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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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2
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Kobryn AE, Maruyama Y, Velázquez-Martínez CA, Yoshida N, Gusarov S. Modeling the interaction of SARS-CoV-2 binding to the ACE2 receptor via molecular theory of solvation. NEW J CHEM 2021. [DOI: 10.1039/d1nj02015c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The angiotensin-converting enzyme 2 (ACE2) protein is a cell gate receptor for the SARS-CoV-2 virus, responsible for the development of symptoms associated with the Covid-19 disease.
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Affiliation(s)
- Alexander E. Kobryn
- Nanotechnology Research Centre, National Research Council Canada, 11421 Saskatchewan Drive NW, Edmonton, Alberta, T6G 2M9, Canada
| | - Yutaka Maruyama
- Architecture Development Team, FLAGSHIP 2020 Project, RIKEN Center for Computational Science, Kobe, Hyogo 650-0047, Japan
| | - Carlos A. Velázquez-Martínez
- 2142-L Katz Group Centre for Research, University of Alberta, 11315-87 Avenue NW, Edmonton, Alberta, T6G 2H5, Canada
| | - Norio Yoshida
- Department of Chemistry, Graduate School of Science, Kyushu University, 744, Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Sergey Gusarov
- Nanotechnology Research Centre, National Research Council Canada, 11421 Saskatchewan Drive NW, Edmonton, Alberta, T6G 2M9, Canada
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3
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Keya JJ, Kabir AMR, Kakugo A. Synchronous operation of biomolecular engines. Biophys Rev 2020; 12:401-409. [PMID: 32125657 PMCID: PMC7242543 DOI: 10.1007/s12551-020-00651-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Accepted: 02/16/2020] [Indexed: 12/12/2022] Open
Abstract
Biomolecular motor systems are the smallest natural machines with an ability to convert chemical energy into mechanical work with remarkably high efficiency. Such attractive features enabled biomolecular motors to become classic tools in soft matter research over the past decade. For designing suitably engineered biomimetic systems, the biomolecular motors can potentially be used as molecular engines that can transform energy and ensure great advantages for the construction of bio-nanodevices and molecular robots. From the optimization of their prolonged lifetime to coordinate them into highly complex and ordered structures, enormous efforts have been devoted to make them useful in the synthetic environment. Synchronous operation of the biomolecular engines is one of the key criteria to coordinate them into certain different patterns, which depends on the local interaction of biomolecular motors. Utilizing chemical and physical stimuli, synchronization of biomolecular motor systems has become possible, which allows them to coordinate into different higher ordered patterns with different modes of functionality. Recently, programmed synchronous operation of the biomolecular engines has also been demonstrated, using a smart biomaterial to build up swarms reminiscent of nature. Here, we review the recent progress in the synchronized operation of biomolecular motors in engineered systems to explicitly program their interaction and further their applications. Such developments in the coordination of biomolecular motors have opened a broad way to explore the construction of future autonomous molecular machines and robots based on synchronization of biomolecular engines.
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Affiliation(s)
- Jakia Jannat Keya
- Faculty of Science, Hokkaido University, Sapporo, Hokkaido, 060-0810, Japan
| | | | - Akira Kakugo
- Faculty of Science, Hokkaido University, Sapporo, Hokkaido, 060-0810, Japan.
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Hokkaido, 060-0810, Japan.
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4
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5
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Blinov N, Wishart DS, Kovalenko A. Solvent Composition Effects on the Structural Properties of the Aβ42 Monomer from the 3D-RISM-KH Molecular Theory of Solvation. J Phys Chem B 2019; 123:2491-2506. [PMID: 30811210 DOI: 10.1021/acs.jpcb.9b00480] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Structural characterization of amyloid (A)β peptides implicated in Alzheimer's disease is a challenging problem due to their intrinsically disordered nature and their high propensity for aggregation. Only limited information is currently available from experiments on conformational properties and aggregation pathways of the peptides in cellular environments. In silico modeling complements experimental information, providing atomistic insight into structure and dynamics of different Aβ species. All-atom explicit solvent molecular dynamics (MD) simulations with a properly selected force field can deliver reliable structural and dynamic information. In the case of intrinsically disordered Aβ peptides, enhanced sampling simulations beyond the nanosecond time scale are required to obtain statistically meaningful results even for simple solvent conditions. To overcome the challenges of conformational sampling in crowded cellular environments, alternative approaches have to be used, including postprocessing of MD data. In this study, we employ the statistical-mechanical, three-dimensional reference interaction site model with the Kovalenko-Hirata closure integral equation molecular theory of solvation to describe solvent composition effects on the conformational equilibrium in a structural ensemble of the Aβ42 (covering residues 1-42) monomer based on a statistical reweighting technique. The methodology enables a computationally efficient prediction on how different factors in the cellular environment, such as solvent composition, nonpolar solvation, and macromolecular crowding, affect the structural properties of the monomer. Similarities have been identified between changes in the structural ensemble caused by nonpolar solvation and crowded environments modeled by ionic solution with large negative ions. In particular, both solvent conditions reduce the random coil content and enhance the helical structure content of the monomer. In contrast to the previous studies, which reported increased α-helical content of peptides in crowded environments, this work attributes these structural features to the difference in solvent exposure of hydrophilic residues of the monomer for different secondary structure elements, rather than to (entropic) excluded volume effects.
