Güleşen, Sevilay

The Regional Student Group Turkey (RSG-Turkey) is officially associated with the International Society for Computational Biology (ISCB) Student Council (SC). At the RSG-Turkey, we aim to contribute to the early-career researchers in computational biology and bioinformatics fields by providing opportunities for improving their academic and technical skills in the field. Over the last ten years, we have built a well-known student-driven academic society in Turkey that organizes numerous events every year and continues to grow with over 650 current members. Celebrating the 10th anniversary of RSG-Turkey, in this communication, we share our experiences, five main lessons we learned, and the steps to establish a long-standing academic community: having a clear mission, building a robust structure, effective communication, turning challenges into opportunities, and building collaborations. We believe that our experiences can help students and academics establish long-standing communities in fast-developing areas like bioinformatics. Copyright: © 2022 Kaya Y et al.

Human acetylcholinesterase (hAChE), an essential enzyme in the central and peripheral nervous system, hydrolyses acetylcholine (ACh) at the cholinergic synapses. Organophosphorus pesticides (OPs), also called nerve agents, can inactivate the hAChE irreversibly and leads to serious morbidity (such as paralysis, cognitive deficiencies, and seizures) and even mortality consequences based on the amount of exposure and rapidness of treatment. Therefore, understanding the inhibition mechanism of hAChE by OPs, such as soman and sarin, is critical since it may guide developing a new and efficient treatment for poisoning by the nerve agents. The effects of soman inhibition on the dynamics of the hAChE were investigated in comparison with the results of the molecular dynamics study of the apo form and another OP adducted, i.e. soman adducted, form of hAChE in 2005. To understand the changes in the protein structure of hAChE after binding soman, 40 MD data were published. In this thesis, we aimed to find how sarin phosphorylation of the active site Ser203 residue of the hAChE affects the protein dynamics and to compare the result with the previously discovered results of the apo and soman-adducted hAChE. First, 40 classical MD simulations for the sarin adducted hAChE were run with the exact parameters of the apo and soman-adducted hAChE simulations. The sarin adducted hAChE was used for the MD simulations. Resulting trajectories were analyzed with RMSD analysis, principal component analysis (PCA), and K-means clustering algorithm calculations to understand the differences between collective motions of the apo, soman adducted, and sarin adducted hAChE. According to the results, the sarin molecule has an alternative pathway for entering and leaving from the active site of the hAChE like the soman molecule. The back door area when it is calculated from the backbone atoms versus the sidechain atoms shows a significant different behavior. The backbone atoms calculation of the sarin-adducted gives similar results with the apo simulation. However, there is a significant third peak at much larger value observed in the calculation of the sarin-adducted sidechain. That might be an alternative pathway for entrance to the molecule. Also, the gorge entrance and back door motion correlation is affected when hAChE is adducted by sarin, depending on correlation analysis. This disruption and the previous mentioned above area results support the hypothesis about alternative pathways for entrance and exit in the protein. All these motions and alternative pathways are critical for the development of the treatment of sarin poisoning. Keywords: Molecular dynamic simulation, acetylcholinesterase, sarin, soman, principal component analysis

Güleşen, Sevilay

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