1
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Coleman H, Saylor Perez J, Schwartz DK, Kaar J, Garcea RL, Randolph TW. Effect of mechanical stresses on viral capsid disruption during droplet formation and drying. Colloids Surf B Biointerfaces 2024; 233:113661. [PMID: 38006709 PMCID: PMC10986848 DOI: 10.1016/j.colsurfb.2023.113661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 11/10/2023] [Accepted: 11/19/2023] [Indexed: 11/27/2023]
Abstract
Identification of the mechanisms by which viruses lose activity during droplet formation and drying is of great importance to understanding the spread of infectious diseases by virus-containing respiratory droplets and to developing thermally stable spray dried live or inactivated viral vaccines. In this study, we exposed suspensions of baculovirus, an enveloped virus, to isolated mechanical stresses similar to those experienced during respiratory droplet formation and spray drying: fluid shear forces, osmotic pressure forces, and surface tension forces at interfaces. DNA released from mechanically stressed virions was measured by SYBR Gold staining to quantify viral capsid disruption. Theoretical estimates of the force exerted by fluid shear, osmotic pressures and interfacial tension forces during respiratory droplet formation and spray drying suggest that osmotic and interfacial stresses have greater potential to mechanically destabilize viral capsids than forces associated with shear stresses. Experimental results confirmed that rapid changes in osmotic pressure, such as those associated with drying of virus-containing droplets, caused significant viral capsid disruption, whereas the effect of fluid shear forces was negligible. Surface tension forces were sufficient to provoke DNA release from virions adsorbed at air-water interfaces, but the extent of this disruption was limited by the time required for virions to diffuse to interfaces. These results demonstrate the effect of isolated mechanical stresses on virus particles during droplet formation and drying.
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Affiliation(s)
- Holly Coleman
- Department of Chemical and Biological Engineering, University of Colorado Boulder, CO 80303, United States
| | - J Saylor Perez
- Department of Chemical and Biological Engineering, University of Colorado Boulder, CO 80303, United States
| | - Daniel K Schwartz
- Department of Chemical and Biological Engineering, University of Colorado Boulder, CO 80303, United States
| | - Joel Kaar
- Department of Chemical and Biological Engineering, University of Colorado Boulder, CO 80303, United States
| | - Robert L Garcea
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, CO 80303, United States
| | - Theodore W Randolph
- Department of Chemical and Biological Engineering, University of Colorado Boulder, CO 80303, United States.
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2
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Maruno T, Ohkubo T, Uchiyama S. Stirring rate affects thermodynamics and unfolding kinetics in isothermal titration calorimetry. J Biochem 2020; 168:53-62. [PMID: 32134445 DOI: 10.1093/jb/mvaa028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 02/10/2020] [Indexed: 11/13/2022] Open
Abstract
Isothermal titration calorimetry (ITC) directly provides thermodynamic parameters depicting the energetics of intermolecular interactions in solution. During ITC experiments, a titration syringe with a paddle is continuously rotating to promote a homogeneous mixing. Here, we clarified that the shape of the paddles (flat, corkscrew and small-pitched corkscrew) and the stirring rates influence on the thermodynamic parameters of protein-ligand interaction. Stirring with the flat paddle at lower and higher rate both yielded a lower exothermic heat due to different reasons. The complete reaction with no incompetent fractions was achieved only when the stirring was performed at 500 or 750 rpm using the small-pitched corkscrew paddle. The evaluation of the protein solution after 1,500 rpm stirring indicated that proteins in the soluble fraction decreased to 94% of the initial amount, among which 6% was at an unfolded state. In addition, a significant increase of micron aggregates was confirmed. Furthermore, a new approach for the determination of the unfolding kinetics based on the time dependence of the total reaction heat was developed. This study demonstrates that a proper stirring rate and paddle shape are essential for the reliable estimation of thermodynamic parameters in ITC experiments.