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Affiliation(s)
- Nikolay Blinov
- Department of Mechanical Engineering , Edmonton , Alberta T6G 1H9 , Canada.,Nanotechnology Research Centre , Edmonton , Alberta T6G 2M9 , Canada
| | - David S Wishart
- Departments of Computing Science and Biological Sciences , University of Alberta , Edmonton , Alberta T6G 2E8 , Canada
| | - Andriy Kovalenko
- Department of Mechanical Engineering , Edmonton , Alberta T6G 1H9 , Canada.,Nanotechnology Research Centre , Edmonton , Alberta T6G 2M9 , Canada
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6
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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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7
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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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8
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Brini E, Fennell CJ, Fernandez-Serra M, Hribar-Lee B, Lukšič M, Dill KA. How Water's Properties Are Encoded in Its Molecular Structure and Energies. Chem Rev 2017; 117:12385-12414. [PMID: 28949513 PMCID: PMC5639468 DOI: 10.1021/acs.chemrev.7b00259] [Citation(s) in RCA: 208] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Indexed: 11/29/2022]
Abstract
How are water's material properties encoded within the structure of the water molecule? This is pertinent to understanding Earth's living systems, its materials, its geochemistry and geophysics, and a broad spectrum of its industrial chemistry. Water has distinctive liquid and solid properties: It is highly cohesive. It has volumetric anomalies-water's solid (ice) floats on its liquid; pressure can melt the solid rather than freezing the liquid; heating can shrink the liquid. It has more solid phases than other materials. Its supercooled liquid has divergent thermodynamic response functions. Its glassy state is neither fragile nor strong. Its component ions-hydroxide and protons-diffuse much faster than other ions. Aqueous solvation of ions or oils entails large entropies and heat capacities. We review how these properties are encoded within water's molecular structure and energies, as understood from theories, simulations, and experiments. Like simpler liquids, water molecules are nearly spherical and interact with each other through van der Waals forces. Unlike simpler liquids, water's orientation-dependent hydrogen bonding leads to open tetrahedral cage-like structuring that contributes to its remarkable volumetric and thermal properties.
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Affiliation(s)
- Emiliano Brini
- Laufer
Center for Physical and Quantitative Biology, Department of Physics and Astronomy, and Department of
Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | - Christopher J. Fennell
- Department
of Chemistry, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Marivi Fernandez-Serra
- Laufer
Center for Physical and Quantitative Biology, Department of Physics and Astronomy, and Department of
Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | - Barbara Hribar-Lee
- Faculty
of Chemistry and Chemical Technology, University
of Ljubljana, Večna
pot 113, SI-1000 Ljubljana, Slovenia
| | - Miha Lukšič
- Faculty
of Chemistry and Chemical Technology, University
of Ljubljana, Večna
pot 113, SI-1000 Ljubljana, Slovenia
| | - Ken A. Dill
- Laufer
Center for Physical and Quantitative Biology, Department of Physics and Astronomy, and Department of
Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
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9
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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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10
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Kobryn AE, Gusarov S, Kovalenko A. A closure relation to molecular theory of solvation for macromolecules. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2016; 28:404003. [PMID: 27549008 DOI: 10.1088/0953-8984/28/40/404003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We propose a closure to the integral equations of molecular theory of solvation, particularly suitable for polar and charged macromolecules in electrolyte solution. This includes such systems as oligomeric polyelectrolytes at a finite concentration in aqueous and various non-aqueous solutions, as well as drug-like compounds in solution. The new closure by Kobryn, Gusarov, and Kovalenko (KGK closure) imposes the mean spherical approximation (MSA) almost everywhere in the solvation shell but levels out the density distribution function to zero (with the continuity at joint boundaries) inside the repulsive core and in the spatial regions of strong density depletion emerging due to molecular associative interactions. Similarly to MSA, the KGK closure reduces the problem to a linear equation for the direct correlation function which is predefined analytically on most of the solvation shells and has to be determined numerically on a relatively small (three-dimensional) domain of strong depletion, typically within the repulsive core. The KGK closure leads to the solvation free energy in the form of the Gaussian fluctuation (GF) functional. We first test the performance of the KGK closure coupled to the reference interaction site model (RISM) integral equations on the examples of Lennard-Jones liquids, polar and nonpolar molecular solvents, including water, and aqueous solutions of simple ions. The solvation structure, solvation chemical potential, and compressibility obtained from RISM with the KGK closure favorably compare to the results of the hypernetted chain (HNC) and Kovalenko-Hirata (KH) closures, including their combination with the GF solvation free energy. We then use the KGK closure coupled to RISM to obtain the solvation structure and thermodynamics of oligomeric polyelectrolytes and drug-like compounds at a finite concentration in electrolyte solution, for which no convergence is obtained with other closures. For comparison, we calculate their solvation structure from molecular dynamics (MD) simulations. We further couple the 3D-RISM integral equation with the 3D-version of the KGK closure, and solve it for molecular mixtures as well as oligomeric polyelectrolytes and drug-like molecules in electrolyte solutions.
