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Nowroz S, Nasrin SR, Kabir AMR, Yamashita T, Kusumoto T, Taira J, Tani M, Ichikawa M, Sada K, Kakugo A. Role of tubulin C-terminal tail on mechanical properties of microtubule. Biochem Biophys Res Commun 2024; 706:149761. [PMID: 38479245 DOI: 10.1016/j.bbrc.2024.149761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 02/29/2024] [Accepted: 03/06/2024] [Indexed: 03/24/2024]
Abstract
Tubulin C-terminal tail (CTT) is a disordered segment extended from each tubulin monomer of αβ tubulin heterodimers, the building blocks of microtubules. The tubulin CTT contributes to the cellular function of microtubules such as intracellular transportation by regulating their interaction with other proteins and cell shape regulation by controlling microtubule polymerization dynamics. Although the mechanical integrity of microtubules is crucial for their functions, the role of tubulin CTT on microtubule mechanical properties has remained elusive. In this work, we investigate the role of tubulin CTTs in regulating the mechanical properties of microtubules by estimating the persistence lengths and investigating the buckling behavior of microtubules with and without CTT. We find that microtubules with intact CTTs exhibit twice the rigidity of microtubules lacking tubulin CTTs. Our study will widen the scope of altering microtubule mechanical properties for its application in nano bio-devices and lead to novel therapeutic approaches for neurodegenerative diseases with altered microtubule properties.
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Affiliation(s)
- Senjuti Nowroz
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-0810, Japan
| | - Syeda Rubaiya Nasrin
- Department of Physics, Division of Physics and Astronomy, Graduate School of Science, Kyoto University, Kyoto, 606-8502, Japan
| | | | - Takefumi Yamashita
- Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, 153-8904, Japan; Deaprtment of Physical Chemistry, School of Pharmacy and Pharmaceutical Sciences, Hoshi University, Tokyo, 142-8501, Japan
| | - Tomoichiro Kusumoto
- Department of Bioscience and Bioinformatics, Graduate School of Computer Science and Systems Engineering, Kyushu Institute of Technology, Iizuka, 820-8502, Japan
| | - Junichi Taira
- Department of Bioscience and Bioinformatics, Graduate School of Computer Science and Systems Engineering, Kyushu Institute of Technology, Iizuka, 820-8502, Japan
| | - Marie Tani
- Department of Physics, Division of Physics and Astronomy, Graduate School of Science, Kyoto University, Kyoto, 606-8502, Japan
| | - Masatoshi Ichikawa
- Department of Physics, Division of Physics and Astronomy, Graduate School of Science, Kyoto University, Kyoto, 606-8502, Japan
| | - Kazuki Sada
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-0810, Japan; Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Akira Kakugo
- Department of Physics, Division of Physics and Astronomy, Graduate School of Science, Kyoto University, Kyoto, 606-8502, Japan.
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2
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Sergeeva IA, Klinov DV, Schäffer TE, Dubrovin EV. Characterization of the effect of chromium salts on tropocollagen molecules and molecular aggregates. Int J Biol Macromol 2023; 242:124835. [PMID: 37201883 DOI: 10.1016/j.ijbiomac.2023.124835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/06/2023] [Accepted: 05/08/2023] [Indexed: 05/20/2023]
Abstract
Though the capability of chromium treatment to improve the stability and mechanical properties of collagen fibrils is well-known, the influence of different chromium salts on collagen molecules (tropocollagen) is not well characterized. In this study, the effect of Cr3+ treatment on the conformation and hydrodynamic properties of collagen was studied using atomic force microscopy (AFM) and dynamic light scattering (DLS). Statistical analysis of contours of adsorbed tropocollagen molecules using the two-dimensional worm-like chain model revealed a reduction of the persistence length (i.e., the increase of flexibility) from ≈72 nm in water to ≈56-57 nm in chromium (III) salt solutions. DLS studies demonstrated an increase of the hydrodynamic radius from ≈140 nm in water to ≈190 nm in chromium (III) salt solutions, which is associated with protein aggregation. The kinetics of collagen aggregation was shown to be ionic strength dependent. Collagen molecules treated with three different chromium (III) salts demonstrated similar properties such as flexibility, aggregation kinetics, and susceptibility to enzymatic cleavage. The observed effects are explained by a model that considers the formation of chromium-associated intra- and intermolecular crosslinks. The obtained results provide novel insights into the effect of chromium salts on the conformation and properties of tropocollagen molecules.
