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Mostafazadeh N, Resnick A, Young YN, Peng Z. Microstructure-based modeling of primary cilia mechanics. Cytoskeleton (Hoboken) 2024; 81:369-381. [PMID: 38676536 DOI: 10.1002/cm.21860] [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: 01/10/2024] [Revised: 04/07/2024] [Accepted: 04/08/2024] [Indexed: 04/29/2024]
Abstract
A primary cilium, made of nine microtubule doublets enclosed in a cilium membrane, is a mechanosensing organelle that bends under an external mechanical load and sends an intracellular signal through transmembrane proteins activated by cilium bending. The nine microtubule doublets are the main load-bearing structural component, while the transmembrane proteins on the cilium membrane are the main sensing component. No distinction was made between these two components in all existing models, where the stress calculated from the structural component (nine microtubule doublets) was used to explain the sensing location, which may be totally misleading. For the first time, we developed a microstructure-based primary cilium model by considering these two components separately. First, we refined the analytical solution of bending an orthotropic cylindrical shell for individual microtubule, and obtained excellent agreement between finite element simulations and the theoretical predictions of a microtubule bending as a validation of the structural component in the model. Second, by integrating the cilium membrane with nine microtubule doublets and simulating the tip-anchored optical tweezer experiment on our computational model, we found that the microtubule doublets may twist significantly as the whole cilium bends. Third, besides being cilium-length-dependent, we found the mechanical properties of the cilium are also highly deformation-dependent. More important, we found that the cilium membrane near the base is not under pure in-plane tension or compression as previously thought, but has significant local bending stress. This challenges the traditional model of cilium mechanosensing, indicating that transmembrane proteins may be activated more by membrane curvature than membrane stretching. Finally, we incorporated imaging data of primary cilia into our microstructure-based cilium model, and found that comparing to the ideal model with uniform microtubule length, the imaging-informed model shows the nine microtubule doublets interact more evenly with the cilium membrane, and their contact locations can cause even higher bending curvature in the cilium membrane than near the base.
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Affiliation(s)
- Nima Mostafazadeh
- Department of Biomedical Engineering, University of Illinois Chicago, Chicago, Illinois, USA
| | - Andrew Resnick
- Department of Physics and Center for Gene Regulation in Health and Disease, Cleveland State University, Cleveland, Ohio, USA
| | - Y-N Young
- Department of Mathematical Sciences, New Jersey Institute of Technology, Newark, New Jersey, USA
| | - Zhangli Peng
- Department of Biomedical Engineering, University of Illinois Chicago, Chicago, Illinois, USA
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2
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Spinello A, Lapenta F, De March M. The avidin-theophylline complex: A structural and computational study. Proteins 2023; 91:1437-1443. [PMID: 37318226 DOI: 10.1002/prot.26538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/12/2023] [Accepted: 05/30/2023] [Indexed: 06/16/2023]
Abstract
The interaction between avidin and its counterpart biotin is one of central importance in biology and has been reproposed and studied at length. However, the binding pocket of avidin is prone to promiscuous binding, able to accommodate even non-biotinylated ligands. Comprehending the factors that distinguish the extremely strong interaction with biotin to other ligands is an important step to fully picture the thermodynamics of these low-affinity complexes. Here, we present the complex between chicken white egg avidin and theophylline (TEP), the xanthine derivative used in the therapy of asthma. In the crystal structure, TEP lies in the biotin-binding pocket with the same orientation and planarity of the aromatic ring of 8-oxodeoxyguanosine. Indeed, its affinity for avidin measured by isothermal titration calorimetry is in the same μM range as those obtained for the previously characterized nucleoside derivatives. By the use of molecular dynamic simulations, we have investigated the most important intermolecular interactions occurring in the avidin-TEP binding pocket and compared them with those obtained for the avidin 8-oxodeoxyguanosine and avidin-biotin complexes. These results testify the capability of avidin to complex purely aromatic molecules.
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Affiliation(s)
- Angelo Spinello
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo, Italy
| | - Fabio Lapenta
- Department of Environmental and Biological Sciences, University of Nova Gorica, Nova Gorica, Slovenia
| | - Matteo De March
- Department of Environmental and Biological Sciences, University of Nova Gorica, Nova Gorica, Slovenia
- Department of Chemical and Pharmacological Sciences, University of Trieste, Trieste, Italy
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3
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Mostafazadeh N, Resnick A, Young YN, Peng Z. Microstructure-Based Modeling of Primary Cilia Mechanics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.14.549117. [PMID: 37503231 PMCID: PMC10370030 DOI: 10.1101/2023.07.14.549117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
A primary cilium, made of nine microtubule doublets enclosed in a cilium membrane, is a mechanosensing organelle that bends under an external mechanical load and sends an intracellular signal through transmembrane proteins activated by cilium bending. The nine microtubule doublets are the main load-bearing structural component, while the transmembrane proteins on the cilium membrane are the main sensing component. No distinction was made between these two components in all existing models, where the stress calculated from the structural component (nine microtubule doublets) was used to explain the sensing location, which may be totally misleading. For the first time, we developed a microstructure-based primary cilium model by considering these two components separately. First, we refined the analytical solution of bending an orthotropic cylindrical shell for individual microtubule, and obtained excellent agreement between finite element simulations and the theoretical predictions of a microtubule bending as a validation of the structural component in the model. Second, by integrating the cilium membrane with nine microtubule doublets, we found that the microtubule doublets may twist significantly as the whole cilium bends. Third, besides being cilium-length-dependent, we found the mechanical properties of the cilium are also highly deformation-dependent. More important, we found that the cilium membrane near the base is not under pure in-plane tension or compression as previously thought, but has significant local bending stress. This challenges the traditional model of cilium mechanosensing, indicating that transmembrane proteins may be activated more by membrane curvature than membrane stretching. Finally, we incorporated imaging data of primary cilia into our microstructure-based cilium model, and found that comparing to the ideal model with uniform microtubule length, the imaging-informed model shows the nine microtubule doublets interact more evenly with the cilium membrane, and their contact locations can cause even higher bending curvature in the cilium membrane than near the base. SIGNIFICANCE Factors regulating the mechanical response of a primary cilium to fluid flow remain unclear. Modeling the microtubule doublet as a composite of two orthotropic shells and the ciliary axoneme as an elastic shell enclosing nine such microtubule doublets, we found that the length distribution of microtubule doublets (inferred from cryogenic electron tomography images) is the primary determining factor in the bending stiffness of primary cilia, rather than just the ciliary length. This implies ciliary-associated transmembrane proteins may be activated by membrane curvature changes rather than just membrane stretching. These insights challenge the traditional view of ciliary mechanosensation and expands our understanding of the different ways in which cells perceive and respond to mechanical stimuli.