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Affiliation(s)
- Takahiro Maruno
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tadayasu Ohkubo
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Susumu Uchiyama
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.,Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan
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3
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Proteostasis Failure in Neurodegenerative Diseases: Focus on Oxidative Stress. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2020; 2020:5497046. [PMID: 32308803 PMCID: PMC7140146 DOI: 10.1155/2020/5497046] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 03/03/2020] [Indexed: 12/11/2022]
Abstract
Protein homeostasis or proteostasis is an essential balance of cellular protein levels mediated through an extensive network of biochemical pathways that regulate different steps of the protein quality control, from the synthesis to the degradation. All proteins in a cell continuously turn over, contributing to development, differentiation, and aging. Due to the multiple interactions and connections of proteostasis pathways, exposure to stress conditions may cause various types of protein damage, altering cellular homeostasis and disrupting the entire network with additional cellular stress. Furthermore, protein misfolding and/or alterations during protein synthesis results in inactive or toxic proteins, which may overload the degradation mechanisms. The maintenance of a balanced proteome, preventing the formation of impaired proteins, is accomplished by two major catabolic routes: the ubiquitin proteasomal system (UPS) and the autophagy-lysosomal system. The proteostasis network is particularly important in nondividing, long-lived cells, such as neurons, as its failure is implicated with the development of neurodegenerative diseases, such as Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis. These neurological disorders share common risk factors such as aging, oxidative stress, environmental stress, and protein dysfunction, all of which alter cellular proteostasis, suggesting that general mechanisms controlling proteostasis may underlay the etiology of these diseases. In this review, we describe the major pathways of cellular proteostasis and discuss how their disruption contributes to the onset and progression of neurodegenerative diseases, focusing on the role of oxidative stress.
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4
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Yu Z, Finch BA, Hale DA. Mixing of Stratified Miscible Liquids in an Unbaffled Tank with Application in High Concentration Protein Drug Product Manufacturing. Ind Eng Chem Res 2018. [DOI: 10.1021/acs.iecr.7b04618] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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5
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Hughes ML, Dougan L. The physics of pulling polyproteins: a review of single molecule force spectroscopy using the AFM to study protein unfolding. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2016; 79:076601. [PMID: 27309041 DOI: 10.1088/0034-4885/79/7/076601] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
One of the most exciting developments in the field of biological physics in recent years is the ability to manipulate single molecules and probe their properties and function. Since its emergence over two decades ago, single molecule force spectroscopy has become a powerful tool to explore the response of biological molecules, including proteins, DNA, RNA and their complexes, to the application of an applied force. The force versus extension response of molecules can provide valuable insight into its mechanical stability, as well as details of the underlying energy landscape. In this review we will introduce the technique of single molecule force spectroscopy using the atomic force microscope (AFM), with particular focus on its application to study proteins. We will review the models which have been developed and employed to extract information from single molecule force spectroscopy experiments. Finally, we will end with a discussion of future directions in this field.
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Affiliation(s)
- Megan L Hughes
- School of Physics and Astronomy, University of Leeds, LS2 9JT, UK. Astbury Centre for Structural and Molecular Biology, University of Leeds, LS2 9JT, UK
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6
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Booth JJ, Shalashilin DV. Fully Atomistic Simulations of Protein Unfolding in Low Speed Atomic Force Microscope and Force Clamp Experiments with the Help of Boxed Molecular Dynamics. J Phys Chem B 2016; 120:700-8. [DOI: 10.1021/acs.jpcb.5b11519] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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7
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Booth J, Vazquez S, Martinez-Nunez E, Marks A, Rodgers J, Glowacki DR, Shalashilin DV. Recent applications of boxed molecular dynamics: a simple multiscale technique for atomistic simulations. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2014; 372:rsta.2013.0384. [PMID: 24982247 PMCID: PMC4084527 DOI: 10.1098/rsta.2013.0384] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
In this paper, we briefly review the boxed molecular dynamics (BXD) method which allows analysis of thermodynamics and kinetics in complicated molecular systems. BXD is a multiscale technique, in which thermodynamics and long-time dynamics are recovered from a set of short-time simulations. In this paper, we review previous applications of BXD to peptide cyclization, solution phase organic reaction dynamics and desorption of ions from self-assembled monolayers (SAMs). We also report preliminary results of simulations of diamond etching mechanisms and protein unfolding in atomic force microscopy experiments. The latter demonstrate a correlation between the protein's structural motifs and its potential of mean force. Simulations of these processes by standard molecular dynamics (MD) is typically not possible, because the experimental time scales are very long. However, BXD yields well-converged and physically meaningful results. Compared with other methods of accelerated MD, our BXD approach is very simple; it is easy to implement, and it provides an integrated approach for simultaneously obtaining both thermodynamics and kinetics. It also provides a strategy for obtaining statistically meaningful dynamical results in regions of configuration space that standard MD approaches would visit only very rarely.