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Affiliation(s)
- Irina A Sergeeva
- Lomonosov Moscow State University, Faculty of Physics, Leninskie Gory 1 bld 2, 119991 Moscow, Russia.
| | - Dmitry V Klinov
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya 1a, 119435 Moscow, Russia
| | - Tilman E Schäffer
- University of Tübingen, Institute of Applied Physics, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Evgeniy V Dubrovin
- Lomonosov Moscow State University, Faculty of Physics, Leninskie Gory 1 bld 2, 119991 Moscow, Russia.
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3
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Dubrovin EV, Barinov NA, Ivanov DA, Klinov DV. Single-molecule AFM study of hyaluronic acid softening in electrolyte solutions. Carbohydr Polym 2023; 303:120472. [PMID: 36657830 DOI: 10.1016/j.carbpol.2022.120472] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 11/30/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022]
Abstract
Investigation of hyaluronic acid (HA) morphology and mechanical properties at a single-molecule level is important for the development of HA based biomaterials. We have developed the atomic force microscopy (AFM) based approach for quantitative characterization of conformation of HA molecules. HA molecules adsorbed on a modified graphitic surface form oriented linear segments. Conformation of HA molecules can be considered as two-dimensional quasi-projection of a three-dimensional conformation locally straightened by a substrate. The persistence length and Young's modulus of biomolecules estimated using wormlike chain model decrease from 15.7 to 9.9 nm, and from ∼21 to ∼13 GPa, respectively, when KCl concentration increases from 0 to 100 mM. The dependence of the persistence length on ionic strength supports the Odijk-Skolnick-Fixman model of polyelectrolyte stiffening in electrolyte solution. The obtained results represent a new insight into the conformation and mechanical characteristics of HA molecules and complement the characterization of this biopolymer by bulk methods.
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Affiliation(s)
- Evgeniy V Dubrovin
- Sirius University of Science and Technology, 1 Olympic Ave, 354340 Sochi, Russian Federation; Moscow Institute of Physics and Technology, Institutskiy Per. 9, Dolgoprudny 141700, Russian Federation; Lomonosov Moscow State University, Leninskie Gory 1 bld. 2, 119991 Moscow, Russian Federation.
| | - Nikolay A Barinov
- Sirius University of Science and Technology, 1 Olympic Ave, 354340 Sochi, Russian Federation; Moscow Institute of Physics and Technology, Institutskiy Per. 9, Dolgoprudny 141700, Russian Federation.
| | - Dmitry A Ivanov
- Sirius University of Science and Technology, 1 Olympic Ave, 354340 Sochi, Russian Federation; Institut de Sciences des Matériaux de Mulhouse - IS2M, CNRS UMR7361, 15 Jean Starcky, Mulhouse 68057, France.
| | - Dmitry V Klinov
- Sirius University of Science and Technology, 1 Olympic Ave, 354340 Sochi, Russian Federation; Moscow Institute of Physics and Technology, Institutskiy Per. 9, Dolgoprudny 141700, Russian Federation.
