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Průša J, Cifra M. Molecular dynamics simulation dataset of a kinesin on tubulin heterodimers in electric field. Data Brief 2024; 52:109765. [PMID: 38370023 PMCID: PMC10873870 DOI: 10.1016/j.dib.2023.109765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 10/30/2023] [Accepted: 10/31/2023] [Indexed: 02/20/2024] Open
Abstract
We present trajectories from non-equilibrium (in electric field) molecular dynamics (MD) simulations of a kinesin motor domain on tubulin heterodimers with two tubulin heterodimers forming neighbouring microtubule protofilaments. The trajectories are for no field (long equilibrium simulation), for four different electric field orientations (X, -X, Y, -Y) and for the X electric field at four different field strengths. We also provide a trajectory for larger simulation box. Our data enable to analyze the electric field effects on kinesin, which ultimately leads to kinesin detachment. This data set was used to understand the effect of electric field orientation and field strength on the kinetics and energetics of the electro-detachment of kinesin [1].
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Affiliation(s)
- Jiří Průša
- Institute of Photonics and Electronics of the Czech Academy of Sciences, Prague, 18200, Czechia
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Vacek J, Zatloukalová M, Dorčák V, Cifra M, Futera Z, Ostatná V. Electrochemistry in sensing of molecular interactions of proteins and their behavior in an electric field. Mikrochim Acta 2023; 190:442. [PMID: 37847341 PMCID: PMC10582152 DOI: 10.1007/s00604-023-05999-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 09/12/2023] [Indexed: 10/18/2023]
Abstract
Electrochemical methods can be used not only for the sensitive analysis of proteins but also for deeper research into their structure, transport functions (transfer of electrons and protons), and sensing their interactions with soft and solid surfaces. Last but not least, electrochemical tools are useful for investigating the effect of an electric field on protein structure, the direct application of electrochemical methods for controlling protein function, or the micromanipulation of supramolecular protein structures. There are many experimental arrangements (modalities), from the classic configuration that works with an electrochemical cell to miniaturized electrochemical sensors and microchip platforms. The support of computational chemistry methods which appropriately complement the interpretation framework of experimental results is also important. This text describes recent directions in electrochemical methods for the determination of proteins and briefly summarizes available methodologies for the selective labeling of proteins using redox-active probes. Attention is also paid to the theoretical aspects of electron transport and the effect of an external electric field on the structure of selected proteins. Instead of providing a comprehensive overview, we aim to highlight areas of interest that have not been summarized recently, but, at the same time, represent current trends in the field.
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Affiliation(s)
- Jan Vacek
- Department of Medical Chemistry and Biochemistry, Faculty of Medicine and Dentistry, Palacky University, Hnevotinska 3, 77515, Olomouc, Czech Republic.
| | - Martina Zatloukalová
- Department of Medical Chemistry and Biochemistry, Faculty of Medicine and Dentistry, Palacky University, Hnevotinska 3, 77515, Olomouc, Czech Republic
| | - Vlastimil Dorčák
- Department of Medical Chemistry and Biochemistry, Faculty of Medicine and Dentistry, Palacky University, Hnevotinska 3, 77515, Olomouc, Czech Republic
| | - Michal Cifra
- Institute of Photonics and Electronics of the Czech Academy of Sciences, Chaberska 1014/57, 18200, Prague, Czech Republic
| | - Zdeněk Futera
- Faculty of Science, University of South Bohemia, Branisovska 1760, 37005, Ceske Budejovice, Czech Republic
| | - Veronika Ostatná
- Institute of Biophysics, The Czech Academy of Sciences, v.v.i., Kralovopolska 135, 61200, Brno, Czech Republic
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Kinoshita Y, Uchida N. Flow patterns and defect dynamics of active nematic liquid crystals under an electric field. Phys Rev E 2023; 108:014605. [PMID: 37583184 DOI: 10.1103/physreve.108.014605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 06/19/2023] [Indexed: 08/17/2023]
Abstract
The effects of an electric field on the flow patterns and defect dynamics of two-dimensional active nematic liquid crystals are numerically investigated. We found that field-induced director reorientation causes anisotropic active turbulence characterized by enhanced flow perpendicular to the electric field. The average flow speed and its anisotropy are maximized at an intermediate field strength. Topological defects in the anisotropic active turbulence are localized and show characteristic dynamics with simultaneous creation of two pairs of defects. A laning state characterized by stripe domains with alternating flow directions is found at a larger field strength near the transition to the uniformly aligned state. We obtained periodic oscillations between the laning state and active turbulence, which resembles an experimental observation of active nematics subject to anisotropic friction.