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Affiliation(s)
- Jonathan Booth
- School of Chemistry, University of Leeds, Leeds LS2 9JT, UK
| | - Saulo Vazquez
- Departamento de Química Física and Centro Singular de Investigación en Química Biológica y Materiales Moleculares, Campus Vida, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Emilio Martinez-Nunez
- Departamento de Química Física and Centro Singular de Investigación en Química Biológica y Materiales Moleculares, Campus Vida, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Alison Marks
- School of Life Sciences, University of Bradford, Bradford BD7 1DP, UK
| | - Jeff Rodgers
- School of Chemistry, University of Bristol, Bristol BS8 1TS, UK
| | - David R Glowacki
- School of Chemistry, University of Bristol, Bristol BS8 1TS, UK Department of Chemistry, Stanford University, Stanford, CA 94305, USA
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8
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Liu L, Werner M, Gershenson A. Collapse of a long axis: single-molecule Förster resonance energy transfer and serpin equilibrium unfolding. Biochemistry 2014; 53:2903-14. [PMID: 24749911 PMCID: PMC4020580 DOI: 10.1021/bi401622n] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Revised: 03/17/2014] [Indexed: 01/25/2023]
Abstract
The energy required for mechanical inhibition of target proteases is stored in the native structure of inhibitory serpins and accessed by serpin structural remodeling. The overall serpin fold is ellipsoidal with one long and two short axes. Most of the structural remodeling required for function occurs along the long axis, while expansion of the short axes is associated with misfolded, inactive forms. This suggests that ellipticity, as typified by the long axis, may be important for both function and folding. Placement of donor and acceptor fluorophores approximately along the long axis or one of the short axes allows single-pair Förster resonance energy transfer (spFRET) to report on both unfolding transitions and the time-averaged shape of different conformations. Equilibrium unfolding and refolding studies of the well-characterized inhibitory serpin α1-antitrypsin reveal that the long axis collapses in the folding intermediates while the monitored short axis expands. These energetically distinct intermediates are thus more spherical than the native state. Our spFRET studies agree with other equilibrium unfolding studies that found that the region around one of the β strands, s5A, which helps define the long axis and must move for functionally required loop insertion, unfolds at low denaturant concentrations. This supports a connection between functionally important structural lability and unfolding in the inhibitory serpins.