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4
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Banerjee A, De R, Das B. Hydrodynamic and conformational characterization of aqueous sodium alginate solutions with varying salinity. Carbohydr Polym 2022; 277:118855. [PMID: 34893264 DOI: 10.1016/j.carbpol.2021.118855] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 11/01/2021] [Accepted: 11/02/2021] [Indexed: 11/18/2022]
Abstract
Insight into the role of electrostatic interactions on the hydrodynamics and conformation of aqueous sodium alginate was gained through viscometry. Alginate chains are found to shrink in salt-free solutions more rapidly with increasing polymer concentration compared to salt-solutions. For salt-free solutions, a reduced polymer concentration of less than 1 suffices to make the alginate coil volume half of that at infinite dilution which becomes invariant when the reduced concentration exceeds 8. In saline media having salt concentration greater than 0.1 mol·L-1, the chains become more flexible, caused by the shielding of intra-chain repulsions. The chains effectively reached unperturbed state when the added salt concentration becomes ≥0.5 mol·L-1. Alginate chains are shown to remain stiff up to about 8-10 monomers within the investigated temperature range. This study explores the possible modification of the individual chain behavior induced by the neighboring chains or by the variation of temperature.
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Affiliation(s)
- Arnab Banerjee
- Department of Chemistry, Presidency University, Kolkata 700 073, India
| | - Ranjit De
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Bijan Das
- Department of Chemistry, Presidency University, Kolkata 700 073, India.
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5
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Kang Y, Zhao X, Han X, Ji X, Chen Q, Pasch H, Lederer A, Liu Y. Conformation and persistence length of chitosan in aqueous solutions of different ionic strengths via asymmetric flow field-flow fractionation. Carbohydr Polym 2021; 271:118402. [PMID: 34364548 DOI: 10.1016/j.carbpol.2021.118402] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 06/01/2021] [Accepted: 07/01/2021] [Indexed: 12/24/2022]
Abstract
Conformation of chitosan in acidic aqueous solutions is strongly influenced by ionic strength, but the conventional employed size exclusion chromatography is limited to high ionic strength. Here we show that conformation of chitosan in acetate buffer down to millimolar ionic strength can be studied via asymmetric flow field-flow fractionation (AF4), where the separation is governed by the diffusion properties of the chitosan molecules and assisted by the electrostatic repulsion of the polyelectrolyte from the channel membrane. The size of chitosan decreases with ionic strength due to increasing screening of the polyelectrolyte effect. The persistence length of chitosan in the solutions, obtained by fitting the conformation plot by the wormlike chain model, decreases linearly with the Debye screening length from 44.5 nm at a salt concentration of 1.25 mM dominated by the electrostatic contribution to 8.6 nm in 800 mM acetate buffer close to its intrinsic persistence length of 7.7 nm.
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Affiliation(s)
- Yu Kang
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China; University of Science and Technology of China, Hefei 230026, China
| | - Xinyue Zhao
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China; University of Science and Technology of China, Hefei 230026, China
| | - Xintong Han
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Xiangling Ji
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China; University of Science and Technology of China, Hefei 230026, China
| | - Quan Chen
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China; University of Science and Technology of China, Hefei 230026, China
| | - Harald Pasch
- Department of Chemistry and Polymer Science, University of Stellenbosch, Private Bag X1, 7602 Matieland, South Africa
| | - Albena Lederer
- Department of Chemistry and Polymer Science, University of Stellenbosch, Private Bag X1, 7602 Matieland, South Africa; Leibniz-Institut für Polymerforschung Dresden e.V., 01069 Dresden, Germany
| | - Yonggang Liu
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China.
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6
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Pal C, Varma S, Majumder S. Oxygen vacancy assisted condensation of DNA molecule observed on ZnO thin film. Biophys Chem 2021; 277:106659. [PMID: 34340002 DOI: 10.1016/j.bpc.2021.106659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 07/15/2021] [Accepted: 07/23/2021] [Indexed: 10/20/2022]
Abstract
An exotic condensation of DNA molecules is observed on the nanostructured ZnO surface. The ZnO nanostructures (NS) fabricated by thermal vapor deposition technique were associated with a large number of oxygen vacancies on the surface. These oxygen vacancies induced changes in the DNA conformation which further reflected through changes in the persistence length of the DNA molecules. This indicates a reinforcement of the bonds and binding in both the phosphate and the base regions of the DNA molecules with the positively charged core vacancy sites on the ZnO nanostructured surface through strong interaction mediated via long-range electrostatic forces which effectively reduced the end-to-end distance of the λ-DNA molecule. This strongly suggests a transition of the λ-DNA molecule through structural modification into a more compact higher-order fractal dimension from its native state.