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Marsan ES, Dreab A, Bayse CA. In silico insights into the dimer structure and deiodinase activity of type III iodothyronine deiodinase from bioinformatics, molecular dynamics simulations, and QM/MM calculations. J Biomol Struct Dyn 2023; 41:4819-4829. [PMID: 35579922 PMCID: PMC9878935 DOI: 10.1080/07391102.2022.2073271] [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: 01/18/2022] [Accepted: 04/27/2022] [Indexed: 01/28/2023]
Abstract
The homodimeric family of iodothyronine deiodinases (Dios) regioselectively remove iodine from thyroid hormones. Currently, structural data has only been reported for the monomer of the mus type III thioredoxin (Trx) fold catalytic domain (Dio3Trx), but the mode of dimerization has not yet been determined. Various groups have proposed dimer structures that are similar to the A-type and B-type dimerization modes of peroxiredoxins. Computational methods are used to compare the sequence of Dio3Trx to related proteins known to form A-type and B-type dimers. Sequence analysis and in silico protein-protein docking methods suggest that Dio3Trx is more consistent with proteins that adopt B-type dimerization. Molecular dynamics (MD) simulations of the refined Dio3Trx dimer constructed using the SymmDock and GalaxyRefineComplex databases indicate stable dimer formation along the β4α3 interface consistent with other Trx fold B-type dimers. Free energy calculations show that the dimer is stabilized by interdimer interactions between the β-sheets and α-helices. A comparison of MD simulations of the apo and thyroxine-bound dimers suggests that the active site binding pocket is not affected by dimerization. Determination of the transition state for deiodination of thyroxine from the monomer structure using QM/MM methods provides an activation barrier consistent with previous small model DFT studies.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Eric S Marsan
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA
| | - Ana Dreab
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA
| | - Craig A Bayse
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA
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Palicha KA, Loganathan P, Sudha V, Harinipriya S. Monte Carlo simulation and experimental validation of plant microtubules cathode in biodegradable battery. Sci Rep 2023; 13:10393. [PMID: 37369685 DOI: 10.1038/s41598-023-36902-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
For the first time, electrochemical methods are utilized to study the response of tubulin monomers (extracted from plant source such as Green Peas: Arachis Hypogea) towards charge perturbations in the form of conductivity, conformational changes via self-assembly and adsorption on Au surface. The obtained dimerization and surface adsorption energetics of the tubulins from Cyclic Voltammetry agree well with the literature value of 6.9 and 14.9 kCal/mol for lateral and longitudinal bond formation energy respectively. In addition to the effects of charge perturbations on change in structure, ionic and electronic conductivity of tubulin with increasing load are investigated and found to be 1.25 Sm-1 and 2.89 mSm-1 respectively. The electronic conductivity is 1.93 times higher than the literature value of 1.5 mSm-1, demonstrating the fact that the microtubules (dimer of tubulins, MTs) from plant source can be used as a semiconductor electrode material in energy conversion and storage applications. Thus, motivated by the Monte Carlo simulation and electrochemical results the MTs extracted from plant source are used as cathode material for energy storage device such as Bio-battery and the Galvanostatic Charge/Discharge studies are carried out in coin cell configuration. The configuration of the bio-battery cell is as follows: Al/CB//PP-1M KCl//MTs/SS; where SS and Al are used as current collectors for cathode and anode respectively, Polypropylene (PP) membrane soaked in 1M KCl as electrolyte and Carbon Black (CB) is the anode material. Another configuration of the cell would be replacement of CB by biopolymer such as ethyl cellulose anode (Al/EC/PP-1M KCl/MTs/SS).
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Affiliation(s)
- Kaushik A Palicha
- Research and Development Center, Ram Charan Co Pvt Ltd - Entity1, Chennai, Tamilnadu, 600 002, India
| | - Pavithra Loganathan
- Department of Physics and Nanotechnology, SRMIST, Kattankulathur, Chennai, Tamilnadu, 603203, India
| | - V Sudha
- Department of Chemistry, SRMIST, Kattankulathur, Chennai, Tamilnadu, 603203, India.
| | - S Harinipriya
- Research and Development Center, Ram Charan Co Pvt Ltd - Entity1, Chennai, Tamilnadu, 600 002, India.
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Hardianto A, Muscifa ZS, Widayat W, Yusuf M, Subroto T. The Effect of Ethanol on Lipid Nanoparticle Stabilization from a Molecular Dynamics Simulation Perspective. Molecules 2023; 28:4836. [PMID: 37375391 DOI: 10.3390/molecules28124836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/14/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023] Open
Abstract
Lipid nanoparticles (LNPs) have emerged as a promising delivery system, particularly for genetic therapies and vaccines. LNP formation requires a specific mixture of nucleic acid in a buffered solution and lipid components in ethanol. Ethanol acts as a lipid solvent, aiding the formation of the nanoparticle's core, but its presence can also affect LNP stability. In this study, we used molecular dynamics (MD) simulations to investigate the physicochemical effect of ethanol on LNPs and gain a dynamic understanding of its impact on the overall structure and stability of LNPs. Our results demonstrate that ethanol destabilizes LNP structure over time, indicated by increased root mean square deviation (RMSD) values. Changes in the solvent-accessible surface area (SASA), electron density, and radial distribution function (RDF) also suggest that ethanol affects LNP stability. Furthermore, our H-bond profile analysis shows that ethanol penetrates the LNP earlier than water. These findings emphasize the importance of immediate ethanol removal in lipid-based systems during LNP production to ensure stability.
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Affiliation(s)
- Ari Hardianto
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Jatinangor 45363, West Java, Indonesia
- Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung 40133, West Java, Indonesia
| | - Zahra Silmi Muscifa
- Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung 40133, West Java, Indonesia
| | - Wahyu Widayat
- Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung 40133, West Java, Indonesia
- Faculty of Pharmacy, Mulawarman University, Samarinda 75119, East Kalimantan, Indonesia
| | - Muhammad Yusuf
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Jatinangor 45363, West Java, Indonesia
- Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung 40133, West Java, Indonesia
| | - Toto Subroto
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Jatinangor 45363, West Java, Indonesia
- Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung 40133, West Java, Indonesia
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Guo W, Ale TA, Sun S, Sanchez JE, Li L. A Comprehensive Study on the Electrostatic Properties of Tubulin-Tubulin Complexes in Microtubules. Cells 2023; 12:cells12020238. [PMID: 36672172 PMCID: PMC9857020 DOI: 10.3390/cells12020238] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/31/2022] [Accepted: 01/02/2023] [Indexed: 01/08/2023] Open
Abstract
Microtubules are key players in several stages of the cell cycle and are also involved in the transportation of cellular organelles. Microtubules are polymerized by α/β tubulin dimers with a highly dynamic feature, especially at the plus ends of the microtubules. Therefore, understanding the interactions among tubulins is crucial for characterizing microtubule dynamics. Studying microtubule dynamics can help researchers make advances in the treatment of neurodegenerative diseases and cancer. In this study, we utilize a series of computational approaches to study the electrostatic interactions at the binding interfaces of tubulin monomers. Our study revealed that among all the four types of tubulin-tubulin binding modes, the electrostatic attractive interactions in the α/β tubulin binding are the strongest while the interactions of α/α tubulin binding in the longitudinal direction are the weakest. Our calculations explained that due to the electrostatic interactions, the tubulins always preferred to form α/β tubulin dimers. The interactions between two protofilaments are the weakest. Thus, the protofilaments are easily separated from each other. Furthermore, the important residues involved in the salt bridges at the binding interfaces of the tubulins are identified, which illustrates the details of the interactions in the microtubule. This study elucidates some mechanistic details of microtubule dynamics and also identifies important residues at the binding interfaces as potential drug targets for the inhibition of cancer cells.
