weight molecular thiol compounds directly affect mechanical protein folding.
Collapse
Affiliation(s)
- Amy E M Beedle
- Department of Physics and Randall Division of Cell and Molecular Biophysics, King's College London, WC2R 2LS London, UK
| | - Marc Mora
- Department of Physics and Randall Division of Cell and Molecular Biophysics, King's College London, WC2R 2LS London, UK
| | - Steven Lynham
- Centre of Excellence for Mass Spectrometry, King's College London, SE5 8AF London, UK
| | - Guillaume Stirnemann
- CNRS Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Univ. Paris Denis Diderot, Sorbonne Paris Cité, PSL Research University, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Sergi Garcia-Manyes
- Department of Physics and Randall Division of Cell and Molecular Biophysics, King's College London, WC2R 2LS London, UK
| |
Collapse
|
11
|
Galior K, Liu Y, Yehl K, Vivek S, Salaita K. Titin-Based Nanoparticle Tension Sensors Map High-Magnitude Integrin Forces within Focal Adhesions. NANO LETTERS 2016; 16:341-8. [PMID: 26598972 PMCID: PMC5592801 DOI: 10.1021/acs.nanolett.5b03888] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Mechanical forces transmitted through integrin transmembrane receptors play important roles in a variety of cellular processes ranging from cell development to tumorigenesis. Despite the importance of mechanics in integrin function, the magnitude of integrin forces within adhesions remains unclear. Literature suggests a range from 1 to 50 pN, but the upper limit of integrin forces remains unknown. Herein we challenge integrins with the most mechanically stable molecular tension probe, which is comprised of the immunoglobulin 27th (I27) domain of cardiac titin flanked with a fluorophore and gold nanoparticle. Cell experiments show that integrin forces unfold the I27 domain, suggesting that integrin forces exceed ∼30-40 pN. The addition of a disulfide bridge within I27 "clamps" the probe and resists mechanical unfolding. Importantly, incubation with a reducing agent initiates SH exchange, thus unclamping I27 at a rate that is dependent on the applied force. By recording the rate of S-S reduction in clamped I27, we infer that integrins apply 110 ± 9 pN within focal adhesions of rat embryonic fibroblasts. The rates of S-S exchange are heterogeneous and integrin subtype-dependent. Nanoparticle titin tension sensors along with kinetic analysis of unfolding demonstrate that a subset of integrins apply tension many fold greater than previously reported.
Collapse
Affiliation(s)
- Kornelia Galior
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA 30322, USA
| | - Yang Liu
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA 30322, USA
| | - Kevin Yehl
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA 30322, USA
| | - Skanda Vivek
- Department of Physics, Emory University, 400 Dowman Drive, Atlanta, GA 30322, USA
| | - Khalid Salaita
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA 30322, USA
| |
Collapse
|
12
|
Wang S, Kaltashov IA. Identification of reduction-susceptible disulfide bonds in transferrin by differential alkylation using O(16)/O(18) labeled iodoacetic acid. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:800-807. [PMID: 25716754 PMCID: PMC4401651 DOI: 10.1007/s13361-015-1082-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 01/13/2015] [Accepted: 01/14/2015] [Indexed: 06/04/2023]
Abstract
Stabilization of native three-dimensional structure has been considered for decades to be the main function of disulfide bonds in proteins. More recently, it was becoming increasingly clear that in addition to this static role, disulfide bonds are also important for many other aspects of protein behavior, such as regulating protein function in a redox-sensitive fashion. Dynamic disulfide bonds can be taken advantage of as candidate anchor sites for site-specific modification (such as PEGylation of conjugation to a drug molecule), but are also frequently implicated in protein aggregation (through disulfide bond scrambling leading to formation of intermolecular covalent linkages). A common feature of all these labile disulfide bonds is their high susceptibility to reduction, as they need to be selectively regulated by either specific local redox conditions in vivo or well-controlled experimental conditions in vitro. The ability to identify labile disulfide bonds in a cysteine-rich protein can be extremely beneficial for a variety of tasks ranging from understanding the mechanistic aspects of protein function to identification of troublesome "hot spots" in biopharmaceutical products. Herein, we describe a mass spectrometry (MS)-based method for reliable identification of labile disulfide bonds, which consists of limited reduction, differential alkylation with an O(18)-labeled reagent, and LC-MS/MS analysis. Application of this method to a cysteine-rich protein transferrin allows the majority of its native disulfide bonds to be measured for their reduction susceptibility, which appears to reflect both solvent accessibility and bond strain energy.
