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Belghit H, Spivak M, Dauchez M, Baaden M, Jonquet-Prevoteau J. From complex data to clear insights: visualizing molecular dynamics trajectories. FRONTIERS IN BIOINFORMATICS 2024; 4:1356659. [PMID: 38665177 PMCID: PMC11043564 DOI: 10.3389/fbinf.2024.1356659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 03/14/2024] [Indexed: 04/28/2024] Open
Abstract
Advances in simulations, combined with technological developments in high-performance computing, have made it possible to produce a physically accurate dynamic representation of complex biological systems involving millions to billions of atoms over increasingly long simulation times. The analysis of these computed simulations is crucial, involving the interpretation of structural and dynamic data to gain insights into the underlying biological processes. However, this analysis becomes increasingly challenging due to the complexity of the generated systems with a large number of individual runs, ranging from hundreds to thousands of trajectories. This massive increase in raw simulation data creates additional processing and visualization challenges. Effective visualization techniques play a vital role in facilitating the analysis and interpretation of molecular dynamics simulations. In this paper, we focus mainly on the techniques and tools that can be used for visualization of molecular dynamics simulations, among which we highlight the few approaches used specifically for this purpose, discussing their advantages and limitations, and addressing the future challenges of molecular dynamics visualization.
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Affiliation(s)
- Hayet Belghit
- Université de Reims Champagne-Ardenne, CNRS, MEDYC, Reims, France
| | - Mariano Spivak
- Université Paris Cité, CNRS, Laboratoire de Biochimie Théorique, Paris, France
| | - Manuel Dauchez
- Université de Reims Champagne-Ardenne, CNRS, MEDYC, Reims, France
| | - Marc Baaden
- Université Paris Cité, CNRS, Laboratoire de Biochimie Théorique, Paris, France
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Skånberg R, Hotz I, Ynnerman A, Linares M. VIAMD: a Software for Visual Interactive Analysis of Molecular Dynamics. J Chem Inf Model 2023; 63:7382-7391. [PMID: 38011026 PMCID: PMC10716899 DOI: 10.1021/acs.jcim.3c01033] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 10/13/2023] [Accepted: 11/06/2023] [Indexed: 11/29/2023]
Abstract
The typical workflow in molecular dynamics (MD) analysis requires several separate tools, often resulting in a lack of synergy and interaction between the individual analysis steps. This article presents VIAMD, an application designed to address this issue by integrating a 3D visualization of molecular trajectories with flexible analysis components. VIAMD uses an interactive scripting interface, allowing for property definition and evaluation. The application provides context-aware suggestions and expression feedback through information and visualizations. The user-defined properties can be explored and analyzed through the various components. This enables correlation with spatial conformations, statistical analysis of distributions, and powerful aggregation of multidimensional properties such as spatial distribution functions. VIAMD has the potential to advance research in many scientific disciplines and is a promising solution for improving the workflow of MD visualization and analysis.
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Affiliation(s)
| | - Ingrid Hotz
- Linköping University, SE-581 83 Linköping, Sweden
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Björk L, Shirani H, Todarwal Y, Linares M, Vidal R, Ghetti B, Norman P, Klingstedt T, Nilsson KPR. Distinct Heterocyclic Moieties Govern the Selectivity of Thiophene-Vinylene-Based Ligands Towards Aβ or Tau Pathology in Alzheime's Disease. European J Org Chem 2023; 26:e202300583. [PMID: 38585413 PMCID: PMC10997339 DOI: 10.1002/ejoc.202300583] [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: 06/16/2023] [Indexed: 04/09/2024]
Abstract
Distinct aggregated proteins are correlated with numerous neurodegenerative diseases and the development of ligands that selectively detect these pathological hallmarks is vital. Recently, the synthesis of thiophene-based optical ligands, denoted bi-thiophene-vinyl-benzothiazoles (bTVBTs), that could be utilized for selective assignment of tau pathology in brain tissue with Alzheime's disease (AD) pathology, was reported. Herein, we investigate the ability of these ligands to selectively distinguish tau deposits from aggregated amyloid-β (Aβ), the second AD associated pathological hallmark, when replacing the terminal thiophene moiety with other heterocyclic motifs. The selectivity for tau pathology was reduced when introducing specific heterocyclic motifs, verifying that specific molecular interactions between the ligands and the aggregates are necessary for selective detection of tau deposits. In addition, ligands having certain heterocyclic moieties attached to the central thiophene-vinylene building block displayed selectivity to aggregated Aβ pathology. Our findings provide chemical insights for the development of ligands that can distinguish between aggregated proteinaceous species consisting of different proteins and might also aid in creating novel agents for clinical imaging of tau pathology in AD.