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Affiliation(s)
| | - Shikha Varma
- Institute of Physics, Bhubaneswar, 751005, India
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7
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Smoler M, Coceano G, Testa I, Bruno L, Levi V. Apparent stiffness of vimentin intermediate filaments in living cells and its relation with other cytoskeletal polymers. Biochim Biophys Acta Mol Cell Res 2020; 1867:118726. [PMID: 32320724 DOI: 10.1016/j.bbamcr.2020.118726] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 04/11/2020] [Accepted: 04/15/2020] [Indexed: 12/12/2022]
Abstract
The cytoskeleton is a complex network of interconnected biopolymers intimately involved in the generation and transmission of forces. Several mechanical properties of microtubules and actin filaments have been extensively explored in cells. In contrast, intermediate filaments (IFs) received comparatively less attention despite their central role in defining cell shape, motility and adhesion during physiological processes as well as in tumor progression. Here, we explored relevant biophysical properties of vimentin IFs in living cells combining confocal microscopy and a filament tracking routine that allows localizing filaments with ~20 nm precision. A Fourier-based analysis showed that IFs curvatures followed a thermal-like behavior characterized by an apparent persistence length (lp*) similar to that measured in aqueous solution. Additionally, we determined that certain perturbations of the cytoskeleton affect lp* and the lateral mobility of IFs as assessed in cells in which either the microtubule dynamic instability was reduced or actin filaments were partially depolymerized. Our results provide relevant clues on how vimentin IFs mechanically couple with microtubules and actin filaments in cells and support a role of this network in the response to mechanical stress.
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8
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Lehman W, Rynkiewicz MJ, Moore JR. A new twist on tropomyosin binding to actin filaments: perspectives on thin filament function, assembly and biomechanics. J Muscle Res Cell Motil 2019; 41:23-38. [PMID: 30771202 DOI: 10.1007/s10974-019-09501-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Accepted: 02/07/2019] [Indexed: 02/07/2023]
Abstract
Tropomyosin, best known for its role in the steric regulation of muscle contraction, polymerizes head-to-tail to form cables localized along the length of both muscle and non-muscle actin-based thin filaments. In skeletal and cardiac muscles, tropomyosin, under the control of troponin and myosin, moves in a cooperative manner between blocked, closed and open positions on filaments, thereby masking and exposing actin-binding sites necessary for myosin crossbridge head interactions. While the coiled-coil signature of tropomyosin appears to be simple, closer inspection reveals surprising structural complexity required to perform its role in steric regulation. For example, component α-helices of coiled coils are typically zippered together along a continuous core hydrophobic stripe. Tropomyosin, however, contains a number of anomalous, functionally controversial, core amino acid residues. We argue that the atypical residues at this interface, including clusters of alanines and a charged aspartate, are required for preshaping tropomyosin to readily fit to the surface of the actin filament, but do so without compromising tropomyosin rigidity once the filament is assembled. Indeed, persistence length measurements of tropomyosin are characteristic of a semi-rigid cable, in this case conducive to cooperative movement on thin filaments. In addition, we also maintain that tropomyosin displays largely unrecognized and residue-specific torsional variance, which is involved in optimizing contacts between actin and tropomyosin on the assembled thin filament. Corresponding twist-induced stiffness may also enhance cooperative translocation of tropomyosin across actin filaments. We conclude that anomalous core residues of tropomyosin facilitate thin filament regulatory behavior in a multifaceted way.
