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Molnar K, Suman SK, Eichelbrenner J, Plancke CN, Robin FB, Labouesse M. Conditional nmy-1 and nmy-2 alleles establish that nonmuscle myosins are required for late Caenorhabditis elegans embryonic elongation. Genetics 2024; 228:iyae109. [PMID: 39053622 DOI: 10.1093/genetics/iyae109] [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: 04/11/2024] [Revised: 04/11/2024] [Accepted: 06/26/2024] [Indexed: 07/27/2024] Open
Abstract
The elongation of Caenorhabditis elegans embryos allows examination of mechanical interactions between adjacent tissues. Muscle contractions during late elongation induce the remodeling of epidermal circumferential actin filaments through mechanotransduction. Force inputs from the muscles deform circumferential epidermal actin filament, which causes them to be severed, eventually reformed, and shortened. This squeezing force drives embryonic elongation. We investigated the possible role of the nonmuscle myosins NMY-1 and NMY-2 in this process using nmy-1 and nmy-2 thermosensitive alleles. Our findings show these myosins act redundantly in late elongation, since double nmy-2(ts); nmy-1(ts) mutants immediately stop elongation when raised to 25°C. Their inactivation does not reduce muscle activity, as measured from epidermis deformation, suggesting that they are directly involved in the multistep process of epidermal remodeling. Furthermore, NMY-1 and NMY-2 inactivation is reversible when embryos are kept at the nonpermissive temperature for a few hours. However, after longer exposure to 25°C double mutant embryos fail to resume elongation, presumably because NMY-1 was seen to form protein aggregates. We propose that the two C. elegans nonmuscle myosin II act during actin remodeling either to bring severed ends or hold them.
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Affiliation(s)
- Kelly Molnar
- Laboratoire de Biologie du Développement-UMR7622, Institut de Biologie Paris Seine, Sorbonne Université, 7-9 quai Saint Bernard 75005 Paris, France
| | - Shashi Kumar Suman
- Laboratoire de Biologie du Développement-UMR7622, Institut de Biologie Paris Seine, Sorbonne Université, 7-9 quai Saint Bernard 75005 Paris, France
| | - Jeanne Eichelbrenner
- Laboratoire de Biologie du Développement-UMR7622, Institut de Biologie Paris Seine, Sorbonne Université, 7-9 quai Saint Bernard 75005 Paris, France
| | - Camille N Plancke
- Laboratoire de Biologie du Développement-UMR7622, Institut de Biologie Paris Seine, Sorbonne Université, 7-9 quai Saint Bernard 75005 Paris, France
| | - François B Robin
- Laboratoire de Biologie du Développement-UMR7622, Institut de Biologie Paris Seine, Sorbonne Université, 7-9 quai Saint Bernard 75005 Paris, France
| | - Michel Labouesse
- Laboratoire de Biologie du Développement-UMR7622, Institut de Biologie Paris Seine, Sorbonne Université, 7-9 quai Saint Bernard 75005 Paris, France
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2
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Shityakov S, Skorb EV, Nosonovsky M. Folding-unfolding asymmetry and a RetroFold computational algorithm. ROYAL SOCIETY OPEN SCIENCE 2023; 10:221594. [PMID: 37153361 PMCID: PMC10154942 DOI: 10.1098/rsos.221594] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 03/30/2023] [Indexed: 05/09/2023]
Abstract
We treat protein folding as molecular self-assembly, while unfolding is viewed as disassembly. Fracture is typically a much faster process than self-assembly. Self-assembly is often an exponentially decaying process, since energy relaxes due to dissipation, while fracture is a constant-rate process as the driving force is opposed by damping. Protein folding takes two orders of magnitude longer than unfolding. We suggest a mathematical transformation of variables, which makes it possible to view self-assembly as time-reversed disassembly, thus folding can be studied as reversed unfolding. We investigate the molecular dynamics modelling of folding and unfolding of the short Trp-cage protein. Folding time constitutes about 800 ns, while unfolding (denaturation) takes only about 5.0 ns and, therefore, fewer computational resources are needed for its simulation. This RetroFold approach can be used for the design of a novel computation algorithm, which, while approximate, is less time-consuming than traditional folding algorithms.
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Affiliation(s)
- Sergey Shityakov
- Infochemistry Scientific Center (ISC), ITMO University, 9 Lomonosova Street, St. Petersburg 191002, Russia
| | - Ekaterina V. Skorb
- Infochemistry Scientific Center (ISC), ITMO University, 9 Lomonosova Street, St. Petersburg 191002, Russia
| | - Michael Nosonovsky
- Infochemistry Scientific Center (ISC), ITMO University, 9 Lomonosova Street, St. Petersburg 191002, Russia
- College of Engineering and Applied Science, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA
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3
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The spectrin cytoskeleton integrates endothelial mechanoresponses. Nat Cell Biol 2022; 24:1226-1238. [PMID: 35817960 DOI: 10.1038/s41556-022-00953-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 06/01/2022] [Indexed: 12/13/2022]
Abstract
Physiological blood flow induces the secretion of vasoactive compounds, notably nitric oxide, and promotes endothelial cell elongation and reorientation parallel to the direction of applied shear. How shear is sensed and relayed to intracellular effectors is incompletely understood. Here, we demonstrate that an apical spectrin network is essential to convey the force imposed by shear to endothelial mechanosensors. By anchoring CD44, spectrins modulate the cell surface density of hyaluronan and sense and translate shear into changes in plasma membrane tension. Spectrins also regulate the stability of apical caveolae, where the mechanosensitive PIEZO1 channels are thought to reside. Accordingly, shear-induced PIEZO1 activation and the associated calcium influx were absent in spectrin-deficient cells. As a result, cell realignment and flow-induced endothelial nitric oxide synthase stimulation were similarly dependent on spectrin. We conclude that the apical spectrin network is not only required for shear sensing but also transmits and distributes the resulting tensile forces to mechanosensors that elicit protective and vasoactive responses.
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4
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Khan MI, Ferdous SF, Adnan A. Mechanical behavior of actin and spectrin subjected to high strain rate: A molecular dynamics simulation study. Comput Struct Biotechnol J 2021; 19:1738-1749. [PMID: 33897978 PMCID: PMC8050423 DOI: 10.1016/j.csbj.2021.03.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 03/21/2021] [Accepted: 03/23/2021] [Indexed: 11/16/2022] Open
Abstract
Recent nanoscopy and super-resolution microscopy studies have substantiated the structural contribution of periodic actin-spectrin lattice to the axonal cytoskeleton of neuron. However, sufficient mechanical insight is not present for spectrin and actin-spectrin network, especially in high strain rate scenario. To quantify the mechanical behavior of actin-spectrin cytoskeleton in such conditions, this study determines individual stretching characteristics of actin and spectrin at high strain rate by molecular dynamics (MD) simulation. The actin-spectrin separation criteria are also determined. It is found that both actin and spectrin have high stiffness when susceptible to high strain rate and show strong dependence on applied strain rate. The stretching stiffness of actin and forced unfolding mechanism of spectrin are in harmony with the current literature. Actin-spectrin model provides novel insight into their interaction and separation stretch. It is shown that the region vulnerable to failure is the actin-spectrin interface at lower strain rate, while it is the inter-repeat region of spectrin at higher strain rate.
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Affiliation(s)
- Md Ishak Khan
- Department of Mechanical and Aerospace Engineering, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Sheikh Fahad Ferdous
- Department of Applied Engineering and Technology Management, Indiana State University, Terre Haute, IN 47809, USA
| | - Ashfaq Adnan
- Department of Mechanical and Aerospace Engineering, University of Texas at Arlington, Arlington, TX 76019, USA
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5
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Manipulation of Focal Adhesion Signaling by Pathogenic Microbes. Int J Mol Sci 2021; 22:ijms22031358. [PMID: 33572997 PMCID: PMC7866387 DOI: 10.3390/ijms22031358] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 01/25/2021] [Accepted: 01/27/2021] [Indexed: 12/22/2022] Open
Abstract
Focal adhesions (FAs) serve as dynamic signaling hubs within the cell. They connect intracellular actin to the extracellular matrix (ECM) and respond to environmental cues. In doing so, these structures facilitate important processes such as cell-ECM adhesion and migration. Pathogenic microbes often modify the host cell actin cytoskeleton in their pursuit of an ideal replicative niche or during invasion to facilitate uptake. As actin-interfacing structures, FA dynamics are also intimately tied to actin cytoskeletal organization. Indeed, exploitation of FAs is another avenue by which pathogenic microbes ensure their uptake, survival and dissemination. This is often achieved through the secretion of effector proteins which target specific protein components within the FA. Molecular mimicry of the leucine-aspartic acid (LD) motif or vinculin-binding domains (VBDs) commonly found within FA proteins is a common microbial strategy. Other effectors may induce post-translational modifications to FA proteins through the regulation of phosphorylation sites or proteolytic cleavage. In this review, we present an overview of the regulatory mechanisms governing host cell FAs, and provide examples of how pathogenic microbes have evolved to co-opt them to their own advantage. Recent technological advances pose exciting opportunities for delving deeper into the mechanistic details by which pathogenic microbes modify FAs.