Collapse
Affiliation(s)
| | - Igor A. Kaltashov
- address correspondence to: Igor A. Kaltashov, Department of Chemistry, University of Massachusetts-Amherst, 140 Thatcher Drive, LSL N369, Amherst, MA 01003, Tel: (413) 545-1460, Fax: (413) 545-4490,
| |
Collapse
|
13
|
Kotamarthi HC, Sharma R, Koti Ainavarapu SR. Single-molecule studies on PolySUMO proteins reveal their mechanical flexibility. Biophys J 2013; 104:2273-81. [PMID: 23708367 DOI: 10.1016/j.bpj.2013.04.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Revised: 04/04/2013] [Accepted: 04/05/2013] [Indexed: 01/08/2023] Open
Abstract
Proteins with β-sandwich and β-grasp topologies are resistant to mechanical unfolding as shown by single-molecule force spectroscopy studies. Their high mechanical stability has generally been associated with the mechanical clamp geometry present at the termini. However, there is also evidence for the importance of interactions other than the mechanical clamp in providing mechanical stability, which needs to be tested thoroughly. Here, we report the mechanical unfolding properties of ubiquitin-like proteins (SUMO1 and SUMO2) and their comparison with those of ubiquitin. Although ubiquitin and SUMOs have similar size and structural topology, they differ in their sequences and structural contacts, making them ideal candidates to understand the variations in the mechanical stability of a given protein topology. We observe a two-state unfolding pathway for SUMO1 and SUMO2, similar to that of ubiquitin. Nevertheless, the unfolding forces of SUMO1 (∼130 pN) and SUMO2 (∼120 pN) are lower than that of ubiquitin (∼190 pN) at a pulling speed of 400 nm/s, indicating their lower mechanical stability. The mechanical stabilities of SUMO proteins and ubiquitin are well correlated with the number of interresidue contacts present in their structures. From pulling speed-dependent mechanical unfolding experiments and Monte Carlo simulations, we find that the unfolding potential widths of SUMO1 (∼0.51 nm) and SUMO2 (∼0.33 nm) are much larger than that of ubiquitin (∼0.19 nm), indicating that SUMO1 is six times and SUMO2 is three times mechanically more flexible than ubiquitin. These findings might also be important in understanding the functional differences between ubiquitin and SUMOs.
Collapse
Affiliation(s)
- Hema Chandra Kotamarthi
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Colaba, Mumbai, India
| | | | | |
Collapse
|
14
|
Bujalowski PJ, Oberhauser AF. Tracking unfolding and refolding reactions of single proteins using atomic force microscopy methods. Methods 2013; 60:151-60. [PMID: 23523554 DOI: 10.1016/j.ymeth.2013.03.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Revised: 03/07/2013] [Accepted: 03/11/2013] [Indexed: 11/26/2022] Open
Abstract
During the last two decades single-molecule manipulation techniques such as atomic force microscopy (AFM) has risen to prominence through their unique capacity to provide fundamental information on the structure and function of biomolecules. Here we describe the use of single-molecule AFM to track protein unfolding and refolding pathways, enzymatic catalysis and the effects of osmolytes and chaperones on protein stability and folding. We will outline the principles of operation for two different AFM pulling techniques: length clamp and force-clamp and discuss prominent applications. We provide protocols for the construction of polyproteins which are amenable for AFM experiments, the preparation of different coverslips, choice and calibration of AFM cantilevers. We also discuss the selection criteria for AFM recordings, the calibration of AFM cantilevers, protein sample preparations and analysis of the obtained data.
Collapse
Affiliation(s)
- Paul J Bujalowski
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, TX 77555, USA
| | | |
Collapse
|
15
|
Liu N, Zhang W. Feeling Inter- or Intramolecular Interactions with the Polymer Chain as Probe: Recent Progress in SMFS Studies on Macromolecular Interactions. Chemphyschem 2012; 13:2238-56. [DOI: 10.1002/cphc.201200154] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2012] [Indexed: 01/30/2023]
|
16
|
Aggarwal V, Kulothungan SR, Balamurali MM, Saranya SR, Varadarajan R, Ainavarapu SRK. Ligand-modulated parallel mechanical unfolding pathways of maltose-binding proteins. J Biol Chem 2011; 286:28056-65. [PMID: 21659518 DOI: 10.1074/jbc.m111.249045] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Protein folding and unfolding are complex phenomena, and it is accepted that multidomain proteins generally follow multiple pathways. Maltose-binding protein (MBP) is a large (a two-domain, 370-amino acid residue) bacterial periplasmic protein involved in maltose uptake. Despite the large size, it has been shown to exhibit an apparent two-state equilibrium unfolding in bulk experiments. Single-molecule studies can uncover rare events that are masked by averaging in bulk studies. Here, we use single-molecule force spectroscopy to study the mechanical unfolding pathways of MBP and its precursor protein (preMBP) in the presence and absence of ligands. Our results show that MBP exhibits kinetic partitioning on mechanical stretching and unfolds via two parallel pathways: one of them involves a mechanically stable intermediate (path I) whereas the other is devoid of it (path II). The apoMBP unfolds via path I in 62% of the mechanical unfolding events, and the remaining 38% follow path II. In the case of maltose-bound MBP, the protein unfolds via the intermediate in 79% of the cases, the remaining 21% via path II. Similarly, on binding to maltotriose, a ligand whose binding strength with the polyprotein is similar to that of maltose, the occurrence of the intermediate is comparable (82% via path I) with that of maltose. The precursor protein preMBP also shows a similar behavior upon mechanical unfolding. The percentages of molecules unfolding via path I are 53% in the apo form and 68% and 72% upon binding to maltose and maltotriose, respectively, for preMBP. These observations demonstrate that ligand binding can modulate the mechanical unfolding pathways of proteins by a kinetic partitioning mechanism. This could be a general mechanism in the unfolding of other large two-domain ligand-binding proteins of the bacterial periplasmic space.