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Affiliation(s)
- William Lehman
- Department of Physiology and Biophysics, Boston University School of Medicine, Boston, MA, USA.
| | - Michael J Rynkiewicz
- Department of Physiology and Biophysics, Boston University School of Medicine, Boston, MA, USA
| | - Jeffrey R Moore
- Department of Biological Sciences, University of Massachusetts-Lowell, Lowell, MA, USA
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9
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Mehrafrooz B, Shamloo A. Mechanical differences between ATP and ADP actin states: A molecular dynamics study. J Theor Biol 2018; 448:94-103. [PMID: 29634959 DOI: 10.1016/j.jtbi.2018.04.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 03/31/2018] [Accepted: 04/06/2018] [Indexed: 11/15/2022]
Abstract
This paper aims to give a comprehensive atomistic modeling of the nanomechanical behavior of actin monomer. Actin is a ubiquitous and essential component of cytoskeleton which forms many different cellular structures. Despite for several years great effort has been devoted to the investigation of mechanical properties of the actin filament, studies on the nanomechanical behavior of actin monomer are still lacking. These scales are, however, important for a complete understanding of the role of actin as an important component in the cytoskeleton structure. Based on the accuracy of atomistic modeling methods such as molecular dynamics simulations, steered molecular dynamics method is performed to assess tension of monomeric G-actin molecule under different types of mechanical loading including axial and lateral. As a result, stress-strain curves are obtained in aqueous solution, with either ATP or ADP bound in the nucleotide binding pocket. The obtained results yield evaluation of the tensile stiffness of a single actin monomer in lateral and normal direction. In order to compare the behavior of ATP and ADP G-actins, the number of hydrogen bonds and nonbonded interactions between the nucleotide and the protein are analyzed. Moreover, The effect of virtual spring of steered molecular dynamics on the mechanical behavior of actin monomer is investigated. The results reveal increasing the virtual spring constant leads to convergence of the stiffness. Moreover, in this paper, a generalized model is proposed to extend the obtained results for the monomeric G-actin scale to the actin filament. Our modeling estimated a persistence length of actin filament 15.41 µm, close to experimental measurements. Moreover, In this paper, the breaking force actin-actin bond is evaluated using steered molecular dynamics simulation. By applying a tensile force, actin-actin bond ruptured at 4197.5 pN.
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Affiliation(s)
- Behzad Mehrafrooz
- Department of Mechanical Engineering, Sharif University of Technology, Tehran, Iran
| | - Amir Shamloo
- Department of Mechanical Engineering, Sharif University of Technology, Tehran, Iran.
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10
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Abstract
Atomic force microscopy (AFM) is widely used to image and study biological molecules. As an example, we have utilized AFM to investigate how the mechanical properties of DNA polymers depend on electrostatics and the strength of DNA base stacking by studying double-stranded DNA molecules incorporating several different neutral and charged base modifications. Here, we describe ten complementary approaches for determining DNA persistence length by AFM imaging. The combination of different approaches provides increased confidence and statistical reliability over existing methods utilizing only a single approach.
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Affiliation(s)
- Justin P Peters
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - L James Maher
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN, USA.
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11
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Huber ST, Kuhm T, Sachse C. Automated tracing of helical assemblies from electron cryo-micrographs. J Struct Biol 2017; 202:1-12. [PMID: 29191673 PMCID: PMC5847486 DOI: 10.1016/j.jsb.2017.11.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 11/24/2017] [Accepted: 11/26/2017] [Indexed: 01/17/2023]
Abstract
Structure determination of helical specimens commonly requires datasets from thousands of micrographs often obtained by automated cryo-EM data acquisition. Interactive tracing of helical assemblies from such a number of micrographs is labor-intense and time-consuming. Here, we introduce an automated tracing tool MicHelixTrace that precisely locates helix traces from micrographs of rigid as well as very flexible helical assemblies with small numbers of false positives. The computer program is fast and has low computational requirements. In addition to helix coordinates required for a subsequent helical reconstruction work-flow, we determine the persistence length of the polymer ensemble. This information provides a useful measure to characterize mechanical properties of helical assemblies and to evaluate the potential for high-resolution structure determination.