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Casuso I, Redondo-Morata L, Rico F. Biological physics by high-speed atomic force microscopy. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2020; 378:20190604. [PMID: 33100165 PMCID: PMC7661283 DOI: 10.1098/rsta.2019.0604] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
While many fields have contributed to biological physics, nanotechnology offers a new scale of observation. High-speed atomic force microscopy (HS-AFM) provides nanometre structural information and dynamics with subsecond resolution of biological systems. Moreover, HS-AFM allows us to measure piconewton forces within microseconds giving access to unexplored, fast biophysical processes. Thus, HS-AFM provides a tool to nourish biological physics through the observation of emergent physical phenomena in biological systems. In this review, we present an overview of the contribution of HS-AFM, both in imaging and force spectroscopy modes, to the field of biological physics. We focus on examples in which HS-AFM observations on membrane remodelling, molecular motors or the unfolding of proteins have stimulated the development of novel theories or the emergence of new concepts. We finally provide expected applications and developments of HS-AFM that we believe will continue contributing to our understanding of nature, by serving to the dialogue between biology and physics. This article is part of a discussion meeting issue 'Dynamic in situ microscopy relating structure and function'.
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Affiliation(s)
- Ignacio Casuso
- Aix-Marseile University, Inserm, CNRS, LAI, 163 Av. de Luminy, 13009 Marseille, France
| | - Lorena Redondo-Morata
- Center for Infection and Immunity of Lille, INSERM U1019, CNRS UMR 8204, 59000 Lille, France
| | - Felix Rico
- Aix-Marseile University, Inserm, CNRS, LAI, 163 Av. de Luminy, 13009 Marseille, France
- e-mail:
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7
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Cotranslational folding cooperativity of contiguous domains of α-spectrin. Proc Natl Acad Sci U S A 2020; 117:14119-14126. [PMID: 32513720 DOI: 10.1073/pnas.1909683117] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Proteins synthesized in the cell can begin to fold during translation before the entire polypeptide has been produced, which may be particularly relevant to the folding of multidomain proteins. Here, we study the cotranslational folding of adjacent domains from the cytoskeletal protein α-spectrin using force profile analysis (FPA). Specifically, we investigate how the cotranslational folding behavior of the R15 and R16 domains are affected by their neighboring R14 and R16, and R15 and R17 domains, respectively. Our results show that the domains impact each other's folding in distinct ways that may be important for the efficient assembly of α-spectrin, and may reduce its dependence on chaperones. Furthermore, we directly relate the experimentally observed yield of full-length protein in the FPA assay to the force exerted by the folding protein in piconewtons. By combining pulse-chase experiments to measure the rate at which the arrested protein is converted into full-length protein with a Bell model of force-induced rupture, we estimate that the R16 domain exerts a maximal force on the nascent chain of ∼15 pN during cotranslational folding.
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8
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Dubey S, Bhembre N, Bodas S, Veer S, Ghose A, Callan-Jones A, Pullarkat P. The axonal actin-spectrin lattice acts as a tension buffering shock absorber. eLife 2020; 9:51772. [PMID: 32267230 PMCID: PMC7190353 DOI: 10.7554/elife.51772] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 04/06/2020] [Indexed: 12/11/2022] Open
Abstract
Axons span extreme distances and are subject to significant stretch deformations during limb movements or sudden head movements, especially during impacts. Yet, axon biomechanics, and its relation to the ultrastructure that allows axons to withstand mechanical stress, is poorly understood. Using a custom developed force apparatus, we demonstrate that chick dorsal root ganglion axons exhibit a tension buffering or strain-softening response, where its steady state elastic modulus decreases with increasing strain. We then explore the contributions from the various cytoskeletal components of the axon to show that the recently discovered membrane-associated actin-spectrin scaffold plays a prominent mechanical role. Finally, using a theoretical model, we argue that the actin-spectrin skeleton acts as an axonal tension buffer by reversibly unfolding repeat domains of the spectrin tetramers to release excess mechanical stress. Our results revise the current viewpoint that microtubules and their associated proteins are the only significant load-bearing elements in axons.
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Affiliation(s)
| | | | - Shivani Bodas
- Indian Institute of Science Education and Research, Pune, India
| | - Sukh Veer
- Raman Research Institute, Bangalore, India
| | - Aurnab Ghose
- Indian Institute of Science Education and Research, Pune, India
| | - Andrew Callan-Jones
- Laboratory of Complex Materials Systems, Paris Diderot University, Paris, France
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Mechanical Unfolding of Spectrin Repeats Induces Water-Molecule Ordering. Biophys J 2020; 118:1076-1089. [PMID: 32027822 DOI: 10.1016/j.bpj.2020.01.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 12/24/2019] [Accepted: 01/02/2020] [Indexed: 02/07/2023] Open
Abstract
Mechanical processes are involved at many stages of the development of living cells, and often external forces applied to a biomolecule result in its unfolding. Although our knowledge of the unfolding mechanisms and the magnitude of the forces involved has evolved, the role that water molecules play in the mechanical unfolding of biomolecules has not yet been fully elucidated. To this end, we investigated with steered molecular dynamics simulations the mechanical unfolding of dystrophin's spectrin repeat 1 and related the changes in the protein's structure to the ordering of the surrounding water molecules. Our results indicate that upon mechanically induced unfolding of the protein, the solvent molecules become more ordered and increase their average number of hydrogen bonds. In addition, the unfolded structures originating from mechanical pulling expose an increasing amount of the hydrophobic residues to the solvent molecules, and the uncoiled regions adapt a convex surface with a small radius of curvature. As a result, the solvent molecules reorganize around the protein's small protrusions in structurally ordered waters that are characteristic of the so-called "small-molecule regime," which allows water to maintain a high hydrogen bond count at the expense of an increased structural order. We also determined that the response of water to structural changes in the protein is localized to the specific regions of the protein that undergo unfolding. These results indicate that water plays an important role in the mechanically induced unfolding of biomolecules. Our findings may prove relevant to the ever-growing interest in understanding macromolecular crowding in living cells and their effects on protein folding, and suggest that the hydration layer may be exploited as a means for short-range allosteric communication.
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10
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Suman SK, Daday C, Ferraro T, Vuong-Brender T, Tak S, Quintin S, Robin F, Gräter F, Labouesse M. The plakin domain of C. elegans VAB-10/plectin acts as a hub in a mechanotransduction pathway to promote morphogenesis. Development 2019; 146:dev183780. [PMID: 31784459 PMCID: PMC7375825 DOI: 10.1242/dev.183780] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 11/18/2019] [Indexed: 12/29/2022]
Abstract
Mechanical forces can elicit a mechanotransduction response through junction-associated proteins. In contrast to the wealth of knowledge available for focal adhesions and adherens junctions, much less is known about mechanotransduction at hemidesmosomes. Here, we focus on the C. elegans plectin homolog VAB-10A, the only evolutionary conserved hemidesmosome component. In C. elegans, muscle contractions induce a mechanotransduction pathway in the epidermis through hemidesmosomes. We used CRISPR to precisely remove spectrin repeats (SRs) or a partially hidden Src homology 3 (SH3) domain within the VAB-10 plakin domain. Deleting the SH3 or SR8 domains in combination with mutations affecting mechanotransduction, or just the part of SR5 shielding the SH3 domain, induced embryonic elongation arrest because hemidesmosomes collapse. Notably, recruitment of GIT-1, the first mechanotransduction player, requires the SR5 domain and the hemidesmosome transmembrane receptor LET-805. Furthermore, molecular dynamics simulations confirmed that forces acting on VAB-10 could make the central SH3 domain, otherwise in contact with SR4, available for interaction. Collectively, our data strongly indicate that the plakin domain plays a central role in mechanotransduction and raise the possibility that VAB-10/plectin might act as a mechanosensor.