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Affiliation(s)
- Alexander E Kobryn
- National Institute for Nanotechnology, National Research Council Canada, 11421 Saskatchewan Drive, Edmonton, Alberta, T6G 2M9, Canada
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11
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SAMPL5: 3D-RISM partition coefficient calculations with partial molar volume corrections and solute conformational sampling. J Comput Aided Mol Des 2016; 30:1115-1127. [PMID: 27585474 DOI: 10.1007/s10822-016-9947-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 08/18/2016] [Indexed: 12/15/2022]
Abstract
Implicit solvent methods for classical molecular modeling are frequently used to provide fast, physics-based hydration free energies of macromolecules. Less commonly considered is the transferability of these methods to other solvents. The Statistical Assessment of Modeling of Proteins and Ligands 5 (SAMPL5) distribution coefficient dataset and the accompanying explicit solvent partition coefficient reference calculations provide a direct test of solvent model transferability. Here we use the 3D reference interaction site model (3D-RISM) statistical-mechanical solvation theory, with a well tested water model and a new united atom cyclohexane model, to calculate partition coefficients for the SAMPL5 dataset. The cyclohexane model performed well in training and testing ([Formula: see text] for amino acid neutral side chain analogues) but only if a parameterized solvation free energy correction was used. In contrast, the same protocol, using single solute conformations, performed poorly on the SAMPL5 dataset, obtaining [Formula: see text] compared to the reference partition coefficients, likely due to the much larger solute sizes. Including solute conformational sampling through molecular dynamics coupled with 3D-RISM (MD/3D-RISM) improved agreement with the reference calculation to [Formula: see text]. Since our initial calculations only considered partition coefficients and not distribution coefficients, solute sampling provided little benefit comparing against experiment, where ionized and tautomer states are more important. Applying a simple [Formula: see text] correction improved agreement with experiment from [Formula: see text] to [Formula: see text], despite a small number of outliers. Better agreement is possible by accounting for tautomers and improving the ionization correction.
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12
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Ghosh C, Bhunia D, Ghosh S, Jana B, Ghosh S, Bhattacharyya K. Fluorescence Probing of Fluctuating Microtubule using a Covalent Fluorescent Probe: Effect of Taxol. ChemistrySelect 2016. [DOI: 10.1002/slct.201600353] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Catherine Ghosh
- Department of Physical Chemistry; Indian Association for the Cultivation of Science; Jadavpur Kolkata- 700032 India
| | - Debmalya Bhunia
- Organic & Medicinal Chemistry Division; CSIR-Indian Institute of Chemical Biology; Jadavpur Kolkata- 700032 India
| | - Shirsendu Ghosh
- Department of Physical Chemistry; Indian Association for the Cultivation of Science; Jadavpur Kolkata- 700032 India
| | - Batakrishna Jana
- Organic & Medicinal Chemistry Division; CSIR-Indian Institute of Chemical Biology; Jadavpur Kolkata- 700032 India
| | - Surajit Ghosh
- Organic & Medicinal Chemistry Division; CSIR-Indian Institute of Chemical Biology; Jadavpur Kolkata- 700032 India
| | - Kankan Bhattacharyya
- Department of Physical Chemistry; Indian Association for the Cultivation of Science; Jadavpur Kolkata- 700032 India
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13
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Natarajan K, Mohan J, Senapati S. Relating nucleotide-dependent conformational changes in free tubulin dimers to tubulin assembly. Biopolymers 2016; 99:282-91. [PMID: 23426572 DOI: 10.1002/bip.22153] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Accepted: 08/29/2012] [Indexed: 11/07/2022]
Abstract
The complex dynamic behavior of microtubules (MTs) is believed to be primarily due to the αβ-tubulin dimer architecture and its intrinsic GTPase activity. Hence, a detailed knowledge of the conformational variations of isolated α-GTP-β-GTP- and α-GTP-β-GDP-tubulin dimers in solution and their implications to interdimer interactions and stability is directly relevant to understand the MT dynamics. An attempt has been made here by combining molecular dynamics (MD) simulations and protein-protein docking studies that unravels key structural features of tubulin dimer in different nucleotide states and correlates their association to tubulin assembly. Results from simulations suggest that tubulin dimers and oligomers attain curved conformations in both GTP and GDP states. Results also indicate that the tubulin C-terminal domain and the nucleotide state are closely linked. Protein-protein docking in combination with MD simulations suggest that the GTP-tubulin dimers engage in relatively stronger interdimer interactions even though the interdimer interfaces are bent in both GTP and GDP tubulin complexes, providing valuable insights on in vitro finding that GTP-tubulin is a better assembly candidate than GDP-tubulin during the MT nucleation and elongation processes.
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Affiliation(s)
- Kathiresan Natarajan
- Department of Biotechnology, Indian Institute of Technology Madras, Chennai 600036, India
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14
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Ayoub AT, Craddock TJA, Klobukowski M, Tuszynski J. Analysis of the strength of interfacial hydrogen bonds between tubulin dimers using quantum theory of atoms in molecules. Biophys J 2015; 107:740-750. [PMID: 25099813 DOI: 10.1016/j.bpj.2014.05.047] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 05/07/2014] [Accepted: 05/23/2014] [Indexed: 11/19/2022] Open
Abstract
Microtubules are key structural elements that, among numerous biological functions, maintain the cytoskeleton of the cell and have a major role in cell division, which makes them important cancer chemotherapy targets. Understanding the energy balance that brings tubulin dimers, the building blocks of microtubules, together to form a microtubule is especially important for revealing the mechanism of their dynamic instability. Several studies have been conducted to estimate various contributions to the free energy of microtubule formation. However, the hydrogen-bond contribution was not studied before as a separate component. In this work, we use concepts such as the quantum theory of atoms in molecules to estimate the per-residue strength of hydrogen bonds contributing to the overall stability that brings subunits together in pair of tubulin heterodimers, across both the longitudinal and lateral interfaces. Our study shows that hydrogen bonding plays a major role in the stability of tubulin systems. Several residues that are crucial to the binding of vinca alkaloids are shown to be strongly involved in longitudinal microtubule stabilization. This indicates a direct relation between the binding of these agents and the effect on the interfacial hydrogen-bonding network, and explains the mechanism of their action. Lateral contacts showed much higher stability than longitudinal ones (-462 ± 70 vs. -392 ± 59 kJ/mol), which suggests a dramatic lateral stabilization effect of the GTP cap in the β-subunit. The role of the M-loop in lateral stability in absence of taxol was shown to be minor. The B-lattice lateral hydrogen bonds are shown to be comparable in strength to the A-lattice ones (-462 ± 70 vs. -472 ± 46 kJ/mol). These findings establish the importance of hydrogen bonds to the stability of tubulin systems.