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Affiliation(s)
- Wenhan Guo
- Computational Science Program, University of Texas at El Paso, El Paso, TX 79902, USA
| | - Tolulope Ayodeji Ale
- Computational Science Program, University of Texas at El Paso, El Paso, TX 79902, USA
| | - Shengjie Sun
- Computational Science Program, University of Texas at El Paso, El Paso, TX 79902, USA
| | - Jason E. Sanchez
- Computational Science Program, University of Texas at El Paso, El Paso, TX 79902, USA
| | - Lin Li
- Computational Science Program, University of Texas at El Paso, El Paso, TX 79902, USA
- Department of Physics, University of Texas at El Paso, El Paso, TX 79902, USA
- Correspondence:
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Discovery of reversible selective monoamine oxidase B inhibitors with anti-acetylcholinesterase activity derived from 4-oxo-N-4-diphenyl butanamides. Future Med Chem 2023; 15:189-210. [PMID: 36799336 DOI: 10.4155/fmc-2022-0169] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023] Open
Abstract
Aim: Multitargeted drugs are essential for the treatment of various neurodegenerative disorders, because of their complex nature. This study aimed to develop novel small molecules as selective monoamine oxidase B (MAO-B) inhibitors with cholinesterase inhibition. Materials & methods: With the help of fragment-based drug design, some 4-oxo-N-4-diphenyl butanamides were designed and synthesized as MAO-B inhibitors with anti-acetylcholinesterase (AChE) activity. Results: Compound 6m showed the best neuroprotection, with reversible selective MAO-B inhibition activity (IC50 = 11.54 ± 0.64 nM). Compounds 6b, 6h, 6j, 6n and 6p (IC50 = 20.90 ± 0.50, 17.25 ± 0.90, 15.85 ± 0.16, 16.81 ± 0.85 and 25.19 ± 0.17 nM, respectively) also appeared as potent and selective MAO-B inhibitors with anti-AChE activity. Conclusion: The present study suggests potent, neuroprotective and nontoxic lead compounds as selective MAO-B inhibitors with anti-AChE activity.
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Hough CM, Purschke DN, Bell C, Kalra AP, Oliva PJ, Huang C, Tuszynski JA, Warkentin BJ, Hegmann FA. Disassembly of microtubules by intense terahertz pulses. BIOMEDICAL OPTICS EXPRESS 2021; 12:5812-5828. [PMID: 34692217 PMCID: PMC8515977 DOI: 10.1364/boe.433240] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 08/12/2021] [Accepted: 08/12/2021] [Indexed: 06/13/2023]
Abstract
The biological effects of terahertz (THz) radiation have been observed across multiple levels of biological organization, however the sub-cellular mechanisms underlying the phenotypic changes remain to be elucidated. Filamentous protein complexes such as microtubules are essential cytoskeletal structures that regulate diverse biological functions, and these may be an important target for THz interactions underlying THz-induced effects observed at the cellular or tissue level. Here, we show disassembly of microtubules within minutes of exposure to extended trains of intense, picosecond-duration THz pulses. Further, the rate of disassembly depends on THz intensity and spectral content. As inhibition of microtubule dynamics is a mechanism of clinically-utilized anti-cancer agents, disruption of microtubule networks may indicate a potential therapeutic mechanism of intense THz pulses.
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Affiliation(s)
- Cameron M. Hough
- Department of Oncology, University of Alberta, Edmonton, AB T6G 2E1, Canada
- Department of Physics, University of Alberta, Edmonton, AB T6G 2E1, Canada
| | - David N. Purschke
- Department of Physics, University of Alberta, Edmonton, AB T6G 2E1, Canada
| | - Clayton Bell
- Department of Oncology, University of Alberta, Edmonton, AB T6G 2E1, Canada
| | - Aarat P. Kalra
- Department of Oncology, University of Alberta, Edmonton, AB T6G 2E1, Canada
- Currently with the Department of Chemistry, Frick Chemistry Laboratory, Princeton University, Princeton, NJ 08540, USA
| | - Patricia J. Oliva
- Department of Physics, University of Alberta, Edmonton, AB T6G 2E1, Canada
| | - Chenxi Huang
- Department of Physics, University of Alberta, Edmonton, AB T6G 2E1, Canada
| | - Jack A. Tuszynski
- Department of Oncology, University of Alberta, Edmonton, AB T6G 2E1, Canada
- Department of Physics, University of Alberta, Edmonton, AB T6G 2E1, Canada
| | - Brad J. Warkentin
- Department of Oncology, University of Alberta, Edmonton, AB T6G 2E1, Canada
| | - Frank A. Hegmann
- Department of Physics, University of Alberta, Edmonton, AB T6G 2E1, Canada
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Shyama M, Lakshmipathi S. Adsorption properties of amino acid-based ionic liquids (AAILs) on edge fluorinated graphene surface – a DFT study. MOLECULAR SIMULATION 2021. [DOI: 10.1080/08927022.2021.1948544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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11
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Klaewkla M, Pichyangkura R, Chunsrivirot S. Computational Design of Oligosaccharide-Producing Levansucrase from Bacillus licheniformis RN-01 to Increase Its Stability at High Temperature. J Phys Chem B 2021; 125:5766-5774. [PMID: 34047564 DOI: 10.1021/acs.jpcb.1c02016] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Levan-type fructooligosaccharides (LFOs) and levan can potentially be used as ingredients in prebiotics, skincare products, and antitumor agents. The Y246S mutant of Bacillus licheniformis RN-01 levansucrase (oligosaccharide-producing levansucrase, OPL) was reported to productively synthesize LFOs; however, OPL's thermostability is low at high temperatures. To enhance OPL structural stability, this study employed molecular dynamics (AMBER) to identify a highly flexible region, as measured by its average root-mean-square fluctuation (RMSF) value, on the OPL surface and computational protein design (Rosetta) to rigidify and increase favorable interactions to increase its structural stability. AMBER identified region nine (residues 277-317) as a highly flexible region that was selected for design because it has the highest number of residues and the second-highest average RMSF, and it is farthest from the active site. Rosetta designed 14 mutants with the best ΔΔG value in each position, where three mutants have better ΔG than OPL. To determine whether their flexibilities and stabilities are lower than those of OPL, all 14 designed mutants were simulated at high temperature (500 K), and we found that K296E, G309S, and A310W mutants were predicted to be more stable and could retain their native structures better than OPL. Our results suggest that enhanced structural stabilities of these mutants are caused by increased hydrogen bond strengths of the designed residues and their neighboring residues. This study designed K296E, G309S, and A310W mutants of OPL with high potential for stability improvement, and they could potentially be used for the effective production of LFOs.