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Affiliation(s)
- Shashi Kumar Suman
- Sorbonne Université, CNRS, Institut de Biologie Paris Seine, Laboratoire de Biologie du Développement/UMR7622,7 Quai St-Bernard, 75005 Paris, France
- Development and Stem Cells Program, IGBMC, CNRS (UMR7104), INSERM (U964), Université de Strasbourg, 1 rue Laurent Fries, BP10142, 67400 Illkirch, France
| | - Csaba Daday
- Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Mathematikon, INF 205, 69120 Heidelberg, Germany
- Heidelberg Institute for Theoretical Studies, Schloß-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany
| | - Teresa Ferraro
- Sorbonne Université, CNRS, Institut de Biologie Paris Seine, Laboratoire de Biologie du Développement/UMR7622,7 Quai St-Bernard, 75005 Paris, France
| | - Thanh Vuong-Brender
- Sorbonne Université, CNRS, Institut de Biologie Paris Seine, Laboratoire de Biologie du Développement/UMR7622,7 Quai St-Bernard, 75005 Paris, France
- Development and Stem Cells Program, IGBMC, CNRS (UMR7104), INSERM (U964), Université de Strasbourg, 1 rue Laurent Fries, BP10142, 67400 Illkirch, France
| | - Saurabh Tak
- Sorbonne Université, CNRS, Institut de Biologie Paris Seine, Laboratoire de Biologie du Développement/UMR7622,7 Quai St-Bernard, 75005 Paris, France
- Development and Stem Cells Program, IGBMC, CNRS (UMR7104), INSERM (U964), Université de Strasbourg, 1 rue Laurent Fries, BP10142, 67400 Illkirch, France
| | - Sophie Quintin
- Development and Stem Cells Program, IGBMC, CNRS (UMR7104), INSERM (U964), Université de Strasbourg, 1 rue Laurent Fries, BP10142, 67400 Illkirch, France
| | - François Robin
- Sorbonne Université, CNRS, Institut de Biologie Paris Seine, Laboratoire de Biologie du Développement/UMR7622,7 Quai St-Bernard, 75005 Paris, France
| | - Frauke Gräter
- Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Mathematikon, INF 205, 69120 Heidelberg, Germany
- Heidelberg Institute for Theoretical Studies, Schloß-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany
| | - Michel Labouesse
- Sorbonne Université, CNRS, Institut de Biologie Paris Seine, Laboratoire de Biologie du Développement/UMR7622,7 Quai St-Bernard, 75005 Paris, France
- Development and Stem Cells Program, IGBMC, CNRS (UMR7104), INSERM (U964), Université de Strasbourg, 1 rue Laurent Fries, BP10142, 67400 Illkirch, France
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11
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Bose D, Chakrabarti A. Localizing the chaperone activity of erythroid spectrin. Cytoskeleton (Hoboken) 2019; 76:383-397. [DOI: 10.1002/cm.21556] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 07/31/2019] [Accepted: 08/06/2019] [Indexed: 02/05/2023]
Affiliation(s)
- Dipayan Bose
- Crystallography and Molecular Biology DivisionSaha Institute of Nuclear Physics Kolkata India
- Homi Bhabha National Institute Mumbai India
| | - Abhijit Chakrabarti
- Crystallography and Molecular Biology DivisionSaha Institute of Nuclear Physics Kolkata India
- Homi Bhabha National Institute Mumbai India
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12
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Distinct mechanical properties in homologous spectrin-like repeats of utrophin. Sci Rep 2019; 9:5210. [PMID: 30914715 PMCID: PMC6435810 DOI: 10.1038/s41598-019-41569-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 03/12/2019] [Indexed: 11/09/2022] Open
Abstract
Patients with Duchenne muscular dystrophy (DMD) lack the protein dystrophin, which is a critical molecular component of the dystrophin-glycoprotein complex (DGC). Dystrophin is hypothesized to function as a molecular shock absorber that mechanically stabilizes the sarcolemma of striated muscle through interaction with the cortical actin cytoskeleton via its N-terminal half and with the transmembrane protein β-dystroglycan via its C-terminal region. Utrophin is a fetal homologue of dystrophin that can subserve many dystrophin functions and is therefore under active investigation as a dystrophin replacement therapy for DMD. Here, we report the first mechanical characterization of utrophin using atomic force microscopy (AFM). Our data indicate that the mechanical properties of spectrin-like repeats in utrophin are more in line with the PEVK and Ig-like repeats of titin rather than those reported for repeats in spectrin or dystrophin. Moreover, we measured markedly different unfolding characteristics for spectrin repeats within the N-terminal actin-binding half of utrophin compared to those in the C-terminal dystroglycan-binding half, even though they exhibit identical thermal denaturation profiles. Our results demonstrate dramatic differences in the mechanical properties of structurally homologous utrophin constructs and suggest that utrophin may function as a stiff elastic element in series with titin at the myotendinous junction.
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13
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Victor dos Santos Junior C, Sader MS, Gonçalves GC, Weissmüller G, Simão RA. Effect of pH on the adsorption and interactions of Bovine Serum Albumin with functionalized silicon nitride surface. Colloids Surf B Biointerfaces 2018; 167:441-447. [DOI: 10.1016/j.colsurfb.2018.03.045] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 03/02/2018] [Accepted: 03/27/2018] [Indexed: 10/17/2022]
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14
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Takahashi H, Rico F, Chipot C, Scheuring S. α-Helix Unwinding as Force Buffer in Spectrins. ACS NANO 2018; 12:2719-2727. [PMID: 29390177 DOI: 10.1021/acsnano.7b08973] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Spectrins are cytoskeletal proteins located at the inner face of the plasma membrane, making connections between membrane anchors and the actin cortex, and between actin filaments. Spectrins share a common structure forming a bundle of 3 α-helices and play a major role during cell deformation. Here, we used high-speed force spectroscopy and steered molecular dynamics simulations to understand the mechanical stability of spectrin, revealing a molecular force buffering function. We find that spectrin acts as a soft spring at short extensions (70-100 Å). Under continuous external stretching, its α-helices unwind, leading to a viscous mechanical response over larger extensions (100-300 Å), represented by a constant-force plateau in force/extension curves. This viscous force buffering emerges from a quasi-equilibrium competition between disruption and re-formation of α-helical hydrogen bonds. Our results suggest that, in contrast to β-sheet proteins, which unfold in a catastrophic event, α-helical spectrins dominantly unwind, providing a viscous force buffer over extensions about 5 times their folded length.
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Affiliation(s)
- Hirohide Takahashi
- U1006 INSERM, Université Aix-Marseille, Parc Scientifique et Technologique de Luminy , 163 Avenue de Luminy , 13009 Marseille , France
- Department of Anesthesiology , Weill Cornell Medicine , 1300 York Avenue , New York , New York 10065 , United States
- Departments of Physiology and Biophysics , Weill Cornell Medicine , 1300 York Avenue , New York , New York 10065 , United States
| | - Felix Rico
- U1006 INSERM, Université Aix-Marseille, Parc Scientifique et Technologique de Luminy , 163 Avenue de Luminy , 13009 Marseille , France
| | - Christophe Chipot
- Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana-Champaign , UMR 7565, Université de Lorraine, B.P. 70239, 54506 Vandœuvre-lès-Nancy Cedex, France, and Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana , Illinois 61801 , United States
| | - Simon Scheuring
- U1006 INSERM, Université Aix-Marseille, Parc Scientifique et Technologique de Luminy , 163 Avenue de Luminy , 13009 Marseille , France
- Department of Anesthesiology , Weill Cornell Medicine , 1300 York Avenue , New York , New York 10065 , United States
- Departments of Physiology and Biophysics , Weill Cornell Medicine , 1300 York Avenue , New York , New York 10065 , United States
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15
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Zeng X, Li K, Yuan R, Gao H, Luo J, Liu F, Wu Y, Wu G, Yan X. Nuclear Envelope-Associated Chromosome Dynamics during Meiotic Prophase I. Front Cell Dev Biol 2018; 5:121. [PMID: 29376050 PMCID: PMC5767173 DOI: 10.3389/fcell.2017.00121] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 12/21/2017] [Indexed: 12/21/2022] Open
Abstract
Chromosome dynamics during meiotic prophase I are associated with a series of major events such as chromosomal reorganization and condensation, pairing/synapsis and recombination of the homologs, and chromosome movements at the nuclear envelope (NE). The NE is the barrier separating the nucleus from the cytoplasm and thus plays a central role in NE-associated chromosomal movements during meiosis. Previous studies have shown in various species that NE-linked chromosome dynamics are actually driven by the cytoskeleton. The linker of nucleoskeleton and cytoskeleton (LINC) complexes are important constituents of the NE that facilitate in the transfer of cytoskeletal forces across the NE to individual chromosomes. The LINCs consist of the inner and outer NE proteins Sad1/UNC-84 (SUN), and Klarsicht/Anc-1/Syne (KASH) domain proteins. Meiosis-specific adaptations of the LINC components and unique modifications of the NE are required during chromosomal movements. Nonetheless, the actual role of the NE in chromosomic dynamic movements in plants remains elusive. This review summarizes the findings of recent studies on meiosis-specific constituents and modifications of the NE and corresponding nucleoplasmic/cytoplasmic adaptors being involved in NE-associated movement of meiotic chromosomes, as well as describes the potential molecular network of transferring cytoplasm-derived forces into meiotic chromosomes in model organisms. It helps to gain a better understanding of the NE-associated meiotic chromosomal movements in plants.
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Affiliation(s)
- Xinhua Zeng
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, China
| | - Keqi Li
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, China
| | - Rong Yuan
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, China
| | - Hongfei Gao
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, China
| | - Junling Luo
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, China
| | - Fang Liu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, China
| | - Yuhua Wu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, China
| | - Gang Wu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, China
| | - Xiaohong Yan
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, China
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16
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Comparative mechanical unfolding studies of spectrin domains R15, R16 and R17. J Struct Biol 2017; 201:162-170. [PMID: 29221897 DOI: 10.1016/j.jsb.2017.12.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 11/08/2017] [Accepted: 12/04/2017] [Indexed: 11/20/2022]
Abstract
Spectrins belong to repetitive three-helix bundle proteins that have vital functions in multicellular organisms and are of potential value in nanotechnology. To reveal the unique physical features of repeat proteins we have studied the structural and mechanical properties of three repeats of chicken brain α-spectrin (R15, R16 and R17) at the atomic level under stretching at constant velocities (0.01, 0.05 and 0.1 Å·ps-1) and constant forces (700 and 900 pN) using molecular dynamics (MD) simulations at T = 300 K. 114 independent MD simulations were performed and their analysis has been done. Despite structural similarity of these domains we have found that R15 is less mechanically stable than R16, which is less stable than R17. This result is in agreement with the thermal unfolding rates. Moreover, we have observed the relationship between mechanical stability, flexibility of the domains and the number of aromatic residues involved in aromatic clusters.