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Affiliation(s)
- Stefan T Huber
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Tanja Kuhm
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Carsten Sachse
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany.
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12
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Abstract
Protein-induced DNA bridging and looping is a common mechanism for various and essential processes in bacterial chromosomes. This mechanism is preserved despite the very different bacterial conditions and their expected influence on the thermodynamic and kinetic characteristics of the bridge formation and stability. Over the last two decades, single-molecule techniques carried out on in vitro DNA systems have yielded valuable results which, in combination with theoretical works, have clarified the effects of different parameters of nucleoprotein complexes on the protein-induced DNA bridging and looping process. In this review, I will outline the features that can be measured for such processes with various single-molecule techniques in use in the field. I will then describe both the experimental results and the theoretical models that illuminate the contribution of the DNA molecule itself as well as that of the bridging proteins in the DNA looping mechanism at play in the nucleoid of E. coli.
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Affiliation(s)
- Catherine Tardin
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, France.
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13
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Kriegel F, Ermann N, Lipfert J. Probing the mechanical properties, conformational changes, and interactions of nucleic acids with magnetic tweezers. J Struct Biol 2017; 197:26-36. [PMID: 27368129 DOI: 10.1016/j.jsb.2016.06.022] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 05/06/2016] [Accepted: 06/28/2016] [Indexed: 11/21/2022]
Abstract
Nucleic acids are central to the storage and transmission of genetic information. Mechanical properties, along with their sequence, both enable and fundamentally constrain the biological functions of DNA and RNA. For small deformations from the equilibrium conformations, nucleic acids are well described by an isotropic elastic rod model. However, external forces and torsional strains can induce conformational changes, giving rise to a complex force-torque phase diagram. This review focuses on magnetic tweezers as a powerful tool to precisely determine both the elastic parameters and conformational transitions of nucleic acids under external forces and torques at the single-molecule level. We review several variations of magnetic tweezers, in particular conventional magnetic tweezers, freely orbiting magnetic tweezers and magnetic torque tweezers, and discuss their characteristic capabilities. We then describe the elastic rod model for DNA and RNA and discuss conformational changes induced by mechanical stress. The focus lies on the responses to torque and twist, which are crucial in the mechanics and interactions of nucleic acids and can directly be measured using magnetic tweezers. We conclude by highlighting several recent studies of nucleic acid-protein and nucleic acid-small-molecule interactions as further applications of magnetic tweezers and give an outlook of some exciting developments to come.
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Abstract
Tropomyosin is a major regulatory protein of contractile systems and cytoskeleton, an actin-binding protein that positions laterally along actin filaments and modulates actin-myosin interaction. About 40 tropomyosin isoforms have been found in a variety of cytoskeleton systems, not necessarily connected with actin-myosin interaction and contraction. Involvement of specific tropomyosin isoforms in the regulation of key cell processes was shown, and specific features of tropomyosin genes and protein structure have been investigated with molecular biology and genetics approaches. However, the mechanisms underlying the effects of tropomyosin on cytoskeleton dynamics are still unclear. As tropomyosin is primarily an F-actin-binding protein, it is important to understand how it interacts both with actin and actin-binding proteins functioning in muscles and cytoskeleton to regulate actin dynamics. This review focuses on biochemical data on the effects of tropomyosin on actin assembly and dynamics, as well as on the modulation of these effects by actin-binding proteins. The data indicate that tropomyosin can efficiently regulate actin dynamics via allosteric conformational changes within actin filaments.
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Affiliation(s)
- Sofia Yu Khaitlina
- Institute of Cytology, Russian Academy of Sciences, Saint-Petersburg, Russia.