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Affiliation(s)
- Methus Klaewkla
- Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok 10330, Thailand
| | - Rath Pichyangkura
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok 10330, Thailand
| | - Surasak Chunsrivirot
- Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok 10330, Thailand.,Department of Biochemistry, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok 10330, Thailand
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12
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Průša J, Ayoub AT, Chafai DE, Havelka D, Cifra M. Electro-opening of a microtubule lattice in silico. Comput Struct Biotechnol J 2021; 19:1488-1496. [PMID: 33815687 PMCID: PMC7985272 DOI: 10.1016/j.csbj.2021.02.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 02/10/2021] [Accepted: 02/12/2021] [Indexed: 11/28/2022] Open
Abstract
Modulation of the structure and function of biomaterials is essential for advancing bio-nanotechnology and biomedicine. Microtubules (MTs) are self-assembled protein polymers that are essential for fundamental cellular processes and key model compounds for the design of active bio-nanomaterials. In this in silico study, a 0.5 μs-long all-atom molecular dynamics simulation of a complete MT with approximately 1.2 million atoms in the system indicated that a nanosecond-scale intense electric field can induce the longitudinal opening of the cylindrical shell of the MT lattice, modifying the structure of the MT. This effect is field-strength- and temperature-dependent and occurs on the cathode side. A model was formulated to explain the opening on the cathode side, which resulted from an electric-field-induced imbalance between electric torque on tubulin dipoles and cohesive forces between tubulin heterodimers. Our results open new avenues for electromagnetic modulation of biological and artificial materials through action on noncovalent molecular interactions.
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Affiliation(s)
- Jiří Průša
- Institute of Photonics and Electronics of the Czech Academy of Sciences, Prague 18251, Czech Republic
| | - Ahmed Taha Ayoub
- Biomolecular Simulation Center, Department of Chemistry, Faculty of Pharmacy, Heliopolis University, Cairo 11777, Egypt
| | - Djamel Eddine Chafai
- Institute of Photonics and Electronics of the Czech Academy of Sciences, Prague 18251, Czech Republic
| | - Daniel Havelka
- Institute of Photonics and Electronics of the Czech Academy of Sciences, Prague 18251, Czech Republic
| | - Michal Cifra
- Institute of Photonics and Electronics of the Czech Academy of Sciences, Prague 18251, Czech Republic
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13
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He J, Zhang L, Liu L. The hydrogen-bond configuration modulates the energy transfer efficiency in helical protein nanotubes. NANOSCALE 2021; 13:991-999. [PMID: 33367447 DOI: 10.1039/d0nr06031c] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Energy transport in proteins is critical to a variety of physical, chemical, and biological processes in living organisms. While strenuous efforts have been made to study vibrational energy transport in proteins, thermal transport processes across the most fundamental building blocks of proteins, i.e. helices, are not well understood. This work studies energy transport in a group of "isomer" helices. The π-helix is shown to have the highest thermal conductivity, 110% higher than that of the α-helix and 207% higher than that of the 310-helix. The H-bond connectivity is found to govern thermal transport mechanisms including the phonon spectral energy density, dispersion, mode-specific transport, group velocity, and relaxation time. The energy transport is strongly correlated with the H-bond strength which is also modulated by the H-bond connectivity. These fundamental insights provide a novel perspective for understanding energy transfer in proteins and guiding a rational molecule-level design of novel materials with configurable H-bonds.
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Affiliation(s)
- Jinlong He
- Department of Mechanical Engineering, Temple University, Philadelphia, PA 19122, USA. and Department of Mechanical and Aerospace Engineering, Utah State University, Logan, Utah 84322, USA
| | - Lin Zhang
- Department of Engineering Mechanics, School of Civil Engineering, Shandong University, Jinan, 250061, P.R. China and Department of Mechanical Engineering and Materials Science, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Ling Liu
- Department of Mechanical Engineering, Temple University, Philadelphia, PA 19122, USA.
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14
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Anderson GA, Behera RN, Gomatam R. Calculation of higher protonation states and of a new resting state for vanadium chloroperoxidase using QM/MM, with an Atom-in-Molecules analysis. J Mol Graph Model 2020; 99:107624. [PMID: 32388271 DOI: 10.1016/j.jmgm.2020.107624] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 03/12/2020] [Accepted: 04/16/2020] [Indexed: 12/18/2022]
Abstract
Earlier QM/MM studies of the resting state of vanadium chloroperoxidase (VCPO) focused on the diprotonated states of the vanadate cofactor. Herein, we report a new extensive QM/MM study that includes the tri- and quadprotonated states of VCPO at neutral pH. We identify certain di- and triprotonated states as being candidates for the resting state based on a comparison of relative energies. The quadprotonated states as well as some of the triprotonated states are ruled out as the resting state. An Atoms-in-Molecules (AIM) analysis of the complex hydrogen bonding around the vanadate cofactor helps to explain the relative energies of the protonation states considered herein, and it also indicates new hydrogen bonding which has not been recognized previously. A Natural Bond Orbital (NBO) study is presented to give a better understanding of the electronic structure of the vanadate co-factor.
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Affiliation(s)
| | - Raghu Nath Behera
- Department of Chemistry, Birla Institute of Technology and Science, Pilani - Goa Campus, Zuarinagar, Goa, 403726, India.
| | - Ravi Gomatam
- Bhaktivedanta Institute and Institute of Semantic Information Sciences and Technology, Juhu Road, Juhu, Mumbai, 400049, India
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15
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Klaewkla M, Pichyangkura R, Charoenwongpaiboon T, Wangpaiboon K, Chunsrivirot S. Computational design of oligosaccharide producing levansucrase from Bacillus licheniformis RN-01 to improve its thermostability for production of levan-type fructooligosaccharides from sucrose. Int J Biol Macromol 2020; 160:252-263. [PMID: 32439436 DOI: 10.1016/j.ijbiomac.2020.05.102] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 05/08/2020] [Accepted: 05/14/2020] [Indexed: 12/27/2022]
Abstract
Levansucrase catalyzes production of levan and levan-type fructooligosaccharides (LFOs) with potential applications in food and pharmaceutical industries such as prebiotics and anti-tumor agents. Previous study found that Y246S mutant of Bacillus licheniformis RN-01 levansucrase (oligosaccharide producing levansucrase, OPL) could effectively produce LFOs but its thermostability is limited at high temperature. In this study, molecular dynamics (MD) and computational protein design were used to create mutants with higher thermostability than OPL by rigidifying highly flexible residues on enzyme surface. MD results show that highly flexible residues suitable for design are K82, N83, D179, and Q308. Two approaches were employed to improve their interactions by allowing them to be amino acids that could potentially form favorable interactions with their neighboring residues or natural amino acids except G, P and C. Flexibilities of designed residues of K82H, N83R, Q308S and K82H/N83R mutants are lower than those of OPL. Experimental results show that characteristics and product patterns of designed mutants are relatively similar to those of OPL. K82H/N83R mutant has higher thermostability than OPL with 1.7-fold increase in t1/2. Circular dichroism result suggests that designed mutations do not drastically affect secondary structures. This study shows how computational technique can engineer enzyme for thermostability improvement.