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17
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Abstract
In this review, I discuss the various methods researchers use to unfold proteins in the lab in order to understand protein folding both
in vitro and
in vivo. The four main techniques, chemical-, heat-, pressure- and force-denaturation, produce distinctly different unfolded conformational ensembles. Recent measurements have revealed different folding kinetics from different unfolding mechanisms. Thus, comparing these distinct unfolded ensembles sheds light on the underlying free energy landscape of folding.
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Affiliation(s)
- Lisa J Lapidus
- Department of Physics and Astronomy, Michigan State University, East Lansing, USA
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18
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Balikov DA, Brady SK, Ko UH, Shin JH, de Pereda JM, Sonnenberg A, Sung HJ, Lang MJ. The nesprin-cytoskeleton interface probed directly on single nuclei is a mechanically rich system. Nucleus 2017. [PMID: 28640691 DOI: 10.1080/19491034.2017.1322237] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
The cytoskeleton provides structure and plays an important role in cellular function such as migration, resisting compression forces, and transport. The cytoskeleton also reacts to physical cues such as fluid shear stress or extracellular matrix remodeling by reorganizing filament associations, most commonly focal adhesions and cell-cell cadherin junctions. These mechanical stimuli can result in genome-level changes, and the physical connection of the cytoskeleton to the nucleus provides an optimal conduit for signal transduction by interfacing with nuclear envelope proteins, called nesprins, within the LINC (linker of the nucleus to the cytoskeleton) complex. Using single-molecule on single nuclei assays, we report that the interactions between the nucleus and the cytoskeleton, thought to be nesprin-cytoskeleton interactions, are highly sensitive to force magnitude and direction depending on whether cells are historically interfaced with the matrix or with cell aggregates. Application of ∼10-30 pN forces to these nesprin linkages yielded structural transitions, with a base transition size of 5-6 nm, which are speculated to be associated with partial unfoldings of the spectrin domains of the nesprins and/or structural changes of histones within the nucleus.
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Affiliation(s)
- Daniel A Balikov
- a Department of Biomedical Engineering , Vanderbilt University , Nashville , TN , USA
| | - Sonia K Brady
- b Department of Chemical and Biomolecular Engineering , Vanderbilt University , Nashville , TN , USA
| | - Ung Hyun Ko
- c Department of Mechanical Engineering , Korea Advanced Institute of Science and Technology , Daejeon , Korea
| | - Jennifer H Shin
- c Department of Mechanical Engineering , Korea Advanced Institute of Science and Technology , Daejeon , Korea
| | - Jose M de Pereda
- d Instituto de Biologia Molecular y Celular del Cancer, Consejo Superior de Investigaciones Cientificas , University of Salamanca , Salamanca , Spain
| | | | - Hak-Joon Sung
- a Department of Biomedical Engineering , Vanderbilt University , Nashville , TN , USA.,f Division of Cardiovascular Medicine, Department of Medicine , Vanderbilt University Medical Center , Nashville , TN , USA.,g Severance Biomedical Science Institute, College of Medicine , Yonsei University , Seoul , Republic of Korea
| | - Matthew J Lang
- b Department of Chemical and Biomolecular Engineering , Vanderbilt University , Nashville , TN , USA.,h Department of Molecular Physiology and Biophysics , Vanderbilt University Medical Center , Nashville , TN , USA.,i SMART-BioSystems and Micromechanics , National University of Singapore , Singapore
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19
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Wołek K, Gómez-Sicilia À, Cieplak M. Determination of contact maps in proteins: A combination of structural and chemical approaches. J Chem Phys 2016; 143:243105. [PMID: 26723590 DOI: 10.1063/1.4929599] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Contact map selection is a crucial step in structure-based molecular dynamics modelling of proteins. The map can be determined in many different ways. We focus on the methods in which residues are represented as clusters of effective spheres. One contact map, denoted as overlap (OV), is based on the overlap of such spheres. Another contact map, named Contacts of Structural Units (CSU), involves the geometry in a different way and, in addition, brings chemical considerations into account. We develop a variant of the CSU approach in which we also incorporate Coulombic effects such as formation of the ionic bridges and destabilization of possible links through repulsion. In this way, the most essential and well defined contacts are identified. The resulting residue-residue contact map, dubbed repulsive CSU (rCSU), is more sound in its physico-chemical justification than CSU. It also provides a clear prescription for validity of an inter-residual contact: the number of attractive atomic contacts should be larger than the number of repulsive ones - a feature that is not present in CSU. However, both of these maps do not correlate well with the experimental data on protein stretching. Thus, we propose to use rCSU together with the OV map. We find that the combined map, denoted as OV+rCSU, performs better than OV. In most situations, OV and OV+rCSU yield comparable folding properties but for some proteins rCSU provides contacts which improve folding in a substantial way. We discuss the likely residue-specificity of the rCSU contacts. Finally, we make comparisons to the recently proposed shadow contact map, which is derived from different principles.
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Affiliation(s)
- Karol Wołek
- Institute of Physics, Polish Academy of Science, Al. Lotników 32/46, 02-668 Warsaw, Poland
| | - Àngel Gómez-Sicilia
- Instituto Cajal, Consejo Superior de Investigaciones Cientificas (CSIC), Av. Doctor Arce, 37, 28002 Madrid, Spain
| | - Marek Cieplak
- Institute of Physics, Polish Academy of Science, Al. Lotników 32/46, 02-668 Warsaw, Poland
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20
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Stauch T, Hoffmann MT, Dreuw A. Spectroscopic Monitoring of Mechanical Forces during Protein Folding by using Molecular Force Probes. Chemphyschem 2016; 17:1486-92. [PMID: 26928925 DOI: 10.1002/cphc.201600016] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Indexed: 11/08/2022]
Abstract
Detailed folding pathways of proteins are still largely unknown. Real-time monitoring of mechanical forces acting in proteins during structural transitions would provide deep insights into these highly complex processes. Here, we propose two molecular force probes that can be incorporated into the protein backbone to gain insight into the magnitude and direction of mechanical forces acting in proteins during natural folding and unfolding through their optical spectroscopic response. In fact, changes in the infrared and Raman spectra are proportional to the mechanical force deforming the force probes, and the relevant bands can be intensified and shifted to a transparent window in the protein spectrum by isotopic substitution. As a result, the proposed molecular force probes can act as "force rulers", allowing the spectroscopic observation and measurement of mechanical forces acting within the proteins under natural conditions without external perturbation.
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Affiliation(s)
- Tim Stauch
- Interdisciplinary Center for Scientific Computing, University of Heidelberg, Im Neuenheimer Feld 368, 69120, Heidelberg, Germany.
| | - Marvin T Hoffmann
- Interdisciplinary Center for Scientific Computing, University of Heidelberg, Im Neuenheimer Feld 368, 69120, Heidelberg, Germany
| | - Andreas Dreuw
- Interdisciplinary Center for Scientific Computing, University of Heidelberg, Im Neuenheimer Feld 368, 69120, Heidelberg, Germany
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21
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Kannan N, Tang VW. Synaptopodin couples epithelial contractility to α-actinin-4-dependent junction maturation. J Cell Biol 2016; 211:407-34. [PMID: 26504173 PMCID: PMC4621826 DOI: 10.1083/jcb.201412003] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
A novel tension-sensitive junctional protein, synaptopodin, can relay biophysical input from cellular actomyosin contractility to induce biochemical changes at cell–cell contacts, resulting in structural reorganization of the junctional complex and epithelial barrier maturation. The epithelial junction experiences mechanical force exerted by endogenous actomyosin activities and from interactions with neighboring cells. We hypothesize that tension generated at cell–cell adhesive contacts contributes to the maturation and assembly of the junctional complex. To test our hypothesis, we used a hydraulic apparatus that can apply mechanical force to intercellular junction in a confluent monolayer of cells. We found that mechanical force induces α-actinin-4 and actin accumulation at the cell junction in a time- and tension-dependent manner during junction development. Intercellular tension also induces α-actinin-4–dependent recruitment of vinculin to the cell junction. In addition, we have identified a tension-sensitive upstream regulator of α-actinin-4 as synaptopodin. Synaptopodin forms a complex containing α-actinin-4 and β-catenin and interacts with myosin II, indicating that it can physically link adhesion molecules to the cellular contractile apparatus. Synaptopodin depletion prevents junctional accumulation of α-actinin-4, vinculin, and actin. Knockdown of synaptopodin and α-actinin-4 decreases the strength of cell–cell adhesion, reduces the monolayer permeability barrier, and compromises cellular contractility. Our findings underscore the complexity of junction development and implicate a control process via tension-induced sequential incorporation of junctional components.