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Affiliation(s)
- Lu Liu
- Department
of Chemistry, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Michael Werner
- Department
of Chemistry, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Anne Gershenson
- Department
of Biochemistry and Molecular Biology, University
of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
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9
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Farrance OE, Hann E, Kaminska R, Housden NG, Derrington SR, Kleanthous C, Radford SE, Brockwell DJ. A force-activated trip switch triggers rapid dissociation of a colicin from its immunity protein. PLoS Biol 2013; 11:e1001489. [PMID: 23431269 PMCID: PMC3576412 DOI: 10.1371/journal.pbio.1001489] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Accepted: 01/09/2013] [Indexed: 01/24/2023] Open
Abstract
A single-molecule force study shows that rapid dissociation of a high-affinity protein interaction can be triggered by site-specific remodelling of one protein partner, and that prevention of remodelling maintains avidity. Colicins are protein antibiotics synthesised by Escherichia coli strains to target and kill related bacteria. To prevent host suicide, colicins are inactivated by binding to immunity proteins. Despite their high avidity (Kd≈fM, lifetime ≈4 days), immunity protein release is a pre-requisite of colicin intoxication, which occurs on a timescale of minutes. Here, by measuring the dynamic force spectrum of the dissociation of the DNase domain of colicin E9 (E9) and immunity protein 9 (Im9) complex using an atomic force microscope we show that application of low forces (<20 pN) increases the rate of complex dissociation 106-fold, to a timescale (lifetime ≈10 ms) compatible with intoxication. We term this catastrophic force-triggered increase in off-rate a trip bond. Using mutational analysis, we elucidate the mechanism of this switch in affinity. We show that the N-terminal region of E9, which has sparse contacts with the hydrophobic core, is linked to an allosteric activator region in E9 (residues 21–30) whose remodelling triggers immunity protein release. Diversion of the force transduction pathway by the introduction of appropriately positioned disulfide bridges yields a force resistant complex with a lifetime identical to that measured by ensemble techniques. A trip switch within E9 is ideal for its function as it allows bipartite complex affinity, whereby the stable colicin:immunity protein complex required for host protection can be readily converted to a kinetically unstable complex whose dissociation is necessary for cellular invasion and competitor death. More generally, the observation of two force phenotypes for the E9:Im9 complex demonstrates that force can re-sculpt the underlying energy landscape, providing new opportunities to modulate biological reactions in vivo; this rationalises the commonly observed discrepancy between off-rates measured by dynamic force spectroscopy and ensemble methods. Many proteins interact with other proteins as part of their function. One method of modulating the activity of protein complexes is to break them apart. Some complexes, however, are extremely kinetically stable and it is unclear how these can dissociate on a biologically relevant timescale. In this study we address this question using protein complexes between colicin E9 (a bacterial toxin) and its immunity protein Im9. These highly avid complexes (with a lifetime of days) must be broken apart for colicin to be activated. By using single-molecule force methods we show that pulling on one end of colicin E9 drastically destabilises the complex so that it dissociates a million-fold faster than its intrinsic rate. We then show that preventing this destabilisation (by the insertion of cross-links that pin the N-terminus of E9 in place) yields a kinetically stable complex. It has previously been postulated that force can destabilise a protein complex by partially unfolding one or more binding partners. Our work provides new experimental evidence that shows this is the case and provides a mechanism for this phenomenon, which we term a trip bond. For the E9:Im9 complex, trip bond behaviour allows a stable complex to be rapidly dissociated by application of a surprisingly small force.
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Affiliation(s)
- Oliver E. Farrance
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, United Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leeds, United Kingdom
| | - Eleanore Hann
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, United Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leeds, United Kingdom
| | - Renata Kaminska
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | | | - Sasha R. Derrington
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, United Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leeds, United Kingdom
| | - Colin Kleanthous
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Sheena E. Radford
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, United Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leeds, United Kingdom
| | - David J. Brockwell
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, United Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leeds, United Kingdom
- * E-mail:
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10
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Bu T, Wang HCE, Li H. Single molecule force spectroscopy reveals critical roles of hydrophobic core packing in determining the mechanical stability of protein GB1. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:12319-12325. [PMID: 22823458 DOI: 10.1021/la301940g] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Understanding molecular determinants of protein mechanical stability is important not only for elucidating how elastomeric proteins are designed and functioning in biological systems but also for designing protein building blocks with defined nanomechanical properties for constructing novel biomaterials. GB1 is a small α/β protein and exhibits significant mechanical stability. It is thought that the shear topology of GB1 plays an important role in determining its mechanical stability. Here, we combine single molecule atomic force microscopy and protein engineering techniques to investigate the effect of side chain reduction and hydrophobic core packing on the mechanical stability of GB1. We engineered seven point mutants and carried out mechanical φ-value analysis of the mechanical unfolding of GB1. We found that three mutations, which are across the surfaces of two subdomains that are to be sheared by the applied stretching force, in the hydrophobic core (F30L, Y45L, and F52L) result in significant decrease in mechanical unfolding force of GB1. The mechanical unfolding force of these mutants drop by 50-90 pN compared with wild-type GB1, which unfolds at around 180 pN at a pulling speed of 400 nm/s. These results indicate that hydrophobic core packing plays an important role in determining the mechanical stability of GB1 and suggest that optimizing hydrophobic interactions across the surfaces that are to be sheared will likely be an efficient method to enhance the mechanical stability of GB1 and GB1 homologues.