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Affiliation(s)
- Ahmed T Ayoub
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Travis J A Craddock
- Graduate School of Computer and Information Sciences and Center for Psychological Studies, Nova Southeastern University, Ft. Lauderdale, Florida
| | | | - Jack Tuszynski
- Department of Physics, University of Alberta, Edmonton, Alberta, Canada.
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15
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Ratkova EL, Palmer DS, Fedorov MV. Solvation thermodynamics of organic molecules by the molecular integral equation theory: approaching chemical accuracy. Chem Rev 2015; 115:6312-56. [PMID: 26073187 DOI: 10.1021/cr5000283] [Citation(s) in RCA: 135] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Ekaterina L Ratkova
- †G. A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences, Akademicheskaya Street 1, Ivanovo 153045, Russia.,‡The Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, Leipzig 04103, Germany
| | - David S Palmer
- ‡The Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, Leipzig 04103, Germany.,§Department of Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral Street, Glasgow, Scotland G1 1XL, United Kingdom
| | - Maxim V Fedorov
- ‡The Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, Leipzig 04103, Germany.,∥Department of Physics, Scottish Universities Physics Alliance (SUPA), University of Strathclyde, John Anderson Building, 107 Rottenrow East, Glasgow G4 0NG, United Kingdom
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16
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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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Bachand GD, Spoerke ED, Stevens MJ. Microtubule-based nanomaterials: Exploiting nature's dynamic biopolymers. Biotechnol Bioeng 2015; 112:1065-73. [PMID: 25728349 DOI: 10.1002/bit.25569] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Revised: 02/09/2015] [Accepted: 02/10/2015] [Indexed: 12/11/2022]
Abstract
For more than a decade now, biomolecular systems have served as an inspiration for the development of synthetic nanomaterials and systems that are capable of reproducing many of unique and emergent behaviors of living systems. One intriguing element of such systems may be found in a specialized class of proteins known as biomolecular motors that are capable of performing useful work across multiple length scales through the efficient conversion of chemical energy. Microtubule (MT) filaments may be considered within this context as their dynamic assembly and disassembly dissipate energy, and perform work within the cell. MTs are one of three cytoskeletal filaments in eukaryotic cells, and play critical roles in a range of cellular processes including mitosis and vesicular trafficking. Based on their function, physical attributes, and unique dynamics, MTs also serve as a powerful archetype of a supramolecular filament that underlies and drives multiscale emergent behaviors. In this review, we briefly summarize recent efforts to generate hybrid and composite nanomaterials using MTs as biomolecular scaffolds, as well as computational and synthetic approaches to develop synthetic one-dimensional nanostructures that display the enviable attributes of the natural filaments.
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Affiliation(s)
- George D Bachand
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, 87185-1303, New Mexico.
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18
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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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19
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Omelyan I, Kovalenko A. Multiple time step molecular dynamics in the optimized isokinetic ensemble steered with the molecular theory of solvation: accelerating with advanced extrapolation of effective solvation forces. J Chem Phys 2014; 139:244106. [PMID: 24387356 DOI: 10.1063/1.4848716] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
We develop efficient handling of solvation forces in the multiscale method of multiple time step molecular dynamics (MTS-MD) of a biomolecule steered by the solvation free energy (effective solvation forces) obtained from the 3D-RISM-KH molecular theory of solvation (three-dimensional reference interaction site model complemented with the Kovalenko-Hirata closure approximation). To reduce the computational expenses, we calculate the effective solvation forces acting on the biomolecule by using advanced solvation force extrapolation (ASFE) at inner time steps while converging the 3D-RISM-KH integral equations only at large outer time steps. The idea of ASFE consists in developing a discrete non-Eckart rotational transformation of atomic coordinates that minimizes the distances between the atomic positions of the biomolecule at different time moments. The effective solvation forces for the biomolecule in a current conformation at an inner time step are then extrapolated in the transformed subspace of those at outer time steps by using a modified least square fit approach applied to a relatively small number of the best force-coordinate pairs. The latter are selected from an extended set collecting the effective solvation forces obtained from 3D-RISM-KH at outer time steps over a broad time interval. The MTS-MD integration with effective solvation forces obtained by converging 3D-RISM-KH at outer time steps and applying ASFE at inner time steps is stabilized by employing the optimized isokinetic Nosé-Hoover chain (OIN) ensemble. Compared to the previous extrapolation schemes used in combination with the Langevin thermostat, the ASFE approach substantially improves the accuracy of evaluation of effective solvation forces and in combination with the OIN thermostat enables a dramatic increase of outer time steps. We demonstrate on a fully flexible model of alanine dipeptide in aqueous solution that the MTS-MD/OIN/ASFE/3D-RISM-KH multiscale method of molecular dynamics steered by effective solvation forces allows huge outer time steps up to tens of picoseconds without affecting the equilibrium and conformational properties, and thus provides a 100- to 500-fold effective speedup in comparison to conventional MD with explicit solvent. With the statistical-mechanical 3D-RISM-KH account for effective solvation forces, the method provides efficient sampling of biomolecular processes with slow and/or rare solvation events such as conformational transitions of hydrated alanine dipeptide with the mean life times ranging from 30 ps up to 10 ns for "flip-flop" conformations, and is particularly beneficial for biomolecular systems with exchange and localization of solvent and ions, ligand binding, and molecular recognition.