Collapse
Affiliation(s)
- Vasudha Aggarwal
- Department of Biological Sciences, Tata Institute of Fundamental Research, Colaba, Mumbai 400 005, India
| | | | | | | | | | | |
Collapse
|
17
|
Abstract
We use single-molecule force clamp spectroscopy (SMFCS) to explore the reactivity of tris(2-carboxyethyl)phosphine (TCEP), 1, 4-dl-dithiothreitol (DTT) and hydrosulfide anion (HS(-)) on disulfide bonds within a mechanically stretched polypeptide. The single-bond level bimolecular nucleophilic substitution (S(N)2) events are recorded at a series of precisely controlled temperatures so that the Arrhenius kinetic parameters, that is, the height of the activation energy barrier (E(a)) and the attempting frequency (A) of the chemical reactions, can be determined. The values of A are typically at the order of 10(7) M(-1) s(-1), which is far lower than that predicted by the transition-state theory, in which A is given by k(B)T/h and around 10(12) M(-1) s(-1) at room temperature. Furthermore, E(a) is derived to be 30-40 kJ/mol, which can be lowered by ∼6-8% with every 100 pN mechanical force applied. The correlation of the A and E(a) with the molecular structures reveals that the relative magnitude of these two parameters cannot be simply judged from the size of the molecule or the nucleophilicity of the attacking atom. The comparison of the influences on the reaction rate induced by force and temperature indicates an equivalent accelerating effect by every 50 pN or 10 K increment, giving for the first time the relationship between mechanical and thermal effects on a single-molecule S(N)2 chemical reaction.
Collapse
Affiliation(s)
| | - Julio M. Fernández
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| |
Collapse
|
18
|
Alegre-Cebollada J, Perez-Jimenez R, Kosuri P, Fernandez JM. Single-molecule force spectroscopy approach to enzyme catalysis. J Biol Chem 2010; 285:18961-6. [PMID: 20382731 DOI: 10.1074/jbc.r109.011932] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Enzyme catalysis has been traditionally studied using a diverse set of techniques such as bulk biochemistry, x-ray crystallography, and NMR. Recently, single-molecule force spectroscopy by atomic force microscopy has been used as a new tool to study the catalytic properties of an enzyme. In this approach, a mechanical force ranging up to hundreds of piconewtons is applied to the substrate of an enzymatic reaction, altering the conformational energy of the substrate-enzyme interactions during catalysis. From these measurements, the force dependence of an enzymatic reaction can be determined. The force dependence provides valuable new information about the dynamics of enzyme catalysis with sub-angstrom resolution, a feat unmatched by any other current technique. To date, single-molecule force spectroscopy has been applied to gain insight into the reduction of disulfide bonds by different enzymes of the thioredoxin family. This minireview aims to present a perspective on this new approach to study enzyme catalysis and to summarize the results that have already been obtained from it. Finally, the specific requirements that must be fulfilled to apply this new methodology to any other enzyme will be discussed.
