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Keywords = IOR matching

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17 pages, 4762 KB  
Article
iBio-GATS—A Semi-Automated Workflow for Structural Modelling of Insect Odorant Receptors
by Vaanathi Chidambara Thanu, Amara Jabeen and Shoba Ranganathan
Int. J. Mol. Sci. 2024, 25(5), 3055; https://doi.org/10.3390/ijms25053055 - 6 Mar 2024
Cited by 4 | Viewed by 2593
Abstract
Insects utilize seven transmembrane (7TM) odorant receptor (iOR) proteins, with an inverted topology compared to G-protein coupled receptors (GPCRs), to detect chemical cues in the environment. For pest biocontrol, chemical attractants are used to trap insect pests. However, with the influx of invasive [...] Read more.
Insects utilize seven transmembrane (7TM) odorant receptor (iOR) proteins, with an inverted topology compared to G-protein coupled receptors (GPCRs), to detect chemical cues in the environment. For pest biocontrol, chemical attractants are used to trap insect pests. However, with the influx of invasive insect pests, novel odorants are urgently needed, specifically designed to match 3D iOR structures. Experimental structural determination of these membrane receptors remains challenging and only four experimental iOR structures from two evolutionarily distant organisms have been solved. Template-based modelling (TBM) is a complementary approach, to generate model structures, selecting templates based on sequence identity. As the iOR family is highly divergent, a different template selection approach than sequence identity is needed. Bio-GATS template selection for GPCRs, based on hydrophobicity correspondence, has been morphed into iBio-GATS, for template selection from available experimental iOR structures. This easy-to-use semi-automated workflow has been extended to generate high-quality models from any iOR sequence from the selected template, using Python and shell scripting. This workflow was successfully validated on Apocrypta bakeri Orco and Machilis hrabei OR5 structures. iBio-GATS models generated for the fruit fly iOR, OR59b and Orco, yielded functional ligand binding results concordant with experimental mutagenesis findings, compared to AlphaFold2 models. Full article
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17 pages, 2004 KB  
Review
A Review on Novel Channel Materials for Particle Image Velocimetry Measurements—Usability of Hydrogels in Cardiovascular Applications
by Christina Maria Winkler, Antonia Isabel Kuhn, Gesine Hentschel and Birgit Glasmacher
Gels 2022, 8(8), 502; https://doi.org/10.3390/gels8080502 - 12 Aug 2022
Cited by 11 | Viewed by 5363
Abstract
Particle image velocimetry (PIV) is an optical and contactless measurement method for analyzing fluid blood dynamics in cardiovascular research. The main challenge to visualization investigated in the current research was matching the channel material’s index of refraction (IOR) to that of the fluid. [...] Read more.
Particle image velocimetry (PIV) is an optical and contactless measurement method for analyzing fluid blood dynamics in cardiovascular research. The main challenge to visualization investigated in the current research was matching the channel material’s index of refraction (IOR) to that of the fluid. Silicone is typically used as a channel material for these applications, so optical matching cannot be proven. This review considers hydrogel as a new PIV channel material for IOR matching. The advantages of hydrogels are their optical and mechanical properties. Hydrogels swell more than 90 vol% when hydrated in an aqueous solution and have an elastic behavior. This paper aimed to review single, double, and triple networks and nanocomposite hydrogels with suitable optical and mechanical properties to be used as PIV channel material, with a focus on cardiovascular applications. The properties are summarized in seven hydrogel groups: PAMPS, PAA, PVA, PAAm, PEG and PEO, PSA, and PNIPA. The reliability of the optical properties is related to low IORs, which allow higher light transmission. On the other hand, elastic modulus, tensile/compressive stress, and nominal tensile/compressive strain are higher for multiple-cross-linked and nanocomposite hydrogels than single mono-cross-linked gels. This review describes methods for measuring optical and mechanical properties, e.g., refractometry and mechanical testing. Full article
(This article belongs to the Special Issue Women’s Special Issue Series: Gels)
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