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Affiliation(s)
- Tianjia Bu
- State Key Laboratory for Supramolecular Structure and Materials, Jilin University, Changchun, Jilin Province, P R China
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11
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Wales DJ, Head-Gordon T. Evolution of the potential energy landscape with static pulling force for two model proteins. J Phys Chem B 2012; 116:8394-411. [PMID: 22432920 DOI: 10.1021/jp211806z] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The energy landscape is analyzed for off-lattice bead models of protein L and protein G as a function of a static pulling force. Two different pairs of attachment points (pulling directions) are compared in each case, namely, residues 1/56 and 10/32. For the terminal residue pulling direction 1/56, the distinct global minimum structures are all extended, aside from the compact geometry that correlates with zero force. The helical turns finally disappear at the highest pulling forces considered. For the 10/32 pulling direction, the changes are more complicated, with a variety of competing arrangements for beads outside the region where the force is directly applied. These alternatives produce frustrated energy landscapes, with low-lying minima separated by high barriers. The calculated folding pathways in the absence of force are in good agreement with previous work. The N-terminal hairpin folds first for protein L and the C-terminal hairpin for protein G, which exhibits an intermediate. However, for a relatively low static force, where the global minimum retains its structure, the folding mechanisms change, sometimes dramatically, depending on the protein and the attachment points. The scaling relations predicted by catastrophe theory are found to hold in the limit of short path lengths.
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Affiliation(s)
- David J Wales
- University Chemical Laboratories, Lensfield Road, Cambridge CB2 1EW, UK.
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12
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Ikeda-Kobayashi A, Taniguchi Y, Brockwell DJ, Paci E, Kawakami M. Prying open single GroES ring complexes by force reveals cooperativity across domains. Biophys J 2012; 102:1961-8. [PMID: 22768953 DOI: 10.1016/j.bpj.2012.03.046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2011] [Revised: 02/29/2012] [Accepted: 03/14/2012] [Indexed: 11/16/2022] Open
Abstract
Understanding how the mechanical properties of a protein complex emerge from the interplay of intra- and interchain interactions is vital at both fundamental and applied levels. To investigate whether interdomain cooperativity affects protein mechanical strength, we employed single-molecule force spectroscopy to probe the mechanical stability of GroES, a homoheptamer with a domelike quaternary stucture stabilized by intersubunit interactions between the first and last β-strands of adjacent domains. A GroES variant was constructed in which each subunit of the GroES heptamer is covalently linked to adjacent subunits by tripeptide linkers and folded domains of protein L are introduced to the heptamer's termini as handle molecules. The force-distance profiles for GroES unfolding showed, for the first time that we know of, a mechanical phenotype whereby seven distinct force peaks, with alternating behavior of unfolding force and contour length (ΔL(c)), were observed with increasing unfolding-event number. Unfolding of (GroES)(7) is initiated by breakage of the interface between domains 1 and 7 at low force, which imparts a polarity to (GroES)(7) that results in two distinct mechanical phenotypes of these otherwise identical protein domains. Unfolding then proceeds by peeling domains off the domelike native structure by sequential repetition of the denaturation of mechanically weak (unfoldon 1) and strong (unfoldon 2) units. These results indicate that domain-domain interactions help to determine the overall mechanical strength and unfolding pathway of the oligomeric structure. These data reveal an unexpected richness in the mechanical behavior of this homopolyprotein, yielding a complex with greater mechanical strength and properties distinct from those that would be apparent for GroES domains in isolation.