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Affiliation(s)
- Igor Omelyan
- National Institute for Nanotechnology, 11421 Saskatchewan Drive, Edmonton, Alberta T6G 2M9, Canada
| | - Andriy Kovalenko
- National Institute for Nanotechnology, 11421 Saskatchewan Drive, Edmonton, Alberta T6G 2M9, Canada
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20
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Zdravković S, Bugay AN, Aru GF, Maluckov A. Localized modulated waves in microtubules. CHAOS (WOODBURY, N.Y.) 2014; 24:023139. [PMID: 24985453 DOI: 10.1063/1.4885777] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
In the present paper, we study nonlinear dynamics of microtubules (MTs). As an analytical method, we use semi-discrete approximation and show that localized modulated solitonic waves move along MT. This is supported by numerical analysis. Both cases with and without viscosity effects are studied.
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Affiliation(s)
- Slobodan Zdravković
- Laboratorija za Atomsku Fiziku (040), Institut za Nuklearne Nauke Vinča, Univerzitet u Beogradu, Poštanski fah 522, 11001 Beograd, Serbia
| | - Aleksandr N Bugay
- Joint Institute for Nuclear Research, Joliot-Curie 6, 141980, Dubna, Moscow Region, Russia
| | - Guzel F Aru
- Joint Institute for Nuclear Research, Joliot-Curie 6, 141980, Dubna, Moscow Region, Russia
| | - Aleksandra Maluckov
- Laboratorija za Atomsku Fiziku (040), Institut za Nuklearne Nauke Vinča, Univerzitet u Beogradu, Poštanski fah 522, 11001 Beograd, Serbia
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21
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Kwiatkowska M, Stępiński D, Popłońska K. Diameters of microtubules change during rotation of the lipotubuloids of Ornithogalum umbellatum
stipule epidermis as a result of varying protofilament monomers sizes and distance between them. Cell Biol Int 2013; 33:1245-52. [DOI: 10.1016/j.cellbi.2009.08.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2008] [Revised: 07/16/2009] [Accepted: 08/25/2009] [Indexed: 11/29/2022]
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22
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Omelyan I, Kovalenko A. Generalised canonical–isokinetic ensemble: speeding up multiscale molecular dynamics and coupling with 3D molecular theory of solvation. MOLECULAR SIMULATION 2013. [DOI: 10.1080/08927022.2012.700486] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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23
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Palmer DS, McDonagh JL, Mitchell JBO, van Mourik T, Fedorov MV. First-Principles Calculation of the Intrinsic Aqueous Solubility of Crystalline Druglike Molecules. J Chem Theory Comput 2012; 8:3322-37. [PMID: 26605739 DOI: 10.1021/ct300345m] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We demonstrate that the intrinsic aqueous solubility of crystalline druglike molecules can be estimated with reasonable accuracy from sublimation free energies calculated using crystal lattice simulations and hydration free energies calculated using the 3D Reference Interaction Site Model (3D-RISM) of the Integral Equation Theory of Molecular Liquids (IET). The solubilities of 25 crystalline druglike molecules taken from different chemical classes are predicted by the model with a correlation coefficient of R = 0.85 and a root mean square error (RMSE) equal to 1.45 log10S units, which is significantly more accurate than results obtained using implicit continuum solvent models. The method is not directly parametrized against experimental solubility data, and it offers a full computational characterization of the thermodynamics of transfer of the drug molecule from crystal phase to gas phase to dilute aqueous solution.
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Affiliation(s)
- David S Palmer
- Department of Physics, University of Strathclyde , John Anderson Building, 107 Rottenrow, Glasgow, Scotland G4 0NG, United Kingdom.,Max Planck Institute for Mathematics in the Sciences , Inselstrasse 22, DE-04103 Leipzig, Germany
| | - James L McDonagh
- Biomedical Sciences Research Complex and EaStCHEM School of Chemistry, University of St. Andrews , Purdie Building, North Haugh, St. Andrews, Scotland KY16 9ST, United Kingdom
| | - John B O Mitchell
- Biomedical Sciences Research Complex and EaStCHEM School of Chemistry, University of St. Andrews , Purdie Building, North Haugh, St. Andrews, Scotland KY16 9ST, United Kingdom
| | - Tanja van Mourik
- Biomedical Sciences Research Complex and EaStCHEM School of Chemistry, University of St. Andrews , Purdie Building, North Haugh, St. Andrews, Scotland KY16 9ST, United Kingdom
| | - Maxim V Fedorov
- Department of Physics, University of Strathclyde , John Anderson Building, 107 Rottenrow, Glasgow, Scotland G4 0NG, United Kingdom.,Max Planck Institute for Mathematics in the Sciences , Inselstrasse 22, DE-04103 Leipzig, Germany
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24
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Gusarov S, Pujari BS, Kovalenko A. Efficient treatment of solvation shells in 3D molecular theory of solvation. J Comput Chem 2012; 33:1478-94. [DOI: 10.1002/jcc.22974] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2011] [Accepted: 03/02/2012] [Indexed: 01/01/2023]
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25
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26
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Blinov N, Dorosh L, Wishart D, Kovalenko A. 3D-RISM-KH approach for biomolecular modelling at nanoscale: thermodynamics of fibril formation and beyond. MOLECULAR SIMULATION 2011. [DOI: 10.1080/08927022.2010.544306] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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27
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Grafmüller A, Voth GA. Intrinsic bending of microtubule protofilaments. Structure 2011; 19:409-17. [PMID: 21397191 DOI: 10.1016/j.str.2010.12.020] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2010] [Revised: 12/20/2010] [Accepted: 12/22/2010] [Indexed: 01/05/2023]
Abstract
The complex polymerization dynamics of the microtubule (MT) plus end are closely linked to the hydrolysis of the GTP nucleotide bound to the β-tubulin. The destabilization is thought to be associated with the conformational change of the tubulin dimers from the straight conformation in the MT lattice to a curved conformation. It remains under debate whether this transformation is directly related to the nucleotide state, or a consequence of the longitudinal or lateral contacts in the MT lattice. Here, we present large-scale atomistic simulations of short tubulin protofilaments with both nucleotide states, starting from both extreme conformations. Our simulations indicate that both interdimer and intradimer contacts in both GDP and GTP-bound tubulin dimers and protofilaments in solution bend. There are no observable differences between the mesoscopic properties of the contacts in GTP and GDP-bound tubulin or the intradime and interdimer interfaces.