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Affiliation(s)
- Linnea Björk
- Department of Physics, Chemistry and Biology, Linköping University, SE-581 83 Linköping, Sweden
| | - Hamid Shirani
- Department of Physics, Chemistry and Biology, Linköping University, SE-581 83 Linköping, Sweden
| | - Yogesh Todarwal
- Division of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-106 91, Stockholm, Sweden
| | - Mathieu Linares
- Division of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-106 91, Stockholm, Sweden
| | - Ruben Vidal
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, 46202 Indiana, USA
| | - Bernardino Ghetti
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, 46202 Indiana, USA
| | - Patrick Norman
- Division of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-106 91, Stockholm, Sweden
| | - Therése Klingstedt
- Department of Physics, Chemistry and Biology, Linköping University, SE-581 83 Linköping, Sweden
| | - K Peter R Nilsson
- Department of Physics, Chemistry and Biology, Linköping University, SE-581 83 Linköping, Sweden
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Strakosas X, Biesmans H, Abrahamsson T, Hellman K, Ejneby MS, Donahue MJ, Ekström P, Ek F, Savvakis M, Hjort M, Bliman D, Linares M, Lindholm C, Stavrinidou E, Gerasimov JY, Simon DT, Olsson R, Berggren M. Metabolite-induced in vivo fabrication of substrate-free organic bioelectronics. Science 2023; 379:795-802. [PMID: 36821679 DOI: 10.1126/science.adc9998] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
Interfacing electronics with neural tissue is crucial for understanding complex biological functions, but conventional bioelectronics consist of rigid electrodes fundamentally incompatible with living systems. The difference between static solid-state electronics and dynamic biological matter makes seamless integration of the two challenging. To address this incompatibility, we developed a method to dynamically create soft substrate-free conducting materials within the biological environment. We demonstrate in vivo electrode formation in zebrafish and leech models, using endogenous metabolites to trigger enzymatic polymerization of organic precursors within an injectable gel, thereby forming conducting polymer gels with long-range conductivity. This approach can be used to target specific biological substructures and is suitable for nerve stimulation, paving the way for fully integrated, in vivo-fabricated electronics within the nervous system.
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Affiliation(s)
- Xenofon Strakosas
- Laboratory of Organic Electronics, Department of Science and Technology, Linköping University, 601 74 Norrköping, Sweden
- Chemical Biology and Therapeutics, Department of Experimental Medical Science, Lund University, SE-221 84 Lund, Sweden
| | - Hanne Biesmans
- Laboratory of Organic Electronics, Department of Science and Technology, Linköping University, 601 74 Norrköping, Sweden
| | - Tobias Abrahamsson
- Laboratory of Organic Electronics, Department of Science and Technology, Linköping University, 601 74 Norrköping, Sweden
| | - Karin Hellman
- Chemical Biology and Therapeutics, Department of Experimental Medical Science, Lund University, SE-221 84 Lund, Sweden
| | - Malin Silverå Ejneby
- Laboratory of Organic Electronics, Department of Science and Technology, Linköping University, 601 74 Norrköping, Sweden
| | - Mary J Donahue
- Laboratory of Organic Electronics, Department of Science and Technology, Linköping University, 601 74 Norrköping, Sweden
| | - Peter Ekström
- Chemical Biology and Therapeutics, Department of Experimental Medical Science, Lund University, SE-221 84 Lund, Sweden
| | - Fredrik Ek
- Chemical Biology and Therapeutics, Department of Experimental Medical Science, Lund University, SE-221 84 Lund, Sweden
| | - Marios Savvakis
- Laboratory of Organic Electronics, Department of Science and Technology, Linköping University, 601 74 Norrköping, Sweden
| | - Martin Hjort
- Chemical Biology and Therapeutics, Department of Experimental Medical Science, Lund University, SE-221 84 Lund, Sweden
| | - David Bliman
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-405 30 Gothenburg, Sweden
- IRLAB Therapeutics AB, Arvid Wallgrens Backe 20, 413 46 Gothenburg, Sweden
| | - Mathieu Linares
- Laboratory of Organic Electronics, Department of Science and Technology, Linköping University, 601 74 Norrköping, Sweden
- Scientific Visualization Group, Department of Science and Technology, Linköping University, 601 74 Norrköping, Sweden
| | - Caroline Lindholm
- Laboratory of Organic Electronics, Department of Science and Technology, Linköping University, 601 74 Norrköping, Sweden
| | - Eleni Stavrinidou
- Laboratory of Organic Electronics, Department of Science and Technology, Linköping University, 601 74 Norrköping, Sweden
| | - Jennifer Y Gerasimov
- Laboratory of Organic Electronics, Department of Science and Technology, Linköping University, 601 74 Norrköping, Sweden
| | - Daniel T Simon
- Laboratory of Organic Electronics, Department of Science and Technology, Linköping University, 601 74 Norrköping, Sweden
| | - Roger Olsson
- Chemical Biology and Therapeutics, Department of Experimental Medical Science, Lund University, SE-221 84 Lund, Sweden
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-405 30 Gothenburg, Sweden
| | - Magnus Berggren
- Laboratory of Organic Electronics, Department of Science and Technology, Linköping University, 601 74 Norrköping, Sweden
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