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Affiliation(s)
- Akiko Ikeda-Kobayashi
- School of Materials Science, Japan Advanced Institute of Science and Technology, Ishikawa, Japan
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13
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The removal of a disulfide bridge in CotA-laccase changes the slower motion dynamics involved in copper binding but has no effect on the thermodynamic stability. J Biol Inorg Chem 2011; 16:641-51. [DOI: 10.1007/s00775-011-0768-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2010] [Accepted: 02/08/2011] [Indexed: 10/18/2022]
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14
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Sacquin-Mora S, Delalande O, Baaden M. Functional modes and residue flexibility control the anisotropic response of guanylate kinase to mechanical stress. Biophys J 2011; 99:3412-9. [PMID: 21081090 DOI: 10.1016/j.bpj.2010.09.026] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2010] [Revised: 09/11/2010] [Accepted: 09/15/2010] [Indexed: 01/27/2023] Open
Abstract
The coupling between the mechanical properties of enzymes and their biological activity is a well-established feature that has been the object of numerous experimental and theoretical works. In particular, recent experiments show that enzymatic function can be modulated anisotropically by mechanical stress. We study such phenomena using a method for investigating local flexibility on the residue scale that combines a reduced protein representation with Brownian dynamics simulations. We performed calculations on the enzyme guanylate kinase to study its mechanical response when submitted to anisotropic deformations. The resulting modifications of the protein's rigidity profile can be related to the changes in substrate binding affinity observed experimentally. Further analysis of the principal components of motion of the trajectories shows how the application of a mechanical constraint on the protein can disrupt its dynamics, thus leading to a decrease of the enzyme's catalytic rate. Eventually, a systematic probe of the protein surface led to the prediction of potential hotspots where the application of an external constraint would produce a large functional response both from the mechanical and dynamical points of view. Such enzyme-engineering approaches open the possibility to tune catalytic function by varying selected external forces.
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Affiliation(s)
- Sophie Sacquin-Mora
- Institut de Biologie Physico-Chimique, Laboratoire de Biochimie Théorique, CNRS UPR9080, Paris, France.
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15
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Arad-Haase G, Chuartzman SG, Dagan S, Nevo R, Kouza M, Mai BK, Nguyen HT, Li MS, Reich Z. Mechanical unfolding of acylphosphatase studied by single-molecule force spectroscopy and MD simulations. Biophys J 2010; 99:238-47. [PMID: 20655852 PMCID: PMC2895382 DOI: 10.1016/j.bpj.2010.04.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2010] [Revised: 03/28/2010] [Accepted: 04/01/2010] [Indexed: 11/30/2022] Open
Abstract
Single-molecule manipulation methods provide a powerful means to study protein transitions. Here we combined single-molecule force spectroscopy and steered molecular-dynamics simulations to study the mechanical properties and unfolding behavior of the small enzyme acylphosphatase (AcP). We find that mechanical unfolding of AcP occurs at relatively low forces in an all-or-none fashion and is decelerated in the presence of a ligand, as observed in solution measurements. The prominent energy barrier for the transition is separated from the native state by a distance that is unusually long for alpha/beta proteins. Unfolding is initiated at the C-terminal strand (beta(T)) that lies at one edge of the beta-sheet of AcP, followed by unraveling of the strand located at the other. The central strand of the sheet and the two helices in the protein unfold last. Ligand binding counteracts unfolding by stabilizing contacts between an arginine residue (Arg-23) and the catalytic loop, as well as with beta(T) of AcP, which renders the force-bearing units of the protein resistant to force. This stabilizing effect may also account for the decelerated unfolding of ligand-bound AcP in the absence of force.