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15
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Block J, Schroeder V, Pawelzyk P, Willenbacher N, Köster S. Physical properties of cytoplasmic intermediate filaments. Biochim Biophys Acta 2015; 1853:3053-64. [PMID: 25975455 DOI: 10.1016/j.bbamcr.2015.05.009] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 04/28/2015] [Accepted: 05/05/2015] [Indexed: 11/29/2022]
Abstract
Intermediate filaments (IFs) constitute a sophisticated filament system in the cytoplasm of eukaryotes. They form bundles and networks with adapted viscoelastic properties and are strongly interconnected with the other filament types, microfilaments and microtubules. IFs are cell type specific and apart from biochemical functions, they act as mechanical entities to provide stability and resilience to cells and tissues. We review the physical properties of these abundant structural proteins including both in vitro studies and cell experiments. IFs are hierarchical structures and their physical properties seem to a large part be encoded in the very specific architecture of the biopolymers. Thus, we begin our review by presenting the assembly mechanism, followed by the mechanical properties of individual filaments, network and structure formation due to electrostatic interactions, and eventually the mechanics of in vitro and cellular networks. This article is part of a Special Issue entitled: Mechanobiology.
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Affiliation(s)
- Johanna Block
- Institut für Röntgenphysik, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Viktor Schroeder
- Institut für Röntgenphysik, Georg-August-Universität Göttingen, Göttingen, Germany; Center for Nanoscale Microscopy and Molecular Physiology of the Brain, Göttingen, Germany
| | - Paul Pawelzyk
- Institute of Mechanical Process Engineering and Mechanics, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Norbert Willenbacher
- Institute of Mechanical Process Engineering and Mechanics, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Sarah Köster
- Institut für Röntgenphysik, Georg-August-Universität Göttingen, Göttingen, Germany; Center for Nanoscale Microscopy and Molecular Physiology of the Brain, Göttingen, Germany.
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16
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Lamour G, Kirkegaard JB, Li H, Knowles TP, Gsponer J. Easyworm: an open-source software tool to determine the mechanical properties of worm-like chains. Source Code Biol Med 2014; 9:16. [PMID: 25093038 PMCID: PMC4106204 DOI: 10.1186/1751-0473-9-16] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 07/02/2014] [Indexed: 11/12/2022]
Abstract
Background A growing spectrum of applications for natural and synthetic polymers, whether in industry or for biomedical research, demands for fast and universally applicable tools to determine the mechanical properties of very diverse polymers. To date, determining these properties is the privilege of a limited circle of biophysicists and engineers with appropriate technical skills. Findings Easyworm is a user-friendly software suite coded in MATLAB that simplifies the image analysis of individual polymeric chains and the extraction of the mechanical properties of these chains. Easyworm contains a comprehensive set of tools that, amongst others, allow the persistence length of single chains and the Young’s modulus of elasticity to be calculated in multiple ways from images of polymers obtained by a variety of techniques (e.g. atomic force microscopy, electron, contrast-phase, or epifluorescence microscopy). Conclusions Easyworm thus provides a simple and efficient tool for specialists and non-specialists alike to solve a common problem in (bio)polymer science. Stand-alone executables and shell scripts are provided along with source code for further development.