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Affiliation(s)
- Nivetha Kannan
- Program in Global Public Health, University of Illinois, Urbana-Champaign, Champaign, IL 61801
| | - Vivian W Tang
- Department of Cell and Developmental Biology, University of Illinois, Urbana-Champaign, Champaign, IL 61801
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22
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Myklebust LM, Horvli O, Raae AJ. RACK1 (receptor for activated C-kinase 1) interactions with spectrin repeat elements. J Mol Recognit 2014; 28:49-58. [PMID: 26268370 DOI: 10.1002/jmr.2411] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2014] [Revised: 06/25/2014] [Accepted: 06/28/2014] [Indexed: 12/12/2022]
Affiliation(s)
- Line M. Myklebust
- Department of Molecular Biology; University of Bergen; HIB, Thormoehlens gt. 55 N-5020 Bergen Norway
| | - Ole Horvli
- Department of Molecular Biology; University of Bergen; HIB, Thormoehlens gt. 55 N-5020 Bergen Norway
| | - Arnt J. Raae
- Department of Molecular Biology; University of Bergen; HIB, Thormoehlens gt. 55 N-5020 Bergen Norway
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23
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Glyakina AV, Likhachev IV, Balabaev NK, Galzitskaya OV. Mechanical stability analysis of the protein L immunoglobulin-binding domain by full alanine screening using molecular dynamics simulations. Biotechnol J 2014; 10:386-94. [PMID: 25425165 DOI: 10.1002/biot.201400231] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 11/07/2014] [Accepted: 11/24/2014] [Indexed: 11/10/2022]
Abstract
This article is the first to study the mechanical properties of the immunoglobulin-binding domain of protein L (referred to as protein L) and its mutants at the atomic level. In the structure of protein L, each amino acid residue (except for alanines and glycines) was replaced sequentially by alanine. Thus, 49 mutants of protein L were obtained. The proteins were stretched at their termini at constant velocity using molecular dynamics simulations in water, i.e. by forced unfolding. 19 out of 49 mutations resulted in a large decrease of mechanical protein stability. These amino acids were affecting either the secondary structure (11 mutations) or loop structures (8 mutations) of protein L. Analysis of mechanical unfolding of the generated protein that has the same topology as protein L but consists of only alanines and glycines allows us to suggest that the mechanical stability of proteins, and specifically protein L, is determined by interactions between certain amino acid residues, although the unfolding pathway depends on the protein topology. This insight can now be used to modulate the mechanical properties of proteins and their unfolding pathways in the desired direction for using them in various biochips, biosensors and biomaterials for medicine, industry, and household purposes.
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Affiliation(s)
- Anna V Glyakina
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia; Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
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24
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Glyakina AV, Balabaev NK, Galzitskaya OV. Experimental and theoretical studies of mechanical unfolding of different proteins. BIOCHEMISTRY (MOSCOW) 2014; 78:1216-27. [PMID: 24460936 DOI: 10.1134/s0006297913110023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Mechanical properties of proteins are important for a wide range of biological processes including cell adhesion, muscle contraction, and protein translocation across biological membranes. It is necessary to reveal how proteins achieve their required mechanical stability under natural conditions in order to understand the biological processes and also to use the knowledge for constructing new biomaterials for medical and industrial purposes. In this connection, it is important to know how a protein will behave in response to various impacts. Theoretical and experimental works on mechanical unfolding of globular proteins will be considered in detail in this review.
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Affiliation(s)
- A V Glyakina
- Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
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25
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Evans DE, Pawar V, Smith SJ, Graumann K. Protein interactions at the higher plant nuclear envelope: evidence for a linker of nucleoskeleton and cytoskeleton complex. FRONTIERS IN PLANT SCIENCE 2014; 5:183. [PMID: 24847341 PMCID: PMC4019843 DOI: 10.3389/fpls.2014.00183] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 04/17/2014] [Indexed: 05/20/2023]
Abstract
Following the description of SAD1/UNC84 (SUN) domain proteins in higher plants, evidence has rapidly increased that plants contain a functional linker of nucleoskeleton and cytoskeleton (LINC) complex bridging the nuclear envelope (NE). While the SUN domain proteins appear to be highly conserved across kingdoms, other elements of the complex are not and some key components and interactions remain to be identified. This mini review examines components of the LINC complex, including proteins of the SUN domain family and recently identified plant Klarsicht/Anc/Syne-1 homology (KASH) domain proteins. First of these to be described were WIPs (WPP domain interacting proteins), which act as protein anchors in the outer NE. The plant KASH homologs are C-terminally anchored membrane proteins with the extreme C-terminus located in the nuclear periplasm; AtWIPs contain a highly conserved X-VPT motif at the C-terminus in contrast to PPPX in opisthokonts. The role of the LINC complex in organisms with a cell wall, and description of further LINC complex components will be considered, together with other potential plant-specific functions.
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Affiliation(s)
- David E. Evans
- *Correspondence: David E. Evans, Department of Biological and Medical Sciences, Oxford Brookes University, Headington Campus, Oxford, OX3 0BP, UK e-mail:
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26
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Valle-Delgado JJ, Urbán P, Fernàndez-Busquets X. Demonstration of specific binding of heparin to Plasmodium falciparum-infected vs. non-infected red blood cells by single-molecule force spectroscopy. NANOSCALE 2013; 5:3673-3680. [PMID: 23306548 DOI: 10.1039/c2nr32821f] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Glycosaminoglycans (GAGs) play an important role in the sequestration of Plasmodium falciparum-infected red blood cells (pRBCs) in the microvascular endothelium of different tissues, as well as in the formation of small clusters (rosettes) between infected and non-infected red blood cells (RBCs). Both sequestration and rosetting have been recognized as characteristic events in severe malaria. Here we have used heparin and pRBCs infected by the 3D7 strain of P. falciparum as a model to study GAG-pRBC interactions. Fluorescence microscopy and fluorescence-assisted cell sorting assays have shown that exogenously added heparin has binding specificity for pRBCs (preferentially for those infected with late forms of the parasite) vs. RBCs. Heparin-pRBC adhesion has been probed by single-molecule force spectroscopy, obtaining an average binding force ranging between 28 and 46 pN depending on the loading rate. No significant binding of heparin to non-infected RBCs has been observed in control experiments. This work represents the first approach to quantitatively evaluate GAG-pRBC molecular interactions at the individual molecule level.
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Affiliation(s)
- Juan José Valle-Delgado
- Nanobioengineering Group, Institute for Bioengineering of Catalonia (IBEC), Baldiri Reixac 10-12, Barcelona E08028, Spain
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27
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Hoffmann T, Dougan L. Single molecule force spectroscopy using polyproteins. Chem Soc Rev 2012; 41:4781-96. [DOI: 10.1039/c2cs35033e] [Citation(s) in RCA: 139] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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28
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The Nonlinear Structure of the Desmoplakin Plakin Domain and the Effects of Cardiomyopathy-Linked Mutations. J Mol Biol 2011; 411:1049-61. [DOI: 10.1016/j.jmb.2011.06.047] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2011] [Revised: 06/21/2011] [Accepted: 06/28/2011] [Indexed: 11/15/2022]
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29
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Sikora M, Sułkowska JI, Cieplak M. Mechanical strength of 17,134 model proteins and cysteine slipknots. PLoS Comput Biol 2009; 5:e1000547. [PMID: 19876372 PMCID: PMC2759523 DOI: 10.1371/journal.pcbi.1000547] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2009] [Accepted: 09/28/2009] [Indexed: 11/29/2022] Open
Abstract
A new theoretical survey of proteins' resistance to constant speed stretching is performed for a set of 17 134 proteins as described by a structure-based model. The proteins selected have no gaps in their structure determination and consist of no more than 250 amino acids. Our previous studies have dealt with 7510 proteins of no more than 150 amino acids. The proteins are ranked according to the strength of the resistance. Most of the predicted top-strength proteins have not yet been studied experimentally. Architectures and folds which are likely to yield large forces are identified. New types of potent force clamps are discovered. They involve disulphide bridges and, in particular, cysteine slipknots. An effective energy parameter of the model is estimated by comparing the theoretical data on characteristic forces to the corresponding experimental values combined with an extrapolation of the theoretical data to the experimental pulling speeds. These studies provide guidance for future experiments on single molecule manipulation and should lead to selection of proteins for applications. A new class of proteins, involving cystein slipknots, is identified as one that is expected to lead to the strongest force clamps known. This class is characterized through molecular dynamics simulations. The advances in nanotechnology have allowed for manipulation of single biomolecules and determination of their elastic properties. Titin was among the first proteins studied in this way. Its unravelling by stretching requires a 204 pN force. The resistance to stretching comes mostly from a localized region known as a force clamp. In titin, the force clamp is simple as it is formed by two parallel β-strands that are sheared on pulling. Studies of a set of under a hundred proteins accomplished in the last decade have revealed a variety of the force clamps that lead to forces ranging from under 20 pN to about 500 pN. This set comprises only a tiny fraction of proteins known. Thus one needs guidance as to what proteins should be considered for specific mechanical properties. Such a guidance is provided here through simulations within simplified coarse-grained models on 17 134 proteins that are stretched at constant speed. We correlate their unravelling forces with two structure classification schemes. We identify proteins with large resistance to unravelling and characterize their force clamps. Quite a few top strength proteins owe their sturdiness to a new type of the force clamp: the cystein slipknot in which the force peak is due to dragging of a piece of the backbone through a closed ring formed by two other pieces of the backbone and two connecting disulphide bonds.