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Affiliation(s)
- Gali Arad-Haase
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Silvia G. Chuartzman
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Shlomi Dagan
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Reinat Nevo
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Maksim Kouza
- Department of Physics, Michigan Technological University, Houghton, Michigan
| | - Binh Khanh Mai
- Saigon Institute for Computational Science and Technology, Ho Chi Minh City, Vietnam
| | - Hung Tien Nguyen
- Saigon Institute for Computational Science and Technology, Ho Chi Minh City, Vietnam
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, Warsaw, Poland
| | - Ziv Reich
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
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16
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Taniguchi Y, Kawakami M. Application of HaloTag protein to covalent immobilization of recombinant proteins for single molecule force spectroscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:10433-10436. [PMID: 20527958 DOI: 10.1021/la101658a] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
We have developed the HaloTag system for the covalent immobilization of polyproteins onto a mica substrate for single molecule force spectroscopy using the atomic force microscope. A recombinant fusion polyprotein of titin I27 with HaloTag7 protein was produced, and the covalent and site-specific attachment on a HaloTag-ligand-modified mica surface was confirmed by force-extension measurements. Two mechanical unfolding intermediates of HaloTag7 protein were found by contour length analysis. This tethering method allows site-specific covalent immobilization of a protein that complements the standard method utilizing thiol-gold interaction, thus facilitating force-extension measurements for cysteine-containing proteins.
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Affiliation(s)
- Yukinori Taniguchi
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
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Sadler DP, Petrik E, Taniguchi Y, Pullen JR, Kawakami M, Radford SE, Brockwell DJ. Identification of a mechanical rheostat in the hydrophobic core of protein L. J Mol Biol 2009; 393:237-48. [PMID: 19683005 PMCID: PMC2796179 DOI: 10.1016/j.jmb.2009.08.015] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2009] [Revised: 07/23/2009] [Accepted: 08/07/2009] [Indexed: 11/22/2022]
Abstract
The ability of proteins and their complexes to withstand or respond to mechanical stimuli is vital for cells to maintain their structural organisation, to relay external signals and to facilitate unfolding and remodelling. Force spectroscopy using the atomic force microscope allows the behaviour of single protein molecules under an applied extension to be investigated and their mechanical strength to be quantified. protein L, a simple model protein, displays moderate mechanical strength and is thought to unfold by the shearing of two mechanical sub-domains. Here, we investigate the importance of side-chain packing for the mechanical strength of protein L by measuring the mechanical strength of a series of protein L variants containing single conservative hydrophobic volume deletion mutants. Of the five thermodynamically destabilised variants characterised, only one residue (I60V) close to the interface between two mechanical sub-domains was found to differ in mechanical properties to wild type (ΔFI60V–WT = − 36 pN at 447 nm s− 1, ΔxuI60V–WT = 0.2 nm). Φ-value analysis of the unfolding data revealed a highly native transition state. To test whether the number of hydrophobic contacts across the mechanical interface does affect the mechanical strength of protein L, we measured the mechanical properties of two further variants. protein L L10F, which increases core packing but does not enhance interfacial contacts, increased mechanical strength by 13 ± 11 pN at 447 nm s− 1. By contrast, protein L I60F, which increases both core and cross-interface contacts, increased mechanical strength by 72 ± 13 pN at 447 nm s− 1. These data suggest a method by which nature can evolve a varied mechanical response from a limited number of topologies and demonstrate a generic but facile method by which the mechanical strength of proteins can be rationally modified.