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Affiliation(s)
- Methus Klaewkla
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok 10330, Thailand; Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok 10330, Thailand
| | - Rath Pichyangkura
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok 10330, Thailand
| | | | - Karan Wangpaiboon
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok 10330, Thailand
| | - Surasak Chunsrivirot
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok 10330, Thailand; Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok 10330, Thailand.
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16
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Kumar D, Singh P, Jayaraj A, Kumar V, Kumari K, Chandra R, Ramappa VK. Selective Docking of Pyranooxazoles Against nsP2 of CHIKV Eluted Through Isothermally and Non‐Isothermally MD simulations. ChemistrySelect 2020. [DOI: 10.1002/slct.202000768] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Durgesh Kumar
- Department of Chemistry A.R.S.D. CollegeUniversity of Delhi Delhi India
- Department of ChemistryUniversity of Delhi Delhi India
| | - Prashant Singh
- Department of Chemistry A.R.S.D. CollegeUniversity of Delhi Delhi India
| | | | - Vinod Kumar
- Special Centre for Nano SciencesJawaharlal Nehru University Delhi 110067 India
| | - Kamlesh Kumari
- Department of Zoology DDU CollegeUniversity of Delhi Delhi India
| | | | - Venkatesh Kumar Ramappa
- Department of ZoologyBabasaheb Bhimrao Ambedkar University Lucknow 226025 Uttar Pradesh India
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17
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Dash J, Ray S, Devi N, Basutkar N, Ambade AV, Pesala B. Fine-tuning of Terahertz resonances in hydrogen-bonded organic molecular complexes. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2019.02.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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18
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Zúñiga MA, Alderete JB, Jaña GA, Navarrete KR, Jiménez VA. Molecular modeling study on the differential microtubule‐stabilizing effect in singly‐ and doubly‐bonded complexes with peloruside A and paclitaxel. Proteins 2019; 87:668-678. [DOI: 10.1002/prot.25692] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 03/15/2019] [Accepted: 04/04/2019] [Indexed: 01/26/2023]
Affiliation(s)
- Matías A. Zúñiga
- Department of Chemical Sciences, Faculty of Exact Sciencies, Universidad Andres BelloSede Concepción Autopista Concepción‐Talcahuano Talcahuano Chile
| | - Joel B. Alderete
- Instituto de Química de Recursos Naturales, Universidad de Talca Casilla Talca Chile
| | - Gonzalo A. Jaña
- Department of Chemical Sciences, Faculty of Exact Sciencies, Universidad Andres BelloSede Concepción Autopista Concepción‐Talcahuano Talcahuano Chile
| | - Karen R. Navarrete
- Department of Chemical Sciences, Faculty of Exact Sciencies, Universidad Andres BelloSede Concepción Autopista Concepción‐Talcahuano Talcahuano Chile
| | - Verónica A. Jiménez
- Department of Chemical Sciences, Faculty of Exact Sciencies, Universidad Andres BelloSede Concepción Autopista Concepción‐Talcahuano Talcahuano Chile
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19
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Jana S, Singh SK. Identification of human tau-tubulin kinase 1 inhibitors: an integrated e-pharmacophore-based virtual screening and molecular dynamics simulation. J Biomol Struct Dyn 2019; 38:886-900. [DOI: 10.1080/07391102.2019.1590242] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Srabanti Jana
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
| | - Sushil Kumar Singh
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
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20
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Organochlorinated pesticides expedite the enzymatic degradation of DNA. Commun Biol 2019; 2:81. [PMID: 30820476 PMCID: PMC6391446 DOI: 10.1038/s42003-019-0326-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Accepted: 01/24/2019] [Indexed: 01/31/2023] Open
Abstract
Extracellular DNA in the environment may play important roles in genetic diversity and biological evolution. However, the influence of environmental persistent organic contaminants such as organochlorinated pesticides (e.g., hexachlorocyclohexanes [HCHs]) on the enzymatic degradation of extracellular DNA has not been elucidated. In this study, we observed expedited enzymatic degradation of extracellular DNA in the presence of α-HCH, β-HCH and γ-HCH. The HCH-expedited DNA degradation was not due to increased deoxyribonuclease I (DNase I) activity. Our spectroscopic and computational results indicate that HCHs bound to DNA bases (most likely guanine) via Van der Waals forces and halogen bonds. This binding increased the helicity and accumulation of DNA base pairs, leading to a more compact DNA structure that exposed more sites susceptible to DNase I and thus expedited DNA degradation. This study provided insight into the genotoxicity and ecotoxicity of pesticides and improved our understanding of DNA persistence in contaminated environments.
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21
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Timmons JJ, Preto J, Tuszynski JA, Wong ET. Tubulin's response to external electric fields by molecular dynamics simulations. PLoS One 2018; 13:e0202141. [PMID: 30231050 PMCID: PMC6145594 DOI: 10.1371/journal.pone.0202141] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 07/27/2018] [Indexed: 02/03/2023] Open
Abstract
Tubulin heterodimers are the building blocks of microtubules and disruption of their dynamics is exploited in the treatment of cancer. Electric fields at certain frequencies and magnitudes are believed to do the same. Here, the tubulin dimer’s response to external electric fields was determined by atomistic simulation. External fields from 50 to 750 kV/cm, applied for 10 ns, caused significant conformational rearrangements that were dependent upon the field’s directionality. Charged and flexible regions, including the α:H1-B2 loop, β:M-loop, and C-termini, were susceptible. Closer inspection of the α:H1-B2 loop in lower strength fields revealed that these effects were consistent and proportional to field strength, and the findings indicate that external electric fields modulate the stability of microtubules through conformational changes to key loops involved in lateral contacts. We also find evidence that tubulin’s curvature and elongation are affected, and external electric fields may bias tubulin towards depolymerization.