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Affiliation(s)
- Mateusz Sikora
- Institute of Physics, Polish Academy of Sciences, Warsaw, Poland
| | - Joanna I. Sułkowska
- Institute of Physics, Polish Academy of Sciences, Warsaw, Poland
- Center for Theoretical Biological Physics, University of California, San Diego, California, USA
| | - Marek Cieplak
- Institute of Physics, Polish Academy of Sciences, Warsaw, Poland
- * E-mail:
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30
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Razafsky D, Hodzic D. Bringing KASH under the SUN: the many faces of nucleo-cytoskeletal connections. ACTA ACUST UNITED AC 2009; 186:461-72. [PMID: 19687252 PMCID: PMC2733748 DOI: 10.1083/jcb.200906068] [Citation(s) in RCA: 197] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The nucleus is the most prominent cellular organelle, and its sharp boundaries suggest the compartmentalization of the nucleoplasm from the cytoplasm. However, the recent identification of evolutionarily conserved linkers of the nucleoskeleton to the cytoskeleton (LINC) complexes, a family of macromolecular assemblies that span the double membrane of the nuclear envelope, reveals tight physical connections between the two compartments. Here, we review the structure and evolutionary conservation of SUN and KASH domain–containing proteins, whose interaction within the perinuclear space forms the “nuts and bolts” of LINC complexes. Moreover, we discuss the function of these complexes in nuclear, centrosomal, and chromosome dynamics, and their connection to human disease.
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Affiliation(s)
- David Razafsky
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, MO 63110, USA
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31
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Genchev GZ, Källberg M, Gürsoy G, Mittal A, Dubey L, Perisic O, Feng G, Langlois R, Lu H. Mechanical signaling on the single protein level studied using steered molecular dynamics. Cell Biochem Biophys 2009; 55:141-52. [PMID: 19669741 DOI: 10.1007/s12013-009-9064-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2009] [Accepted: 07/22/2009] [Indexed: 01/16/2023]
Abstract
Efficient communication between the cell and its external environment is of the utmost importance to the function of multicellular organisms. While signaling events can be generally characterized as information exchange by means of controlled energy conversion, research efforts have hitherto mainly been concerned with mechanisms involving chemical and electrical energy transfer. Here, we review recent computational efforts addressing the function of mechanical force in signal transduction. Specifically, we focus on the role of steered molecular dynamics (SMD) simulations in providing details at the atomic level on a group of protein domains, which play a fundamental role in signal exchange by responding properly to mechanical strain. We start by giving a brief introduction to the SMD technique and general properties of mechanically stable protein folds, followed by specific examples illustrating three general regimes of signal transfer utilizing mechanical energy: purely mechanical, mechanical to chemical, and chemical to mechanical. Whenever possible the physiological importance of the example at hand is stressed to highlight the diversity of the processes in which mechanical signaling plays a key role. We also provide an overview of future challenges and perspectives for this rapidly developing field.
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Affiliation(s)
- Georgi Z Genchev
- Bioinformatics Program, Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, 60607, USA
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32
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Ackbarow T, Keten S, Buehler MJ. A multi-timescale strength model of alpha-helical protein domains. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2009; 21:035111. [PMID: 21817269 DOI: 10.1088/0953-8984/21/3/035111] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Here we report a constitutive model that characterizes the strength of an alpha-helical protein domain subjected to tensile deformation, covering more than ten orders of magnitude in timescales. The model elucidates multiple physical mechanisms of failure in dependence on the deformation rate, quantitatively linking atomistic simulation results with experimental strength measurements of alpha-helical protein domains. The model provides a description of the strength of alpha-helices based on fundamental physical parameters such as the H-bond energy and the polypeptide's persistence length, showing that strength is controlled by energetic, nonequilibrium processes at high rates and by thermodynamical, equilibrium processes at low rates. Our model provides a novel perspective on the strength of protein domains at ultra-slow pulling speeds relevant under physiologic and experimental conditions.
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Affiliation(s)
- Theodor Ackbarow
- Laboratory for Atomistic and Molecular Mechanics, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue Room 1-235A&B, Cambridge, MA, USA. Max-Planck Institute of Colloids and Interfaces, Science Park Golm, 14424 Potsdam, Germany
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33
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Actomyosin interaction: mechanical and energetic properties in different nucleotide binding states. Int J Mol Sci 2008; 9:1927-1943. [PMID: 19325727 PMCID: PMC2635604 DOI: 10.3390/ijms9101927] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2008] [Revised: 10/08/2008] [Accepted: 10/10/2008] [Indexed: 11/17/2022] Open
Abstract
The mechanics of the actomyosin interaction is central in muscle contraction and intracellular trafficking. A better understanding of the events occurring in the actomyosin complex requires the examination of all nucleotide-dependent states and of the energetic features associated with the dynamics of the cross-bridge cycle. The aim of the present study is to estimate the interaction strength between myosin in nucleotide-free, ATP, ADP·Pi and ADP states and actin monomer. The molecular models of the complexes were constructed based on cryo-electron microscopy maps and the interaction properties were estimated by means of a molecular dynamics approach, which simulate the unbinding of the complex applying a virtual spring to the core of myosin protein. Our results suggest that during an ATP hydrolysis cycle the affinity of myosin for actin is modulated by the presence and nature of the nucleotide in the active site of the myosin motor domain. When performing unbinding simulations with a pulling rate of 0.001 nm/ps, the maximum pulling force applied to the myosin during the experiment is about 1nN. Under these conditions the interaction force between myosin and actin monomer decreases from 0.83 nN in the nucleotide-free state to 0.27 nN in the ATP state, and increases to 0.60 nN after ATP hydrolysis and Pi release from the complex (ADP state).
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Aprodu I, Soncini M, Redaelli A. Interaction forces and interface properties of KIF1A kinesin-alphabeta tubulin complex assessed by molecular dynamics. J Biomech 2008; 41:3196-201. [PMID: 18829030 DOI: 10.1016/j.jbiomech.2008.08.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2008] [Revised: 08/14/2008] [Accepted: 08/15/2008] [Indexed: 11/27/2022]
Abstract
Kinesin is a microtubule-based motor protein that generates motion involved in intracellular trafficking and cell division. Even if the force-generating and enzymatic properties of kinesin were extensively studied, the molecular basis of its interaction with the microtubule is still not well understood. The aim of the present study is to provide a detailed description, in terms of conformational changes and interaction properties, of the kinesin-alphabeta tubulin complex during a cycle of ATP hydrolysis. Four different nucleotide-dependent conformations (nucleotide-free, ATP, ADP.Pi and ADP) of the kinesin-alphabeta tubulin were constructed and investigated by performing molecular dynamics simulations. Computational results show that small conformational changes, in the order of few Angstrom, occurring in the kinesin structure reflect on its affinity for the filament substrate. Indeed the rotation of the alpha4 helix due to the transition from the bound (ADP.Pi) to the unbound (ADP) state, when the Pi is released from the complex, coupled with the modification occurred in the loop L9 of switch I domain are associated to a marked decrease (approximately 45%) of the maximum interaction force between the kinesin motor and the tubulin dimer.
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Affiliation(s)
- Iuliana Aprodu
- Department of Bioengineering, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano, Italy.
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35
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Aprodu I, Soncini M, Redaelli A. Mechanical Characterization of Motor Proteins: A Molecular Dynamics Approach. MACROMOL THEOR SIMUL 2008. [DOI: 10.1002/mats.200800033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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36
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Selection of optimal variants of Gō-like models of proteins through studies of stretching. Biophys J 2008; 95:3174-91. [PMID: 18567634 DOI: 10.1529/biophysj.107.127233] [Citation(s) in RCA: 112] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Gō-like models of proteins are constructed based on the knowledge of the native conformation. However, there are many possible choices of a Hamiltonian for which the ground state coincides with the native state. Here, we propose to use experimental data on protein stretching to determine what choices are most adequate physically. This criterion is motivated by the fact that stretching processes usually start with the native structure, in the vicinity of which the Gō-like models should work the best. Our selection procedure is applied to 62 different versions of the Gō model and is based on 28 proteins. We consider different potentials, contact maps, local stiffness energies, and energy scales--uniform and nonuniform. In the latter case, the strength of the nonuniformity was governed either by specificity or by properties related to positioning of the side groups. Among them is the simplest variant: uniform couplings with no i, i + 2 contacts. This choice also leads to good folding properties in most cases. We elucidate relationship between the local stiffness described by a potential which involves local chirality and the one which involves dihedral and bond angles. The latter stiffness improves folding but there is little difference between them when it comes to stretching.