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Affiliation(s)
- David P Sadler
- Astbury Centre for Structural Molecular Biology, Institute of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
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Bee JS, Stevenson JL, Mehta B, Svitel J, Pollastrini J, Platz R, Freund E, Carpenter JF, Randolph TW. Response of a concentrated monoclonal antibody formulation to high shear. Biotechnol Bioeng 2009; 103:936-43. [PMID: 19370772 PMCID: PMC2724069 DOI: 10.1002/bit.22336] [Citation(s) in RCA: 133] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
There is concern that shear could cause protein unfolding or aggregation during commercial biopharmaceutical production. In this work we exposed two concentrated immunoglobulin-G1 (IgG1) monoclonal antibody (mAb, at >100 mg/mL) formulations to shear rates between 20,000 and 250,000 s(-1) for between 5 min and 30 ms using a parallel-plate and capillary rheometer, respectively. The maximum shear and force exposures were far in excess of those expected during normal processing operations (20,000 s(-1) and 0.06 pN, respectively). We used multiple characterization techniques to determine if there was any detectable aggregation. We found that shear alone did not cause aggregation, but that prolonged exposure to shear in the stainless steel parallel-plate rheometer caused a very minor reversible aggregation (<0.3%). Additionally, shear did not alter aggregate populations in formulations containing 17% preformed heat-induced aggregates of a mAb. We calculate that the forces applied to a protein by production shear exposures (<0.06 pN) are small when compared with the 140 pN force expected at the air-water interface or the 20-150 pN forces required to mechanically unfold proteins described in the atomic force microscope (AFM) literature. Therefore, we suggest that in many cases, air-bubble entrainment, adsorption to solid surfaces (with possible shear synergy), contamination by particulates, or pump cavitation stresses could be much more important causes of aggregation than shear exposure during production.
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Affiliation(s)
- Jared S. Bee
- University of Colorado, Department of Chemical and Biological Engineering, Room: ECCH 111, Campus Box 0424, 1111 Engineers Dr, Boulder, Colorado 80309-0424, Telephone: 303-492-4776
| | | | - Bhavya Mehta
- Drug Product & Device Development, Amgen Inc., Thousand Oaks, CA 91320
| | - Juraj Svitel
- Formulation and Analytical Resources, Amgen Inc., Thousand Oaks, CA 91320
| | - Joey Pollastrini
- Formulation and Analytical Resources, Amgen Inc., Thousand Oaks, CA 91320
| | | | - Erwin Freund
- Drug Product & Device Development, Amgen Inc., Thousand Oaks, CA 91320
| | - John F. Carpenter
- Department of Pharmaceutical Sciences, University of Colorado Health Sciences Center, Denver, Colorado 80262
| | - Theodore W. Randolph
- University of Colorado, Department of Chemical and Biological Engineering, Room: ECCH 111, Campus Box 0424, 1111 Engineers Dr, Boulder, Colorado 80309-0424, Telephone: 303-492-4776
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Sacquin-Mora S, Lavery R. Modeling the mechanical response of proteins to anisotropic deformation. Chemphyschem 2009; 10:115-8. [PMID: 19006155 DOI: 10.1002/cphc.200800480] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Sophie Sacquin-Mora
- Laboratoire de Biochimie Théorique, CNRS UPR9080, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France.
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Folding scene investigation: membrane proteins. Curr Opin Struct Biol 2009; 19:8-13. [PMID: 19157854 PMCID: PMC2670978 DOI: 10.1016/j.sbi.2008.12.005] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2008] [Accepted: 12/04/2008] [Indexed: 11/23/2022]
Abstract
Investigations into protein folding have concentrated on experimentally tractable proteins with the result that membrane protein folding remains unsolved. New evidence is providing insight into the nature of the interactions stabilising the folded state of α-helical membrane proteins as well as giving hints on the character of the folding transition state. These developments show that classical methods used for water-soluble proteins can be successfully adapted for membrane proteins. The advances, coupled with increasing numbers of solved crystal structures, augur well for future research into the mechanisms of membrane protein folding.
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Schlierf M, Rief M. Surprising Simplicity in the Single-Molecule Folding Mechanics of Proteins. Angew Chem Int Ed Engl 2009; 48:820-2. [DOI: 10.1002/anie.200804723] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Schlierf M, Rief M. Überraschend einfache Einzelmolekülmechanik der Faltung von Proteinen. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200804723] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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