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Affiliation(s)
- Andrea Grafmüller
- Department of Chemistry, James Franck Institute, and Computation Institute, University of Chicago, 5735 S. Ellis Avenue, Chicago, IL 60637, USA
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28
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Palmer DS, Frolov AI, Ratkova EL, Fedorov MV. Toward a Universal Model To Calculate the Solvation Thermodynamics of Druglike Molecules: The Importance of New Experimental Databases. Mol Pharm 2011; 8:1423-9. [DOI: 10.1021/mp200119r] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- David S. Palmer
- Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, DE-04103 Leipzig, Germany
| | - Andrey I. Frolov
- Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, DE-04103 Leipzig, Germany
| | - Ekaterina L. Ratkova
- Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, DE-04103 Leipzig, Germany
| | - Maxim V. Fedorov
- Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, DE-04103 Leipzig, Germany
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29
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Yamazaki T, Kovalenko A. Spatial Decomposition of Solvation Free Energy Based on the 3D Integral Equation Theory of Molecular Liquid: Application to Miniproteins. J Phys Chem B 2010; 115:310-8. [DOI: 10.1021/jp1082938] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Takeshi Yamazaki
- National Institute for Nanotechnology, 11421 Saskatchewan Drive, Edmonton, Alberta, T6G 2M9, Canada, and Department of Mechanical Engineering, University of Alberta, Edmonton, Alberta, T6G 2G8, Canada
| | - Andriy Kovalenko
- National Institute for Nanotechnology, 11421 Saskatchewan Drive, Edmonton, Alberta, T6G 2M9, Canada, and Department of Mechanical Engineering, University of Alberta, Edmonton, Alberta, T6G 2G8, Canada
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30
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Palmer DS, Frolov AI, Ratkova EL, Fedorov MV. Towards a universal method for calculating hydration free energies: a 3D reference interaction site model with partial molar volume correction. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2010; 22:492101. [PMID: 21406779 DOI: 10.1088/0953-8984/22/49/492101] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
We report a simple universal method to systematically improve the accuracy of hydration free energies calculated using an integral equation theory of molecular liquids, the 3D reference interaction site model. A strong linear correlation is observed between the difference of the experimental and (uncorrected) calculated hydration free energies and the calculated partial molar volume for a data set of 185 neutral organic molecules from different chemical classes. By using the partial molar volume as a linear empirical correction to the calculated hydration free energy, we obtain predictions of hydration free energies in excellent agreement with experiment (R = 0.94, σ = 0.99 kcal mol (- 1) for a test set of 120 organic molecules).
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Affiliation(s)
- David S Palmer
- Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, DE-04103 Leipzig, Germany
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31
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Boudreaux MK, Osborne CD, Herre AC, Rivera ER, Spangler EA. Unique structure of the M loop region of β1-tubulin may contribute to size variability of platelets in the family Felidae. Vet Clin Pathol 2010; 39:417-23. [DOI: 10.1111/j.1939-165x.2010.00256.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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32
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Genheden S, Luchko T, Gusarov S, Kovalenko A, Ryde U. An MM/3D-RISM approach for ligand binding affinities. J Phys Chem B 2010; 114:8505-16. [PMID: 20524650 DOI: 10.1021/jp101461s] [Citation(s) in RCA: 118] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have modified the popular MM/PBSA or MM/GBSA approaches (molecular mechanics for a biomolecule, combined with a Poisson-Boltzmann or generalized Born electrostatic and surface area nonelectrostatic solvation energy) by employing instead the statistical-mechanical, three-dimensional molecular theory of solvation (also known as 3D reference interaction site model, or 3D-RISM-KH) coupled with molecular mechanics or molecular dynamics ( Blinov , N. ; et al. Biophys. J. 2010 ; Luchko , T. ; et al. J. Chem. Theory Comput. 2010 ). Unlike the PBSA or GBSA semiempirical approaches, the 3D-RISM-KH theory yields a full molecular picture of the solvation structure and thermodynamics from the first principles, with proper account of chemical specificities of both solvent and biomolecules, such as hydrogen bonding, hydrophobic interactions, salt bridges, etc. We test the method on the binding of seven biotin analogues to avidin in aqueous solution and show it to work well in predicting the ligand-binding affinities. We have compared the results of 3D-RISM-KH with four different generalized Born and two Poisson-Boltzmann methods. They give absolute binding energies that differ by up to 208 kJ/mol and mean absolute deviations in the relative affinities of 10-43 kJ/mol.
