• Genomics & Informatics
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• v.20 no.3
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• pp.33.1-33.17
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• 2022

Nervous necrosis virus (NNV) is a deadly infectious disease that affects several fish species. It has been found that the NNV utilizes grouper heat shock cognate protein 70 (GHSC70) to enter the host cell. Thus, blocking the virus entry by targeting the responsible protein can protect the fishes from disease. The main objective of the study was to evaluate the inhibitory potentiality of 70 compounds of Azadirachta indica (Neem plant) which has been reported to show potential antiviral activity against various pathogens, but activity against the NNV has not yet been reported. The binding affinity of 70 compounds was calculated against the GHSC70 with the docking and molecular dynamics (MD) simulation approaches. Both the docking and MD methods predict 4 (PubChem CID: 14492795, 10134, 5280863, and 11119228) inhibitory compounds that bind strongly with the GHSC70 protein with a binding affinity of -9.7, -9.5, -9.1, and -9.0 kcal/mol, respectively. Also, the ADMET (absorption, distribution, metabolism, excretion, and toxicity) properties of the compounds confirmed the drug-likeness properties. As a result of the investigation, it may be inferred that Neem plant compounds may act as significant inhibitors of viral entry into the host cell. More in-vitro testing is needed to establish their effectiveness.

• Molecules and Cells
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• v.46 no.8
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• pp.513-525
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• 2023

Orange carotenoid protein (OCP) of photosynthetic cyanobacteria binds to ketocarotenoids noncovalently and absorbs excess light to protect the host organism from light-induced oxidative damage. Herein, we found that mutating valine 40 in the α3 helix of Gloeocapsa sp. PCC 7513 (GlOCP1) resulted in blue- or red-shifts of 6-20 nm in the absorption maxima of the lit forms. We analyzed the origins of absorption maxima shifts by integrating X-ray crystallography, homology modeling, molecular dynamics simulations, and hybrid quantum mechanics/molecular mechanics calculations. Our analysis suggested that the single residue mutations alter the polar environment surrounding the bound canthaxanthin, thereby modulating the degree of charge transfer in the photoexcited state of the chromophore. Our integrated investigations reveal the mechanism of color adaptation specific to OCPs and suggest a design principle for color-specific photoswitches.

• Journal of the Korean Society of Earth Science Education
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• v.15 no.3
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• pp.354-372
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• 2022

The purpose of this study is to explore the philosophical position of various scientific theories based on the scientific worldviews for science education. In addition, it aims to expand science education, which has usually dealt with epistemology and methodology, to ontology, that is, to the problem of metaphysics. It can be said that there exists a physical realism, traditionally defined as a strong determinism of the metaphysical belief. That is fixed and unchanging objective scientific knowledge independent of our minds, which was established by Newton, Einstein and Schridinger. What can be seen in the natural laws of dynamics can be called 'mathematicization'. Einstein also shook the traditional views to some extent through the theory of relativity, but his theory was still close to traditional thinking. On the contrary, to escape from this rigid determinism, we need anthropomorphic concepts such as 'possibility' and 'chance'. It is a characteristic of the modern scientific worldviews that leads the change of scientific theory from a classically strong deterministic thought to a weak deterministic accidental accident, probability theory, and a naturalistic point of view. This can be said to correspond to Darwin's theory of evolution and quantum mechanics. We can have three types of epistemological worlds that justify this ontological worldviews. These are rationalism, empiricism and naturalism. In many cases, science education does not tell us what kind of metaphysical beliefs the scientific theories we deal with in the field of education are based on. Also, science education focuses only on the understanding of scientific knowledge. However, it can be said that true knowledge can bring understanding only when it is connected to the knowledge of learned knowledge and the learner's own metaphysical belief in the world. Therefore, in the future, science education needs to connect various scientific theories based on scientific worldviews and philosophical position and present them to students.