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Affiliation(s)
- Yutaka Kinoshita
- Department of Physics, Tohoku University, Sendai 980-8578, Japan
| | - Nariya Uchida
- Department of Physics, Tohoku University, Sendai 980-8578, Japan
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Průša J, Cifra M. Electro-detachment of kinesin motor domain from microtubule in silico. Comput Struct Biotechnol J 2023; 21:1349-1361. [PMID: 36814722 PMCID: PMC9939557 DOI: 10.1016/j.csbj.2023.01.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 01/15/2023] [Accepted: 01/15/2023] [Indexed: 01/22/2023] Open
Abstract
Kinesin is a motor protein essential in cellular functions, such as intracellular transport and cell-division, as well as for enabling nanoscopic transport in bio-nanotechnology. Therefore, for effective control of function for nanotechnological applications, it is important to be able to modify the function of kinesin. To circumvent the limitations of chemical modifications, here we identify another potential approach for kinesin control: the use of electric forces. Using full-atom molecular dynamics simulations (247,358 atoms, total time ∼ 4.4 μs), we demonstrate, for the first time, that the kinesin-1 motor domain can be detached from a microtubule by an intense electric field within the nanosecond timescale. We show that this effect is field-direction dependent and field-strength dependent. A detailed analysis of the electric forces and the work carried out by electric field acting on the microtubule-kinesin system shows that it is the combined action of the electric field pulling on the β-tubulin C-terminus and the electric-field-induced torque on the kinesin dipole moment that causes kinesin detachment from the microtubule. It is shown, for the first time in a mechanistic manner, that an electric field can dramatically affect molecular interactions in a heterologous functional protein assembly. Our results contribute to understanding of electromagnetic field-biomatter interactions on a molecular level, with potential biomedical and bio-nanotechnological applications for harnessing control of protein nanomotors.
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Tassinari R, Cavallini C, Olivi E, Facchin F, Taglioli V, Zannini C, Marcuzzi M, Ventura C. Cell Responsiveness to Physical Energies: Paving the Way to Decipher a Morphogenetic Code. Int J Mol Sci 2022; 23:ijms23063157. [PMID: 35328576 PMCID: PMC8949133 DOI: 10.3390/ijms23063157] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 03/10/2022] [Accepted: 03/11/2022] [Indexed: 02/04/2023] Open
Abstract
We discuss emerging views on the complexity of signals controlling the onset of biological shapes and functions, from the nanoarchitectonics arising from supramolecular interactions, to the cellular/multicellular tissue level, and up to the unfolding of complex anatomy. We highlight the fundamental role of physical forces in cellular decisions, stressing the intriguing similarities in early morphogenesis, tissue regeneration, and oncogenic drift. Compelling evidence is presented, showing that biological patterns are strongly embedded in the vibrational nature of the physical energies that permeate the entire universe. We describe biological dynamics as informational processes at which physics and chemistry converge, with nanomechanical motions, and electromagnetic waves, including light, forming an ensemble of vibrations, acting as a sort of control software for molecular patterning. Biomolecular recognition is approached within the establishment of coherent synchronizations among signaling players, whose physical nature can be equated to oscillators tending to the coherent synchronization of their vibrational modes. Cytoskeletal elements are now emerging as senders and receivers of physical signals, "shaping" biological identity from the cellular to the tissue/organ levels. We finally discuss the perspective of exploiting the diffusive features of physical energies to afford in situ stem/somatic cell reprogramming, and tissue regeneration, without stem cell transplantation.
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Affiliation(s)
- Riccardo Tassinari
- ELDOR LAB, National Laboratory of Molecular Biology and Stem Cell Engineering, National Institute of Biostructures and Biosystems, CNR, Via Gobetti 101, 40129 Bologna, Italy; (R.T.); (C.C.); (E.O.); (V.T.); (C.Z.)
| | - Claudia Cavallini
- ELDOR LAB, National Laboratory of Molecular Biology and Stem Cell Engineering, National Institute of Biostructures and Biosystems, CNR, Via Gobetti 101, 40129 Bologna, Italy; (R.T.); (C.C.); (E.O.); (V.T.); (C.Z.)
| | - Elena Olivi
- ELDOR LAB, National Laboratory of Molecular Biology and Stem Cell Engineering, National Institute of Biostructures and Biosystems, CNR, Via Gobetti 101, 40129 Bologna, Italy; (R.T.); (C.C.); (E.O.); (V.T.); (C.Z.)
| | - Federica Facchin
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Via Massarenti 9, 40138 Bologna, Italy;
| | - Valentina Taglioli
- ELDOR LAB, National Laboratory of Molecular Biology and Stem Cell Engineering, National Institute of Biostructures and Biosystems, CNR, Via Gobetti 101, 40129 Bologna, Italy; (R.T.); (C.C.); (E.O.); (V.T.); (C.Z.)
| | - Chiara Zannini
- ELDOR LAB, National Laboratory of Molecular Biology and Stem Cell Engineering, National Institute of Biostructures and Biosystems, CNR, Via Gobetti 101, 40129 Bologna, Italy; (R.T.); (C.C.); (E.O.); (V.T.); (C.Z.)
| | - Martina Marcuzzi
- INBB, Biostructures and Biosystems National Institute, Viale Medaglie d’Oro 305, 00136 Rome, Italy;
| | - Carlo Ventura
- ELDOR LAB, National Laboratory of Molecular Biology and Stem Cell Engineering, National Institute of Biostructures and Biosystems, CNR, Via Gobetti 101, 40129 Bologna, Italy; (R.T.); (C.C.); (E.O.); (V.T.); (C.Z.)
- Correspondence: ; Tel.: +39-347-920-6992
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