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37
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Sandal M, Valle F, Tessari I, Mammi S, Bergantino E, Musiani F, Brucale M, Bubacco L, Samorì B. Conformational equilibria in monomeric alpha-synuclein at the single-molecule level. PLoS Biol 2008; 6:e6. [PMID: 18198943 PMCID: PMC2174973 DOI: 10.1371/journal.pbio.0060006] [Citation(s) in RCA: 155] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2007] [Accepted: 11/26/2007] [Indexed: 01/24/2023] Open
Abstract
Human α-Synuclein (αSyn) is a natively unfolded protein whose aggregation into amyloid fibrils is involved in the pathology of Parkinson disease. A full comprehension of the structure and dynamics of early intermediates leading to the aggregated states is an unsolved problem of essential importance to researchers attempting to decipher the molecular mechanisms of αSyn aggregation and formation of fibrils. Traditional bulk techniques used so far to solve this problem point to a direct correlation between αSyn's unique conformational properties and its propensity to aggregate, but these techniques can only provide ensemble-averaged information for monomers and oligomers alike. They therefore cannot characterize the full complexity of the conformational equilibria that trigger the aggregation process. We applied atomic force microscopy–based single-molecule mechanical unfolding methodology to study the conformational equilibrium of human wild-type and mutant αSyn. The conformational heterogeneity of monomeric αSyn was characterized at the single-molecule level. Three main classes of conformations, including disordered and “β-like” structures, were directly observed and quantified without any interference from oligomeric soluble forms. The relative abundance of the “β-like” structures significantly increased in different conditions promoting the aggregation of αSyn: the presence of Cu2+, the pathogenic A30P mutation, and high ionic strength. This methodology can explore the full conformational space of a protein at the single-molecule level, detecting even poorly populated conformers and measuring their distribution in a variety of biologically important conditions. To the best of our knowledge, we present for the first time evidence of a conformational equilibrium that controls the population of a specific class of monomeric αSyn conformers, positively correlated with conditions known to promote the formation of aggregates. A new tool is thus made available to test directly the influence of mutations and pharmacological strategies on the conformational equilibrium of monomeric αSyn. Natively unstructured proteins defy the classical “one sequence–one structure” paradigm of protein science. In pathological conditions, monomers of these proteins can aggregate in the cell, a process that underlies neurodegenerative diseases such as Alzheimer and Parkinson. A key step in the aggregation process—the formation of misfolded intermediates—remains obscure. To shed light on this process, we characterized the folding and conformational diversity of αSyn, a natively unstructured protein involved in Parkinson disease, by mechanically stretching single molecules of this protein and recording their mechanical properties. These experiments permitted us to observe directly and quantify three main classes of conformations that, under in vitro physiological conditions, exist simultaneously in the αSyn sample. We found that one class of conformations, “β-like” structures, is directly related to αSyn aggregation. In fact, their relative abundance increases drastically in three different conditions known to promote the formation of αSyn fibrils. We expect that a critical concentration of αSyn with a “β-like” structure must be reached to trigger fibril formation. This critical concentration is therefore controlled by a chemical equilibrium. Novel pharmacological strategies can now be tailored to act upstream, before the aggregation process ensues, by targeting this equilibrium. To this end, single-molecule force spectroscopy can be an effective tool to tailor and test new pharmacological agents. A single-molecule study detects structured and unstructured conformers in equilibrium in monomeric α-synuclein. The β-like conformers increase with pathological mutations and under other conditions known to promote aggregation.
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Affiliation(s)
- Massimo Sandal
- Department of Biochemistry “G. Moruzzi”, University of Bologna, Bologna, Italy
| | - Francesco Valle
- Department of Biochemistry “G. Moruzzi”, University of Bologna, Bologna, Italy
- National Center on Nanostructures and BioSystems at Surfaces (S3) INFM-CNR, Modena, Italy
- * To whom correspondence should be addressed. E-mail: (FV); (BS)
| | | | - Stefano Mammi
- Department of Chemical Sciences, University of Padova, Padova, Italy
| | | | - Francesco Musiani
- Department of Biochemistry “G. Moruzzi”, University of Bologna, Bologna, Italy
| | - Marco Brucale
- Department of Biochemistry “G. Moruzzi”, University of Bologna, Bologna, Italy
| | - Luigi Bubacco
- Department of Biology, University of Padova, Padova, Italy
| | - Bruno Samorì
- Department of Biochemistry “G. Moruzzi”, University of Bologna, Bologna, Italy
- National Center on Nanostructures and BioSystems at Surfaces (S3) INFM-CNR, Modena, Italy
- * To whom correspondence should be addressed. E-mail: (FV); (BS)
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38
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Paramore S, Ayton GS, Voth GA. Transient violations of the second law of thermodynamics in protein unfolding examined using synthetic atomic force microscopy and the fluctuation theorem. J Chem Phys 2007; 127:105105. [PMID: 17867784 DOI: 10.1063/1.2764487] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The synthetic atomic force microscopy (AFM) method is developed to simulate a periodically replicated atomistic system subject to force and length fluctuations characteristic of an AFM experiment. This new method is used to examine the forced-extension and subsequent rupture of the alpha-helical linker connecting periodic images of a spectrin protein repeat unit. A two-dimensional potential of mean force (PMF) along the length and a reaction coordinate describing the state of the linker was calculated. This PMF reveals that the basic material properties of the spectrin repeat unit are sensitive to the state of linker, an important feature that cannot be accounted for in a one-dimensional PMF. Furthermore, nonequilibrium simulations were generated to examine the rupture event in the context of the fluctuation theorem. These atomistic simulations demonstrate that trajectories which are in apparent violation of the second law can overcome unfolding barriers at significantly reduced rupture forces.
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Affiliation(s)
- Sterling Paramore
- Center for Biophysical Modeling and Simulation and Department of Chemistry, University of Utah, Salt Lake City, Utah 84112-0850, USA
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39
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Valle F, Sandal M, Samorì B. The interplay between chemistry and mechanics in the transduction of a mechanical signal into a biochemical function. Phys Life Rev 2007. [DOI: 10.1016/j.plrev.2007.06.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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40
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Abstract
We make a survey of resistance of 7510 proteins to mechanical stretching at constant speed as studied within a coarse-grained molecular dynamics model. We correlate the maximum force of resistance with the native structure, predict proteins which should be especially strong, and identify the nature of their force clamps.
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41
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Hann E, Kirkpatrick N, Kleanthous C, Smith DA, Radford SE, Brockwell DJ. The effect of protein complexation on the mechanical stability of Im9. Biophys J 2007; 92:L79-81. [PMID: 17351013 PMCID: PMC1852351 DOI: 10.1529/biophysj.106.102475] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Force mode microscopy can be used to examine the effect of mechanical manipulation on the noncovalent interactions that stabilize proteins and their complexes. Here we describe the effect of complexation by the high affinity protein ligand E9 on the mechanical resistance of the simple four-helical protein, Im9. When concatenated into a construct of alternating I27 domains, Im9 unfolded below the thermal noise limit of the instrument ( approximately 20 pN). Complexation of E9 had little effect on the mechanical resistance of Im9 (unfolding force approximately 30 pN) despite the high avidity of this complex (K(d) approximately 10 fM).
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Affiliation(s)
- Eleanore Hann
- Institute of Molecular and Cellular Biology, University of Leeds, United Kingdom
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42
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Forman JR, Clarke J. Mechanical unfolding of proteins: insights into biology, structure and folding. Curr Opin Struct Biol 2007; 17:58-66. [PMID: 17251000 DOI: 10.1016/j.sbi.2007.01.006] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2006] [Revised: 12/13/2006] [Accepted: 01/12/2007] [Indexed: 10/23/2022]
Abstract
Since user-friendly atomic force microscopes came onto the market a few years ago, scientists have explored the response of many proteins to applied force. This field has now matured beyond the phenomenological with exciting recent developments, particularly with regards to research into biological questions. For example, detailed mechanistic studies have suggested how mechanically active proteins perform their functions. Also, in vitro forced unfolding has been compared with in vivo protein import and degradation. Additionally, investigations have been carried out that probe the relationship between protein structure and response to applied force, an area that has benefited significantly from synergy between experiments and simulations. Finally, recent technological developments offer exciting new avenues for experimental studies.
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Affiliation(s)
- Julia R Forman
- Cambridge University Department of Chemistry, MRC Centre for Protein Engineering, Lensfield Road, Cambridge CB2 1EW, UK
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43
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Randles LG, Rounsevell RWS, Clarke J. Spectrin domains lose cooperativity in forced unfolding. Biophys J 2007; 92:571-7. [PMID: 17085494 PMCID: PMC1751415 DOI: 10.1529/biophysj.106.093690] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2006] [Accepted: 10/10/2006] [Indexed: 11/18/2022] Open
Abstract
Spectrin is a multidomain cytoskeletal protein, the component three-helix bundle domains are expected to experience mechanical force in vivo. In thermodynamic and kinetic studies, neighboring domains of chicken brain alpha-spectrin R16 and R17 have been shown to behave cooperatively. Is this cooperativity maintained under force? The effect of force on these spectrin domains was investigated using atomic force microscopy. The response of the individual domains to force was compared to that of the tandem repeat R1617. Importantly, nonhelical linkers (all-beta immunoglobulin domains) were used to avoid formation of nonnative helical linkers. We show that, in contrast to previous studies on spectrin repeats, only 3% of R1617 unfolding events gave an increase in contour length consistent with cooperative two-domain unfolding events. Furthermore, the unfolding forces for R1617 were the same as those for the unfolding of R16 or R17 alone. This is a strong indication that the cooperative unfolding behavior observed in the stopped-flow studies is absent between these spectrin domains when force is acting as a denaturant. Our evidence suggests that the rare double unfolding events result from misfolding between adjacent repeats. We suggest that this switch from cooperative to independent behavior allows multidomain proteins to maintain integrity under applied force.
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Affiliation(s)
- Lucy G Randles
- Department of Chemistry, University of Cambridge, MRC Centre for Protein Engineering, Cambridge, United Kingdom
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44
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Soncini M, Vesentini S, Ruffoni D, Orsi M, Deriu MA, Redaelli A. Mechanical response and conformational changes of alpha-actinin domains during unfolding: a molecular dynamics study. Biomech Model Mechanobiol 2006; 6:399-407. [PMID: 17115122 DOI: 10.1007/s10237-006-0060-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2006] [Accepted: 10/13/2006] [Indexed: 10/23/2022]
Abstract
Alpha-actinin is a cytoskeleton-binding protein involved in the assembly and regulation of the actin filaments. In this work molecular dynamics method was applied to investigate the mechanical behaviour of the human skeletal muscle alpha-actinin. Five configurations were unfolded at an elongation speed of 0.1 nm/ps in order to investigate the conformational changes occurring during the extension process. Moreover, a sensitivity analysis at different velocities was performed for one of the R2-R3 spectrin-like repeat configuration extracted in order to evaluate the effect of the pulling speed on the mechanical behaviour of the molecule. Two different behaviours were recognized with respect to the pulling speed. In particular, at speed higher than 0.025 nm/ps a continuous rearrangement without evident force peaks was obtained, on the contrary at lower speed evident peaks in the range 500-750 pN were detected. R3 repeat resulted more stable than R2 during mechanical unfolding, due to the lower hydrophobic surface available to the solvent. The characterization of the R2-R3 units can be useful for the development of cytoskeleton network models based on stiffness values obtained by analyses performed at the molecular level.