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Affiliation(s)
- Samuel Genheden
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
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33
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Blinov N, Dorosh L, Wishart D, Kovalenko A. Association thermodynamics and conformational stability of beta-sheet amyloid beta(17-42) oligomers: effects of E22Q (Dutch) mutation and charge neutralization. Biophys J 2010; 98:282-96. [PMID: 20338850 DOI: 10.1016/j.bpj.2009.09.062] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2008] [Revised: 09/16/2009] [Accepted: 09/17/2009] [Indexed: 12/21/2022] Open
Abstract
Amyloid fibrils are associated with many neurodegenerative diseases. It was found that amyloidogenic oligomers, not mature fibrils, are neurotoxic agents related to these diseases. Molecular mechanisms of infectivity, pathways of aggregation, and molecular structure of these oligomers remain elusive. Here, we use all-atom molecular dynamics, molecular mechanics combined with solvation analysis by statistical-mechanical, three-dimensional molecular theory of solvation (also known as 3D-RISM-KH) in a new MM-3D-RISM-KH method to study conformational stability, and association thermodynamics of small wild-type Abeta(17-42) oligomers with different protonation states of Glu(22), as well the E22Q (Dutch) mutants. The association free energy of small beta-sheet oligomers shows near-linear trend with the dimers being thermodynamically more stable relative to the larger constructs. The linear (within statistical uncertainty) dependence of the association free energy on complex size is a consequence of the unilateral stacking of monomers in the beta-sheet oligomers. The charge reduction of the wild-type Abeta(17-42) oligomers upon protonation of the solvent-exposed Glu(22) at acidic conditions results in lowering the association free energy compared to the wild-type oligomers at neutral pH and the E22Q mutants. The neutralization of the peptides because of the E22Q mutation only marginally affects the association free energy, with the reduction of the direct electrostatic interactions mostly compensated by the unfavorable electrostatic solvation effects. For the wild-type oligomers at acidic conditions such compensation is not complete, and the electrostatic interactions, along with the gas-phase nonpolar energetic and the overall entropic effects, contribute to the lowering of the association free energy. The differences in the association thermodynamics between the wild-type Abeta(17-42) oligomers at neutral pH and the Dutch mutants, on the one hand, and the Abeta(17-42) oligomers with protonated Glu(22), on the other, may be explained by destabilization of the inter- and intrapeptide salt bridges between Asp(23) and Lys(28). Peculiarities in the conformational stability and the association thermodynamics for the different models of the Abeta(17-42) oligomers are rationalized based on the analysis of the local physical interactions and the microscopic solvation structure.
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Affiliation(s)
- Nikolay Blinov
- National Institute for Nanotechnology, National Research Council of Canada, Edmonton, Alberta, Canada
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Luchko T, Gusarov S, Roe DR, Simmerling C, Case DA, Tuszynski J, Kovalenko A. Three-dimensional molecular theory of solvation coupled with molecular dynamics in Amber. J Chem Theory Comput 2010; 6:607-624. [PMID: 20440377 PMCID: PMC2861832 DOI: 10.1021/ct900460m] [Citation(s) in RCA: 201] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present the three-dimensional molecular theory of solvation (also known as 3D-RISM) coupled with molecular dynamics (MD) simulation by contracting solvent degrees of freedom, accelerated by extrapolating solvent-induced forces and applying them in large multi-time steps (up to 20 fs) to enable simulation of large biomolecules. The method has been implemented in the Amber molecular modeling package, and is illustrated here on alanine dipeptide and protein G.
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Affiliation(s)
- Tyler Luchko
- National Institute for Nanotechnology, 11421 Saskatchewan Drive, Edmonton, Alberta, T6G 2M9, Canada
- Department of Mechanical Engineering, University of Alberta, Edmonton, Alberta, T6G 2G8, Canada
| | - Sergey Gusarov
- National Institute for Nanotechnology, 11421 Saskatchewan Drive, Edmonton, Alberta, T6G 2M9, Canada
| | - Daniel R. Roe
- National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD 20899-8443
| | - Carlos Simmerling
- Department of Chemistry, Graduate Program in Biochemistry and Structural Biology, and Center for Structural Biology, Stony Brook University, Stony Brook, New York 11794-3400
- Computational Science Center, Brookhaven National Laboratory, Upton, New York 11973
| | - David A. Case
- BioMaPS Institute, Rutgers University, Piscataway, NJ
- Department of Chemistry & Chemical Biology, Rutgers University, Piscataway, NJ
| | - Jack Tuszynski
- Department of Oncology, University of Alberta, Edmonton, Alberta, Canada
| | - Andriy Kovalenko
- National Institute for Nanotechnology, 11421 Saskatchewan Drive, Edmonton, Alberta, T6G 2M9, Canada
- Department of Mechanical Engineering, University of Alberta, Edmonton, Alberta, T6G 2G8, Canada
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35
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Li Q, Gusarov S, Evoy S, Kovalenko A. Electronic Structure, Binding Energy, and Solvation Structure of the Streptavidin−Biotin Supramolecular Complex: ONIOM and 3D-RISM Study. J Phys Chem B 2009; 113:9958-67. [DOI: 10.1021/jp902668c] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Qingbin Li
- National Institute for Nanotechnology, 11421 Saskatchewan Drive, Edmonton, Alberta, T6G 2M9, Canada, and Department of Mechanical Engineering and Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Alberta, Canada T6G 2R3
| | - Sergey Gusarov
- National Institute for Nanotechnology, 11421 Saskatchewan Drive, Edmonton, Alberta, T6G 2M9, Canada, and Department of Mechanical Engineering and Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Alberta, Canada T6G 2R3
| | - Stephane Evoy
- National Institute for Nanotechnology, 11421 Saskatchewan Drive, Edmonton, Alberta, T6G 2M9, Canada, and Department of Mechanical Engineering and Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Alberta, Canada T6G 2R3
| | - Andriy Kovalenko
- National Institute for Nanotechnology, 11421 Saskatchewan Drive, Edmonton, Alberta, T6G 2M9, Canada, and Department of Mechanical Engineering and Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Alberta, Canada T6G 2R3
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36