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Affiliation(s)
- Guillaume Lamour
- Centre for High-Throughput Biology, University of British Colombia, Vancouver, BC V6T 1Z4, Canada ; Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada ; Department of Biochemistry & Molecular Biology, University of British Colombia, Vancouver, BC V6T 2A1, Canada
| | | | - Hongbin Li
- Department of Biochemistry & Molecular Biology, University of British Colombia, Vancouver, BC V6T 2A1, Canada
| | - Tuomas Pj Knowles
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Jörg Gsponer
- Centre for High-Throughput Biology, University of British Colombia, Vancouver, BC V6T 1Z4, Canada ; Department of Biochemistry & Molecular Biology, University of British Colombia, Vancouver, BC V6T 2A1, Canada
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Abodinar A, Smith AM, Morris GA. A novel method to estimate the stiffness of carbohydrate polyelectrolyte polymers based on the ionic strength dependence of zeta potential. Carbohydr Polym 2014; 112:6-9. [PMID: 25129709 DOI: 10.1016/j.carbpol.2014.05.063] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Revised: 05/22/2014] [Accepted: 05/23/2014] [Indexed: 10/25/2022]
Abstract
Polysaccharides have received a great deal of attention from, for example, the food, cosmetic and pharmaceutical industries. Their conformations (flexibility/stiffness) span a wide range of conformational flexibilities with large hydrated volumes, these properties are important in relation to polysaccharide structure-function relationships. Perhaps the simplest parameter available to estimate the dilute solution conformation of polysaccharides is the Smidsrød-Haug stiffness parameter (B) where the stiffness of polyelectrolytes can be estimated by measuring the intrinsic viscosity at a number of different ionic strengths. In this paper we propose an alternative method for estimating the Smidsrød-Haug stiffness parameter (B) using the ionic strength dependency of zeta potential. For this purpose we have studied a number of different polysaccharides.
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Affiliation(s)
- Atiga Abodinar
- Department of Chemical Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield HD1 3DH, UK
| | - Alan M Smith
- Department of Pharmacy, School of Applied Sciences, University of Huddersfield, Huddersfield HD1 3DH, UK
| | - Gordon A Morris
- Department of Chemical Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield HD1 3DH, UK.
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Takatsuki H, Bengtsson E, Månsson A. Persistence length of fascin-cross-linked actin filament bundles in solution and the in vitro motility assay. Biochim Biophys Acta Gen Subj 2014; 1840:1933-42. [PMID: 24418515 DOI: 10.1016/j.bbagen.2014.01.012] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Revised: 01/05/2014] [Accepted: 01/06/2014] [Indexed: 11/16/2022]
Abstract
BACKGROUND Bundles of unipolar actin filaments (F-actin), cross-linked via the actin-binding protein fascin, are important in filopodia of motile cells and stereocilia of inner ear sensory cells. However, such bundles are also useful as shuttles in myosin-driven nanotechnological applications. Therefore, and for elucidating aspects of biological function, we investigate if the bundle tendency to follow straight paths (quantified by path persistence length) when propelled by myosin motors is directly determined by material properties quantified by persistence length of thermally fluctuating bundles. METHODS Fluorescent bundles, labeled with rhodamine-phalloidin, were studied at fascin:actin molar ratios: 0:1 (F-actin), 1:7, 1:4 and 1:2. Persistence lengths (Lp) were obtained by fitting the cosine correlation function (CCF) to a single exponential function: <cos(θ(0)-θ(s))>=exp(-s/(2Lp)) where θ(s) is tangent angle; s: path or contour lengths. < > denotes averaging over filaments. RESULTS Bundle-Lp (bundles<15μm long) increased from ~10 to 150μm with increased fascin:actin ratio. The increase was similar for path-Lp (path<15μm), with highly linear correlation. For longer bundle paths, the CCF-decay deviated from a single exponential, consistent with superimposition of the random path with a circular path as suggested by theoretical analysis. CONCLUSIONS Fascin-actin bundles have similar path-Lp and bundle-Lp, both increasing with fascin:actin ratio. Path-Lp is determined by the flexural rigidity of the bundle. GENERAL SIGNIFICANCE The findings give general insight into mechanics of cytoskeletal polymers that interact with molecular motors, aid rational development of nanotechnological applications and have implications for structure and in vivo functions of fascin-actin bundles.
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Affiliation(s)
- Hideyo Takatsuki
- Department of Chemistry and Biomedical Sciences, Linnaeus University, Kalmar SE-391 82, Sweden
| | - Elina Bengtsson
- Department of Chemistry and Biomedical Sciences, Linnaeus University, Kalmar SE-391 82, Sweden
| | - Alf Månsson
- Department of Chemistry and Biomedical Sciences, Linnaeus University, Kalmar SE-391 82, Sweden.
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