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Affiliation(s)
- Monica Soncini
- Department of Bioengineering, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133, Milan, Italy.
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45
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Paramore S, Voth GA. Examining the influence of linkers and tertiary structure in the forced unfolding of multiple-repeat spectrin molecules. Biophys J 2006; 91:3436-45. [PMID: 16891371 PMCID: PMC1614492 DOI: 10.1529/biophysj.106.091108] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The unfolding pathways of multiple-repeat spectrin molecules were examined using steered molecular dynamics (SMD) simulations to forcibly unfold double- and triple-repeat spectrin molecules. Although SMD has previously been used to study other repeating-domain proteins, spectrin offers a unique challenge in that the linker connecting repeat units has a definite secondary structure, that of an alpha-helix. Therefore, the boundary conditions imposed on a double- or triple-repeat spectrin must be carefully considered if any relationship to the real system is to be deduced. This was accomplished by imposing additional forces on the system which ensure that the terminal alpha-helices behave as if there were no free noncontiguous helical ends. The results of the SMD simulations highlight the importance of the rupture of the alpha-helical linker on the subsequent unfolding events. Rupture of the linker propagates unfolding in the adjacent repeat units by destabilizing the tertiary structure, ultimately resulting in complete unfolding of the affected repeat unit. Two dominant classes of unfolding pathways are observed after the initial rupture of a linker which involve either rupture of another linker (possibly adjacent) or rupture of the basic tertiary structure of a repeat unit. The relationship between the force response observed on simulation timescales and those of experiment or physiological conditions is also discussed.
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Affiliation(s)
- Sterling Paramore
- Department of Chemistry, Center for Biophysical Modeling and Simulation, University of Utah, Salt Lake City, 84112-0850, USA
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46
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Paramore S, Ayton GS, Mirijanian DT, Voth GA. Extending a spectrin repeat unit. I: linear force-extension response. Biophys J 2005; 90:92-100. [PMID: 16227506 PMCID: PMC1367040 DOI: 10.1529/biophysj.105.066969] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Nonequilibrium molecular dynamics simulations were used to calculate the elastic properties of a spectrin repeat unit. A contiguous alpha-helical linker was constructed by employing periodic boundary conditions, allowing a novel scheme for evaluating the thermodynamic force as a function of extension. By measuring the force-extension response under small extensions, spectrin was observed to behave primarily as an elastic material with a spring constant of 1700 +/- 100 pN/nm. The implications of this spring constant, in terms of the properties of the spectrin tetramer, are also discussed.
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Affiliation(s)
- Sterling Paramore
- Center for Biophysical Modeling and Simulation and Department of Chemistry, University of Utah, Salt Lake City, Utah, USA
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47
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Abstract
A spectrin repeat unit was subject to extension using cyclic expansion nonequilibrium molecular dynamics. Periodic boundary conditions were used to examine the effects of the contiguous alpha-helical linker on the force response. The measured force-extension curve shows a linear increase in the force response when the spectrin repeat unit is extended by approximately 0.4 nm. After that point, the force response peaks and subsequently declines. The peak in the force response marks the point where the spectrin repeat unit undergoes a change in its material properties from a strongly elastic material to a mostly viscous one, on the timescales of the simulations. The force peak is also correlated with rupture of the alpha-helical linker, and is likely the event responsible for the peaks in the sawtooth-pattern force-extension curves measured by atomic force microscopy experiments. Rupture of the linker involves simultaneously breaking approximately four hydrogen bonds that maintain the alpha-helical linker. After this initial rupture, the linker undergoes simple helix-to-coil transitions as the spectrin repeat unit continues to be extended. The implications of linker rupture in the interpretation of unfolding and atomic force microscopy experiments are also discussed.
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Affiliation(s)
- Sterling Paramore
- Center for Biophysical Modeling and Simulation and Department of Chemistry, University of Utah, Salt Lake City, Utah, USA
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48
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West DK, Brockwell DJ, Olmsted PD, Radford SE, Paci E. Mechanical resistance of proteins explained using simple molecular models. Biophys J 2005; 90:287-97. [PMID: 16214858 PMCID: PMC1367027 DOI: 10.1529/biophysj.105.071035] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Recent experiments have demonstrated that proteins unfold when two atoms are mechanically pulled apart, and that this process is different to when heated or when a chemical denaturant is added to the solution. Experiments have also shown that the response of proteins to external forces is very diverse, some of them being "hard," and others "soft." Mechanical resistance originates from the presence of barriers on the energy landscape; together, experiment and simulation have demonstrated that unfolding occurs through alternative pathways when different pairs of atoms undergo mechanical extension. Here we use simulation to probe the mechanical resistance of six structurally diverse proteins when pulled in different directions. For this, we use two very different models: a detailed, transferable one, and a coarse-grained, structure-based one. The coarse-grained model gives results that are surprisingly similar to the detailed one and qualitatively agree with experiment; i.e., the mechanical resistance of different proteins or of a single protein pulled in different directions can be predicted by simulation. The results demonstrate the importance of pulling direction relative to the local topology in determining mechanical stability, and rationalize the effect of the location of importation/degradation tags on the rates of mitochondrial import or protein degradation in vivo.
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Affiliation(s)
- Daniel K West
- School of Physics & Astronomy, School of Biochemistry & Microbiology, and Institute of Molecular Biophysics, University of Leeds, Leeds, United Kingdom
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49
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Dugdale TM, Dagastine R, Chiovitti A, Mulvaney P, Wetherbee R. Single adhesive nanofibers from a live diatom have the signature fingerprint of modular proteins. Biophys J 2005; 89:4252-60. [PMID: 16169972 PMCID: PMC1366990 DOI: 10.1529/biophysj.105.062489] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The adhesive and mechanical properties of a cell-substratum adhesive secreted by live diatom cells were examined in situ using atomic force microscopy. The resulting force curves have a regular saw-tooth pattern, the characteristic fingerprint of modular proteins, and when bridged between tip and surface can repeatedly be stretched and relaxed resulting in precisely overlaying saw-tooth curves (up to approximately 600 successive cycles). The average rupture force of the peaks is 0.794 +/- 0.007 (mean +/- SE) nN at a loading rate of 0.8 microm/s and the average persistence length is 0.026 +/- <0.001 (mean +/- SE) nm (fit using the worm-like chain model). We propose that we are pulling on single adhesive nanofibers, each a cohesive unit composed of a set number of modular proteins aligned in register. Furthermore, we can observe and differentiate when up to three adhesive nanofibers are pulled based upon multimodal distributions of force and persistence length. The high force required for bond rupture, high extensibility (approximately 1.2 microm), and the accurate and rapid refolding upon relaxation, together provide strong and flexible properties ideally suited for the cell-substratum adhesion of this fouling diatom and allow us to understand the mechanism responsible for the strength of adhesion.
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Affiliation(s)
- T M Dugdale
- School of Botany, School of Chemical and Biomolecular Engineering, University of Melbourne, Melbourne, Australia
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50
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Brockwell DJ, Beddard GS, Paci E, West DK, Olmsted PD, Smith DA, Radford SE. Mechanically unfolding the small, topologically simple protein L. Biophys J 2005; 89:506-19. [PMID: 15863479 PMCID: PMC1366550 DOI: 10.1529/biophysj.105.061465] [Citation(s) in RCA: 139] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
beta-sheet proteins are generally more able to resist mechanical deformation than alpha-helical proteins. Experiments measuring the mechanical resistance of beta-sheet proteins extended by their termini led to the hypothesis that parallel, directly hydrogen-bonded terminal beta-strands provide the greatest mechanical strength. Here we test this hypothesis by measuring the mechanical properties of protein L, a domain with a topology predicted to be mechanically strong, but with no known mechanical function. A pentamer of this small, topologically simple protein is resistant to mechanical deformation over a wide range of extension rates. Molecular dynamics simulations show the energy landscape for protein L is highly restricted for mechanical unfolding and that this protein unfolds by the shearing apart of two structural units in a mechanism similar to that proposed for ubiquitin, which belongs to the same structural class as protein L, but unfolds at a significantly higher force. These data suggest that the mechanism of mechanical unfolding is conserved in proteins within the same fold family and demonstrate that although the topology and presence of a hydrogen-bonded clamp are of central importance in determining mechanical strength, hydrophobic interactions also play an important role in modulating the mechanical resistance of these similar proteins.
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Affiliation(s)
- David J Brockwell
- School of Biochemistry and Microbiology, Institute of Molecular Biophysics, Centre for Chemical Dynamics, University of Leeds, Leeds, United Kingdom.
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