Collapse
|
19
|
Hofbauer F, Frank I. Disulfide Bond Cleavage: A Redox Reaction Without Electron Transfer. Chemistry 2010; 16:5097-101. [DOI: 10.1002/chem.200902831] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
20
|
Iozzi MF, Helgaker T, Uggerud E. Assessment of theoretical methods for the determination of the mechanochemical strength of covalent bonds. Mol Phys 2009. [DOI: 10.1080/00268970903401041] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
21
|
|
22
|
Abstract
Single-molecule force-clamp spectroscopy offers a novel platform for mechanically denaturing proteins by applying a constant force to a polyprotein. A powerful emerging application of the technique is that, by introducing a disulfide bond in each protein module, the chemical kinetics of disulfide bond cleavage under different stretching forces can be probed at the single-bond level. Even at forces much lower than that which can rupture the chemical bond, the breaking of the S-S bond at the presence of various chemical reducing agents is significantly accelerated. Our previous work demonstrated that the rate of thiol/disulfide exchange reaction is force-dependent and well-described by an Arrhenius term of the form r = A(exp((FΔx(r) - E(a))/k(B)T)[nucleophile]). From Arrhenius fits to the force dependency of the reduction rate, we measured the bond elongation parameter, Δx(r), along the reaction coordinate to the transition state of the S(N)2 reaction cleaved by different nucleophiles and enzymes, never before observed by any other technique. For S-S cleavage by various reducing agents, obtaining the Δx(r) value can help depicting the energy landscapes and elucidating the mechanisms of the reactions at the single-molecule level. Small nucleophiles, such as 1,4-dl-dithiothreitol (DTT), tris(2-carboxyethyl)phosphine (TCEP), and l-cysteine, react with the S-S bond with monotonically increasing rates under the applied force, while thioredoxin enzymes exhibit both stretching-favored and -resistant reaction-rate regimes. These measurements demonstrate the power of the single-molecule force-clamp spectroscopy approach in providing unprecedented access to chemical reactions.
Collapse
|
23
|
|
24
|
Dumont E, Loos PF, Assfeld X. Factors governing electron capture by small disulfide loops in two-cysteine peptides. J Phys Chem B 2008; 112:13661-9. [PMID: 18837539 DOI: 10.1021/jp806465e] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Integrated molecular orbital-molecular orbital (IMOMO) calculations on 17 short disulfide-bridged peptides (up to 16 residues, with at most five intraloop residues) were performed to elucidate some factors controlling their electron capture. These illustrative systems display contrasted behaviors, shedding light on several criteria of differentiation: size, shape, and rigidity of the disulfide-linking loop, intramolecular hydrogen bonds, etc. The geometrical malleability of disulfide radical anions, whose existence and role as intermediate have been evidenced, is discussed. The disulfide elongation (by ca. 0.7 A) upon electron capture induces "soft" structural damages for these turn structures, with a weakening or cleavage of vicinal hydrogen bond(s). On the basis of a series of six Cys-Alan-Cys peptides, it is proposed that electron affinity reflects the topological frustration of these short and highly constrained structures. Results for a series of amino acid mutations are analyzed for the Cys-Xxx-Yyy-Cys motif, common to redox enzymes of the thioredoxin superfamily.
Collapse
Affiliation(s)
- Elise Dumont
- Equipe de Chimie et Biochimie Théoriques, UMR 7565 CNRS-UHP, Institut Jean Barriol, (FR CNRS 2843), Faculté des Sciences et Techniques, Nancy-Université, B.P. 239, 54506 Vandoeuvre-lès-Nancy, France.
| | | | | |
Collapse
|
25
|
Koti Ainavarapu SR, Wiita AP, Dougan L, Uggerud E, Fernandez JM. Single-molecule force spectroscopy measurements of bond elongation during a bimolecular reaction. J Am Chem Soc 2008; 130:6479-87. [PMID: 18433129 DOI: 10.1021/ja800180u] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
It is experimentally challenging to directly obtain structural information of the transition state (TS), the high-energy bottleneck en route from reactants to products, for solution-phase reactions. Here, we use single-molecule experiments as well as high-level quantum chemical calculations to probe the TS of disulfide bond reduction, a bimolecular nucleophilic substitution (S N2) reaction. We use an atomic force microscope in force-clamp mode to apply mechanical forces to a protein disulfide bond and obtain force-dependent rate constants of the disulfide bond reduction initiated by a variety of nucleophiles. We measure distances to the TS or bond elongation (Delta x), along a 1-D reaction coordinate imposed by mechanical force, of 0.31 +/- 0.05 and 0.44 +/- 0.03 A for thiol-initiated and phosphine-initiated disulfide bond reductions, respectively. These results are in agreement with quantum chemical calculations, which show that the disulfide bond at the TS is longer in phosphine-initiated reduction than in thiol-initiated reduction. We also investigate the effect of solvent environment on the TS geometry by incorporating glycerol into the aqueous solution. In this case, the Delta x value for the phosphine-initiated reduction is decreased to 0.28 +/- 0.04 A whereas it remains unchanged for thiol-initiated reduction, providing a direct test of theoretical calculations of the role of solvent molecules in the reduction TS of an S N2 reaction. These results demonstrate that single-molecule force spectroscopy represents a novel experimental tool to study mechanochemistry and directly probe the sub-ångström changes in TS structure of solution-phase reactions. Furthermore, this single-molecule method opens new doors to gain molecular level understanding of chemical reactivity when combined with quantum chemical calculations.
Collapse
|