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Affiliation(s)
- Joshua J. Timmons
- Brain Tumor Center & Neuro-Oncology Unit, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jordane Preto
- Department of Physics, University of Alberta, Edmonton, Canada
| | - Jack A. Tuszynski
- Department of Physics, University of Alberta, Edmonton, Canada
- Department of Oncology, University of Alberta, Edmonton, Canada
- Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Corso Duca degli Abruzzi, Torino, Italy
| | - Eric T. Wong
- Brain Tumor Center & Neuro-Oncology Unit, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail:
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22
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Castro-Alvarez A, Pineda O, Vilarrasa J. Further Insight into the Interactions of the Cytotoxic Macrolides Laulimalide and Peloruside A with Their Common Binding Site. ACS OMEGA 2018; 3:1770-1782. [PMID: 31458493 PMCID: PMC6641392 DOI: 10.1021/acsomega.7b01723] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Accepted: 01/23/2018] [Indexed: 06/10/2023]
Abstract
The binding site of the macrolides laulimalide and peloruside A, which is different from that of the clinically useful drugs paclitaxel/taxol and ixabepilone (tax site), is known to be between two adjacent β-tubulin units (ext site). Here, we report our study of the binding of these molecules to an α1β1/α2β2-tubulin "tetramer" model. AutoDock 4.2.6//AutoDock Vina dockings predicted that the affinities of laulimalide and peloruside A for the tax site are quite similar to those for the ext site. However, molecular dynamics (MD) simulations indicated that only when these two ligands are located at the ext site, there are contacts that help stabilize the system, favoring the β1/β2 interactions. The binding affinity of laulimalide for this site is stronger than that of peloruside A, but this is compensated for by additional β1/β2 contacts that are induced by peloruside A. MD studies also suggested that epothilones at the tax site and either laulimalide or peloruside A at the ext site cause similar stabilizing effects (mainly linking the M-loop of β1 and loop H1-B2 of β2). In a "hexamer" model (3 units of αβ-tubulin), the effects are confirmed. Metadynamics simulations of laulimalide and peloruside A, which are reported for the first time, suggest that peloruside A produces a stronger change in the M-loop, which explains the stabilization of the β1/β2 interaction.
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23
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Zúñiga MA, Alderete JB, Jaña GA, Fernandez PA, Ramos MJ, Jiménez VA. Modulation of lateral and longitudinal interdimeric interactions in microtubule models by Laulimalide and Peloruside A association: A molecular modeling approach on the mechanism of microtubule stabilizing agents. Chem Biol Drug Des 2018; 91:1042-1055. [DOI: 10.1111/cbdd.13168] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 12/27/2017] [Accepted: 12/31/2017] [Indexed: 01/10/2023]
Affiliation(s)
- Matías A. Zúñiga
- Departamento de Ciencias Químicas; Facultad de Ciencias Exactas; Universidad Andres Bello; Talcahuano Chile
| | - Joel B. Alderete
- Departamento de Química Orgánica; Facultad de Ciencias Químicas; Universidad de Concepción; Concepción Chile
| | - Gonzalo A. Jaña
- Departamento de Ciencias Químicas; Facultad de Ciencias Exactas; Universidad Andres Bello; Talcahuano Chile
| | | | - Maria J. Ramos
- Faculdade de Ciencias; Universidad do Porto; Porto Portugal
| | - Verónica A. Jiménez
- Departamento de Ciencias Químicas; Facultad de Ciencias Exactas; Universidad Andres Bello; Talcahuano Chile
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24
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Barsegov V, Ross JL, Dima RI. Dynamics of microtubules: highlights of recent computational and experimental investigations. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2017; 29:433003. [PMID: 28812545 DOI: 10.1088/1361-648x/aa8670] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Microtubules are found in most eukaryotic cells, with homologs in eubacteria and archea, and they have functional roles in mitosis, cell motility, intracellular transport, and the maintenance of cell shape. Numerous efforts have been expended over the last two decades to characterize the interactions between microtubules and the wide variety of microtubule associated proteins that control their dynamic behavior in cells resulting in microtubules being assembled and disassembled where and when they are required by the cell. We present the main findings regarding microtubule polymerization and depolymerization and review recent work about the molecular motors that modulate microtubule dynamics by inducing either microtubule depolymerization or severing. We also discuss the main experimental and computational approaches used to quantify the thermodynamics and mechanics of microtubule filaments.
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Affiliation(s)
- Valeri Barsegov
- Department of Chemistry, University of Massachusetts, Lowell, MA 01854, United States of America
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25
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Ayoub AT, Staelens M, Prunotto A, Deriu MA, Danani A, Klobukowski M, Tuszynski JA. Explaining the Microtubule Energy Balance: Contributions Due to Dipole Moments, Charges, van der Waals and Solvation Energy. Int J Mol Sci 2017; 18:ijms18102042. [PMID: 28937650 PMCID: PMC5666724 DOI: 10.3390/ijms18102042] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 09/12/2017] [Accepted: 09/13/2017] [Indexed: 12/14/2022] Open
Abstract
Microtubules are the main components of mitotic spindles, and are the pillars of the cellular cytoskeleton. They perform most of their cellular functions by virtue of their unique dynamic instability processes which alternate between polymerization and depolymerization phases. This in turn is driven by a precise balance between attraction and repulsion forces between the constituents of microtubules (MTs)—tubulin dimers. Therefore, it is critically important to know what contributions result in a balance of the interaction energy among tubulin dimers that make up microtubules and what interactions may tip this balance toward or away from a stable polymerized state of tubulin. In this paper, we calculate the dipole–dipole interaction energy between tubulin dimers in a microtubule as part of the various contributions to the energy balance. We also compare the remaining contributions to the interaction energies between tubulin dimers and establish a balance between stabilizing and destabilizing components, including the van der Waals, electrostatic, and solvent-accessible surface area energies. The energy balance shows that the GTP-capped tip of the seam at the plus end of microtubules is stabilized only by −9 kcal/mol, which can be completely reversed by the hydrolysis of a single GTP molecule, which releases +14 kcal/mol and destabilizes the seam by an excess of +5 kcal/mol. This triggers the breakdown of microtubules and initiates a disassembly phase which is aptly called a catastrophe.
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Affiliation(s)
- Ahmed Taha Ayoub
- Medicinal Chemistry Department, Heliopolis University, Cairo-Belbeis Desert Rd, El-Nahda, El-Salam, Cairo Governorate 11777, Egypt.
| | - Michael Staelens
- Department of Physics, University of Alberta, Edmonton, AB T6G 2E1, Canada.
| | - Alessio Prunotto
- Istituto Dalle Molle di Studi sull'Intelligenza Artificiale (IDSIA), Scuola Universitaria Professionale Della Svizzera Italiana (SUPSI), Università Della Svizzera Italiana (USI), Centro Galleria 2, Manno CH-6928, Switzerland.
| | - Marco A Deriu
- Istituto Dalle Molle di Studi sull'Intelligenza Artificiale (IDSIA), Scuola Universitaria Professionale Della Svizzera Italiana (SUPSI), Università Della Svizzera Italiana (USI), Centro Galleria 2, Manno CH-6928, Switzerland.
| | - Andrea Danani
- Istituto Dalle Molle di Studi sull'Intelligenza Artificiale (IDSIA), Scuola Universitaria Professionale Della Svizzera Italiana (SUPSI), Università Della Svizzera Italiana (USI), Centro Galleria 2, Manno CH-6928, Switzerland.
| | - Mariusz Klobukowski
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada.