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Dima RI, Joshi H. Probing the origin of tubulin rigidity with molecular simulations. Proc Natl Acad Sci U S A 2008; 105:15743-8. [PMID: 18840679 PMCID: PMC2572946 DOI: 10.1073/pnas.0806113105] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2008] [Indexed: 11/18/2022] Open
Abstract
Tubulin heterodimers are the building blocks of microtubules, a major component of the cytoskeleton, whose mechanical properties are fundamental for the life of the cell. We uncover the microscopic origins of the mechanical response in microtubules by probing features of the energy landscape of the tubulin monomers and tubulin heterodimer. To elucidate the structures of the unfolding pathways and reveal the multiple unfolding routes, we performed simulations of a self-organized polymer (SOP) model of tubulin. The SOP representation, which is a coarse-grained description of chains, allows us to perform force-induced simulations at loading rates and time scales that closely match those used in single-molecule experiments. We show that the forced unfolding of each monomer involves a bifurcation in the pathways to the stretched state. After the unfolding of the C-term domain, the unraveling continues either from the N-term domain or from the middle domain, depending on the monomer and the pathway. In contrast to the unfolding complexity of the monomers, the dimer unfolds according to only one route corresponding to the unraveling of the C-term domain and part of the middle domain of beta-tubulin. We find that this surprising behavior is due to the viscoelastic properties of the interface between the monomers. We map precise features of the complex energy landscape of tubulin by surveying the structures of the various metastable intermediates, which, in the dimer case, are characterized only by changes in the beta-tubulin monomer.
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Affiliation(s)
- Ruxandra I Dima
- Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221, USA.
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37
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Hydration effects on the HET-s prion and amyloid-beta fibrillous aggregates, studied with three-dimensional molecular theory of solvation. Biophys J 2008; 95:4540-8. [PMID: 18689456 DOI: 10.1529/biophysj.107.123000] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
We study the thermodynamic properties of the experimental fragments of the amyloid fibril made of the HET-s prion proteins (the infectious element of the filamentous fungus Podospora anserina) and of amyloid-beta proteins (the major component of Alzheimer's disease-associated plaques) by using the three-dimensional molecular theory of solvation. The full quantitative picture of hydration effects, including the hydration thermodynamics and hydration structure around the fragments, is presented. For both the complexes, the hydration entropic effects dominate, which results in the entropic part offsetting the unfavorable energetic part of the free energy change upon the association. This is in accord with the fact that the hydrophobic cooperativity plays an essential role in the formation of amyloid fibrils. By calculating the partial molar volume of the proteins, we found that the volume change upon the association in both the systems is large and positive, with the implication that high pressure causes destabilization of the fibril. This observation is in good agreement with the recent experimental results. We also found that both the HET-s and amyloid-beta pentamers have loose intermolecular packing with voids. The three-dimensional molecular theory of solvation predicts that water molecules can be locked in the interior cavities along the fibril axis for both the HET-s and amyloid-beta proteins. We provide a detailed molecular picture of the structural water localized in the interior of the fibrils. Our results suggest that the interior hydration plays an important role in the structural stability of fibrils.
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Pampaloni F, Florin EL. Microtubule architecture: inspiration for novel carbon nanotube-based biomimetic materials. Trends Biotechnol 2008; 26:302-10. [PMID: 18433902 DOI: 10.1016/j.tibtech.2008.03.002] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2007] [Revised: 03/05/2008] [Accepted: 03/10/2008] [Indexed: 01/06/2023]
Abstract
Microtubules are self-assembling biological nanotubes that are essential for cell motility, cell division and intracellular trafficking. Microtubules have outstanding mechanical properties, combining high resilience and stiffness. Such a combination allows microtubules to accomplish multiple cellular functions and makes them interesting for material sciences. We review recent experiments that elucidate the relationship between molecular architecture and mechanics in microtubules and examine analogies and differences between microtubules and carbon nanotubes, which are their closest equivalent in nanotechnology. We suggest that a long-term goal in bionanotechnology should be mimicking the properties of microtubules and microtubule bundles to produce new functional nanomaterials.
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Affiliation(s)
- Francesco Pampaloni
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, D-69117 Heidelberg, Germany.
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39
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Abstract
Recent modeling efforts to estimate energies of tubulin-tubulin bonds shed light on a delicate balance between competing mechanical forces maintaining microtubule walls. Here we formulate two important refinements to the explanation of bond energetics. First, energy surface calculations in the elastic filament approximation reveal a finite stabilizing barrier assumed a simple Lennard-Jones-like potential for protein bonds. The presence of a guanosine triphosphate (GTP) cap represented by straight segments is necessary, as it is predicted for a long time. In the lack of such a cap, the protofilaments are either in an absolutely stable or absolutely unstable state. Second, our calculations show that this barrier appears only if the mechanical energy associated with the conformational change after GTP hydrolysis (curling energy) is larger than the strength of lateral bonds. The overall energy balance we propose supports continuous assembly of GTP dimers, a metastable state in the presence of a finite GTP cap and energetically driven disassembly of guanosine diphosphate protofilaments.
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Affiliation(s)
- Viktória Hunyadi
- Department of Physics of Complex Systems, Eötvös University, Pázmány Péter s. 1/A, H-1117 Budapest, Hungary
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