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26
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Ghadari R. Nitrogen doped nanographene structures; study on the adsorption of nucleobases, nucleotides, and their triphosphate derivatives using mixed docking, MD, and QM/MM approaches. J Chem Phys 2017; 146:044105. [PMID: 28147537 DOI: 10.1063/1.4974088] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The interactions of the nucleobases, nucleotides, and their triphosphate derivatives in both neutral and anionic forms with the nitrogen doped graphenes (NG) were studied using docking and molecular dynamic simulation methods. In docking studies, based on binding energy results, the anionic species and nucleobases were showing the most and the least tendency toward the surface of the NG, respectively. The molecular mechanic/Poisson-Boltzmann surface area results revealed similar results, except for the anionic species; in these studies, the anionic species showed a lesser affinity toward the NG. The time-dependent density functional theory studies were carried out to investigate the effects of the NG on the electronic nature of the investigated ligands; a red-shift in all of the cases was observed. The results of binding energy decomposition and atoms in molecules studies showed that the interactions are van der Waals in nature. The graphitic, pyridinic, and pyrrolic nitrogen atoms which were considered in this study behaved similar to each other.
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Affiliation(s)
- Rahim Ghadari
- Computational Chemistry Laboratory, Department of Organic and Biochemistry, Faculty of Chemistry, University of Tabriz, 5166616471 Tabriz, Iran
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27
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Deformation pattern in vibrating microtubule: Structural mechanics study based on an atomistic approach. Sci Rep 2017; 7:4227. [PMID: 28652626 PMCID: PMC5484714 DOI: 10.1038/s41598-017-04272-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 05/12/2017] [Indexed: 12/27/2022] Open
Abstract
The mechanical properties of microtubules are of great importance for understanding their biological function and for applications in artificial devices. Although microtubule mechanics has been extensively studied both theoretically and experimentally, the relation to its molecular structure is understood only partially. Here, we report on the structural analysis of microtubule vibration modes calculated by an atomistic approach. Molecular dynamics was applied to refine the atomic structure of a microtubule and a Cα elastic network model was analyzed for its normal modes. We mapped fluctuations and local deformations up to the level of individual aminoacid residues. The deformation is mode-shape dependent and principally different in α-tubulins and β-tubulins. Parts of the tubulin dimer sequence responding specifically to longitudinal and radial stress are identified. We show that substantial strain within a microtubule is located both in the regions of contact between adjacent dimers and in the body of tubulins. Our results provide supportive evidence for the generally accepted assumption that the mechanics of microtubules, including its anisotropy, is determined by the bonds between tubulins.
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28
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Igamberdiev AU, Shklovskiy-Kordi NE. The quantum basis of spatiotemporality in perception and consciousness. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2017; 130:15-25. [PMID: 28232245 DOI: 10.1016/j.pbiomolbio.2017.02.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 02/16/2017] [Indexed: 12/21/2022]
Abstract
Living systems inhabit the area of the world which is shaped by the predictable space-time of physical objects and forces that can be incorporated into their perception pattern. The process of selecting a "habitable" space-time is the internal quantum measurement in which living systems become embedded into the environment that supports their living state. This means that living organisms choose a coordinate system in which the influence of measurement is minimal. We discuss specific roles of biological macromolecules, in particular of the cytoskeleton, in shaping perception patterns formed in the internal measurement process. Operation of neuron is based on the transmission of signals via cytoskeleton where the digital output is generated that can be decoded through a reflective action of the perceiving agent. It is concluded that the principle of optimality in biology as formulated by Liberman et al. (BioSystems 22, 135-154, 1989) is related to the establishment of spatiotemporal patterns that are maximally predictable and can hold the living state for a prolonged time. This is achieved by the selection of a habitable space approximated to the conditions described by classical physics.
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Affiliation(s)
- Abir U Igamberdiev
- Department of Biology, Memorial University of Newfoundland, St. John's, NL A1B 3X9, Canada.
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29
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Liu N, Pidaparti R, Wang X. Effect of amino acid mutations on intra-dimer tubulin–tubulin binding strength of microtubules. Integr Biol (Camb) 2017; 9:925-933. [DOI: 10.1039/c7ib00113d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Binding strength inside αβ-tubulin dimers of a microtubule (MT) with atomic resolutions are of importance in determining the structural stability of the MT as well as designing self-assembled functional structures from it. Through simulations, this study proposes a new strategy to tune the binding strength inside microtubules through point mutations of amino acids on the intra-dimer interface.
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Affiliation(s)
- Ning Liu
- College of Engineering
- University of Georgia
- Athens
- USA
| | | | - Xianqiao Wang
- College of Engineering
- University of Georgia
- Athens
- USA
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30
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Tuszynski JA, Wenger C, Friesen DE, Preto J. An Overview of Sub-Cellular Mechanisms Involved in the Action of TTFields. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2016; 13:E1128. [PMID: 27845746 PMCID: PMC5129338 DOI: 10.3390/ijerph13111128] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Revised: 10/23/2016] [Accepted: 11/07/2016] [Indexed: 12/13/2022]
Abstract
Long-standing research on electric and electromagnetic field interactions with biological cells and their subcellular structures has mainly focused on the low- and high-frequency regimes. Biological effects at intermediate frequencies between 100 and 300 kHz have been recently discovered and applied to cancer cells as a therapeutic modality called Tumor Treating Fields (TTFields). TTFields are clinically applied to disrupt cell division, primarily for the treatment of glioblastoma multiforme (GBM). In this review, we provide an assessment of possible physical interactions between 100 kHz range alternating electric fields and biological cells in general and their nano-scale subcellular structures in particular. This is intended to mechanistically elucidate the observed strong disruptive effects in cancer cells. Computational models of isolated cells subject to TTFields predict that for intermediate frequencies the intracellular electric field strength significantly increases and that peak dielectrophoretic forces develop in dividing cells. These findings are in agreement with in vitro observations of TTFields' disruptive effects on cellular function. We conclude that the most likely candidates to provide a quantitative explanation of these effects are ionic condensation waves around microtubules as well as dielectrophoretic effects on the dipole moments of microtubules. A less likely possibility is the involvement of actin filaments or ion channels.
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Affiliation(s)
- Jack A Tuszynski
- Department of Oncology, University of Alberta, Edmonton, AB T6G 1Z2, Canada.
- Department of Physics, University of Alberta, Edmonton, AB T6G 2E1, Canada.
| | - Cornelia Wenger
- The Institute of Biophysics and Biomedical Engineering, Faculdade de Ciências, Universidade de Lisboa, Lisboa 1749-016, Portugal.
| | - Douglas E Friesen
- Department of Oncology, University of Alberta, Edmonton, AB T6G 1Z2, Canada.
| | - Jordane Preto
- Department of Oncology, University of Alberta, Edmonton, AB T6G 1Z2, Canada.
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31
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Churchill CDM, Klobukowski M, Tuszynski JA. Elucidating the mechanism of action of the clinically approved taxanes: a comprehensive comparison of local and allosteric effects. Chem Biol Drug Des 2015; 86:1253-66. [PMID: 26032329 DOI: 10.1111/cbdd.12595] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 04/29/2015] [Accepted: 05/14/2015] [Indexed: 12/26/2022]
Abstract
The clinically approved taxanes (paclitaxel, docetaxel and cabazitaxel) target the tubulin protein in microtubules. Despite the clinical success of these agents, the mechanism of action of this class of drugs remains elusive, making rational design of taxanes difficult. Molecular dynamics simulations of these three taxanes with the αβ-tubulin heterodimer examine the similarities and differences in the effects of the drugs on tubulin, probing both local and allosteric effects. Despite their structural similarity, the drugs adopt different conformations in the binding site on β-tubulin. The taxanes similarly increase the helical character of α- and β-tubulins. No correlations are found between microtubule assembly and (i) binding affinity or (ii) the role of the M-loop in enhancing lateral contacts. Instead, changes in intra- and interdimer longitudinal contacts are indicative of the mechanism of action of the taxanes. We find β:H1-S1', and more importantly β:H9 and β:H10, play a role translating the effect of local drug binding in β-tubulin to an allosteric effect in α-tubulin and propose that the displacement of these secondary structures towards α-tubulin may be used as a predictor of the effect of taxanes on the tubulin heterodimers in rational drug design approaches.
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Affiliation(s)
- Cassandra D M Churchill
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, AB, T6G 2G2, Canada
| | - Mariusz Klobukowski
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, AB, T6G 2G2, Canada
| | - Jack A Tuszynski
- Department of Oncology, University of Alberta, Cross Cancer Institute 11560 University Avenue, Edmonton, AB, T6G 1Z2, Canada.,Department of Physics, University of Alberta, 4-181 CCIS, Edmonton, AB, T6G 2E1, Canada
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Ayoub AT, Klobukowski M, Tuszynski JA. Detailed Per-residue Energetic Analysis Explains the Driving Force for Microtubule Disassembly. PLoS Comput Biol 2015; 11:e1004313. [PMID: 26030285 PMCID: PMC4452272 DOI: 10.1371/journal.pcbi.1004313] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 05/05/2015] [Indexed: 11/19/2022] Open
Abstract
Microtubules are long filamentous hollow cylinders whose surfaces form lattice structures of αβ-tubulin heterodimers. They perform multiple physiological roles in eukaryotic cells and are targets for therapeutic interventions. In our study, we carried out all-atom molecular dynamics simulations for arbitrarily long microtubules that have either GDP or GTP molecules in the E-site of β-tubulin. A detailed energy balance of the MM/GBSA inter-dimer interaction energy per residue contributing to the overall lateral and longitudinal structural stability was performed. The obtained results identified the key residues and tubulin domains according to their energetic contributions. They also identified the molecular forces that drive microtubule disassembly. At the tip of the plus end of the microtubule, the uneven distribution of longitudinal interaction energies within a protofilament generates a torque that bends tubulin outwardly with respect to the cylinder's axis causing disassembly. In the presence of GTP, this torque is opposed by lateral interactions that prevent outward curling, thus stabilizing the whole microtubule. Once GTP hydrolysis reaches the tip of the microtubule (lateral cap), lateral interactions become much weaker, allowing tubulin dimers to bend outwards, causing disassembly. The role of magnesium in the process of outward curling has also been demonstrated. This study also showed that the microtubule seam is the most energetically labile inter-dimer interface and could serve as a trigger point for disassembly. Based on a detailed balance of the energetic contributions per amino acid residue in the microtubule, numerous other analyses could be performed to give additional insights into the properties of microtubule dynamic instability.
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Affiliation(s)
- Ahmed T. Ayoub
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | | | - Jack A. Tuszynski
- Department of Oncology, University of Alberta, Edmonton, Alberta, Canada
- Department of Physics, University of Alberta, Edmonton, Alberta, Canada
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Cosic I, Lazar K, Cosic D. Prediction of Tubulin Resonant Frequencies Using the Resonant Recognition Model (RRM). IEEE Trans Nanobioscience 2015; 14:491-496. [DOI: 10.1109/tnb.2014.2365851] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Cosic I, Cosic D, Lazar K. Is it possible to predict electromagnetic resonances in proteins, DNA and RNA? ACTA ACUST UNITED AC 2015. [DOI: 10.1140/epjnbp/s40366-015-0020-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Kononova O, Kholodov Y, Theisen KE, Marx KA, Dima RI, Ataullakhanov FI, Grishchuk EL, Barsegov V. Tubulin bond energies and microtubule biomechanics determined from nanoindentation in silico. J Am Chem Soc 2014; 136:17036-45. [PMID: 25389565 PMCID: PMC4277772 DOI: 10.1021/ja506385p] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
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Microtubules,
the primary components of the chromosome segregation
machinery, are stabilized by longitudinal and lateral noncovalent
bonds between the tubulin subunits. However, the thermodynamics of
these bonds and the microtubule physicochemical properties are poorly
understood. Here, we explore the biomechanics of microtubule polymers
using multiscale computational modeling and nanoindentations in silico of a contiguous microtubule fragment. A close
match between the simulated and experimental force–deformation
spectra enabled us to correlate the microtubule biomechanics with
dynamic structural transitions at the nanoscale. Our mechanical testing
revealed that the compressed MT behaves as a system of rigid elements
interconnected through a network of lateral and longitudinal elastic
bonds. The initial regime of continuous elastic deformation of the
microtubule is followed by the transition regime, during which the
microtubule lattice undergoes discrete structural changes, which include
first the reversible dissociation of lateral bonds followed by irreversible
dissociation of the longitudinal bonds. We have determined the free
energies of dissociation of the lateral (6.9 ± 0.4 kcal/mol)
and longitudinal (14.9 ± 1.5 kcal/mol) tubulin–tubulin
bonds. These values in conjunction with the large flexural rigidity
of tubulin protofilaments obtained (18,000–26,000 pN·nm2) support the idea that the disassembling microtubule is capable
of generating a large mechanical force to move chromosomes during
cell division. Our computational modeling offers a comprehensive quantitative
platform to link molecular tubulin characteristics with the physiological
behavior of microtubules. The developed in silico nanoindentation method provides a powerful tool for the exploration
of biomechanical properties of other cytoskeletal and multiprotein
assemblies.
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Affiliation(s)
- Olga Kononova
- Department of Chemistry, University of Massachusetts , Lowell, Massachusetts 01854, United States
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